With the ever increasing amount of high-throughput molecular profile data, biologists need versatile tools to enable them to quickly and succinctly analyze their data. Furthermore, pathway databases have grown increasingly robust with the KEGG database at the forefront. Previous tools have color-coded the genes on different pathways using differential expression analysis. Unfortunately, they do not adequately capture the relationships of the genes amongst one another. Structure Enrichment Analysis (SEA) thus seeks to take biological analysis to the next level. SEA accomplishes this goal by highlighting for users the sub-pathways of a biological pathways that best correspond to their molecular profile data in an easy to use GUI interface.

A Amazônia hospeda a maior floresta tropical do planeta, considerada um \"hotspot\" de biodiversidade. O aumento das ações antropogênicas nas ultimas décadas (desmatamento e queimadas) tem ocasionado perdas irreparáveis na diversidade biológica, contribuindo significativamente nas mudanças climáticas por meio de alterações dos fluxos hidrológicos e emissão excessiva de gases relacionados ao efeito estufa, dentre os quais o metano. Assim, na busca de uma melhor compreensão dessas alterações é de fundamental importância o estudo das comunidades microbianas associadas ao consumo do metano. Este trabalho teve como objetivo avaliar o impacto das alterações no uso da terra sobre a estrutura genômica e das comunidades bacterianas associadas a oxidação do metano presentes no solo, buscando a combinação de análises independentes (de comunidades) e dependentes de cultivo (enriquecimento e cultivo), juntamente com o acesso aos genomas montados de bactérias metanotróficas. Amostras provenientes de diferentes usos do solo e regiões da floresta amazônica foram coletadas, em sistemas de florestas primárias, florestas secundárias e pastagens na região de Santarém (PA), e florestas primárias e pastagens em Ariquemes (RO). Os solos coletados foram adicionados ao meio enriquecido com metano para estimular o metabolismo das bacterias metanotróficas. Tanto nas amostras originais como nas oriundas dos enriquecimentos, foram realizadas quantificações do gene pmoA pela técnica de PCR quantitativo (qPCR) e caracterização da comunidade total (bactérias e arquéias) e metanotróficas por meio do sequênciamento da região V4-V5 do gene 16S rRNA. Foram também realizadas análises de network e isolamentos de bactérias, na busca de uma maior compreensão sobre as correlações e associações microbianas das amostras. Por fim, o acesso ao metagenoma de amostras enriquecidas e montagens de genomas por metagenoma (MAG - Metagenome Assembled Genome), permitiu comparar a estrutura genômica do operon pmoCAB oriunda de diferentes solos. Os resultados mostraram que estrutura da comunidade total e metanotrófica se alteram com a conversão do solo florestal em pastagem, de maneiras distintas nas áreas amostradas, e com comportamento diferenciado ao longo dos enriquecimentos. O filo Acidobacteria mostrou-se característico de solos florestais, enquanto Actinobacteria, Firmicutes e Bacteoidetes de pastagens, ao passo que a abundância relativa e a riqueza de metanotróficos foi mais elevada em solos de pastagens. Também ocorrem alterações nas interações microbianas, mostrando que florestas possuem correlações mais estáveis que solos de pastagem, porém diferentes entre as áreas estudadas. Estas correlações também são notadas na associação de bactérias metanotróficas com outros grupos, como os gêneros Burkholderia, Pseudomonas, Flavisobacter e Cupriavidus. Em resumo, observa-se que há diferenciação no enriquecimento de bactérias metanotróficas nos diferentes solos e áreas, e os genomas montados indicam a possibilidade de metabolismos distintos. Estes dados contribuem para a compreensão das alterações, em diferentes níveis, da comunidade microbiana nos ambientes de conversão do uso do solo. / The Amazon hosts the largest rainforest on the planet, considered a biodiversity \"hotspot\". The increase in anthropogenic actions in the last decades (deforestation and burning) has caused irreparable losses in biological diversity, contributing significantly to climate change through changes in hydrological flows and excessive emissions of greenhouse gases, including methane. Thus, in the search for the best understanding of these changes, it is of fundamental importance to study the microbial communities associated with methane consumption. This work aimed to evaluate the impact of changes in land use on the genomic structure and bacterial communities associated with the oxidation of methane in the soil, seeking the combination of independent (community) and dependent analyzes (enrichment and growth), along with access to the genomes assembled from methanotrophic bacteria. Samples from different soil uses and regions of the Amazon rainforest were collected, such as primary forests, secondary forests and pastures in the Santarém region (PA) and primary forests and pastures in Ariquemes (RO). The collected soils were added to the methane-enriched medium to stimulate the metabolism of the methanotrophic bacteria. In both the original and the enriched samples, were performed quantifications of the pmoA gene by the quantitative PCR technique (qPCR) and characterization of the total community (bacteria and archaea) and methanotrophic by the sequencing of the V4-V5 region of the 16S rRNA gene. Network analyzes and bacterial isolations were also carried out in order to obtain a better understanding of the microbial correlations and associations