EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

Optimization of flocculation process and continuous filtration for sea water primary treatment filtration to reduce SDI for entree to reverse osmosis system

Today , Providing drinking water and process water is one of the major problems in most countries ; the surface water often need to be treated to achieve necessary quality, and in this way, technological and also financial difficulties cause great restrictions in operating the treatment units. Although water supply by simple and cheap systems has been one of the important objectives in most scientific and research centers in the world, still a great percent of population in developing countries, especially in rural areas, don't benefit well quality water. One of the big and available sources for providing acceptable water is sea water. There are two ways to treat sea water first evaporation and second reverse osmosis system. Nowadays R.O system has been used for desalination because of low budget price and easily to operate and maintenance. The sea water should be pretreated before R.O plants, because there is some difficulties in raw sea water that can decrease yield point of membranes in R.O system. The subject of this research may be useful in this way, and we hope to be able to achieve complete success in design and construction of useful pretreatment systems for R.O plant. One of the most important units in the sea water pretreatment plant is filtration, the conventional method for filtration is pressurized sand filters, and the subject of this research is about new filtration which is called continuous back wash sand filtration (CBWSF). The CBWSF designed and tested in this research may be used more economically with less difficulty. It consists two main parts first shell body and second central part comprising of airlift pump, raw water feeding pipe, air supply hose, backwash chamber and sand washer as well as inlet and outlet connections. The CBWSF is a continuously operating filter, i.e. the filter does not have to be taken out of operation for backwashing or cleaning. Inlet water is fed through the sand bed while the sand bed is moving downwards. The water gets filtered while the sand becomes dirty. Simultaneously, the dirty sand is cleaned in the sand washer and the suspended solids are discharged in backwash water. We analyze the behavior of CBWSF in pretreatment of sea water instead of pressurized sand filter. There is one important factor which is not suitable for R.O membranes, it is bio-fouling. This factor is defined by Silt Density Index (SDI).measured by SDI. In this research has been focused on decreasing of SDI and NTU. Based on this goal, the prototype of pretreatment had been designed and manufactured to test. The system design was done mainly by using the design fundamentals of CBWSF. The automatic backwash sand filter can be used in small and also big water supply schemes. In big water treatment plants, the units of filters perform the filtration and backwash stages separately, and in small treatment plants, the unit is usually compacted to achieve less energy consumption. The analysis of the system showed that it may be used feasibly for water treating, especially for limited population. The construction is rapid, simple and economic, and its performance is high enough because no mobile mechanical part is used in it, so it may be proposed as an effective method to improve the water quality and consequently the hygiene level in the remote places of the country.

Ecological effects of flow and temperature regimes on fish communities in temperate rivers

Les organismes aquatiques sont adaptés à une grande variabilité hydrique et thermique des rivières. Malgré ceci, la régulation des eaux suscite des changements aux débits qui peuvent provoquer des impacts négatifs sur la biodiversité et les processus écologiques en rivière. Celle-ci peut aussi causer des modifications au niveau des régimes thermiques et des caractéristiques de l’habitat du poisson. Des données environnementales et biologiques décrivant l’habitat du poisson existent, mais elles sont incomplètes pour plusieurs rivières au Canada et de faible qualité, limitant les relations quantitatives débit-température-poissons à un petit nombre de rivières ou à une région étudiée. La recherche menée dans le cadre de mon doctorat concerne les impacts de la génération d'hydroélectricité sur les rivières; soit les changements aux régimes hydriques et thermiques reliés à la régulation des eaux sur la variation des communautés ichtyologiques qui habitent les rivières régulées et naturelles au Canada. Suite à une comparaison d’échantillonnage de pêche, une méthode constante pour obtenir des bons estimés de poisson (richesse, densité et biomasse des espèces) a été établie pour évaluer la structure de la communauté de poissons pour l’ensemble des rivières ciblées par l’étude. Afin de mieux comprendre ces changements environnementaux, les principales composantes décrivant ces régimes ont été identifiées et l’altération des régimes hydriques pour certaines rivières régulées a été quantifiée. Ces résultats ont servi à établir la relation significative entre le degré de changement biotique et le degré de changement hydrique pour illustrer les différences entre les régimes de régulation. Pour faire un complément aux indices biotiques déjà calculés pour l’ensemble des communautés de poissons (diversité, densité et biomasse des espèces par rivière), les différences au niveau des guildes de poissons ont été quantifiées pour expliquer les divers effets écologiques dus aux changements de régimes hydriques et thermiques provenant de la gestion des barrages. Ces derniers résultats servent à prédire pour quels traits écologiques ou groupes d’espèces de poissons les composantes hydriques et thermiques sont importantes. De plus, ces derniers résultats ont servi à mettre en valeur les variables décrivant les régimes thermiques qui ne sont pas toujours inclues dans les études hydro-écologiques. L’ensemble des résultats de cette thèse ont des retombées importantes sur la gestion des rivières en évaluant, de façon cohérente, l’impact de la régulation des rivières sur les communautés de poissons et en développant des outils de prévision pour la restauration des écosystèmes riverains.

