A subset-oriented algorithm for minimizing the number of steps required for synthesis of cyclic-peptide libraries

Libraries of cyclic peptides are being synthesized using combinatorial chemistry for high throughput screening in the drug discovery process. This paper describes the min_syn_steps.cpp program (available at http://www.imb.uq.edu.au/groups/smythe/tran), which after inputting a list of cyclic peptides to be synthesized, removes cyclic redundant sequences and calculates synthetic strategies which minimize the synthetic steps as well as the reagent requirements. The synthetic steps and reagent requirements could be minimized by finding common subsets within the sequences for block synthesis. Since a brute-force approach to search for optimum synthetic strategies is impractically large, a subset-orientated approach is utilized here to limit the size of the search. (C) 2002 Elsevier Science Ltd. All rights reserved.

Colony-stimulating factor-1 suppresses responses to CpG DNA and expression of toll-like receptor 9 but enhances responses to lipopolysaccharide in murine macrophages

During bacterial infections, the balance between resolution of infection and development of sepsis is dependent upon the macrophage response to bacterial products. We show that priming of murine bone marrow-derived macrophages (BMMs) with CSF-1 differentially regulates the response to two such stimuli, LPS and immunostimulatory (CpG) DNA. CSF-1 pretreatment enhanced IL-6, IL-12, and TNF-alpha production in response to LPS but suppressed the same response to CpG DNA. CSF-1 also regulated cytokine gene expression in response to CpG DNA and LPS; CpG DNA-induced IL-12 p40, IL-12 p35, and TNF-alpha mRNAs were all suppressed by CSF-1 pretreatment. CSF-1 pretreatment enhanced LPS-induced IL-12 p40 mRNA but not TNF-alpha and IL-12 p35 mRNAs, suggesting that part of the priming effect is posttranscriptional. CSF-1 pretreatment also suppressed CpG DNA-induced nuclear translocation of NF-kappaB and phosphorylation of the mitogen-activated protein kinases p38 and extracellular signal-related kinases-1/2 in BMMs, indicating that early events in CpG DNA signaling were regulated by CSF-1. Expression of Toll-like receptor (TLR)9, which is necessary for responses to CpG DNA, was markedly suppressed by CSF-1 in both BMMs and thioglycolate-elicited peritoneal macrophages. CSF-1 also down-regulated expression of TLR1, TLR2, and TLR6, but not the LPS receptor, TLR4, or TLR5. Hence, CSF-1 may regulate host responses to pathogens through modulation of TLR expression. Furthermore, these results suggest that CSF-1 and CSF-1R antagonists may enhance the efficacy of CpG DNA in vivo.

An augmented Lanczos algorithm for the efficient computation of a dot-product of a function of a large sparse symmetric matrix

The Lanczos algorithm is appreciated in many situations due to its speed. and economy of storage. However, the advantage that the Lanczos basis vectors need not be kept is lost when the algorithm is used to compute the action of a matrix function on a vector. Either the basis vectors need to be kept, or the Lanczos process needs to be applied twice. In this study we describe an augmented Lanczos algorithm to compute a dot product relative to a function of a large sparse symmetric matrix, without keeping the basis vectors.

Growth hormone receptor and insulin-like growth factor-I immunoreactivity in osteoclast-like cells during tooth eruption in the toothless (Osteopetrotic) rat following treatment with colony-stimulating factor-1

