Bioinformatic analysis for exploring relationships between genes and gene products

To carry out their specific roles in the cell, genes and gene products often work together in groups, forming many relationships among themselves and with other molecules. Such relationships include physical protein-protein interaction relationships, regulatory relationships, metabolic relationships, genetic relationships, and much more. With advances in science and technology, some high throughput technologies have been developed to simultaneously detect tens of thousands of pairwise protein-protein interactions and protein-DNA interactions. However, the data generated by high throughput methods are prone to noise. Furthermore, the technology itself has its limitations, and cannot detect all kinds of relationships between genes and their products. Thus there is a pressing need to investigate all kinds of relationships and their roles in a living system using bioinformatic approaches, and is a central challenge in Computational Biology and Systems Biology. This dissertation focuses on exploring relationships between genes and gene products using bioinformatic approaches. Specifically, we consider problems related to regulatory relationships, protein-protein interactions, and semantic relationships between genes. A regulatory element is an important pattern or "signal", often located in the promoter of a gene, which is used in the process of turning a gene "on" or "off". Predicting regulatory elements is a key step in exploring the regulatory relationships between genes and gene products. In this dissertation, we consider the problem of improving the prediction of regulatory elements by using comparative genomics data. With regard to protein-protein interactions, we have developed bioinformatics techniques to estimate support for the data on these interactions. While protein-protein interactions and regulatory relationships can be detected by high throughput biological techniques, there is another type of relationship called semantic relationship that cannot be detected by a single technique, but can be inferred using multiple sources of biological data. The contributions of this thesis involved the development and application of a set of bioinformatic approaches that address the challenges mentioned above. These included (i) an EM-based algorithm that improves the prediction of regulatory elements using comparative genomics data, (ii) an approach for estimating the support of protein-protein interaction data, with application to functional annotation of genes, (iii) a novel method for inferring functional network of genes, and (iv) techniques for clustering genes using multi-source data.

Development of risk based treatability and engineering measures for reducing exposure to lead contaminated media in the Miami inner city, Florida

A major consequence of contamination at the local level’s population as it relates to environmental health and environmental engineering is childhood lead poisoning. Environmental contamination is one of the pressing environmental concerns facing the world today. Current approaches often focus on large contaminated industrial size sites that are designated by regulatory agencies for site remediation. Prior to this study, there were no known published studies conducted at the local and smaller scale, such as neighborhoods, where often much of the contamination is present to remediate. An environmental health study of local lead-poisoning data in Liberty City, Little Haiti and eastern Little Havana in Miami-Dade County, Florida accounted for a disproportionately high number of the county’s reported childhood lead poisoning cases. An engineering system was developed and designed for a comprehensive risk management methodology that is distinctively applicable to the geographical and environmental conditions of Miami-Dade County, Florida. Furthermore, a scientific approach for interpreting environmental health concerns, while involving detailed environmental engineering control measures and methods for site remediation in contained media was developed for implementation. Test samples were obtained from residents and sites in those specific communities in Miami-Dade County, Florida (Gasana and Chamorro 2002). Currently lead does not have an Oral Assessment, Inhalation Assessment, and Oral Slope Factor; variables that are required to run a quantitative risk assessment. However, various institutional controls from federal agencies’ standards and regulation for contaminated lead in media yield adequate maximum concentration limits (MCLs). For this study an MCL of .0015 (mg/L) was used. A risk management approach concerning contaminated media involving lead demonstrates that the linkage of environmental health and environmental engineering can yield a feasible solution.

Domestic Politics in the Dominican Republic after the Earthquake in Haiti

Despite historical tensions between the Dominican Republic and Haiti, Dominicans appear to have put aside their resentment in favor of supporting Haitians after the earthquake that devastated the neighbor nation in January 2010. Over the past several months, there has been unprecedented cooperation between the Dominican Republic and Haiti, with little evidence of a negative impact on domestic politics in the Dominican Republic. In fact, the high ratings of President Leonel Fernández and the results of the May Parliamentary elections may suggest that how the Fernández administration handled the Haitian crisis did not have a negative impact on citizens’ perception. However, the issue of Haitian immigration remains very sensitive in the Dominican Republic, and has the potential to become the major concern on the domestic political front. As of June 2010, the Haitian crisis seemed to have little or no impact on Dominican politics, as the following points indicate: The May 16, 2010 Parliamentary elections increased President Fernández political party to 31 out of 32 Senate seats, and 105 out of 183 Chamber of Deputies seats; this is a total increase of 18 seats from the previous term. Polls indicate that President Fernández has a 54 percent approval rating. Polls also indicate that Haiti is not among the most pressing issues of concern to Dominican citizens. Instead, 65 percent of the population identifies drug trafficking and corruption as the greatest concerns. The immigration debate will remain the major consideration in domestic politics in the Dominican Republic; 62.4 percent of Dominicans polled think that the military should be strengthened along the DR-Haitian border.