Ecotoxicological assessment of sediments from the Port of Santos and the disposal sites of dredged material

A dragagem dos sedimentos do Canal de Santos é necessária para permitir o trânsito de navios que operam no Porto de Santos. As áreas de disposição do material dragado estão situadas na zona costeira, em frente à Baía de Santos. Este estudo visou avaliar a qualidade dos sedimentos do Canal de Santos e das áreas de disposição atuais e antigas, utilizando testes de toxicidade de sedimento integral com anfípodos e de toxicidade de elutriatos com embriões de ouriço do mar. As amostras do Canal de Santos foram consideradas as mais tóxicas: todas as amostras dessa área foram consideradas significativamente tóxicas. Além disso, algumas amostras das áreas de disposição exibiram toxicidade. Os resultados mostraram, portanto, que os sedimentos apresentam evidências de degradação em sua qualidade, porém novos estudos devem ser conduzidos visando determinar as relações entre contaminação e toxicidade. Os resultados sugerem ainda que a disposição dos sedimentos dragados deva ser reavaliada.

Integrated sediment quality assessment in Paranagua Estuarine System, Southern Brazil

Sediment quality from Paranagua Estuarine System (PES), a highly important port and ecological zone, was evaluated by assessing three lines of evidence: (1) sediment physical-chemical characteristics; (2) sediment toxicity (elutriates, sediment-water interface, and whole sediment); and (3) benthic community structure. Results revealed a gradient of increasing degradation of sediments (i.e. higher concentrations of trace metals, higher toxicity, and impoverishment of benthic community structure) towards inner PES. Data integration by principal component analysis (PCA) showed positive correlation between some contaminants (mainly As, Cr, Ni, and Pb) and toxicity in samples collected from stations located in upper estuary and one station placed away from contamination sources. Benthic community structure seems to be affected by both pollution and natural fine characteristics of the sediments, which reinforces the importance of a weight-of-evidence approach to evaluate sediments of PES. (C) 2008 Elsevier B.V. All rights reserved.

A simple approach to integrate the ecotoxicological and chemical data for the establishment of environmental risk levels