of the samples. Finally, the access to the metagenome of enriched samples and genome assemblies by metagenome (MAG - Metagenome Assembled Genome) allowed comparing the genomic structure of the pmoCAB operon from different soils. The results showed that the structure of the total and methanotrophic community analyzed changes with the conversion of the forest soil to pasture, in different ways in the sampled areas and in enriched soils. The phyla Acidobacteria showed to be characteristic of forest soils, while Actinobacteria, Firmicutes, and Bacteroides of pastures and the relative abundance and richness of methanotrophic are higher in pastures soils. The changes were observed for microbial interactions, showing that forests have more stable correlations than pasture soils, but different between the areas studied. These correlations are also noted in the association of methanotrophic bacteria with other groups, such as the genera Burkholderia, Pseudomonas, Flavisobacter and Cupriavidus. In summary, it was observed differentiation in the enrichment of methanotrophic bacteria in the different soils and areas, and the assembled genomes indicate the possibility of different metabolisms. These data contribute to the understanding of the changes, at different levels, of the microbial community in the land use conversion environments.

Att vara berövad sin frihet och sina valmöjligheter kan få stora konsekvenser i en individs hälsa och livssituation. Intagna riskerar att, efter avtjänat straff, släppas ut i samhället med begränsad förmåga att fungera självständigt, försämrat hälsotillstånd och med hög återfallsrisk. Ett aktivitetsvetenskapligt perspektiv är användbart för att förstå och utveckla interventioner som syftar till att upprätthålla och utveckla förmågor i det dagliga livet och utvecklandet av roller för att stödja framgångsrik återgång i samhället. Syftet med studien var att beskriva arbetsterapeutiska insatser och dess betydelse för intagna på straffrättsliga institutioner. En litteraturöversikt valdes och sökningar genomfördes i databaserna Web of Science, Cinahl, PubMed, Amed, Socindex och Academic Search Elite. Sju artiklar inkluderades för kvalitetsgranskning och analys. Resultatet visade en variation av interventioner där fokus låg på den generella livssituation de intagna befann sig i alternativt aktuell målgrupps specifika problematik. Gemensamt, inom samtliga instanser, var behovet av att öva upp sociala och kommunikativa förmågor. Viktiga betydelser som framkom var att intagna hade möjlighet till visst självbestämmande och att aktiviteter hade ett tydligt syfte för att upplevas som meningsfulla och terapeutiska. Studien visade att trots restriktioner till följd av säkerhetsaspekter, är det möjligt att genomföra klientcentrerade interventioner som har en positiv inverkan på intagnas hälsa, beteenden, självkänsla och utförandekapacitet. Arbetsterapeuten har en viktig roll i det rehabiliterande arbetet för att motverka kriminellt beteende och erbjuda redskap som underlättar övergången till samhället och minskar risken för återfall.

A conversão de áreas de florestas da Amazônia em áreas agrícolas e pastoris desregula processos relacionados ao estoque de carbono, sendo considerada depois da queima de combustíveis fósseis a atividade que mais contribui com a emissão de gases do efeito estufa, dentre os quais se encontra o metano. A produção de metano é intermediada pelas arquéias metanogênicas, que atuam na decomposição anaeróbia da matéria orgânica. Portanto, para compreender as alterações do fluxo desse gás no ecossistema amazônico, é necessário que as comunidades microbianas envolvidas nesse processo sejam estudadas. Dessa forma, o presente estudo teve por objetivo monitorar e caracterizar comunidades de arquéias metanogênicas, por análises de enriquecimento destas comunidades, em amostras de solo provenientes de floresta primária, floresta secundária e pastagem da região amazônica. As amostras de solo foram colocadas em meio enriquecido com a adição de acetato, metanol ou H2:CO2, separadamente, para estimular os metabolismos aceticlástico, metilotrófico e hidrogenotrófico. O monitoramento desses cultivos foi realizado por análises de emissão de metano por cromatografia gasosa, quantificação do gene mcrA pela técnica de PCR quantitativo (qPCR) e caracterização da comunidade metanogênica por meio de microscopia e sequenciamento da região V4-V5 do gene 16S rRNA. Analisando a emissão de metano entre os três tipos de fontes de carbono para as três amostras de solo, os enriquecimentos com metanol apresentaram uma produção maior de metano em relação as amostras com o acetato e muito superior aos cultivos com atmosfera de H2:CO2. A maior média de produção de metano ocorreu nos enriquecimentos com metanol, indicando que a via metilotrófica embora considerada alternativa, pode ser importante na produção de metano no solo amazônico. Por meio da técnica de qPCR foi possível quantificar o gene mcrA das amostras de pastagens logo no tempo inicial da incubação, o que não foi possível para as amostras florestais. No tempo final, o número de cópias desse gene foi similar para os três perfis de solo. Foi possível observar pela caracterização fenotípica dos enriquecimentos agregados de células característicos do gênero Methanosarcina, gênero que foi identificado posteriormente pelo sequenciamento do gene 16S rRNA, além de células em formatos de bastonetes e cocos. Os resultados do sequenciamento permitiram identificar 7 grupos distintos de arqueias metanogênicas, afiliados aos filos Euryarchaeota e Bathyarchaeota. Nas