Implicit eyewitness memory

After a crime has occurred, one of the most pressing objectives for investigators is to identify and interview any eyewitness that can provide information about the crime. Depending on his or her training, the investigative interviewer will use (to varying degrees) mostly yes/no questions, some cued and multiple-choice questions, with few open-ended questions. When the witness cannot generate any more details about the crime, one assumes the eyewitness' memory for the critical event has been exhausted. However, given what we know about memory, is this a safe assumption? In line with the extant literature on human cognition, if one assumes (a) an eyewitness has more available memories of the crime than he or she has accessible and (b) only explicit probes have been used to elicit information, then one can argue this eyewitness may still be able to provide additional information via implicit memory tests. In accordance with these notions, the present study had two goals: demonstrate that (1) eyewitnesses can reveal memory implicitly for a detail-rich event and (2) particularly for brief crimes, eyewitnesses can reveal memory for event details implicitly that were inaccessible when probed for explicitly. Undergraduates (N = 227) participated in a psychological experiment in exchange for research credit. Participants were presented with one of three stimulus videos (brief crime vs. long crime vs. irrelevant video). Then, participants either completed a series of implicit memory tasks or worked on a puzzle for 5 minutes. Lastly, participants were interviewed explicitly about the previous video via free recall and recognition tasks. Findings indicated that participants who viewed the brief crime provided significantly more crime-related details implicitly than those who viewed the long crime. The data also showed participants who viewed the long crime provided marginally more accurate details during free recall than participants who viewed the brief crime. Furthermore, participants who completed the implicit memory tasks provided significantly less accurate information during the explicit interview than participants who were not given implicit memory tasks. This study was the first to investigate implicit memory for eyewitnesses of a crime. To determine its applied value, additional empirical work is required.

Factors influencing movements and foraging ecology of American alligators (Alligator mississippiensis) in a dynamic subtropical coastal ecosystem

Top predators can have large effects on community and population dynamics but we still know relatively little about their roles in ecosystems and which biotic and abiotic factors potentially affect their behavioral patterns. Understanding the roles played by top predators is a pressing issue because many top predator populations around the world are declining rapidly yet we do not fully understand what the consequences of their potential extirpation could be for ecosystem structure and function. In addition, individual behavioral specialization is commonplace across many taxa, but studies of its prevalence, causes, and consequences in top predator populations are lacking. In this dissertation I investigated the movement, feeding patterns, and drivers and implications of individual specialization in an American alligator (Alligator mississippiensis ) population inhabiting a dynamic subtropical estuary. I found that alligator movement and feeding behaviors in this population were largely regulated by a combination of biotic and abiotic factors that varied seasonally. I also found that the population consisted of individuals that displayed an extremely wide range of movement and feeding behaviors, indicating that individual specialization is potentially an important determinant of the varied roles of alligators in ecosystems. Ultimately, I found that assuming top predator populations consist of individuals that all behave in similar ways in terms of their feeding, movements, and potential roles in ecosystems is likely incorrect. As climate change and ecosystem restoration and conservation activities continue to affect top predator populations worldwide, individuals will likely respond in different and possibly unexpected ways.