O presente trabalho utilizou métodos multivariados e matemáticos para integrar dados químicos e ecotoxicológicos obtidos para o Sistema Estuarino de Santos e para a região próxima à zona de lançamento do emissário submarino de Santos, com a finalidade de estabelecer com maior exatidão os riscos ambientais, e assim identificar áreas prioritárias e orientar programas de controle e políticas públicas. Para ambos os conjuntos de dados, as violações de valores numéricos de qualidade de sedimento tenderam a estar associadas com a ocorrência de toxicidade. Para o estuário, essa tendência foi corroborada pelas correlações entre a toxicidade e as concentrações de HPAs e Cu, enquanto para a região do emissário, pela correlação entre toxicidade e conteúdo de mercúrio no sedimento. Valores normalizados em relação às medias foram calculados para cada amostra, permitindo classificá-las de acordo com a toxicidade e a contaminação. As análises de agrupamento confirmaram os resultados das classificações. Para os dados de sistema estuarino, houve a separação das amostras em três categorias: as estações SSV-2, SSV-3 e SSV-4 encontram-se sob maior risco, seguidas da estação SSV-6. As estações SSV-1 e SSV-5 demonstraram melhores condições. Já em relação ao emissário, as amostras 1 e 2 apresentaram melhores condições, enquanto a estação 5 pareceu apresentar um maior risco, seguida das estações 3 e 4 que tiveram apenas alguns indícios de alteração.

Hidrocarbonetos policíclicos aromáticos em sedimentos de fundo do estuário do rio Potengi, região da grande Natal (RN): implicações ambientais

Estuaries are environments prone to the input of chemical pollutants of various kinds and origins, including polycyclic aromatic hydrocarbons (PAHs). Anthropogenic PAHs may have two possible sources: pyrolytic (with four or more aromatic rings and low degree of alkylation) and petrogenic (with two and three aromatic rings and high degree of alkylation). This study aimed to evaluate the levels, distribution and possible sources of polycyclic aromatic hydrocarbons in the estuary of the Potengi river, Natal, Brazil. Samples of bottom sediments were collected in the final 12 km of the estuary until its mouth to the sea, where the urbanization of the Great Natal is more concentrated. Sampling was performed on 12 cross sections, with three stations each, totaling 36 samples, identified as T1 to T36. The non alkylated and alkylated PAHs were analyzed by gas chromatography coupled to mass spectrometry (GC / MS). PAHs were detected in all 36 stations with total concentration on each varying 174-109407 ng g-1. These values are comparable to those of several estuarine regions worldwide with high anthropogenic influence, suggesting the record of diffuse contamination installed in the estuary. PAHs profiles were similar for most stations. In 32 of the 36 stations, low molecular weight PAHs (with 2 and 3 ring: naphthalene, phenanthrene and their alkylated homologues) prevailed, which ranged from 54% to 100% of the total PAH, indicating that leaks, spills and combustion fuels are the dominant source of PAH pollution in the estuary. The level of contamination by PAHs in most stations suggests that there is potential risk of occasional adverse biological effects, but in some stations adverse impacts on the biota may occur frequently. The diagnostic ratios could differentiate sources of PAHs in sediments of the estuary, which were divided into three groups: petrogenic, pyrolytic and mixing of sources. The urban concentration of the Great Natal and the various industrial activities associated with it can be blamed as potential sources of PAHs in bottom sediments of the estuary studied. The data presented highlight the need to control the causes of existing pollution in the estuary

CHARACTERIZING THE FIRST HISTORIC ERUPTION OF NABRO, ERITREA: INSIGHTS FROM THERMAL AND UV REMOTE SENSING

June 2011 saw the first historic eruption of Nabro volcano, one of an ongoing sequence of eruptions in the Afar-Red Sea region since 2005. It halted air travel in northern Africa, contaminated food and water sources, and displaced thousands from their homes. Due to its remote location, little was known about this event in terms of the quantity of erupted products and the timing and mechanisms of their emplacement. Geographic isolation, previous quiescence and regional civil unrest meant that this volcano was effectively unmonitored at the time of eruption, and opportunities for field study are limited. Using free, publicly available satellite data, I examined rates of lava effusion and SO2 emission in order to quantify the amount of erupted products and understand the temporal evolution of the eruption, as well as explore what information can be gleaned about eruption mechanisms using remote sensing data. These data revealed a bimodal eruption, beginning with explosive activity marked by high SO2 emission totalling 1824 - 2299 KT, and extensive ash fall of 270 - 440 km2. This gave way to a period of rapid effusion, producing a ~17 km long lava flow, and a volume of ~22.1 x 106 m3. Mass balance between the SO2 and lava flows reveals no sulfur 'excess', suggesting that nearly all of the degassed magma was extruded. The 2011 eruption of Nabro lasted nearly 6 weeks, and may be considered the second largest historic eruption in Africa. Work such as this highlights the importance of satellite remote sensing for studying and monitoring volcanoes, particularly those in remote regions that may be otherwise inaccessible.

