GRID and docking analyses reveal a molecular basis for flavonoid inhibition of src-family kinase activity

Flavonoids reduce cardiovascular disease risk through anti-inflammatory, anti-coagulant and anti-platelet actions. One key flavonoid inhibitory mechanism is blocking kinase activity that drives these processes. Flavonoids attenuate activities of kinases including phosphoinositide-3-kinase (PI3K), Fyn, Lyn, Src, Syk, PKC, PIM1/2, ERK, JNK, and PKA. X-ray crystallographic analyses of kinase-flavonoid complexes show that flavonoid ring systems and their hydroxyl substitutions are important structural features for their binding to kinases. A clearer understanding of structural interactions of flavonoids with kinases is necessary to allow construction of more potent and selective counterparts. We examined flavonoid (quercetin, apigenin and catechin) interactions with Src-family kinases (Lyn, Fyn and Hck) applying the Sybyl docking algorithm and GRID. A homology model (Lyn) was used in our analyses to demonstrate that high quality predicted kinase structures are suitable for flavonoid computational studies. Our docking results revealed potential hydrogen bond contacts between flavonoid hydroxyls and kinase catalytic site residues. Identification of plausible contacts indicated that quercetin formed the most energetically stable interactions, apigenin lacked hydroxyl groups necessary for important contacts, and the non-planar structure of catechin could not support predicted hydrogen bonding patterns. GRID analysis using a hydroxyl functional group supported docking results. Based on these findings, we predicted that quercetin would inhibit activities of Src-family kinases with greater potency than apigenin and catechin. We validated this prediction using in vitro kinase assays. We conclude that our study can be used as a basis to construct virtual flavonoid interaction libraries to guide drug discovery using these compounds as molecular templates.

Micro-abrasion of flint artefacts by mobile sediments: a taphonomic approach

Fluvial redeposition of stone artifacts is a major complicating factor in the interpretation of Lower Palaeolithic open-air archaeological sites. However, the microscopic examination of lithic surfaces may provide valuable background information on the transport history of artifacts, particularly in low energy settings. Replica flint artifacts were therefore abraded in an annular flume and examined with a scanning electron microscope. Results showed that abrasion time, sediment size, and artifact transport mode were very sensitive predictors of microscopic surface abrasion, ridge width, and edge damage (p < 0.000). These results suggest that patterns of micro-abrasion of stone artifacts may enhance understanding of archaeological assemblage formation in fluvial contexts

Exploring smart grid possibilities: a complex systems modelling approach

Smart grid research has tended to be compartmentalised, with notable contributions from economics, electrical engineering and science and technology studies. However, there is an acknowledged and growing need for an integrated systems approach to the evaluation of smart grid initiatives. The capacity to simulate and explore smart grid possibilities on various scales is key to such an integrated approach but existing models – even if multidisciplinary – tend to have a limited focus. This paper describes an innovative and flexible framework that has been developed to facilitate the simulation of various smart grid scenarios and the interconnected social, technical and economic networks from a complex systems perspective. The architecture is described and related to realised examples of its use, both to model the electricity system as it is today and to model futures that have been envisioned in the literature. Potential future applications of the framework are explored, along with its utility as an analytic and decision support tool for smart grid stakeholders.

The three faces of bounded reliability: Alfred Chandler and the micro-foundations of management theory

Alfred Chandler, the celebrated business historian, provided detailed descriptions of the reasons for failed human commitments and the managerial tools needed to prevent/remediate such failings in the context of large business firms. Chandler's historical narrative identifies three distinct “faces” of bounded reliability—opportunism, benevolent preference reversal, and identity-based discordance—as the main drivers of commitment failure. Adopting bounded reliability (BRel) as a micro-foundation in management studies will raise the quality and relevance of scholarly recommendations to improve managerial decision making and action, because analysis of BRel challenges closely mirrors the real-world problems facing practicing managers.