"To hold the world in contempt": The British Empire, war, and the Irish and Indian nationalist press, 1899–1914

The era between the close of the nineteenth century and the onset of the First World War witnessed a marked increase in radical agitation among Indian and Irish nationalists. The most outspoken political leaders of the day founded a series of widely circulated newspapers in India and Ireland, placing these editors in the enviable position of both reporting and creating the news. Nationalist journalists were in the vanguard of those pressing vocally for an independent India and Ireland, and together constituted an increasingly problematic contingent for the British Empire. The advanced-nationalist press in Ireland and the nationalist press in India took the lead in facilitating the exchange of provocative ideas--raising awareness of perceived imperial injustices, offering strategic advice, and cementing international solidarity. Irish and Indian press coverage of Britain's imperial wars constituted one of the premier weapons in the nationalists' arsenal, permitting them to build support for their ideology and forward their agenda in a manner both rapid and definitive. Directing their readers' attention to conflicts overseas proved instructive in how the Empire dealt with those who resisted its policies, and also showcased how it conducted its affairs with its allies. As such, critical press coverage of the Boxer Rebellion, Boer War, Russo-Japanese War, and World War I bred disaffection for the Empire, while attempts by the Empire to suppress the critiques further alienated the public. This dissertation offers the first comparative analysis of the major nationalist press organs in India and Ireland, using the prism of war to illustrate the increasingly persuasive role of the press in promoting resistance to the Empire. It focuses on how the leading Indian and Irish editors not only fostered a nationalist agenda within their own countries, but also worked in concert to construct a global anti-imperialist platform. By highlighting the anti-imperial rhetoric of the nationalist press in India and Ireland and illuminating their strategies for attaining self-government, this study deepens understanding of the seeds of nationalism, making a contribution to comparative imperial scholarship, and demonstrating the power of the media to alter imperial dynamics and effect political change.

Catholic student movements in Latin America: Cuba and Brazil, 1920s to 1960s

This dissertation examines the ideological development of the Catholic University Student (JUC) movements in Cuba and Brazil during the Cold War and their organizational predecessors and intellectual influences in interwar Europe. Transnational Catholicism prioritized the attempt to influence youth and in particular, university students, within the context of Catholic nations within Atlantic civilization in the middle of the twentieth century. This dissertation argues that the Catholic university movements achieved a relatively high level of social and political influence in a number of countries in Latin America and that the experience of the Catholic student activists led them to experience ideological conflict and in some cases, rupture, with the conservative ideology of the Catholic hierarchy. Catholic student movements flourished after World War II in the context of an emerging youth culture. The proliferation of student organizations became part of the ideological battlefield of the Cold War. Catholic university students also played key roles in the Cuban Revolution (1957-1959) and in the attempted political and social reforms in Brazil under President João Goulart (1961-1964). ^ The JUC, under the guidance of the Church hierarchy, attempted to avoid aligning itself with either ideological camp in the Cold War, but rather to chart a Third Way between materialistic capitalism and atheistic socialism. Thousands of students in over 70 nations were intensively trained to think critically about pressing social issues. This paper will to place the Catholic Student movement in Cuba in the larger context of transnational Catholic university movements using archival evidence, newspaper accounts and secondary sources. Despite the hierarchy's attempt to utilize students as a tool of influence, the actual lived experience of students equipped them to think critically about social issues, and helped lay a foundation for the progressive student politics of the late 1960s and the rise of liberation theology in the 1970s. ^

The Next Generation of Scientists: Examining the Experiences of Graduate Students in Network-Level Social-Ecological Science

By integrating the research and resources of hundreds of scientists from dozens of institutions, network-level science is fast becoming one scientific model of choice to address complex problems. In the pursuit to confront pressing environmental issues such as climate change, many scientists, practitioners, policy makers, and institutions are promoting network-level research that integrates the social and ecological sciences. To understand how this scientific trend is unfolding among rising scientists, we examined how graduate students experienced one such emergent social-ecological research initiative, Integrated Science for Society and Environment, within the large-scale, geographically distributed Long Term Ecological Research (LTER) Network. Through workshops, surveys, and interviews, we found that graduate students faced challenges in how they conceptualized and practiced social-ecological research within the LTER Network. We have presented these conceptual challenges at three scales: the individual/project, the LTER site, and the LTER Network. The level of student engagement with and knowledge of the LTER Network was varied, and students faced different institutional, cultural, and logistic barriers to practicing social-ecological research. These types of challenges are unlikely to be unique to LTER graduate students; thus, our findings are relevant to other scientific networks implementing new social-ecological research initiatives.

