Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.

Faddeev-Jackiw canonical path integral quantization for a general scenario, its proper vertices and generating functionals

We generalize the Faddeev-Jackiw canonical path integral quantization for the scenario of a Jacobian with J=1 to that for the general scenario of non-unit Jacobian, give the representation of the quantum transition amplitude with symplectic variables and obtain the generating functionals of the Green function and connected Green function. We deduce the unified expression of the symplectic field variable functions in terms of the Green function or the connected Green function with external sources. Furthermore, we generally get generating functionals of the general proper vertices of any n-points cases under the conditions of considering and not considering Grassmann variables, respectively; they are regular and are the simplest forms relative to the usual field theory.

BRST quantization and canonical Ward identity of the supersymmetric electromagnetic interaction system

According to the method of path integral quantization for the canonical constrained system in Becchi-Rouet-Stora-Tyutin scheme, the supersymmetric electromagnetic interaction system was quantized. Both the Hamiltonian of the supersymmetric electromagnetic interaction system in phase space and the quantization procedure were simplified. The BRST generator was constructed, and the BRST transformations of supersymmetric fields were gotten; the effective action was calculated, and the generating functional for the Green function was achieved; also, the gauge generator was constructed, and the gauge transformation of the system was obtained. Finally, the Ward-Takahashi identities based on the canonical Noether theorem were calculated, and two relations between proper vertices and propagators were obtained.

Dendrimer films as matrices for electrochemical fabrication of novel gold/palladium bimetallic nanostructures

Electrodeposition of novel Au/Pd bimetallic nanostructures with dendrimer films as matrices has been reported. The dendrimers exhibited highly open structures arising from protonation of amines and this made them have good penetrability for solvent molecules. The unique properties of dendrimers obviously affected the morphologies and compositions of deposited bimetallic nanostructures compared with those from unmodified surfaces. Field-emitted scanning electron microscopy, energy dispersive spectroscopy, X-ray photoelectron spectroscopy and UV-vis spectroscopy were used to characterize these nanostructures.

Electrochemical biosensors based on advanced bioimmobilization matrices

Biosensors have experienced rapid, extensive development. To maintain the bioactivity of biomolecules and to give the electrochemical output signal required, appropriate bioimmobilization matrices for biomolecules are critical.In this review, we describe some advanced membrane materials (including hydrogels, sol-gel-derived organic-inorganic composites and lipid membranes), introduce electrochemical biosensors based on bioimmobilization materials and describe their performance.Biosensors operating in extreme conditions and displaying direct electron transfer with electrodes based on these advanced membrane materials are attractive. Recent developments in nanomaterials include biosensors, so we emphasize the intersection of nanomaterials with advanced membrane materials in biosensors.

Relationship between luminescence and matrices in the system Al2O3-B2O3-Ce2O3

The system Al2O3-B2O3-Ce2O3, with Al/B ratio varying from 4.5 to 2 and Ce/(Al + B) = 0.02, has been prepared at the temperature from 1 200 to 1 400 degrees C. Relationship between luminescence and matrices in the system Al2O3-B2O3-Ce2O3 was investigated. It was found that some changes of the matrices occurred with Al/B ratio varying from 4.5 to 2. These results lead to a great change in luminescence properties, indicating variation of Ce-surroundings of crystal field. With the decrease of the ratio from 3 to 2, the excitation and emission peaks shift to shorter wavelengths. it was also found that a new type of rare earth luminescent materials was obtained with appropriate Al/B ratio.

A NEW SCHEME FOR ASSIGNMENT OF A CANONICAL CONNECTION TABLE

A new algorithm for deriving canonical numbering of atoms in a molecular graph has been developed. Some graph invariants, such as node properties, degree (connectivity), topological path, the smallest node ring index, etc., are encoded together to partit

Relative Affine Structure: Canonical Model for 3D from 2D Geometry and Applications

We propose an affine framework for perspective views, captured by a single extremely simple equation based on a viewer-centered invariant we call "relative affine structure". Via a number of corollaries of our main results we show that our framework unifies previous work --- including Euclidean, projective and affine --- in a natural and simple way, and introduces new, extremely simple, algorithms for the tasks of reconstruction from multiple views, recognition by alignment, and certain image coding applications.

Boundary triplets and M-functions for non-selfadjoint operators, with applications to elliptic PDEs and block operator matrices

B.M. Brown, M. Marletta, S. Naboko, I. Wood: Boundary triplets and M-functions for non-selfadjoint operators, with applications to elliptic PDEs and block operator matrices, J. London Math. Soc., June 2008; 77: 700-718. The full text of this article will be made available in this repository in June 2009 Sponsorship: EPSRC,INTAS

Diseño y desarrollo de herramientas en cerámica, La Calera. Asistencia técnica para el mejoramiento de la pasta cerámica y proceso de secado de piezas de alfarería San Sebastián. Mejoramiento de la pasta cerámica y proceso de secado de piezas de alfarería. Acondicionamiento y manejo de hornos, Momil. Mejoramiento de la pasta cerámica y proceso de secado de piezas de alfarería. Asistencia para la elaboración de matrices y moldes para piezas de cerámica acondicionamiento y manejo de hornos, Ciénaga De Oro y Planeta Rica.