Bayesian analysis of uncertainty in the GlobCover 2009 land cover product at climate model grid scale

Land cover data derived from satellites are commonly used to prescribe inputs to models of the land surface. Since such data inevitably contains errors, quantifying how uncertainties in the data affect a model’s output is important. To do so, a spatial distribution of possible land cover values is required to propagate through the model’s simulation. However, at large scales, such as those required for climate models, such spatial modelling can be difficult. Also, computer models often require land cover proportions at sites larger than the original map scale as inputs, and it is the uncertainty in these proportions that this article discusses. This paper describes a Monte Carlo sampling scheme that generates realisations of land cover proportions from the posterior distribution as implied by a Bayesian analysis that combines spatial information in the land cover map and its associated confusion matrix. The technique is computationally simple and has been applied previously to the Land Cover Map 2000 for the region of England and Wales. This article demonstrates the ability of the technique to scale up to large (global) satellite derived land cover maps and reports its application to the GlobCover 2009 data product. The results show that, in general, the GlobCover data possesses only small biases, with the largest belonging to non–vegetated surfaces. In vegetated surfaces, the most prominent area of uncertainty is Southern Africa, which represents a complex heterogeneous landscape. It is also clear from this study that greater resources need to be devoted to the construction of comprehensive confusion matrices.

Influence of dentin cavity surface finishing on micro-tensile bond strength of adhesives

The current trend toward minimal-invasive dentistry has introduced innovative techniques for cavity preparation. Chemical vapor deposition (CVD) and laser-irradiation technology have been employed as an alternative to the common use of regular burs in high-speed turbines. Objectives. The purpose of this study was to assess the influence of alternative techniques for cavity preparation on the bonding effectiveness of different adhesives to dentin, and to evaluate the morphological characteristics of dentin prepared with those techniques. Methods. One etch&rinse adhesive (OptiBond FL, Kerr) and three self-etch systems (Adper Prompt L-Pop, 3M ESPE; Clearfil SE Bond, Kuraray; Clearfil S3 Bond, Kuraray) were applied on dentin prepared with a regular bur in a turbine, with a CVD bur in a turbine, with a CVD tip in ultrasound and with an ErCr:YSGG laser. The micro-tensile bond strength (mu TBS) was determined after storage in water for 24 h at 37 degrees C, and morphological evaluation was performed by means of field -emission -gun scanning electron microscopy (Feg-SEM). Results. Feg-SEM evaluation revealed different morphological features on the dentin surface after the usage of both the conventional and alternative techniques for cavity preparation, more specifically regarding smear-layer thickness and surface roughness. CVD bur-cut, CVD ultra-sonoabraded and laser-irradiated dentin resulted in lower mu TBSs than conventionally bur-cut dentin, irrespective of the adhesive employed. Significance. The techniques, such as CVD diamond-bur cutting, CVD diamond ultra-sonoabrasion and laser-irradiation, used for cavity preparation may affect the bonding effectiveness of adhesives to dentin, irrespective of their acidity or approach. (C) 2007 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

A new micro-whip scorpion species from Brazilian Amazonia (Arachnida, Schizomida, Hubbardiidae), with the description of a new synapomorphy for Uropygi

Surazomus uarini n. sp. is described and illustrated based on specimens collected by beating on understory vegetation of Amazonian ""terra firme"" upland rain forests. A new cuticular structure, possibly a gland opening, is described on the female tarsus I and terminal flagellum. A putatively homologous structure is reported from the same body parts in all Undescribed species of Rowlandius Reddell and Cokendolpher 1995; Stenochrus portoricensis Chamberlin 1922; Mastigoproctus maximus (Tarnani 1889), and Thelyphonellus amazonicus (Butler 1872); suggesting it new synapomorphy for the clade Uropygi (i.e., Schizomida + Thelyphonida).

Grid job scheduling using Route with Genetic Algorithm support

In 2006 the Route load balancing algorithm was proposed and compared to other techniques aiming at optimizing the process allocation in grid environments. This algorithm schedules tasks of parallel applications considering computer neighborhoods (where the distance is defined by the network latency). Route presents good results for large environments, although there are cases where neighbors do not have an enough computational capacity nor communication system capable of serving the application. In those situations the Route migrates tasks until they stabilize in a grid area with enough resources. This migration may take long time what reduces the overall performance. In order to improve such stabilization time, this paper proposes RouteGA (Route with Genetic Algorithm support) which considers historical information on parallel application behavior and also the computer capacities and load to optimize the scheduling. This information is extracted by using monitors and summarized in a knowledge base used to quantify the occupation of tasks. Afterwards, such information is used to parameterize a genetic algorithm responsible for optimizing the task allocation. Results confirm that RouteGA outperforms the load balancing carried out by the original Route, which had previously outperformed others scheduling algorithms from literature.

