GONOME: measuring correlations between GO terms and genomic positions

Background: Current methods to find significantly under- and over-represented gene ontology (GO) terms in a set of genes consider the genes as equally probable balls in a bag, as may be appropriate for transcripts in micro-array data. However, due to the varying length of genes and intergenic regions, that approach is inappropriate for deciding if any GO terms are correlated with a set of genomic positions. Results: We present an algorithm - GONOME - that can determine which GO terms are significantly associated with a set of genomic positions given a genome annotated with (at least) the starts and ends of genes. We show that certain GO terms may appear to be significantly associated with a set of randomly chosen positions in the human genome if gene lengths are not considered, and that these same terms have been reported as significantly over-represented in a number of recent papers. This apparent over-representation disappears when gene lengths are considered, as GONOME does. For example, we show that, when gene length is taken into account, the term development is not significantly enriched in genes associated with human CpG islands, in contradiction to a previous report. We further demonstrate the efficacy of GONOME by showing that occurrences of the proteosome-associated control element (PACE) upstream activating sequence in the S. cerevisiae genome associate significantly to appropriate GO terms. An extension of this approach yields a whole-genome motif discovery algorithm that allows identification of many other promoter sequences linked to different types of genes, including a large group of previously unknown motifs significantly associated with the terms 'translation' and 'translational elongation'. Conclusion: GONOME is an algorithm that correctly extracts over-represented GO terms from a set of genomic positions. By explicitly considering gene size, GONOME avoids a systematic bias toward GO terms linked to large genes. Inappropriate use of existing algorithms that do not take gene size into account has led to erroneous or suspect conclusions. Reciprocally GONOME may be used to identify new features in genomes that are significantly associated with particular categories of genes.

RELIGIÃO E ETNICIDADE: O HERÓI CABOCLO BERNARDO E A CONSTRUÇÃO DA IDENTIDADE ÉTNICA NA VILA DE REGÊNCIA AUGUSTA - ES

Na Vila de Regência Augusta, às margens do Rio Doce no município de Linhares - ES, uma intricada dinâmica sócio-religiosa reveste de atribuições religiosas um herói cujo feito remonta os finais do século XIX. Bernardo José dos Santos, morador da vila, ficaria conhecido em âmbito nacional como o herói Caboclo Bernardo ao ser homenageado por Princesa Isabel, por realizar o salvamento de 128 dos 142 tripulantes do naufrágio do Navio de Guerra Imperial Marinheiro , próximo à foz do Rio Doce. O evento e suas conseqüências tornaram-se um marco na história da vila, inclusive o assassinato do herói nos meados da segunda década do século XX. Na continuidade narrativa, ritual e simbólica do ato heróico do Caboclo Bernardo esta investigação lança suas preocupações. Atualmente acontece na vila, todos os anos, a Festa de Caboclo Bernardo, uma festividade para onde convergem religiosos de diversas etnias tupiniquim, botocudo, negros e caboclos com o intuito de prestar homenagens ao herói na capela que leva seu nome. Neste sentido, esta etnografia pretende analisar o processo de construção da identidade étnico-religiosa na vila, pois, ele acontece concomitantemente e está umbilicalmente relacionado ao processo que eleva o herói ao patamar dos santos padroeiros das bandas de congo na região. Para isso, analisado será o contexto dramático onde a identidade da vila é construída; as confluências históricas, narrativas e simbólicas que contribuem para a atual configuração da identidade; e o contexto político-institucional organizado em torno do Caboclo Bernardo, paradigma central da construção da identidade. O método etnográfico, a antropologia interpretativa e a antropologia visual forneceram os contornos metodológicos desta investigação, que se constituiu como uma descrição densa.(AU)

O CADERNO FOLHETIM E O JORNALISMO CULTURAL DA FOLHA DE S. PAULO (1977 - 1989)