Macroinvertebrate abundance in tropical Andean streams, Ecuador

Deforestation in the tropical Andes is affecting ecological conditions of streams, and determination of how much forest should be retained is a pressing task for conservation, restoration and management strategies. We calculated and analyzed eight benthic metrics (structural, compositional and water quality indices) and a physical-chemical composite index with gradients of vegetation cover to assess the effects of deforestation on macroinvertebrate communities and water quality of 23 streams in southern Ecuadorian Andes. Using a geographical information system (GIS), we quantified vegetation cover at three spatial scales: the entire catchment, the riparian buffer of 30 m width extending the entire stream length, and the local scale defined for a stream reach of 100 m in length and similar buffer width. Macroinvertebrate and water quality metrics had the strongest relationships with vegetation cover at catchment and riparian scales, while vegetation cover did not show any association with the macroinvertebrate metrics at local scale. At catchment scale, the water quality metrics indicate that ecological condition of Andean streams is good when vegetation cover is over 70%. Further, macroinvertebrate community assemblages were more diverse and related in catchments largely covered by native vegetation (>70%). Overall, our results suggest that retaining an important quantity of native vegetation cover within the catchments and a linkage between headwater and riparian forests help to maintain and improve stream biodiversity and water quality in Andean streams affected by deforestation. Also, this research proposes that a strong regulation focused to the management of riparian buffers can be successful when decision making is addressed to conservation/restoration of Andean catchments.

Densificação e microestrutura de um compósito Mo-Cu preparado a partir de um pó de heptamolibidato de amônia e cobre

The Cu-Mo system is a composite used in the electrical industry as material for electrical contact and resistance welding electrode as well as the heat sink and microwave absorber in microelectronic devices. The use of this material in such applications is due to the excellent properties of thermal and electrical conductivity and the possibility of adjustment of its coefficient of thermal expansion to meet those of materials used as substrates in the semiconductor micoreletrônic industry. Powder metallurgy through the processes of milling, pressing shaping and sintering is a viable technique for consolidation of such material. However, the mutual insolubility of both phases and the low wettability of liquid Cu on Mo impede its densification. However, the mutual insolubility of both phases and the low wettability of liquid Cu on Mo impede its densification. The mechanical alloying is a technique for preparation of powders used to produce nanocrystalline composite powder with amorphous phase or extended solid solution, which increases the sinterability immiscible systems such as the Mo-Cu. This paper investigates the influence of ammonium heptamolybdate (HMA) and the mechanical alloying in the preparation of a composite powder HMA-20% Cu and the effect of this preparation on densification and structure of MoCu composite produced. HMA and Cu powders in the proportion of 20% by weight of Cu were prepared by the techniques of mechanical mixing and mechanical alloying in a planetary mill. These were milled for 50 hours. To observe the evolution of the characteristics of the particles, powder samples were taken after 2, 10, 15, 20, 30 and 40 hours of milling. Cylindrical samples 5 to 8 mm in diameter and 3 to 4 mm thickness were obtained by pressing at 200 MPa to the mixed powders so as to ground. These samples were sintered at 1200 ° C for 60 minutes under an atmosphere of H2. To determine the effect of heating rate on the structure of the material during the decomposition and reduction of HMA, rates of 2, 5 and 10 ° C / min were used .. The post and the structures of the sintered samples were characterized by SEM and EDS. The density of the green and sintered bodies was measured using the geometric method (weight / volume). Vickers microhardness with a load of 1 N for 15 s were performed on sintered structures. The density of the sintered structures 10 ° C / min. reached 99% of theoretical density, how the density of sintered structures to 2 ° C / min. reached only 90% of the theoretical density