Micro Far-Infrared Reflectivity of CaNb(2)O(6) Single Crystal Fibers Grown by the Laser-Heated Pedestal Growth Technique

CaNb(2)O(6) single crystal fibers were grown by the laser-heated pedestal growth technique, directly from the starting reagents. Optically transparent fibers were obtained in the form of rods with elliptical cross-section, free from cracks, impurities, and secondary phases, with an average diameter of 0.4 mm and about 20 mm of length. The fibers grew within the orthorhombic Pbcn columbite structure, with the growth axis nearly parallel to the crystallographic a-direction. The parameters b and c were parallel to the shorter and larger ellipsis axes. A special setup using a microscope was developed to obtain the far-infrared reflectivity spectra of these micrometer-sized fibers, allowing the identification and assignment of 34 of the 38 polar phonons foreseen for the material. From these phonons, the intrinsic dielectric constant ( = 18.2) and quality factor ( of 185 THz) could be estimated, showing the potential of the material for applications in microwave circuitry. These results, along with previous polarized Raman data (Cryst. Growth Des. 2010, 10, 1569), allow us to present a comprehensive set of optical phonon modes and to discuss the potential use of designed CaNb(2)O(6) microcrystals in compact optical devices.

Scheduling Grid Applications with Software Requirements

The aim of task scheduling is to minimize the makespan of applications, exploiting the best possible way to use shared resources. Applications have requirements which call for customized environments for their execution. One way to provide such environments is to use virtualization on demand. This paper presents two schedulers based on integer linear programming which schedule virtual machines (VMs) in grid resources and tasks on these VMs. The schedulers differ from previous work by the joint scheduling of tasks and VMs and by considering the impact of the available bandwidth on the quality of the schedule. Experiments show the efficacy of the schedulers in scenarios with different network configurations.

Application execution management on the InteGrade opportunistic grid middleware

The InteGrade project is a multi-university effort to build a novel grid computing middleware based on the opportunistic use of resources belonging to user workstations. The InteGrade middleware currently enables the execution of sequential, bag-of-tasks, and parallel applications that follow the BSP or the MPI programming models. This article presents the lessons learned over the last five years of the InteGrade development and describes the solutions achieved concerning the support for robust application execution. The contributions cover the related fields of application scheduling, execution management, and fault tolerance. We present our solutions, describing their implementation principles and evaluation through the analysis of several experimental results. (C) 2010 Elsevier Inc. All rights reserved.

Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts

Schistosoma mansoni is a well-adapted blood-dwelling parasitic helminth, persisting for decades in its human host despite being continually exposed to potential immune attack. Here, we describe in detail micro-exon genes (MEG) in S. mansoni, some present in multiple copies, which represent a novel molecular system for creating protein variation through the alternate splicing of short (<= 36 bp) symmetric exons organized in tandem. Analysis of three closely related copies of one MEG family allowed us to trace several evolutionary events and propose a mechanism for micro-exon generation and diversification. Microarray experiments show that the majority of MEGs are up-regulated in life cycle stages associated with establishment in the mammalian host after skin penetration. Sequencing of RT-PCR products allowed the description of several alternate splice forms of micro-exon genes, highlighting the potential use of these transcripts to generate a complex pool of protein variants. We obtained direct evidence for the existence of such pools by proteomic analysis of secretions from migrating schistosomula and mature eggs. Whole-mount in situ hybridization and immunolocalization showed that MEG transcripts and proteins were restricted to glands or epithelia exposed to the external environment. The ability of schistosomes to produce a complex pool of variant proteins aligns them with the other major groups of blood parasites, but using a completely different mechanism. We believe that our data open a new chapter in the study of immune evasion by schistosomes, and their ability to generate variant proteins could represent a significant obstacle to vaccine development.