The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).

Solar sensitivity experiments for the pre-industrial time period using the comprehensive global climate model CCSM3 (Community Climate System Model 3)

The Southern Hemisphere Westerly Winds (SWW) constitute an important zonal circulation that influences large-scale precipitation patterns and ocean circulation. Variations in their intensity and latitudinal position have been suggested to exert a strong influence on the CO2 budget in the Southern Ocean, thus making them a potential factor affecting the global climate. The possible influence of solar forcing on SWW variability during the Holocene is addressed. Solar sensitivity experiments with a comprehensive global climate model (CCSM3) are carried out to study the response of SWW to solar variability. In addition, It is shown that a high-resolution iron record from the Chilean continental slope (41° S), which is interpreted to reflect changes in the position of the SWW, is significantly correlated with reconstructed solar activity during the past 3000 years. Taken together, the proxy and model results suggest that centennial-scale periods of lower (higher) solar activity caused equatorward (southward) shifts of the annual mean SWW.

The model T Ford car, its construction, operation and repair; a complete practical treatise explaining the operating principles of all parts of the Ford automobile, with complete instructions for driving and maintenance; includes the most thorough and easily understood illustrated instructions on Ford repairing ever published; based on five years' experience of a Ford operator--invaluable to all Ford owners, dealers, salesmen, drivers and repair men--every phase of the subject treated in a non-technical yet comprehensive manner,

Mode of access: Internet.

A conceptual model of organized primary care and comprehensive community health services.

Mode of access: Internet.

Transient simulations for present and last interglacials using a comprehensive coupled climate model CCSM3 (Community Climate System Model 3.0), links to model result files in NetCDF format

Transient simulations are widely used in studying the past climate as they provide better comparison with any exisiting proxy data. However, multi-millennial transient simulations using coupled climate models are usually computationally very expensive. As a result several acceleration techniques are implemented when using numerical simulations to recreate past climate. In this study, we compare the results from transient simulations of the present and the last interglacial with and without acceleration of the orbital forcing, using the comprehensive coupled climate model CCSM3 (Community Climate System Model 3). Our study shows that in low-latitude regions, the simulation of long-term variations in interglacial surface climate is not significantly affected by the use of the acceleration technique (with an acceleration factor of 10) and hence, large-scale model-data comparison of surface variables is not hampered. However, in high-latitude regions where the surface climate has a direct connection to the deep ocean, e.g. in the Southern Ocean or the Nordic Seas, acceleration-induced biases in sea-surface temperature evolution may occur with potential influence on the dynamics of the overlying atmosphere. The data provided here are from both accelerated and non-accelerated runs as decadal mean values.

A comprehensive study of multiplicative attribute graph model

Graphs are powerful tools to describe social, technological and biological networks, with nodes representing agents (people, websites, gene, etc.) and edges (or links) representing relations (or interactions) between agents. Examples of real-world networks include social networks, the World Wide Web, collaboration networks, protein networks, etc. Researchers often model these networks as random graphs. In this dissertation, we study a recently introduced social network model, named the Multiplicative Attribute Graph model (MAG), which takes into account the randomness of nodal attributes in the process of link formation (i.e., the probability of a link existing between two nodes depends on their attributes). Kim and Lesckovec, who defined the model, have claimed that this model exhibit some of the properties a real world social network is expected to have. Focusing on a homogeneous version of this model, we investigate the existence of zero-one laws for graph properties, e.g., the absence of isolated nodes, graph connectivity and the emergence of triangles. We obtain conditions on the parameters of the model, so that these properties occur with high or vanishingly probability as the number of nodes becomes unboundedly large. In that regime, we also investigate the property of triadic closure and the nodal degree distribution.

Phospholipases and the network of auxin signal transduction with ABP1 and TIR1 as two receptors: a comprehensive and provocative model

Three types of phospholipases, phospholipase D, secreted phospholipase A2, and patatin-related phospholipase A (pPLA) have functions in auxin signal transduction. Potential linkage to auxin receptors ABP1 or TIR1, their rapid activation or post-translational activation mechanisms, and downstream functions regulated by these phospholipases is reviewed and discussed. Only for pPLA all aspects are known at least to some detail. Evidence is gathered that all these signal reactions are located in the cytosol and seem to merge on regulation of PIN-catalyzed auxin efflux transport proteins. As a consequence, auxin concentration in the nucleus is also affected and this regulates the E3 activity of this auxin receptor. We showed that ABP1, PIN2, and pPLA, all outside the nucleus, have an impact on regulation of auxin-induced genes within 30 min. We propose that regulation of PIN protein activities and of auxin efflux transport are the means to coordinate ABP1 and TIR1 activity and that no physical contact between components of the ABP1-triggered cytosolic pathways and TIR1-triggered nuclear pathways of signaling is necessary to perform this.