In the toothless (tl/tl) osteopetrotic rat, teeth form but fail to erupt. Treatment of tl/tl rats with colony-stimulating factor-1 (CSF-1) activates bone resorption by osteoclasts, permits tooth eruption, and up-regulates the immunoreactivity of bone marrow mononuclear cells to growth hormone receptor (GHr) and insulin-like growth factor (IGF)-I. This study examined the distribution of tartrate-resistant acid phosphatase (TRAP) and immunoreactivity for GHr and IGF-I in osteoclast-like cells located on the alveolar bone margin, adjacent to the lower first molar crown, in 14-day-old normal and tl/tl rats, following treatment with CSF-1. Osteoclast-like cells demonstrated a positive reaction for TRAP, GHr, and IGF-I in all groups. However, in tl/tl tissue, osteoclast-like cells were generally negative for GHr. There was no significant difference in the total number of TRAP, GHr, and IGF-I-positive osteoclast-like cells on the adjacent bone margin in normal, normal treated with CSF-1, and tl/tl rats. CSF-1 treatment of the tl/tl rat significantly increased the total number of osteoclast-like cells, which were positive for TRAP (p < 0.001), GHr (p < 0.05) and IGF-I (P < 0.01).

The tree cut and merge algorithm for estimation of network reliability

This article presents Monte Carlo techniques for estimating network reliability. For highly reliable networks, techniques based on graph evolution models provide very good performance. However, they are known to have significant simulation cost. An existing hybrid scheme (based on partitioning the time space) is available to speed up the simulations; however, there are difficulties with optimizing the important parameter associated with this scheme. To overcome these difficulties, a new hybrid scheme (based on partitioning the edge set) is proposed in this article. The proposed scheme shows orders of magnitude improvement of performance over the existing techniques in certain classes of network. It also provides reliability bounds with little overhead.

A new mite from an arboreal ant (Formicidae : Polyrachis sp.): Myrmozercon iainkayi n. sp (Mesostigmata : Laelapidae)

Previously, two species of Myrmozercon (= Myrmonyssus) have been described from ground-nesting Australian ants in the genus Iridiomyrmex. Herein a new species, Myrmozercon iainkayi, infesting workers and alate adults of a leaf-nesting species of Polyrachis ant is described. The new species has a number of unusual or unique characters, including coxal hypertrichy (6-6-6-4 for legs I-IV, respectively), and based on the structure of its mouthparts, appears to be a haemolymph-feeding parasite.

A genetic algorithm/method of moments approach to the optimization of an RF coil for MRI applications - Theoretical considerations - Abstract

A Combined Genetic Algorithm and Method of Moments design methods is presented for the design of unusual near-field antennas for use in Magnetic Resonance Imaging systems. The method is successfully applied to the design of an asymmetric coil structure for use at 190MHz and demonstrates excellent radiofrequency field homogeneity.

G??nero, ra??a e espa??os de poder: o caso de Maria Ant??nia e Geraldo

O caso relata uma situa????o de promo????o em ??rg??o p??blico na qual dois funcion??rios ??? uma mulher negra e um homem branco - se mostram como candidatos ao cargo. S??o apresentados os perfis e habilidades profissionais dos dois servidores e, ao final, a decis??o tomada pelo Secret??rio, chefe de ambos. O estudo suscita discuss??es sobre pr??ticas discriminat??rias nos espa??os de poder das institui????es p??blicas e o papel do dirigente para combater ou difundir tais pr??ticas. Pode ser aplicado em cursos sobre lideran??a, gest??o de pessoas e ??tica e servi??o p??blico

O licenciamento ambiental para hidrel??tricas do Rio Madeira: Santo Ant??nio e Jirau

O caso relata o processo de concess??o de licenciamento ambiental para a constru????o de Santo Ant??nio e Jirau, duas usinas hidrel??tricas no estado de Rond??nia. A proposta foi apresentada em um contexto no qual d??ficits energ??ticos colocavam o pa??s em estado de alerta, o que ampliou a press??o para projetos de aproveitamento hidrel??trico de grande porte. Era um dos projetos do Programa de Acelera????o do Crescimento (PAC), o que lhe confere car??ter priorit??rio. A concess??o de licen??a de viabilidade ambiental (licen??a pr??via) constitui pr??-requisito para ser iniciada a licita????o das obras das usinas. Iniciado em 2002, o processo de licenciamento estendeu-se at?? agosto de 2007, quando foi aprovado com medidas de controle da fauna, flora e subst??ncias t??xicas, e a prote????o das popula????es locais. O tema foi escolhido para estudo de caso por envolver m??ltiplos atores e interesses e enfocar um amplo e demorado processo de media????es e negocia????es multilaterais. O caso foi desenhado para ser aplicado em oficina de negocia????es, para alunos com conhecimentos pr??vios sobre teoria das negocia????es, permitindo articular aspectos te??ricos com a dimens??o pr??tica relatada pela experi??ncia. O caso tamb??m fornece elementos para an??lise da participa????o dos atores pol??ticos, conflitos, gera????o de alian??as e consensos e para discuss??es sobre tomada de decis??o