Boreal forest fire impacts on lower troposphere carbon monoxide and ozone levels at the regional to hemispheric scales

Tropospheric ozone (O3) and carbon monoxide (CO) pollution in the Northern Hemisphere is commonly thought to be of anthropogenic origin. While this is true in most cases, copious quantities of pollutants are emitted by fires in boreal regions, and the impact of these fires on CO has been shown to significantly exceed the impact of urban and industrial sources during large fire years. The impact of boreal fires on ozone is still poorly quantified, and large uncertainties exist in the estimates of the fire-released nitrogen oxides (NO x ), a critical factor in ozone production. As boreal fire activity is predicted to increase in the future due to its strong dependence on weather conditions, it is necessary to understand how these fires affect atmospheric composition. To determine the scale of boreal fire impacts on ozone and its precursors, this work combined statistical analysis of ground-based measurements downwind of fires, satellite data analysis, transport modeling and the results of chemical model simulations. The first part of this work focused on determining boreal fire impact on ozone levels downwind of fires, using analysis of observations in several-days-old fire plumes intercepted at the Pico Mountain station (Azores). The results of this study revealed that fires significantly increase midlatitude summertime ozone background during high fire years, implying that predicted future increases in boreal wildfires may affect ozone levels over large regions in the Northern Hemisphere. To improve current estimates of NOx emissions from boreal fires, we further analyzed ΔNOy /ΔCO enhancement ratios in the observed fire plumes together with transport modeling of fire emission estimates. The results of this analysis revealed the presence of a considerable seasonal trend in the fire NOx /CO emission ratio due to the late-summer changes in burning properties. This finding implies that the constant NOx /CO emission ratio currently used in atmospheric modeling is unrealistic, and is likely to introduce a significant bias in the estimated ozone production. Finally, satellite observations were used to determine the impact of fires on atmospheric burdens of nitrogen dioxide (NO2 ) and formaldehyde (HCHO) in the North American boreal region. This analysis demonstrated that fires dominated the HCHO burden over the fires and in plumes up to two days old. This finding provides insights into the magnitude of secondary HCHO production and further enhances scientific understanding of the atmospheric impacts of boreal fires.

WRITING A COMMUNITY GUIDEBOOK FOR EVALUATING LOW-GRADE GEOTHERMAL ENERGY FROM FLOODED UNDERGROUND MINES FOR HEATING AND COOLING BUILDINGS

When underground mines close they often fill with water from ground and surface sources; each mine can contain millions to billions of gallons of water. This water, heated by the Earth’s geothermal energy, reaches temperatures ideal for heat pumps. The sheer scale of these flooded underground mines presents a unique opportunity for large scale geothermal heat pump setups which would not be as economically, socially, and environmentally feasible anywhere else. A literature search revealed approximately 30 instances of flooded underground mines being used to heat and cool buildings worldwide. With thousands of closed/abandoned underground mines in the U.S. and a million estimated globally, why hasn’t this opportunity been more widely adopted? This project has found perception and lack of knowledge about the feasibility to be key barriers. To address these issues, this project drafted a guidebook for former mining communities titled A Community Guide to Mine Water Geothermal Heating and Cooling.

