Theoretical and numerical analysis of a heat pump model utilizing Dufour effect

A heat pump model utilizing the Dufour effect is proposed and studied by numerical and theoretical analysis. Numerically, we perform MD simulations of this system and measure the cooling power and the coefficient of performance (COP) as figures of merit. Theoretically, we calculate the cooling power and the COP from the henomenological equations describing this system by using the linear irreversible thermodynamics and compare the theoretical results with the MD results.Comment: 13 pages, 16 figures(10 captions), published versio

ODB: a database of operons accumulating known operons across multiple genomes

Operon structures play an important role in co-regulation in prokaryotes. Although over 200 complete genome sequences are now available, databases providing genome-wide operon information have been limited to certain specific genomes. Thus, we have developed an ODB (Operon DataBase), which provides a data retrieval system of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The current version of our database contains about 2000 known operon information in more than 50 genomes and about 13 000 putative operons in more than 200 genomes. This system integrates four types of associations: genome context, gene co-expression obtained from microarray data, functional links in biological pathways and the conservation of gene order across the genomes. These associations are indicators of the genes that organize an operon, and the combination of these indicators allows us to predict more reliable operons. Furthermore, our system validates these predictions using known operon information obtained from the literature. This database integrates known literature-based information and genomic data. In addition, it provides an operon prediction tool, which make the system useful for both bioinformatics researchers and experimental biologists. Our database is accessible at

Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli

BACKGROUND: Operon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptional units vary with changing environmental conditions. Information about such complicated operons is helpful for predicting and analyzing operon structures, as well as understanding gene functions and transcriptional regulation. RESULTS: We systematically analyzed the experimentally verified transcriptional units (TUs) in Bacillus subtilis and Escherichia coli obtained from ODB and RegulonDB. To understand the relationships between TUs and operons, we defined a new classification system for adjacent gene pairs, divided into three groups according to the level of gene co-regulation: operon pairs (OP) belong to the same TU, sub-operon pairs (SOP) that are at the transcriptional boundaries within an operon, and non-operon pairs (NOP) belonging to different operons. Consequently, we found that the levels of gene co-regulation was correlated to intergenic distances and gene expression levels. Additional analysis revealed that they were also correlated to the levels of conservation across about 200 prokaryotic genomes. Most interestingly, we found that functional associations in SOPs were more observed in the environmental and genetic information processes. CONCLUSION: Complicated operon strucutures were correlated with genome organization and gene expression profiles. Such intricately regulated operons allow functional differences depending on environmental conditions. These regulatory mechanisms are helpful in accommodating the variety of changes that happen around the cell. In addition, such differences may play an important role in the evolution of gene order across genomes

Molecular dynamics simulations on interaction between dislocation and Y2O3 nanocluster in FE

For a new insight on the mechanical properties of oxide dispersion strengthened (ODS) steels from atomistic viewpoints, we have implemented molecular dynamics simulations on the interaction between Y2O3 nanocluster and dislocation in bcc Fe. There is so far no all-round interatomic potential function that can represent all the bonding state, i.e. metal, ion and covalent systems, so that we have adopted rough approximation. That is, each atom in Y2O3 is not discriminated but treated as “monatomic” pseudo-atom; and its motion is represented with the simple pairwise potential function as same as Johnson potential for Fe. The potential parameters are fitted to the energy change in the hcp infinite crystal, by using the ab-initio density functional theory(DFT) calculation for explicitly discriminated Y and O. We have set edge/screw dislocation in the centre of periodic slab cell, and approached it to the “YO” monatomic nano-cluster coherently precipitated in bcc-Fe matrix. The dislocation behavior is discussed by changing the size and periodic distance of the nano-cluster. Among the many useful results, we have obtained a conclusion that the edge dislocation is strongly trapped by YO sphere larger than the diameter of d =0 .9nm, while the screw dislocation shows various behavior, e.g. it cuts through the precipiate without remarkable resistance if the dislocation line tension is high, or it changes the slip plane leaving jogs at the position anterior to the precipiate with loose line tensio

iPath2.0: interactive pathway explorer

iPath2.0 is a web-based tool (http://pathways.embl.de) for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems as annotated to date. Nodes in the map correspond to various chemical compounds and edges represent series of enzymatic reactions. In two other maps, iPath2.0 provides an overview of secondary metabolite biosynthesis and a hand-picked selection of important regulatory pathways and other functional modules, allowing a more general overview of protein functions in a genome or metagenome. iPath2.0′s main interface is an interactive Flash-based viewer, which allows users to easily navigate and explore the complex pathway maps. In addition to the default pre-computed overview maps, iPath offers several data mapping tools. Users can upload various types of data and completely customize all nodes and edges of iPath2.0′s maps. These customized maps give users an intuitive overview of their own data, guiding the analysis of various genomics and metagenomics projects

Overexpression of DNA Polymerase ζAffects Cisplatin Resistance in Ovarian Cancer: An Immunohistochemical Study