O caderno semanal Folhetim, da Folha de S. Paulo, foi publicado entre 1977 e 1989. Teve três fases distintas, caracterizadas pela semelhança com a imprensa alternativa (no período 1977-1979), pela abertura de espaços à discussão sobre a retomada da democracia, sobre temas sociais e por uma aproximação com as universidades (1979-1982) e pela publicação de ensaios altamente especializados (1982-1989). Procura-se analisar os fatores determinantes dessas reorientações editoriais do Folhetim, como a influência do mercado de jornais, do processo de abertura política e das reformas operadas na Folha a partir de 1974.(AU)

Polymer fractionation by continuous chromatography

A review is given of general chromatographic theory, the factors affecting the performance of chromatographi c columns, and aspects of scale-up of the chromatographic process. The theory of gel permeation chromatography (g. p. c.) is received, and the results of an experimental study to optimize the performance of an analytical g.p.c. system are reported. The design and construction of a novel sequential continuous chromatographic refining unit (SCCR3), for continuous liquid-liquid chromatography applications, is described. Counter-current operation is simulated by sequencing a system of inlet and outlet port functions around a connected series of fixed, 5.1 cm internal diameter x 70 cm long, glass columns. The number of columns may be varied, and, during this research, a series of either twenty or ten columns was used. Operation of the unit for continuous fractionation of a dextran polymer (M. W. - 30,000) by g.p.c. is reported using 200-400 µm diameter porous silica beads (Spherosil XOB07S) as packing, and distilled water for the mobile phase. The effects of feed concentration, feed flow rate, and mobile and stationary phase flow rates have been investigated, by means of both product, and on-column, concentrations and molecular weight distributions. The ability to operate the unit successfully at on-column concentrations as high as 20% w/v dextran has been demonstrated, and removal of both high and low molecular weight ends of a polymer feed distribution, to produce products meeting commercial specifications, has been achieved. Equivalent throughputs have been as high as 2.8 tonnes per annum for ten columns, based on continuous operation for 8000 hours per annum. A concentration dependence of the equilibrium distribution coefficient, KD observed during continuous fractionation studies, is related to evidence in the literature and experimental results obtained on a small-scale batch column. Theoretical treatments of the counter-current chromatographic process are outlined, and a preliminary computer simulation of the SCCR3 unit t is presented.

Flow patterns on distillation trays

Studies into the two-phase flow patterns produced on a sieve tray were carried out using an air-water simulator of 2.44 m in diameter. The flow patterns were investigated by a number of methods, direct observation using directional flow pointers; by water-cooling to simulate mass transfer; and by measurement of the height of clear liquid across the tray with manometers. The flow rates used were designed to show how the flow pattern changed with the change in the gas and liquid rates. The results from water-only studies on an un-perforated tray were compared with those produced on a sieve tray with holes of 12.7 mm diameter. The presence of regions on the sides of the tray where the liquid was circulating was noted from the water-only experiments. The presence and magnitude of the circulations was reduced when the air was passed through the liquid. These were similar to the findings of Hine (1990) and Chambers (1993). When circulation occurred, the flow separated at the ends of the inlet downcomer and circulations of up to 30% of the tray area were observed. Water-cooling and the manometer measurements were used to show the effect of the flow pattern on the tray efficiency and the height of clear liquid respectively. The efficiency was severely reduced by the presence of circulations. The height of clear liquid tended to rise in these areas. A comparison of data collected on trays with different hole diameters showed that the larger hole diameter inhibited the on-set of separation to a greater extent than small hole diameters. The tray efficiency was affected by a combination of the better mixing on smaller hole trays and detrimental effect of greater circulation on these trays. Work on a rectangular tray geometry was carried out to assess the effect of hole size on the height of clear liquid. It was found that the gradient on the outlet half of the tray was very small and that the highest clear liquid height was given by the highest hole size. Overall, the experiments helped to clarify the effect that the flow pattern had on the operation of the tray. It is hoped that the work can be of use in the development of models to predict the flow pattern and hence the tray efficiency.