Organized Labor and U.S. Foreign Policy: The Solidarity Center in Historical Context

During the Cold War the foreign policy of the American Federation of Labor and Congress of Industrial Organizations (AFL-CIO), was heavily criticized by scholars and activists for following the lead of the U.S. state in its overseas operations. In a wide range of states, the AFL-CIO worked to destabilize governments selected by the U.S. state for regime change, while in others the Federation helped stabilize client regimes of the U.S. state. In 1997 the four regional organizations that previously carried out AFL-CIO foreign policy were consolidated into the American Center for International Labor Solidarity (Solidarity Center). My dissertation is an attempt to analyze whether the foreign policy of the AFL-CIO in the Solidarity Center era is marked by continuity or change with past practices. At the same time, this study will attempt to add to the debate over the role of non-governmental organizations (NGOs) in the post-Cold War era, and its implications for future study. Using the qualitative “process-tracing” detailed by of Alexander George and Andrew Bennett (2005) my study examines a wide array of primary and secondary sources, including documents from the NED and AFL-CIO, in order to analyze the relationship between the Solidarity Center and the U.S. state from 2002-2009. Furthermore, after analyzing broad trends of NED grants to the Solidarity Center, this study examines three dissimilar case studies including Venezuela, Haiti, and Iraq and the Middle East and North African (MENA) region to further explore the connections between U.S. foreign policy goals and the Solidarity Center operations. The study concludes that the evidence indicates continuity with past AFL-CIO foreign policy practices whereby the Solidarity Center follows the lead of the U.S. state. It has been found that the patterns of NED funding indicate that the Solidarity Center closely tailors its operations abroad in areas of importance to the U.S. state, that it is heavily reliant on state funding via the NED for its operations, and that the Solidarity Center works closely with U.S. allies and coalitions in these regions. Finally, this study argues for the relevance of “top-down” NGO creation and direction in the post-Cold War era.

Switching Patterns and Steady-State Analysis of Grid-Connected and Stand-Alone Single-Stage Boost-Inverters for PV Applications

Renewable or sustainable energy (SE) sources have attracted the attention of many countries because the power generated is environmentally friendly, and the sources are not subject to the instability of price and availability. This dissertation presents new trends in the DC-AC converters (inverters) used in renewable energy sources, particularly for photovoltaic (PV) energy systems. A review of the existing technologies is performed for both single-phase and three-phase systems, and the pros and cons of the best candidates are investigated. In many modern energy conversion systems, a DC voltage, which is provided from a SE source or energy storage device, must be boosted and converted to an AC voltage with a fixed amplitude and frequency. A novel switching pattern based on the concept of the conventional space-vector pulse-width-modulated (SVPWM) technique is developed for single-stage, boost-inverters using the topology of current source inverters (CSI). The six main switching states, and two zeros, with three switches conducting at any given instant in conventional SVPWM techniques are modified herein into three charging states and six discharging states with only two switches conducting at any given instant. The charging states are necessary in order to boost the DC input voltage. It is demonstrated that the CSI topology in conjunction with the developed switching pattern is capable of providing the required residential AC voltage from a low DC voltage of one PV panel at its rated power for both linear and nonlinear loads. In a micro-grid, the active and reactive power control and consequently voltage regulation is one of the main requirements. Therefore, the capability of the single-stage boost-inverter in controlling the active power and providing the reactive power is investigated. It is demonstrated that the injected active and reactive power can be independently controlled through two modulation indices introduced in the proposed switching algorithm. The system is capable of injecting a desirable level of reactive power, while the maximum power point tracking (MPPT) dictates the desirable active power. The developed switching pattern is experimentally verified through a laboratory scaled three-phase 200W boost-inverter for both grid-connected and stand-alone cases and the results are presented.