Making Fedora easier to implement with Fez: A free open source content model and workflow management front-end to Fedora

The University of Queensland, Australia has developed Fez, a world-leading user-interface and management system for Fedora-based institutional repositories, which bridges the gap between a repository and users. Christiaan Kortekaas, Andrew Bennett and Keith Webster will review this open source software that gives institutions the power to create a comprehensive repository solution without the hassle..

A comprehensive study on carbon dioxide reforming of methane over Ni/gamma-Al2O3 catalysts

Carbon dioxide reforming of methane into syngas over Ni/gamma-Al2O3 catalysts was systematically studied. Effects of reaction parameters on catalytic activity and carbon deposition over Ni/gamma-Al2O3 catalysts were investigated. It is found that reduced NiA1204, metal nickel, and active species of carbon deposited were the active sites for this reaction. Carbon deposition on Ni/gamma Al2O3 varied depending on the nickel loading and reaction temperature and is the major cause of catalyst deactivation. Higher nickel loading produced more coke on the catalysts, resulting in rapid deactivation and plugging of the reactor. At 5 wt % Ni/gamma-Al2O3 catalyst exhibited high activity and much lesser magnitude of deactivation in 140 h. Characterization of carbon deposits on the catalyst surface revealed that there are two kinds of carbon species (oxidized and -C-C-) formed during the reaction and they showed different reactivities toward hydrogenation and oxidation. Kinetic studies showed that the activation energy for CO production in this reaction amounted to 80 kJ/mol and the rate of CO production could be described by a Langmuir-Hinshelwood model.

Comprehensive structural characterization of MCM-41: From mesopores to particles

In the present work the meso- and macro-structural characteristics of the mesoporous adsorbent MCM-41 have been estimated with the help of various techniques. The structure is found to comprise four different length scales: that of the mesopores, the crystallites, the grains and of the particles. It was found that the surface area estimated by the use of small angle scattering techniques is higher, while that estimated by mercury porosimetry is much lower, than that obtained from gas adsorption methods. Based on the macropore characterization by mercury porosimetry, and the considerable macropore area determined, it is seen that the actual mesopore area of MCM-41 may be significantly lower than the BET area. TEM studies indicated that MCM-41 does not have an ideal mesopore structure; however, it may still be treated as a model mesoporous material for gas adsorption studies because of the large radius of curvature of the channels.

Transcriptional Response of Peripheral Lymphocytes to Early Fibrosarcoma: A Model System for Cancer Detection Based on Hybridization Signatures

Since circulating leukocytes, mainly B and T cells, continuously maintain vigilant and comprehensive immune surveillance, these cells could be used as reporters for signs of infection or other pathologies, including cancer. Activated lymphocyte clones trigger a sensitive transcriptional response, which could be identified by gene expression profiling. To assess this hypothesis, we conducted microarray analysis of the gene expression profile of lymphocytes isolated from immunocompetent BALB/c mice subcutaneously injected with different numbers of tumorigenic B61 fibrosarcoma cells. Flow cytometry demonstrated that the number of circulating T (CD3(+)CD4(+) or CD3(+)CD8(+)) or B (CD19(+)) cells did not change. However, the lymphocytes isolated from tumor cell-injected animals expressed a unique transcriptional profile that was identifiable before the development of a palpable tumor mass. This finding demonstrates that the transcriptional response appears before alterations in the main lymphocyte subsets and that the gene expression profile of peripheral lymphocytes can serve as a sensitive and accurate method for the early detection of cancer. Exp Biol Med 234:802-812, 2009

A general hazard model for lifetime data in the presence of cure rate

Historically, the cure rate model has been used for modeling time-to-event data within which a significant proportion of patients are assumed to be cured of illnesses, including breast cancer, non-Hodgkin lymphoma, leukemia, prostate cancer, melanoma, and head and neck cancer. Perhaps the most popular type of cure rate model is the mixture model introduced by Berkson and Gage [1]. In this model, it is assumed that a certain proportion of the patients are cured, in the sense that they do not present the event of interest during a long period of time and can found to be immune to the cause of failure under study. In this paper, we propose a general hazard model which accommodates comprehensive families of cure rate models as particular cases, including the model proposed by Berkson and Gage. The maximum-likelihood-estimation procedure is discussed. A simulation study analyzes the coverage probabilities of the asymptotic confidence intervals for the parameters. A real data set on children exposed to HIV by vertical transmission illustrates the methodology.