Flow patterns on sieve trays

Studies into gas-liquid flow patterns were carried out on commercial scale sieve trays where the ratio of froth depth to flow path length is typical of that found in practice. Experiments were conducted on a 2.44 m diameter air-water distillation simulator, in which flow patterns were investigated by direct observation, using directional flow pointers; by water cooling, to simulate mass transfer; and by height of clear liquid measurements across the tray. The flow rates used are typical of those found in practice. The approach adopted was to investigate the effect of the gas flow on the liquid flow by comparing water only flow patterns across an unperforated tray with air-water flow patterns on perforated trays. Initial gas-liquid contacting experiments on the 6.35 mm hole tray showed that, under certain conditions, the gas flow pattern beneath the test tray can have a significant effect on the tray liquid flow pattern such that gas-driven liquid circulation was produced. This was found to be a function of this particular air-water simulator design, and as far as is known this is the first time that this phenomenon has been observed. Consequently non-uniform gas flow effects were removed by modification of the gas distribution system. By eliminating gas circulation effects, the effect of the gas flow on the separation of liquid flow was similar to that obtained on the 1.0 mm hole tray (Hine, 1990). That is, flow separation occurred at the ends of the inlet downcomer which produced large circulating zones along the tray segments both on the non-perforated and perforated trays. The air when forced through the liquid, inhibited circulating flow such that it only occurred at high water inlet velocities. With the 6.35 mm hole tray, the growth and velocity of circulating flow was reduced at high superficial air velocities, and in the experiments to simulate distillation, liquid was in forward flow over most of the tray.

Modernizing Legacy Physics Applications for Reuse in Web and SOA

This paper concerns the application of recent information technologies for creating a software system for numerical simulations in the domain of plasma physics and in particular metal vapor lasers. The presented work is connected with performing modernization of legacy physics software for reuse on the web and inside a Service-Oriented Architecture environment. Applied and described is the creation of Java front-ends of legacy C++ and FORTRAN codes. Then the transformation of some of the scientific components into web services, as well as the creation of a web interface to the legacy application, is presented. The use of the BPEL language for managing scientific workflows is also considered.

Selections, Paracompactness and Compactness

2000 Mathematics Subject Classification: 54C60, 54C65, 54D20, 54D30.

Short-term changes in phosphorus storage in an oligotrophic Everglades wetland ecosystem receiving experimental nutrient enrichment

Natural, unenriched Everglades wetlands are known to be limited by phosphorus (P) and responsive to P enrichment. However, whole-ecosystem evaluations of experimental P additions are rare in Everglades or other wetlands. We tested the response of the Everglades wetland ecosystem to continuous, low-level additions of P (0, 5, 15, and 30 μg L−1 above ambient) in replicate, 100 m flow-through flumes located in unenriched Everglades National Park. After the first six months of dosing, the concentration and standing stock of phosphorus increased in the surface water, periphyton, and flocculent detrital layer, but not in the soil or macrophytes. Of the ecosystem components measured, total P concentration increased the most in the floating periphyton mat (30 μg L−1: mean = 1916 μg P g−1, control: mean = 149 μg P g−1), while the flocculent detrital layer stored most of the accumulated P (30 μg L−1: mean = 1.732 g P m−2, control: mean = 0.769 g P m−2). Significant short-term responses of P concentration and standing stock were observed primarily in the high dose (30 μg L−1 above ambient) treatment. In addition, the biomass and estimated P standing stock of aquatic consumers increased in the 30 and 5 μg L−1 treatments. Alterations in P concentration and standing stock occurred only at the upstream ends of the flumes nearest to the point source of added nutrient. The total amount of P stored by the ecosystem within the flume increased with P dosing, although the ecosystem in the flumes retained only a small proportion of the P added over the first six months. These results indicate that oligotrophic Everglades wetlands respond rapidly to short-term, low-level P enrichment, and the initial response is most noticeable in the periphyton and flocculent detrital layer.