DNA polymerase ζ (Pol ζ) participates in translesional bypass replication. Pol ζ has been shown to be an important contributor to cis-diamminedichloroplatinum (II)(DDP; cisplatin) -induced genomic instability and the subsequent emergence of resistance in vitro. We immunohistochemically examined the expression of Pol ζ in ovarian cancer tissues to determine whether its expression affects the DDP resistance of human ovarian cancers and also to determine whether Pol ζ expression is a prognostic factor for ovarian cancers. We assessed 76 archival, formalin-fixed, paraffin-embedded tissue samples obtained from patients with epithelial ovarian cancers who underwent their first operation between 2003 and 2011. An ovarian cancer tissue array was also used in this study. Immunohistochemical staining of Pol ζ was performed using an anti-human Pol ζ monoclonal rabbit antibody. The strength of expression of Pol ζ was compared with the DDP resistance and clinical features of the study population. The Pol ζ over-expression in ovarian cancer tissue which compared with epithelial cells in normal ovaries was not affected by the histological types, FIGO stage, or patient age, but Pol ζ was significantly more overexpressed in the DDP-resistant group than in the DDP-sensitive group (P = 0.043). Pol ζ over-expression did not significantly affect the survival rate of the ovarian cancer patients; however, the Pol ζ positive group tended to have a poorer long-term prognosis. In conclusion, ovarian carcinoma patients with Pol ζ over-expression are likely to be resistant to DDP, especially in cases of recurrent disease. These results confirm the previous findings in vitro, wherein Pol ζ modulated the cytotoxicity and mutagenicity of DDP

Bio-based wrinkled surfaces harnessed from biological design principles of wood and peroxidase activity

A new and simple approach for surface wrinkling inspired by polymer assemblies in wood fibers is introduced. A hard skin is synthesized on a linear polysaccharide support that resembles the structural units of the cell wall. This skin, a wood mimetic layer, is produced through immersion in a solution containing phenolic precursor and subsequent surface reaction by horseradish peroxidase. A patterned surface with micron‐scale wrinkles is formed upon drying and as a result of inhomogeneous shrinkage. We demonstrate that the design of the wrinkled surfaces can be controlled by the molecular structure of the phenolic precursor, temperature, and drying stress. It is noteworthy that this is a totally bio‐based system involving green materials and processes

Wood-mimetic skins prepared using horseradish peroxidase catalysis to induce surface wrinkling of chitosan film upon drying

We previously developed bio-based wrinkled surfaces induced by wood-mimetic skins upon drying in which microscopic wrinkles were fabricated on a chitosan (CS) film by immersing it in a phenolic acid solution, followed by horseradish peroxidase (HRP)-catalyzed surface reaction and drying. However, the detailed structure of the resulting wood-mimetic skins, including crosslinking mode and thickness, has not been clarified due to the difficulty of the analysis. Here, we prepare wrinkled films using ferulic acid (FE), vanillic acid (VA), and homovanillic acid (HO) and characterize their structures to clarify the unknown characteristics of wood-mimetic skin. Chemical and structural analyses of wood-mimetic skins prepared using VA and HO indicate that the crosslinking structure in the skin is composed of ionic bonds between CS and an oligophenolic residue generated by the HRP-catalyzed reaction on the CS surface. Moreover, the quantity of these ionic bonds is related to the skin hardness and wrinkle size. Finally, SEM and TOF-SIMS analyses indicate that the skin thickness is on the submicron order (<200 nm)

顎舌骨筋運動ニューロンと一次求心線維のシナプス接合について

Horseradish peroxidase conjugated with wheat germ agglutinin (HRP-WGA) was injected into the muscle branch of the mylohyoid nerve in rats. HRP-labeled neuronal cell bodies were observed ipsilaterally in the caudal portion of the trigeminal mesencephalic nucleus and the ventromedial division of the trigeminal motor nucleus (Vmo.vm). Electron microscope observations were carried out on sections through Vmo.vm containing HRP-labeled cell bodies. Synaptic contacts were found between HRP-labeled axon terminals and HRP-labeled nerve cells. The results suggested that mylohyoid muscle spindle afferents are synaptic contacts on the mylohyoid motoneurons

Case Report Case Report of Atlantoaxial Rotatory Fixation after Cochlear Implantation

Atlantoaxial rotatory fixation (AARF) is a relatively rare condition and is mainly seen in children. We report of a 7-year-old girl suffering from AARF after cochlear implantation (CI). Fortunately, early diagnosis based on three-dimensional computed tomography (3DCT) was made, and the patient was cured with conservative therapy. Nontraumatic AARF, which is also known as Grisel&apos;s syndrome and occurs subsequent to neck infections or ear, nose, and throat (ENT) surgery, represents only a small fraction of AARF cases. Two factors are mainly thought to contribute to the pathogenesis of the condition estimated, namely, (i) neck immaturity in children and (ii) infiltration by inflammatory mediators around the upper neck joint, easily permitted by the neck vasculature. AARF should be suspected in case of torticollis developing after ENT surgery