Electromagnetic-thermal analysis of an RF rectangular resonant cavity applicator for hyperthermia targeting deep-seated tumors using a human body model with blood flow and fat layer

Maxwell's and heat transfer equations were coupled and solved to determine the heating characteristics of an RF rectangular resonant cavity applicator for hyperthermia before the clinical stage. A simple human body model with blood flow and a fat layer was constructed. The region unaffected by tumor was shielded from electromagnetic fields by using conductive caps. The surface of the human model that was exposed to the electromagnetic fields was cooled with pure water bolus. Calculated results show that this applicator can heat a deep-seated tumor

Natural and Artifical Change in Primary Productivity for 200 Years Recorded in the Coastal Lagoon Sediment

地質調査所Scedule:17-18 March 2003, Vemue: Kanazawa, Japan, Kanazawa Citymonde Hotel, Project Leader : Hayakawa, Kazuichi, Symposium Secretariat: XO kamata, Naoto, Edited by:Kamata, Naoto

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

We identified 531 and 616 putative HIF-1α target sites by ChIP-Seq in the cancerous cell line DLD-1 and the non-cancerous cell line TIG-3, respectively. We also examined the positions and expression levels of transcriptional start sites (TSSs) in these cell lines using our TSS-Seq method. We observed that 121 and 48 genes in DLD-1 and TIG-3 cells, respectively, had HIF-1α binding sites in proximal regions of the previously reported TSSs that were up-regulated at the transcriptional level. In addition, 193 and 123 of the HIF-1α target sites, respectively, were located in proximal regions of previously uncharacterized TSSs, namely, TSSs of putative alternative promoters of protein-coding genes or promoters of putative non-protein-coding transcripts. The hypoxic response of DLD-1 cells was more significant than that of TIG-3 cells with respect to both the number of target sites and the degree of induced changes in transcript expression. The Nucleosome-Seq and ChIP-Seq analyses of histone modifications revealed that the chromatin formed an open structure in regions surrounding the HIF-1α binding sites, but this event occurred prior to the actual binding of HIF-1α. Different cellular histories may be encoded by chromatin structures and determine the activation of specific genes in response to hypoxic shock. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11568-011-9150-9) contains supplementary material, which is available to authorized users

Prediction of protein motions from amino acid sequence and its application to protein-protein interaction

BACKGROUND: Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of motions: internal and external ones. The former is deformation of the segment itself, but the latter involves only rotational and translational motions as a rigid body. Normal Model Analysis (NMA) can derive these two motions, but its application remains limited because it necessitates the gathering of complete structural information. RESULTS: In this work, we present a novel method for predicting two kinds of protein motions in ordered structures. The prediction uses only information from the amino acid sequence. We prepared a dataset of the internal and external motions of segments in many proteins by application of NMA. Subsequently, we analyzed the relation between thermal motion assessed from X-ray crystallographic B-factor and internal/external motions calculated by NMA. Results show that attributes of amino acids related to the internal motion have different features from those related to the B-factors, although those related to the external motion are correlated strongly with the B-factors. Next, we developed a method to predict internal and external motions from amino acid sequences based on the Random Forest algorithm. The proposed method uses information associated with adjacent amino acid residues and secondary structures predicted from the amino acid sequence. The proposed method exhibited moderate correlation between predicted internal and external motions with those calculated by NMA. It has the highest prediction accuracy compared to a naïve model and three published predictors. CONCLUSIONS: Finally, we applied the proposed method predicting the internal motion to a set of 20 proteins that undergo large conformational change upon protein-protein interaction. Results show significant overlaps between the predicted high internal motion regions and the observed conformational change regions

Cerebral hierarchies: predictive processing, precision and the pulvinar

This paper considers neuronal architectures from a computational perspective and asks what aspects of neuroanatomy and neurophysiology can be disclosed by the nature of neuronal computations? In particular, we extend current formulations of the brain as an organ of inference—based upon hierarchical predictive coding—and consider how these inferences are orchestrated. In other words, what would the brain require to dynamically coordinate and contextualize its message passing to optimize its computational goals? The answer that emerges rests on the delicate (modulatory) gain control of neuronal populations that select and coordinate (prediction error) signals that ascend cortical hierarchies. This is important because it speaks to a hierarchical anatomy of extrinsic (between region) connections that form two distinct classes, namely a class of driving (first-order) connections that are concerned with encoding the content of neuronal representations and a class of modulatory (second-order) connections that establish context—in the form of the salience or precision ascribed to content. We explore the implications of this distinction from a formal perspective (using simulations of feature–ground segregation) and consider the neurobiological substrates of the ensuing precision-engineered dynamics, with a special focus on the pulvinar and attention

Crystallization of polypropylene near the surface in injection-molded plaques: A comparison of morphology and a numerical analysis

Skin morphology formation on injection-molded isotactic polypropylene (PP) was investigated using micro-beam synchrotron wide-angle X-ray diffraction and numerical simulation. The 1-20 Î?m depth range was characterized with an X-ray beam of 0.273 Î?m Ï? 0.389 Î?m in size. From an evaluation of doping nucleating agents (NA) in PP, the NAs did not work at a depth of 1 Î?m. α-specified NA affected crystallization within a 5-Î?m depth. β-specified PP showed α-form crystallinity at the 5-20 Î?m depth. The mesomorphic crystal near the surface showed extremely high orientation. From viscoelastic flow simulation, PP molecules near the surface were oriented in the flow direction by extensional flow in the flow front, but freezing occurred faster than flow-induced crystallization. It was estimated that the delay of crystallization occurred during the transient temperature. The deformation rate did not cause a difference in crystal morphology near the surface, but the cooling rate did. Copyright © 2009 Society of Plastics Engineers

A Novel Plasmid Carrying Capsule Gene Cluster Found in Lactococcus garvieae Isolated from Filefish

Lactococcus garvieae is recognized as a crucial bacterial pathogen of freshwater and marine fish species. It has been divided into two serological phenotypes, namely KG? and KG+. Difference of the two phenotypes is owing to the presence or absence of polysaccharide capsule, and a phenotypic change from KG? to KG+ occurs during stocking of isolates for a long period or by repeated subculturing. We found that the phenotypic change occurred more readily in L. garvieae isolates from cultured filefish, thread-sail filefish Stephanolepis cirrhifer and black scraper Thamnaconus modestus, than those from other fish species. Thus we studied the gene cluster for capsular polysaccharide biosynthesis (capsule gene cluster) of a filefish isolate, strain BSLG13015, and revealed that the strain possessed the same capsule gene cluster as those from other fish species, but that it was integrated in a newly identified plasmid. The plasmid, a size of 31,654 bp and circular, was named pBSLG13015. It was detected in all of KG? filefish isolates but not in KG+ filefish isolates or L. garvieae from other fish species. It is highly probable that the easier change from KG? to KG+ in L. garvieae filefish isolates is attributed to the loss of the plasmid