Functionalized carbon nanotube nanoelectrodes for biomolecular recognition

The objective of this research is to develop nanoscale ultrasensitive transducers for detection of biological species at molecular level using carbon nanotubes as nanoelectrodes. Rapid detection of ultra low concentration or even single DNA molecules are essential for medical diagnosis and treatment, pharmaceutical applications, gene sequencing as well as forensic analysis. Here the use of functionalized single walled carbon nanotubes (SWNT) as nanoscale detection platform for rapid detection of single DNA molecules is demonstrated. The detection principle is based on obtaining electrical signal from a single amine terminated DNA molecule which is covalently bridged between two ends of an SWNT separated by a nanoscale gap. The synthesis, fabrication, chemical functionalization of nanoelectrodes and DNA attachment were optimized to perform reliable electrical characterization these molecules. Using this detection system fundamental study on charge transport in DNA molecule of both genomic and non genomic sequences is performed. We measured an electrical signal of about 30 pA through a hybridized DNA molecule of 80 base pair in length which encodes a portion of sequence of H5N1 gene of avian Influenza A virus. Due the dynamic nature of the DNA molecules the local environment such as ion concentration, pH and temperature significantly influence its physical properties. We observed a decrease in DNA conductance of about 33% in high vacuum conditions. The counterion variation was analyzed by changing the buffer from sodium acetate to tris(hydroxymethyl) aminomethane, which resulted in a two orders of magnitude increase in the conductivity of the DNA. The fabrication of large array of identical SWNT nanoelectrodes was achieved by using ultralong SWNTs. Using these nanoelectrode array we have investigated the sequence dependent charge transport in DNA. A systematic study performed on PolyG - PolyC sequence with varying number of intervening PolyA - PolyT pairs showed a decrease in electrical signal from 180 pA (PolyG - PolyC) to 30 pA with increasing number of the PolyA - PolyT pairs. This work also led to the development of ultrasensitive nanoelectrodes based on enzyme functionalized vertically aligned high density multiwalled CNTs for electrochemical detection of cholesterol. The nanoelectrodes exhibited selectively detection of cholesterol in the presence of common interferents found in human blood.

Short-term changes in phosphorus storage in an oligotrophic Everglades wetland ecosystem receiving experimental nutrient enrichment

Natural, unenriched Evergladeswetlands are known to be limited by phosphorus(P) and responsive to P enrichment. However,whole-ecosystem evaluations of experimental Padditions are rare in Everglades or otherwetlands. We tested the response of theEverglades wetland ecosystem to continuous,low-level additions of P (0, 5, 15, and30 μg L−1 above ambient) in replicate,100 m flow-through flumes located in unenrichedEverglades National Park. After the first sixmonths of dosing, the concentration andstanding stock of phosphorus increased in thesurface water, periphyton, and flocculentdetrital layer, but not in the soil or macrophytes. Of the ecosystem components measured, total P concentration increased the most in the floating periphyton mat (30 μg L−1: mean = 1916 μg P g−1, control: mean =149 μg P g−1), while the flocculentdetrital layer stored most of the accumulated P(30 μg L−1: mean = 1.732 g P m−2,control: mean = 0.769 g P m−2). Significant short-term responsesof P concentration and standing stock wereobserved primarily in the high dose (30 μgL−1 above ambient) treatment. Inaddition, the biomass and estimated P standingstock of aquatic consumers increased in the 30and 5 μg L−1 treatments. Alterationsin P concentration and standing stock occurredonly at the upstream ends of the flumes nearestto the point source of added nutrient. Thetotal amount of P stored by the ecosystemwithin the flume increased with P dosing,although the ecosystem in the flumes retainedonly a small proportion of the P added over thefirst six months. These results indicate thatoligotrophic Everglades wetlands respondrapidly to short-term, low-level P enrichment,and the initial response is most noticeable inthe periphyton and flocculent detrital layer.

Project POWER: Promoting Our Will Through Education and Research

Project POWER utilized participatory action research to critically examine issues facing students in an urban high school, setting the stage for the co-creation of spaces for student-teacher dialogue. The project culminated in a dialogue between the students and their future teachers at a university in Miami, Florida.