[152] hojas : ilustraciones.

An Independent-Connection Model for Traffic Matrices

A common assumption made in traffic matrix (TM) modeling and estimation is independence of a packet's network ingress and egress. We argue that in real IP networks, this assumption should not and does not hold. The fact that most traffic consists of two-way exchanges of packets means that traffic streams flowing in opposite directions at any point in the network are not independent. In this paper we propose a model for traffic matrices based on independence of connections rather than packets. We argue that the independent connection (IC) model is more intuitive, and has a more direct connection to underlying network phenomena than the gravity model. To validate the IC model, we show that it fits real data better than the gravity model and that it works well as a prior in the TM estimation problem. We study the model's parameters empirically and identify useful stability properties. This justifies the use of the simpler versions of the model for TM applications. To illustrate the utility of the model we focus on two such applications: synthetic TM generation and TM estimation. To the best of our knowledge this is the first traffic matrix model that incorporates properties of bidirectional traffic.

Sugar matrices in stabilization of bioactives by dehydration

Development of functional foods with bioactive components requires component stability in foods and ingredients. Stabilization of sensitive bioactive components can be achieved by entrapment or encapsulation of these components in solid food matrices. Lactose or trehalose was used as the structure-forming material for the entrapment of hydrophilic ascorbic acid and thiamine hydrochloride or the encapsulation of oil particles containing hydrophobic α-tocopherol. In the delivery of hydrophobic components, milk protein isolate, soy protein isolate, or whey protein isolate were used as emulsifiers and, in some cases, applied in excess amount to form matrices together with sugars. Dehydrated amorphous structures with bioactives were produced by freezing and freeze-drying. Experimental results indicated that: (i) lactose and trehalose showed similar water sorption and glass transition but very different crystallization behavior as pure sugars; (ii) the glass transition of sugar-based systems was slightly affected by the presence of other components in anhydrous systems but followed closely that of sugar after water plasticization; (iii) sugar crystallization in mixture systems was composition-dependent; (iv) the stability of bioactives was better retained in the amorphous matrices, although small losses of stability were observed for hydrophilic components above glass transition and for hydrophobic components as a function of water activity; (v) sugar crystallization caused significant loss of hydrophilic bioactives as a result of the exclusion from the continuous crystalline phase; (vi) loss of hydrophobic bioactives upon sugar crystallization was a result of dramatic change of emulsion properties and the exclusion of oil particles from the protecting structure; (vii) the double layers at the hydrophilic-hydrophobic interfaces improved the stability of hydrophobic bioactives in dehydrated systems. The present study provides information on the physical and chemical stability of sugar-based dehydrated delivery systems, which could be helpful in designing foods and ingredients containing bioactive components with improved storage stability.

Characterisation of the role of canonical BMP-Smad 1/5/8 signalling in the development of ventral midbrain dopaminergic neurons

Ventral midbrain (VM) dopaminergic (DA) neurons, which project to the dorsal striatum via the nigrostriatal pathway, are progressively degenerated in Parkinson’s disease (PD). The identification of the instructive factors that regulate midbrain DA neuron development, and the subsequent elucidation of the molecular bases of their effects, is vital. Such an understanding would facilitate the generation of transplantable DA neurons from stem cells and the identification of developmentally-relevant neurotrophic factors, the two most promising therapeutic approaches for PD. Two related members of the bone morphogenetic protein (BMP) family, BMP2 and growth/differentiation factor (GDF) 5, which signal via a canonical Smad 1/5/8 signalling pathway, have been shown to have neurotrophic effects on midbrain DA neurons both in vitro and in vivo, and may function to regulate VM DA neuronal development. However, the molecular (signalling pathway(s)) and cellular (direct neuronal or indirect via glial cells) mechanisms of their effects remain to be elucidated. The present thesis hypothesised that canonical Smad signalling mediates the direct effects of BMP2 and GDF5 on the development of VM DA neurons. By activating, modulating and/or inhibiting various components of the BMP-Smad signalling pathway, this research demonstrated that GDF5- and BMP2-induced neurite outgrowth from midbrain DA neurons is dependent on BMP type I receptor activation of the Smad signalling pathway. The role of glial cell-line derived neurotrophic factor (GDNF)-signalling, dynamin-dependent endocytosis and Smad interacting protein-1 (Sip1) regulation, in the neurotrophic effects of BMP2 and GDF5 were determined. Finally, the in vitro development of VM neural stem cells (NSCs) was characterised, and the ability of GDF5 and BMP2 to induce these VM NSCs towards DA neuronal differentiation was investigated. Taken together, these experiments identify GDF5 and BMP2 as novel regulators of midbrain DA neuronal induction and differentiation, and demonstrate that their effects on DA neurons are mediated by canonical BMPR-Smad signalling.