Automated traffic route identification through the shared nearest neighbour algorithm

Many organisations need to extract useful information from huge amounts of movement data. One example is found in maritime transportation, where the automated identification of a diverse range of traffic routes is a key management issue for improving the maintenance of ports and ocean routes, and accelerating ship traffic. This paper addresses, in a first stage, the research challenge of developing an approach for the automated identification of traffic routes based on clustering motion vectors rather than reconstructed trajectories. The immediate benefit of the proposed approach is to avoid the reconstruction of trajectories in terms of their geometric shape of the path, their position in space, their life span, and changes of speed, direction and other attributes over time. For clustering the moving objects, an adapted version of the Shared Nearest Neighbour algorithm is used. The motion vectors, with a position and a direction, are analysed in order to identify clusters of vectors that are moving towards the same direction. These clusters represent traffic routes and the preliminary results have shown to be promising for the automated identification of traffic routes with different shapes and densities, as well as for handling noise data.

Multi-centre validation of an automatic algorithm for fast 4D myocardial segmentation in cine CMR datasets

Quantitative analysis of cine cardiac magnetic resonance (CMR) images for the assessment of global left ventricular morphology and function remains a routine task in clinical cardiology practice. To date, this process requires user interaction and therefore prolongs the examination (i.e. cost) and introduces observer variability. In this study, we sought to validate the feasibility, accuracy, and time efficiency of a novel framework for automatic quantification of left ventricular global function in a clinical setting.

Lanczos algorithm on the grassmann manifold

5th. European Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS 2008) 8th. World Congress on Computational Mechanics (WCCM8)

IOPT Petri Net State Space Generation Algorithm with Maximal-Step Execution Semantics

This paper presents an algorithm to efficiently generate the state-space of systems specified using the IOPT Petri-net modeling formalism. IOPT nets are a non-autonomous Petri-net class, based on Place-Transition nets with an extended set of features designed to allow the rapid prototyping and synthesis of system controllers through an existing hardware-software co-design framework. To obtain coherent and deterministic operation, IOPT nets use a maximal-step execution semantics where, in a single execution step, all enabled transitions will fire simultaneously. This fact increases the resulting state-space complexity and can cause an arc "explosion" effect. Real-world applications, with several million states, will reach a higher order of magnitude number of arcs, leading to the need for high performance state-space generator algorithms. The proposed algorithm applies a compilation approach to read a PNML file containing one IOPT model and automatically generate an optimized C program to calculate the corresponding state-space.

Genetic algorithm methodology applied to intelligent house control

In recent years the use of several new resources in power systems, such as distributed generation, demand response and more recently electric vehicles, has significantly increased. Power systems aim at lowering operational costs, requiring an adequate energy resources management. In this context, load consumption management plays an important role, being necessary to use optimization strategies to adjust the consumption to the supply profile. These optimization strategies can be integrated in demand response programs. The control of the energy consumption of an intelligent house has the objective of optimizing the load consumption. This paper presents a genetic algorithm approach to manage the consumption of a residential house making use of a SCADA system developed by the authors. Consumption management is done reducing or curtailing loads to keep the power consumption in, or below, a specified energy consumption limit. This limit is determined according to the consumer strategy and taking into account the renewable based micro generation, energy price, supplier solicitations, and consumers’ preferences. The proposed approach is compared with a mixed integer non-linear approach.