Obtenção de Mo2C com adição de Co por reação gás-sólido em reator de leito fixo

Sulfur compounds emissions have been, on the late years, subject to more severe environmental laws due to its impact on the environment (causing the acid rain phenomena) and on human health. It has also been object of much attention from the refiners worldwide due to its relationship with equipment’s life, which is decreased by corrosion, and also with products’ quality, as the later may have its color, smell and stability altered by the presence of such compounds. Sulfur removal can be carried out by hydrotreating (HDT) which is a catalytic process. Catalysts for HDS are traditionally based on Co(Ni)-Mo(W)/Al2O3. However, in face of the increased contaminants’ content on crude oil, and stricter legislation on emissions, the development of new, more active and efficient catalysts is pressing. Carbides of refractory material have been identified as potential materials for this use. The addition of a second metal to carbides may enhance catalytic activities by increasing the density of active sites. In the present thesis Mo2C with Co addition was produced in a fixed bed reactor via gas-solid reaction of CH4 (5%) and H2(95%) with a precursor made of a mix of ammonium heptamolybdate [(NH4)6[Mo7O24].4H2O] and cobalt nitrate[Co(NO3)2.6H2O] at stoichiometric amounts. Precursors’ where analyzed by XRF, XRD, SEM and TG/DTA. Carboreduction reactions were carried out at 700 and 750°C with two cobalt compositions (2,5 and 5%). Reaction’s products were characterized by XRF, XRD, SEM, TOC, BET and laser granulometry. It was possible to obtain Mo2C with 2,5 and 5% cobalt addition as a single phase at 750°C with nanoscale crystallite sizes. At 700°C, however, both MoO2 and Mo2C phases were found by XRD. No Co containing phases were found by XRD. XRF, however, confirmed the intended Co content added. SEM images confirmed XRD data. The increase on Co content promoted a more severe agglomeration of the produced powder. The same effect was noted when the reaction temperature was increased. The powder synthesized at 750°C with 2,5% Co addition TOC analysis indicated the complete conversion from oxide material to carbide, with a 8,9% free carbon production. The powder produced at this temperature with 5% Co addition was only partially converted (86%)

Estudo de duas pseudoligas de Nb-Cu obtidas pela rota da metalurgia do pó

The Nb-Cu pseudoalloys present themselves as potential substitutes for the alloys from a well known system and already commercially applied, as the W-Cu alloys, used in applications such as heat sinks, electrical contacts and coils for the generation of high magnetic fields. Because it is an immiscible system, where there is mutual insolubility and low wettability of the liquid Cu on the Nb surface, the processing route used in this work was the Powder Metallurgy. Two Nb alloys were used, with additions of 10% and 20% in weight of Cu, and times of 20, 30 and 40 hours for the high energy milling of the starting powders. The milling evolution of the powders is presented through the characterization techniques, such as the LASER diffraction for particle size, XRD, SEM, EDS, DSC, dilatometry, TEM and chemical analysis. After the milling, portions of the loads were submitted to the annealing heat treatment. The process used for the samples consolidation was the hot pressing, which has been applied both on some milled powders samples, as on the annealed powders. Subsequent heat treatments were performed in the samples at temperatures of 1000ºC (solid phase) and 1100ºC (in the Cu liquid phase). All sets of consolidated samples, and also the two sets of the heat treated, were analyzed by XRD, SEM, EDS, density and Vickers microhardness. Moreover, other Nb powder samples with 10% and 20% in weight of Cu obtained by simple mechanical mixing, were consolidated, thermally treated and characterized with the same techniques applied to the others, and the results were compared among themselves. Despite the difficulty of consolidation and densification of the two pseudoalloys of the Nb-Cu system of this study, on the route that passes through the HEM, samples were obtained with densities around 90% of the theoretical density. And, on the processing route of which were only mixed, the values reached up to 97%. Therefore, in this work are also emphasized the processes that made possible these results.

Estudo da incorporação de cinza e chamote gerado pela cerâmica vermelha ao próprio processo industrial

The ceramics industry generates waste at various stages of that process, defective products, waste from burning solid fuels, among others. This waste is dumped in landfills, garbage dumps or directly on roads, which has a negative environmental impact. This paper presents a study to incorporate the waste of algaroba wood and chamote (scrap pieces of ceramic already sintered), in to the ceramic material for making sealing blocks. The methodological procedures consist in the characterization of chemical and mineralogical residues, raw materials, and physical-mechanical of the formulations of mixes with clay, silt and waste. By pressing test pieces were produced using a pressure of 200 kgf/cm², varying compositions in the range of 0%, 5%, 10% and 15% by weight of residue. The sintering was performed in a muffle furnace, with the temperature levels of 850 ° C, 900 ° C, 950 ° C, 1000 ° C and 1050 ° C. The evaluated physical and mechanical properties were: Water Absorption, Linear Shrinkage Burning, Apparent Porosity, Apparent Density and Mechanical Resistance to Flexion. Analysis was carried out by Scanning Electron Microscopy on fracture surfaces of the specimens. Evaluation of linear shrinkage property drying and firing , water absorption and mechanical resistance to compression of the sealing blocks 5% wood ash residue, sintered at 900 °C hold temperature in the laboratory the products manufactured on an industrial scale. The main results, it was found on the viability of using the residues of algaroba wood and to confer refractory properties of the ceramic product. The main results, it was concluded feasibility of using the ash residues algaroba wood to impart refractory properties to the ceramic product and the residue of chamote, being derived from the own ceramic product not interfere with the properties, when used in a percentage of up to 5%.Since the residue of chamote being derived from the ceramic product itself had no effect on the properties. Studies in the laboratory have shown that the incorporation of up to 5% of these residues may be adopted as an alternative technology to reduce the environmental impact caused by the industrial sector, without compromising the final properties of the material, since the results on an industrial scale showed absorption values 11.66 and 11.74 of water and waste products respectively, within the parameters of NBR - 15,270, since the mechanical strength was 1.25 MPa and 0.94 MPa respectively for products with and without residue, lower than the minimum required by the technical standard that is 1.5 MPa.