A generalised dynamic model for char particle gasification with structure evolution and peripheral fragmentation

A generalised model for the prediction of single char particle gasification dynamics, accounting for multi-component mass transfer with chemical reaction, heat transfer, as well as structure evolution and peripheral fragmentation is developed in this paper. Maxwell-Stefan analysis is uniquely applied to both micro and macropores within the framework of the dusty-gas model to account for the bidisperse nature of the char, which differs significantly from the conventional models that are based on a single pore type. The peripheral fragmentation and random-pore correlation incorporated into the model enable prediction of structure/reactivity relationships. The occurrence of chemical reaction within the boundary layer reported by Biggs and Agarwal (Chem. Eng. Sci. 52 (1997) 941) has been confirmed through an analysis of CO/CO2 product ratio obtained from model simulations. However, it is also quantitatively observed that the significance of boundary layer reaction reduces notably with the reduction of oxygen concentration in the flue gas, operational pressure and film thickness. Computations have also shown that in the presence of diffusional gradients peripheral fragmentation occurs in the early stages on the surface, after which conversion quickens significantly due to small particle size. Results of the early commencement of peripheral fragmentation at relatively low overall conversion obtained from a large number of simulations agree well with experimental observations reported by Feng and Bhatia (Energy & Fuels 14 (2000) 297). Comprehensive analysis of simulation results is carried out based on well accepted physical principles to rationalise model prediction. (C) 2001 Elsevier Science Ltd. AH rights reserved.

Tsunamigenic earthquakes in the Gulf of Cadiz: fault model and recurrence

The Gulf of Cadiz, as part of the Azores-Gibraltar plate boundary, is recognized as a potential source of big earthquakes and tsunamis that may affect the bordering countries, as occurred on 1 November 1755. Preparing for the future, Portugal is establishing a national tsunami warning system in which the threat caused by any large-magnitude earthquake in the area is estimated from a comprehensive database of scenarios. In this paper we summarize the knowledge about the active tectonics in the Gulf of Cadiz and integrate the available seismological information in order to propose the generation model of destructive tsunamis to be applied in tsunami warnings. The fault model derived is then used to estimate the recurrence of large earthquakes using the fault slip rates obtained by Cunha et al. (2012) from thin-sheet neotectonic modelling. Finally we evaluate the consistency of seismicity rates derived from historical and instrumental catalogues with the convergence rates between Eurasia and Nubia given by plate kinematic models.

The gambin model provides a superior fit to species abundance distributions with a single free parameter : evidence, implementation and interpretation

The species abundance distribution (SAD) has been a central focus of community ecology for over fifty years, and is currently the subject of widespread renewed interest. The gambin model has recently been proposed as a model that provides a superior fit to commonly preferred SAD models. It has also been argued that the model's single parameter (α) presents a potentially informative ecological diversity metric, because it summarises the shape of the SAD in a single number. Despite this potential, few empirical tests of the model have been undertaken, perhaps because the necessary methods and software for fitting the model have not existed. Here, we derive a maximum likelihood method to fit the model, and use it to undertake a comprehensive comparative analysis of the fit of the gambin model. The functions and computational code to fit the model are incorporated in a newly developed free-to-download R package (gambin). We test the gambin model using a variety of datasets and compare the fit of the gambin model to fits obtained using the Poisson lognormal, logseries and zero-sum multinomial distributions. We found that gambin almost universally provided a better fit to the data and that the fit was consistent for a variety of sample grain sizes. We demonstrate how α can be used to differentiate intelligibly between community structures of Azorean arthropods sampled in different land use types. We conclude that gambin presents a flexible model capable of fitting a wide variety of observed SAD data, while providing a useful index of SAD form in its single fitted parameter. As such, gambin has wide potential applicability in the study of SADs, and ecology more generally.