Mutation at the Human D1S80 Minisatellite Locus

Little is known about the general biology of minisatellites. The purpose of this study is to examine repeat mutations from the D1S80 minisatellite locus by sequence analysis to elucidate the mutational process at this locus. This is a highly polymorphic minisatellite locus, located in the subtelomeric region of chromosome 1. We have analyzed 90,000 human germline transmission events and found seven (7) mutations at this locus. The D1S80 alleles of the parentage trio, the child, mother, and the alleged father were sequenced and the origin of the mutation was determined. Using American Association of Blood Banks (AABB) guidelines, we found a male mutation rate of 1 . 0 4 × 1 0− 4 and a female mutation rate of 5 . 1 8 × 1 0− 5 with an overall mutation rate of approximately 7 . 7 7 × 1 0− 5. Also, in this study, we found that the identified mutations are in close proximity to the center of the repeat array rather than at the ends of the repeat array. Several studies have examined the mutational mechanisms of the minisatellites according to infinite allele model (IAM) and the one-step stepwise mutation model (SMM). In this study, we found that this locus fits into the one-step mutation model (SMM) mechanism in six out of seven instances similar to STR loci.

Unidades geoambientais e áreas de preservação permanente como instrumentos de auxílio para o planejamento ambiental - o caso da via costeira de Natal-RN

Brazilian law provides a series of rules and policies which regulate space use and occupancy as well as guide environmental planning. Among those are the Permanent Preservation Areas (PPAs) which purpose is to ensure the preservation of elements that are essential to maintain the environmental function and landscape. Another important instrument identifier of spaces are geoenvironmental units, which are synthesis elements grouping areas of similar characteristics and can be used for the analysis of risk, fragility and potential use of spaces. The geoenvironmental units are defined by more complex processes (information integration), focusing not only on individual elements, but being determined from a systemic analysis. Is It possible to identify and delineate APPs from the identification and determination of geoenvironmental units? The aim of this study was to evaluate the potential of geoenvironmental units in the process of identification and delineation of APPs a see how much of the study area, the area by the Coast line in Natal/RN, is still good for occupation. It was used the physiognomic method, in which the limits of the units are plotted on a synthetic document (aerial photographs), valuing aspects of relief in a range of detail by the analysis of systemic categories (element, structure, function and interaction), observed. The methodology used allowed the identification and delineation of eleven geoenvironmental units and, from these, it was possible to identify and delineate four out of the five PPAs occurring in the study area. Only a small space of 1.2 ha of the study area is not considered APP by law. Thus, the occupation of the unoccupied area by the Coast line is not feasible from a legal standpoint. The geoenvironmental units as well as the identified and delineated APPs in the area by the Coast line are spaces which preservation is guaranteed by law in various scopes and are necessary to maintain the environmental functions of the area. The planning for the use and occupation of the area should involve the recovery of degraded areas and the creation of elements that make possible the use as well as attract the community, as provided in the initial planning, by ensuring the public utility and social interest in the Project.

Vulnerabilidade socioambiental no município de Natal, RN

Contemporary society lives surrounded by various types of risks, causing individuals to be taken by a constant feeling of fear and insecurity, as the negative risks, always bring some harm to the population directly or indirectly involved. The city of Natal has several risk areas, especially on the outskirts of the city, due to the occupation of spaces that have laws and / or natural physical limitations as well as the lack of urban organization, thus increasing the vulnerability of the population living in these areas. The principal objective of this research was to map the areas of social vulnerability and natural hazards in Natal, taking into account the interrelationships between social vulnerability and differential exposure to natural hazards. Therefore, it was necessary to establish, according to the methodology used, the degree of social vulnerability and vulnerability to natural hazard in which individuals are subject, to establish the relationship between society/ risks. In this case, the methodology proposed by Crepani (2001) which is based on ecodynamic Tricart (1977), which classifies the areas of risk and the degree of vulnerability of these areas according to the morphodynamic processes for preparation of the Vulnerability Index was used Physical natural, and for organizing the social Vulnerability Index adopted an adaptation of the Paulista social Vulnerability Index, prepared by SEADE (Fundação Sistema Estadual de Análise de Dados) of the State of São Paulo, drawing on data that denote social disadvantage at the census tract level. Then, with the superposition of these two indices, it was elaborated a Socioenvironmental Vulnerability Index. Thus, it is concluded that besides spatialize areas of risk which indicates the degree of vulnerability of individuals potentially exposed to natural hazard.