Analytic structure of radiation boundary kernels for blackhole perturbations

Exact outer boundary conditions for gravitational perturbations of the Schwarzschild metric feature integral convolution between a time-domain boundary kernel and each radiative mode of the perturbation. For both axial (Regge-Wheeler) and polar (Zerilli) perturbations, we study the Laplace transform of such kernels as an analytic function of (dimensionless) Laplace frequency. We present numerical evidence indicating that each such frequency-domain boundary kernel admits a "sum-of-poles" representation. Our work has been inspired by Alpert, Greengard, and Hagstrom's analysis of nonreflecting boundary conditions for the ordinary scalar wave equation.Comment: revtex4, 14 pages, 12 figures, 3 table

Thermodynamics of aggregation of two proteins

We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is used for numerical calculations. We find that a dimer can be formed spontaneously as a thermodynamically stable state when the system is small enough. It implies the possibility that the aggregation of proteins in a cell is triggered when they are confined in a small region by, for example, being surrounded by other macromolecules.We also find that the dimer exhibits a transition between unstable state and metastable state in the infinite system.Comment: jpsj2.cls, 7 pages, 14 figures; misconfigurations of Fig.Nos. correcte

Information Loss in Coarse Graining of Polymer Configurations via Contact Matrices

Contact matrices provide a coarse grained description of the configuration omega of a linear chain (polymer or random walk) on Z^n: C_{ij}(omega)=1 when the distance between the position of the i-th and j-th step are less than or equal to some distance "a" and C_{ij}(omega)=0 otherwise. We consider models in which polymers of length N have weights corresponding to simple and self-avoiding random walks, SRW and SAW, with "a" the minimal permissible distance. We prove that to leading order in N, the number of matrices equals the number of walks for SRW, but not for SAW. The coarse grained Shannon entropies for SRW agree with the fine grained ones for n <= 2, but differs for n >= 3.Comment: 18 pages, 2 figures, latex2e Main change: the introduction is rewritten in a less formal way with the main results explained in simple term

Nanofiltration of aerobically-treated palm oil mill effluent: Characterization of the size of colour compounds using synthetic dyes and polyethylene glycols

Membrane-based separation is one of the emerging technologies that have garnered significant interest in recent years for the treatment process of palm oil mill effluent (POME). As documented in the literature, different types of membrane processes such as ultrafiltration (UF), nanofiltration (NF) and reverse osmosis (RO) were used for the POME treatment and the efficiency of separation varied depending on the membrane properties. Unlike the previous works that used membranes to treat POME, the main focus of this current work is to utilize NF membrane to characterize the size of colour compounds in the aerobically-treated POME (AT-POME). Two different markers, i.e., synthetic dyes and polyethylene glycols (PEGs) with molecular weight (MW) in the range of 200-1000 g/mol were used to characterize the colour compounds in the AT-POME. Results showed that dyes are more suitable compared to PEGs for the characterization because dyes possessed negative charge similar as the colour compounds in the AT-POME. By using dyes as the markers, it was found that the size of the colour compounds in the AT-POME was at MW of 300-400 g/mol. Precise determination of the size of colour compounds in the AT-POME is of importance as it could provide useful information on the selection of ideal membrane properties (in particular pore size or molecular weight cut-off) to achieve complete solute separation

Protein design in a lattice model of hydrophobic and polar amino acids

A general strategy is described for finding which amino acid sequences have native states in a desired conformation (inverse design). The approach is used to design sequences of 48 hydrophobic and polar aminoacids on three-dimensional lattice structures. Previous studies employing a sequence-space Monte-Carlo technique resulted in the successful design of one sequence in ten attempts. The present work also entails the exploration of conformations that compete significantly with the target structure for being its ground state. The design procedure is successful in all the ten cases.Comment: RevTeX, 12 pages, 1 figur

