MHCWeb: Converting a WWW database into a knowledge-based collaborative environment

The World Wide Web (WWW) is useful for distributing scientific data. Most existing web data resources organize their information either in structured flat files or relational databases with basic retrieval capabilities. For databases with one or a few simple relations, these approaches are successful, but they can be cumbersome when there is a data model involving multiple relations between complex data. We believe that knowledge-based resources offer a solution in these cases. Knowledge bases have explicit declarations of the concepts in the domain, along with the relations between them. They are usually organized hierarchically, and provide a global data model with a controlled vocabulary, We have created the OWEB architecture for building online scientific data resources using knowledge bases. OWEB provides a shell for structuring data, providing secure and shared access, and creating computational modules for processing and displaying data. In this paper, we describe the translation of the online immunological database MHCPEP into an OWEB system called MHCWeb. This effort involved building a conceptual model for the data, creating a controlled terminology for the legal values for different types of data, and then translating the original data into the new structure. The 0 WEB environment allows for flexible access to the data by both users and computer programs.

Sperm environment affects offspring quality in broadcast spawning marine invertebrates

The provisioning of offspring can have far-reaching consequences for later life in a wide range of organisms and generally this provisioning is thought to be under maternal influence or control. In experiments with a broadcast-spawning ascidian, we found that the size of offspring was determined by egg size and the abundance of sperm present during fertilization. Larger eggs were fertilized at low sperm concentrations, whilst smaller eggs were successfully fertilized at high sperm concentrations. These differences in fertilized egg size resulted in differences in the development rate, hatching success and mean size of the subsequent larvae. Our results suggest that, in contrast to females that reproduce by other mating systems, free-spawning mothers lack some control over the provisioning of offspring. Furthermore, because males can alter the sperm environment, they can exert paternal (non-genetic) control over key offspring characteristics.

Developing a reliable audit instrument to measure the physical environment for physical activity

Background: The physical environment plays an important role in influencing participation in physical activity, although which factors of the physical environment have the greatest effect on patterns of activity remain to be determined. We describe the development of a comprehensive instrument to measure the physical environmental factors that may influence walking and cycling in local neighborhoods and report on its reliability. Methods: Following consultation with experts from a variety of fields and a literature search, we developed a Systematic Pedestrian and Cycling Environmental Scan (SPACES) instrument and used it to collect data over a total of 1987 kilometers of roads in metropolitan Perth, Western Australia. The audit instrument is available from the first author on request. Additional environmental information was collected using desktop methods and geographic information systems (GIS) technology. We assessed inter- and intra-rater reliability of the instrument among the 16 observers who collected the data. Results: The observers reported that the audit instrument was easy to use. Both inter- and intra-rater reliability of the environmental scan instrument were generally high. Conclusions: Our instrument provides a reliable, practical, and easy to-use method for collecting detailed street-level data on physical environmental factors that are potential influences on walking in local neighborhoods.

Sources of variation in larval quality for free-spawning marine invertebrates: Egg size and the local sperm environment

There has been growing interest in the effects of variation in larval quality on the post-larval performance of adult marine invertebrates. Variation in egg/larval size is an obvious source of variation in larval quality but sources of variation have received little attention. For broadcast spawners, larval size may vary according to the local sperm environment but the generality of this result is unclear. Here, we show that, for a solitary ascidian, a polychaete and an echinoid, larval size is affected by the concentration of sperm present during fertilization. Larvae that are produced at high sperm concentrations are smaller than larvae that are produced from eggs exposed to low sperm concentrations. We also show that for three ascidians and an asteroid, egg size increases with maternal body size. These differences in larval size are likely to affect larval and subsequent adult performance in the field. Given that sperm concentrations in the field can fluctuate widely, it is likely that larval quality in free-spawning marine invertebrates will also vary widely.

The food business environment and the role of China and Brazil building a ""food bridge""

Purpose - The purpose of this paper is to discuss the economic crisis of 2008/2009 and the major impacts on developing nations and food-producing countries Within this macro-environment of food chains, there is concern that food inflation might come back sooner than expected The role of China as one of the major food consumers in the future, and Brazil, as the major food producer, is described as the food bridge, and an agenda of common development of these countries suggested. Design/methodology/approach - This paper reviews literature on muses of food inflation, production shortages, and investigation of programs to solve the problem in the future, it is also based on author`s personal insights and experience of working on this field in the last 15 years, and recent discussions in forums and interviews Findings - The major factors that jointly caused food prices increase in 2007/2008 were population growth, Income distribution, urbanization, dollar devaluations, commodity funds, social programs, production shortages, and bionic`s A list of ten policies is suggested. horizontal expansion of food production, vertical expansion, reduction in transaction costs, in protectionism and other taxes, investment in logistics, technology and better coordination, contracts, new generation of fertilizers and to use the best sources of biofuels. Originality/value - Two major outputs from this paper are the ""food demand model"" that inserts in one model the trends and muses of food inflation and the solutions, and the ""food bridge concept"" that also aligns in one box the imminent major food chain cooperation between China and Brazil