Estudo da incorporação de cinza e chamote gerado pela cerâmica vermelha ao próprio processo industrial

The ceramics industry generates waste at various stages of that process, defective products, waste from burning solid fuels, among others. This waste is dumped in landfills, garbage dumps or directly on roads, which has a negative environmental impact. This paper presents a study to incorporate the waste of algaroba wood and chamote (scrap pieces of ceramic already sintered), in to the ceramic material for making sealing blocks. The methodological procedures consist in the characterization of chemical and mineralogical residues, raw materials, and physical-mechanical of the formulations of mixes with clay, silt and waste. By pressing test pieces were produced using a pressure of 200 kgf/cm², varying compositions in the range of 0%, 5%, 10% and 15% by weight of residue. The sintering was performed in a muffle furnace, with the temperature levels of 850 ° C, 900 ° C, 950 ° C, 1000 ° C and 1050 ° C. The evaluated physical and mechanical properties were: Water Absorption, Linear Shrinkage Burning, Apparent Porosity, Apparent Density and Mechanical Resistance to Flexion. Analysis was carried out by Scanning Electron Microscopy on fracture surfaces of the specimens. Evaluation of linear shrinkage property drying and firing , water absorption and mechanical resistance to compression of the sealing blocks 5% wood ash residue, sintered at 900 °C hold temperature in the laboratory the products manufactured on an industrial scale. The main results, it was found on the viability of using the residues of algaroba wood and to confer refractory properties of the ceramic product. The main results, it was concluded feasibility of using the ash residues algaroba wood to impart refractory properties to the ceramic product and the residue of chamote, being derived from the own ceramic product not interfere with the properties, when used in a percentage of up to 5%.Since the residue of chamote being derived from the ceramic product itself had no effect on the properties. Studies in the laboratory have shown that the incorporation of up to 5% of these residues may be adopted as an alternative technology to reduce the environmental impact caused by the industrial sector, without compromising the final properties of the material, since the results on an industrial scale showed absorption values 11.66 and 11.74 of water and waste products respectively, within the parameters of NBR - 15,270, since the mechanical strength was 1.25 MPa and 0.94 MPa respectively for products with and without residue, lower than the minimum required by the technical standard that is 1.5 MPa.

Seismic Retrofitting of a Historic Structure with Limited Construction Documentation

Many buildings constructed during the middle of the 20th century were constructed with criteria that fall short of current requirements. Although shortcomings are possible in all aspects of the design, the inadequacies in terms of seismic design present a more pressing issue to human life. This risk has been seen in various earthquakes that have struck Italy recently, and subsequently, the codes have been altered to account for this underestimated danger. Structures built after these changes remain at risk and must be retrofitted depending on their use. This report centers around the Giovanni Michelucci Institute of Mathematics at the University of Bologna and the work required to modify the building so that it can withstand 60% of the current design requirements. The goal of this particular report is to verify the previous reports written in Italian and present an accurate analysis along with intervention suggestions for this particular building. The work began with an investigation into the previous sources and work to find out how the structure had been interpreted. After understanding the building, corrections were made where required, and the failing elements were organized graphically to more easily show where the building needed the most work. Once the critical zones were mapped, remediation techniques were tested on the top floor, and the modeling techniques and effects of the interventions were presented to assist in further work on the structure.