amostras iniciais de pastagens foram identificadas sequências que se afiliaram a todos esses grupos, enquanto as amostras florestais apresentaram sequencias afiliadas apenas ao gênero Methanosarcina. A composição final da comunidade das amostras de pastagens foi similar a inicial, porém mais abundante. Os enriquecimentos de amostras de solo de floresta primária e secundária apresentaram uma composição distinta, devido ao enriquecimento de grupos que não foram identificados no início da incubação. Os resultados obtidos mostraram que embora as arqueias metanogênicas estejam em baixa abundância nos solos florestais, podem ser enriquecidos quando submetidos a condições favoráveis, atingindo produção de metano e alcançando composição similar as amostras de pastagens. / Amazonian forest conversion into agricultural and livestock areas disrupts processes related to carbon stock, being considered, after the fossil fuels burning, the activity contributes most to greenhouse gases emission, of which is methane. Methane production is mediated by methanogenic archaea, acting in organic matter anaerobic decomposition. Therefore, to understand the changes in the flow of this gas in the Amazonian ecosystem, it is necessary to study microbial communities involved in this process. This study aims to monitor and characterize methanogenic archaeal communities by population enrichment from soil samples collected in primary, secondary and pasture of the Amazon region. Soil samples were placed into an enriched medium and received separately acetate, methanol, and H2:CO2 to stimulate the three metabolism types: acetoclastic, methylotrophic and hydrogenotrophic. Monitoring was performed by methane emission analysis by gas chromatography, mcrA quantification by the quantitative PCR and the community characterization was performed by microscopy and sequencing of the V4-V5 region of the 16S rRNA gene. Analyzing the methane emission by the three types of carbon sources in the three soil samples, methanol enrichments presented a higher methane yield than the acetate samples and much larger than cultures with H2:CO2. These results indicate that methylotrophic pathway, although considered as an alternative, may be important in methane production in the Amazonian soil. Was possible to quantify the mcrA gene by qPCR from pasture samples at the initial incubation time, which was not possible for forest samples. In incubation final time, copies number of this gene was similar for the three soil profiles. The phenotypic characterization of enrichments revealed aggregated cells, characteristic of the genus Methanosarcina, later identified by 16S rRNA sequencing. The cells in rod-shaped and cocci formats were also observed. Was identify by sequencing 7 different methanogenic archaeas groups affiliated with Euryarchaeota and Bathyarchaeota phylum. In the initial pasture samples, were identified sequences affiliated with all these groups, while forest samples presented sequences affiliated with only a Methanosarcina genus. Pasture samples showed a final community composition similar to initial, however more abundant. Soil samples enrichment from primary and secondary forest presented a distinct composition due to groups enrichment that was not identified at incubation beginning. These results showed that although methanogenic archaeas are in low abundance in forest soils, they can be enriched when submitted to favorable conditions, archive methane production and reaching similar composition pasture samples.

Birks' unjust enrichment formula was intended to provide a common descriptive structure to all the instances where there was recovery. He did not, however, engage in an analysis of the various reasons why courts awarded restitution. My thesis seeks to fill this gap. I argue that without such an account Birks work is incomplete. According to Birks, for example, money and services both amounted to enrichments and so should be considered together. But there are some differences and similarities between money and services. In order to be able to group them together Birks needs to be able to say that the reasons for giving recovery in money and service cases are similar enough that they can be grouped together. The same goes for all the unjust factors. The point is, the generalisation that Birks sought to do, can only properly be done if one is attuned to the reasons why recovery is granted in each of those cases. If the reasons are similar then the generalisation makes sense. But if they are not then it does not make sense to so generalise. The argument of the thesis is that there three relevant principles to justifying unjust enrichment: the Property Principle, the Benefit-Burden Principle and the Autonomy Principle. The Property Principle states that one should not have property belonging to another. The Benefit-Burden Principle states that if one takes a benefit then one must bear the associated burdens; to put it more colloquially: you have to take the rough with the smooth. These first two principles provide reasons for considering a situation to be defective and the last principle provides a constraint for the operation of the first two. It is there to ensure that the imposition of liability will not unduly affect the autonomy of the defendant. Based on that the thesis proposes that the scope of the unjust enrichment formula be trimmed down to only cover defective transfers of money and other assets. For the other cases, a different analytical structure is needed. This is because the reasons for recovery in those cases are different.