Offspring size effects in the marine environment: A field test for a colonial invertebrate

A central tenet of life-history theory is the presence of a trade-off between the size and number of offspring that a female can produce for a given clutch. A crucial assumption of this trade-off is that larger offspring perform better than smaller offspring. Despite the importance of this assumption empirical, field-based tests are rare, especially for marine organisms. We tested this assumption for the marine invertebrate, Diplosoma listerianum, a colonial ascidian that commonly occurs in temperate marine communities. Colonies that came from larger larvae had larger feeding structures than colonies that came from smaller larvae. Colonies that came from larger larvae also had higher survival and growth after 2 weeks in the field than colonies that came from smaller larvae. However, after 3 weeks in the field the colonies began to fragment and we could not detect an effect of larval size. We suggest that offspring size can have strong effects on the initial recruitment of D. listerianum but because of the tendency of this species to fragment, offspring size effects are less persistent in this species than in others.

MINERALOGY AND GENESIS OF SMECTITES IN AN ALKALINE-SALINE ENVIRONMENT OF PANTANAL WETLAND, BRAZIL

Smectite formation in alkaline-saline environments has been attributed to direct precipitation from solution and/or transformation from precursor minerals, but these mechanisms are not universally agreed upon in the literature. The objective of this work was to investigate the mineralogy of smectites in the soils surrounding a representative alkaline-saline lake of Nhecolandia, a sub-region of the Pantanal wetland, Brazil, and then to identify the mechanisms of their formation. Soils were sampled along a toposequence and analyzed by X-ray diffraction, transmission electron microscopy-energy dispersive X-ray analysis, and inductively coupled plasma-mass spectrometry. Water was collected along a transect involving the studied toposequence and equilibrium diagrams were calculated using the databases PHREEQC and AQUA. The fine-clay fraction is dominated by smectite, mica, and kaolinite. Smectites are concentrated at two places in the toposequence: an upper zone, which includes the soil horizons rarely reached by the lake-level variation; and a lower zone, which includes the surface horizon within the area of seasonal lake-level variation. Within the upper zone, the smectite is dioctahedral, rich in Al and Fe, and is classified as ferribeidellite. This phase is interstratified with mica and vermiculite and has an Fe content similar to that of the mica identified. These characteristics suggest that the ferribeidellite originates from transformation of micas and that vermiculite is an intermediate phase in this transformation. Within the lower zone, smectites are dominantly trioctahedral, Mg-rich, and are saponitic and stevensitic minerals. In addition, samples enriched in these minerals have much smaller rare-earth element (REE) contents than other soil samples. The water chemistry shows a geochemical control of Mg and saturation with respect to Mg-smectites in the more saline waters. The REE contents, water chemistry, and the presence of Mg-smectite where maximum evaporation is expected, suggest that saponitic and stevensitic minerals originate by chemical precipitation from the water column of the alkaline-saline lake.

Inhibition of NF kappa B leads to an intracellular reducing environment in human monocyte-derived immature dendritic cells

Inhibition of NFkB by the compound Bay 11–7082 (Bay) induces tolerogenic properties in dendritic cells (DC). While activation of NFkB can be induced by reactive oxygen species (ROS) and thiol/disulfide redox states, the consequences of NFkB blockade on ROS/redox state is not known. To generate immature DC, monocytes were cultured in GM-CSF and IL-4 (with or without Bay) for 48 h. Genes potentially involved in redox regulation were determined using microarray technology and validated using FACS, real-time PCR or western blotting. ROS were measured using two fluorescent dyes DHR-123 and DHE (to detect H2O2 or O2 respectively). We found increased expression of genes associated with reductants such as thioredoxin reductase (TrxR1) and glutathione (GSH), although those associated with the breakdown of H2O2 such as glutathione peroxidase, peroxiredoxins and catalase were decreased. Interestingly, Bay-treated DC produced less ROS in comparison to control DC under basal conditions and following stimulation with various pro-oxidants. In conclusion, Bay-treated DC display not only tolerogenic properties but also an intracellular reducing environment and an impaired ability to produce ROS. We are currently investigating whether exogenous ROS can interfere with the tolerogenic properties of Bay-treated DC.