Spin relaxation in (110) and (001) InAs/GaSb superlattices

We report an enhancement of the electron spin relaxation time (T1) in a (110) InAs/GaSb superlattice by more than an order of magnitude (25 times) relative to the corresponding (001) structure. The spin dynamics were measured using polarization sensitive pump probe techniques and a mid-infrared, subpicosecond PPLN OPO. Longer T1 times in (110) superlattices are attributed to the suppression of the native interface asymmetry and bulk inversion asymmetry contributions to the precessional D'yakonov Perel spin relaxation process. Calculations using a nonperturbative 14-band nanostructure model give good agreement with experiment and indicate that possible structural inversion asymmetry contributions to T1 associated with compositional mixing at the superlattice interfaces may limit the observed spin lifetime in (110) superlattices. Our findings have implications for potential spintronics applications using InAs/GaSb heterostructures.Comment: 4 pages, 2 figure

Association between cyclo-oxygenase-2 overexpression and missense p53 mutations in gastric cancer

Wild-type p53 competitively binds to the promoter region of COX-2 in vitro and inhibits its transcription. We examined the association between p53 mutation and COX-2 expression in gastric cancer. COX-2 over-expression was seen in 19 (48.7%) cases. These tumours had more lymph-node metastasis (P = 0.048) and tended to have a poorer survival (P = 0.07). Missense mutations of p53 were detected in 20 (51.3%) patients and had a significantly stronger COX-2 expression than tumours without p53 mutation (P = 0.016). Our results suggest a link between p53 mutation and COX-2 overexpression in gastric cancer. © 2001 Cancer Research Campaign http://www.bjcancer.co

A method for encoding clinical datasets with SNOMED CT

<p>Abstract</p> <p>Background</p> <p>Over the past decade there has been a growing body of literature on how the Systematised Nomenclature of Medicine Clinical Terms (SNOMED CT) can be implemented and used in different clinical settings. Yet, for those charged with incorporating SNOMED CT into their organisation's clinical applications and vocabulary systems, there are few detailed encoding instructions and examples available to show how this can be done and the issues involved. This paper describes a heuristic method that can be used to encode clinical terms in SNOMED CT and an illustration of how it was applied to encode an existing palliative care dataset.</p> <p>Methods</p> <p>The encoding process involves: identifying input data items; cleaning the data items; encoding the cleaned data items; and exporting the encoded terms as output term sets. Four outputs are produced: the SNOMED CT reference set; interface terminology set; SNOMED CT extension set and unencodeable term set.</p> <p>Results</p> <p>The original palliative care database contained 211 data elements, 145 coded values and 37,248 free text values. We were able to encode ~84% of the terms, another ~8% require further encoding and verification while terms that had a frequency of fewer than five were not encoded (~7%).</p> <p>Conclusions</p> <p>From the pilot, it would seem our SNOMED CT encoding method has the potential to become a general purpose terminology encoding approach that can be used in different clinical systems.</p

Insights into the O-Acetylation Reaction of Hydroxylated Heterocyclic Amines by Human Arylamine N-Acetyltransferases: A Computational Study

A computational study was performed to better understand the differences between human arylamine N-acetyltransferase (NAT) 1 and 2. Homology models were constructed from available crystal structures and comparisons of the active site residues 125, 127, and 129 for these two enzymes provide insight into observed substrate differences. The NAT2 model provided a basis for understanding how some of the common mutations may affect the structure of the protein. Molecular dynamics simulations of the human NAT models and the template structure (NAT from Mycobacterium smegmatis) were performed and showed the models to be stable and reasonable. Docking studies of hydroxylated heterocyclic amines in the models of NAT1 and NAT2 probed the differences exhibited by these two proteins with mutagenic agents. The hydroxylated heterocyclic amines were only able to fit into the NAT2 active site, and an alternative binding site by the P-loop was found using our models and will be discussed. Additionally, quantum mechanical calculations were performed to study the O-acetylation reaction of the hydroxylated heterocyclic amines N-OH MeIQx and N-OH PhIP. This study has given us insight into why there are substrate differences among isoenzymes and explains some of the polymorphic activity differences