Atlantic Threads: Singer in Spain and Mexico, 1860-1940

This dissertation examines the role of Singer in the modernization of sewing practices in Spain and Mexico from 1860 to 1940. Singer marketing was founded on gendered views of women’s work and gendered perceptions of the home. These connected with sewing practices in Spain and Mexico, where home sewing remained economically and culturally important throughout the 1940s. "Atlantic Threads" is the first study of the US-owned multinational in the Hispanic World. I demonstrate that sewing practices, and especially practices related to home sewing that have been considered part of the private sphere and therefore not an important historical matter, contributed to the building of one the first global corporation. I examine Singer corporate records and business strategies that have not been considered by other scholars such as the creation of the Embroidery Department in the late nineteen-century. Likewise, this dissertation challenges traditional narratives that have assumed that Spain and Mexico were peripheral to modernity. I look at Singer corporate records in Spain and Mexico and at regional government and cultural sources to demonstrate how Singer integrated Spain and Mexico within its business organization. Singer's marketing was focused on the consumer, which contributed to make the company part of local sewing businesses and cultures.

An Islanding Detection Method based on Impedance Estimation and Grid Identification for Grid-Tie Distributed Power Generation Systems

Power system policies are broadly on track to escalate the use of renewable energy resources in electric power generation. Integration of dispersed generation to the utility network not only intensifies the benefits of renewable generation but also introduces further advantages such as power quality enhancement and freedom of power generation for the consumers. However, issues arise from the integration of distributed generators to the existing utility grid are as significant as its benefits. The issues are aggravated as the number of grid-connected distributed generators increases. Therefore, power quality demands become stricter to ensure a safe and proper advancement towards the emerging smart grid. In this regard, system protection is the area that is highly affected as the grid-connected distributed generation share in electricity generation increases. Islanding detection, amongst all protection issues, is the most important concern for a power system with high penetration of distributed sources. Islanding occurs when a portion of the distribution network which includes one or more distributed generation units and local loads is disconnected from the remaining portion of the grid. Upon formation of a power island, it remains energized due to the presence of one or more distributed sources. This thesis introduces a new islanding detection technique based on an enhanced multi-layer scheme that shows superior performance over the existing techniques. It provides improved solutions for safety and protection of power systems and distributed sources that are capable of operating in grid-connected mode. The proposed active method offers negligible non-detection zone. It is applicable to micro-grids with a number of distributed generation sources without sacrificing the dynamic response of the system. In addition, the information obtained from the proposed scheme allows for smooth transition to stand-alone operation if required. The proposed technique paves the path towards a comprehensive protection solution for future power networks. The proposed method is converter-resident and all power conversion systems that are operating based on power electronics converters can benefit from this method. The theoretical analysis is presented, and extensive simulation results confirm the validity of the analytical work.

Factors influencing the use of evidence based practice among physiotherapists and occupational therapists in their clinical work

Background: Evidence-based practice (EBP) is a process through which research is applied in daily clinical practice. Occupational therapists (OTs) and physiotherapists (PTs) are expected to work in line with EBP in order to optimise health care resources. This expectation is too seldom fulfilled. Consequently, research findings may not be implemented in clinical practice in a timely manner, or at all. To remedy this situation, additional knowledge is needed regarding what factors influence the process of EBP among practitioners. The purpose of the present study was to identify factors that influence the use of EBP and the experienced effects of the use of EBP among PTs and OTs in their clinical work. Method: This was a qualitative interview study that consisted of six group interviews involving either OTs or PTs employed by the Jönköping County Council in the South of Sweden. Resulting data were analysed using content analysis. Results: The analysis resulted in the following categories: “definition of evidence and EBP”, “sources of evidence”, “barriers to acquiring evidence and to using evidence in clinical work”, “factors that facilitate the acquisition of evidence and the use of evidence in clinical work”, and “personal experiences of using EBP”. Basing clinical practice on scientific evidence evoked positive experiences, although an ambivalent view towards acting on clinical experience was evident. Participants reported that time for and increased knowledge about searching for, evaluating, and implementing EBP were needed. Conclusion: Because OTs are more oriented towards professional theories and models, and PTs are more focused on randomised controlled trials of interventions, different strategies appear to be needed to increase EBP in these two professions. Management support was considered vital to the implementation of EBP. However, the personal obligation to work in line with EBP must also be emphasised; the participants apparently underestimate its importance.