Thyroid and the environment: exposure to excessive nutritional iodine increases the prevalence of thyroid disorders in Sao Paulo, Brazil

Objective: To evaluate the prevalence of chronic autoimmune thyroiditis (CAT) and iodine-induced hypothyroidism, hyperthyroidism (overt and subclinical). and goiter in a population exposed to excessive iodine intake for 5 years (table salt iodine concentrations: 40-100 mg/kg salt). Design: This was a population-based, cross-sectional study with 1085 participants randomly selected from a metropolitan area in Sao Paulo, Brazil, and conducted during the first semester of 2004. Methods: Thyroid ultrasound examination was performed in all participants and samples of urine and blood were collected from each subject. Serum levels of thyroid-stimulating hormone, free thyroxine, and anti-thyroid peroxidase (TPO) antibodies, urinary iodine concentration. thyroid volume, and thyroid echogenicity were evaluated. We also analyzed table salt iodine concentrations. Results: At the time the study was conducted, table salt iodine concentrations were within the new official limits (20-60 mg/kg salt). Nevertheless, in 45.6%, of the participants, urinary iodine excretion was excessive (above 300 mu g/l) and, in 14.1%, it was higher than 400 mu g/l. The prevalence of CAT (including atrophic thyroiditis) was 16.9% (183/1085), women were more affected than men (21.5 vs 9.1% respectively, P=0.02). Hypothyroidism was detected in 8.0%, (87/1085) of the Population with CAT. Hyperthyroidism was diagnosed in 3.3% of the individuals (36/1085) and goiter was identified in 3.1% (34/1085). Conclusions: Five years of excessive iodine intake by the Brazilian population may have increased the prevalence of CAT and hypothyroidism in subjects genetically predisposed to thyroid autoimmune diseases. Appropriate screening for early detection of thyroid dysfunction may be considered during excessive nutritional iodine intake.

Analysis of workplace injuries in a dental school environment

Workplace injuries at the University of Queensland Dental School during the period 1992-1994 were assessed to determine their incidence, and the associated indirect costs, causal factors, and appropriate preventive strategies. Overall, dental chairside assistants experienced a higher incidence of injuries than students both on a per worker and per time basis. Of the injuries with a low risk of cross-infection, burns and scalds from sterilizing equipment, and eye injuries in laboratories were the most common. This emphasizes the importance of wearing appropriate protective equipment in areas outside the treatment zone, and the need for signage and education. Common causes of sharps injuries were burs left in handpieces, two-handed needle recapping, and cleaning of probes in the sterilizing room. Changes to techniques and equipment would prevent such incidents. A range of factors which contribute to the calculation of indirect costs following injuries in the dental workplace are identified.

Trialing wetlands to treat coal mining wastewaters in a low rainfall, high evaporation environment

The large number of wetlands treating mining wastewaters around the world have mostly been constructed in temperate environments. Wetlands have yet to be proven in low rainfall, high evaporation environments and such conditions are common in many parts of Australia. BHP Australia Coal is researching whether wetlands have potential in central Queensland to treat coal mining wastewaters. In this region, mean annual rainfall is < 650 mm and evaporation > 2 000 mm. A pilot-scale wetland system has been constructed at an open-cut coal mine. The system comprises six treatment cells, each 125 m long and 10 m wide. The system is described in the paper and some initial results presented. Results over the first fourteen months of operation have shown that although pH has not increased enough to enable reuse or release of the water, sulfate reduction has been observed in parts of the system, as shown by the characteristic black precipitate and smell of hydrogen sulfide emanating from the wetlands. These encouraging signs have led to experiments aimed at identifying the factors limiting sulfate reduction. The first experiment, described herein, included four treatments where straw was overlain by soil and the water level varied, being either at the top of the straw, at the top of the soil, or about 5 cm above the soil. The effect of inoculating with sulfate-reducing bacteria was investigated. Two controls were included, one covered and one open, to enable the effect of evaporation to be determined. The final treatment consisted of combined straw/cattle manure overlain with soil. Results showed that sulfate reduction did occur, as demonstrated by pH increases and lowering of sulfate levels. Mean pH of the water was significantly higher after 19 days; in the controls, pH was < 3.3, whereas in the treatments, pH ranged from 5.4 to 6.7. The best improvement in sulfate levels occurred in the straw/cattle manure treatment. (C) 1997 IAWQ. Published by Elsevier Science Ltd.

Ideal soliton environment using parametric band gaps

Simultaneous solitary wave solutions for laser propagation in nonlinear parametric media with up to (3 + 1) dimensions are proved to exist. The combination of the large dispersion of a Bragg grating and the strong nonlinearity of chi((2)) optical material results in stable behavior with short interaction distances and low power requirements. The solutions are obtained by using the effective mass approximation to reduce the coupled propagation equations to those describing a dispersive parametric nonlinear waveguide, and are verified by solving the complete set of coupled band-gap equations numerically.