Motivation Translational bioinformatics(TBI) has been defined as ‘the development and application of informatics methods that connect molecular entities to clinical entities’ [1], which has emerged as a systems theory approach to bridge the huge wealth of biomedical data into clinical actions using a combination of innovations and resources across the entire spectrum of biomedical informatics approaches [2]. The challenge for TBI is the availability of both comprehensive knowledge based on genes and the corresponding tools that allow their analysis and exploitation. Traditionally, biological researchers usually study one or only a few genes at a time, but in recent years high throughput technologies such as gene expression microarrays, protein mass-spectrometry and next-generation DNA and RNA sequencing have emerged that allow the simultaneous measurement of changes on a genome-wide scale. These technologies usually result in large lists of interesting genes, but meaningful biological interpretation remains a major challenge. Over the last decade, enrichment analysis has become standard practice in the analysis of such gene lists, enabling systematic assessment of the likelihood of differential representation of defined groups of genes compared to suitably annotated background knowledge. The success of such analyses are highly dependent on the availability and quality of the gene annotation data. For many years, genes were annotated by different experts using inconsistent, non-standard terminologies. Large amounts of variation and duplication in these unstructured annotation sets, made them unsuitable for principled quantitative analysis. More recently, a lot of effort has been put into the development and use of structured, domain specific vocabularies to annotate genes. The Gene Ontology is one of the most successful examples of this where genes are annotated with terms from three main clades; biological process, molecular function and cellular component. However, there are many other established and emerging ontologies to aid biological data interpretation, but are rarely used. For the same reason, many bioinformatic tools only support analysis analysis using the Gene Ontology. The lack of annotation coverage and the support for them in existing analytical tools to aid biological interpretation of data has become a major limitation to their utility and uptake. Thus, automatic approaches are needed to facilitate the transformation of unstructured data to unlock the potential of all ontologies, with corresponding bioinformatics tools to support their interpretation. Approaches In this thesis, firstly, similar to the approach in [3,4], I propose a series of computational approaches implemented in a new tool OntoSuite-Miner to address the ontology based gene association data integration challenge. This approach uses NLP based text mining methods for ontology based biomedical text mining. What differentiates my approach from other approaches is that I integrate two of the most wildly used NLP modules into the framework, not only increasing the confidence of the text mining results, but also providing an annotation score for each mapping, based on the number of pieces of evidence in the literature and the number of NLP modules that agreed with the mapping. Since heterogeneous data is important in understanding human disease, the approach was designed to be generic, thus the ontology based annotation generation can be applied to different sources and can be repeated with different ontologies. Secondly, in respect of the second challenge proposed by TBI, to increase the statistical power of the annotation enrichment analysis, I propose OntoSuite-Analytics, which integrates a collection of enrichment analysis methods into a unified open-source software package named topOnto, in the statistical programming language R. The package supports enrichment analysis across multiple ontologies with a set of implemented statistical/topological algorithms, allowing the comparison of enrichment results across multiple ontologies and between different algorithms. Results The methodologies described above were implemented and a Human Disease Ontology (HDO) based gene annotation database was generated by mining three publicly available database, OMIM, GeneRIF and Ensembl variation. With the availability of the HDO annotation and the corresponding ontology enrichment analysis tools in topOnto, I profiled 277 gene classes with human diseases and generated ‘disease environments’ for 1310 human diseases. The exploration of the disease profiles and disease environment provides an overview of known disease knowledge and provides new insights into disease mechanisms. The integration of multiple ontologies into a disease context demonstrates how ‘orthogonal’ ontologies can lead to biological insight that would have been missed by more traditional single ontology analysis.

O presente estudo tem por objetivo demonstrar que, nas hipóteses em que alguém intervém na esfera jurídica alheia e obtém benefícios econômicos sem causar danos ao titular do direito ou, causando danos, o lucro obtido pelo ofensor é superior aos danos causados, as regras da responsabilidade civil, isoladamente, não são suficientes, à luz do ordenamento jurídico brasileiro, enquanto sanção eficaz pela violação de um interesse merecedor de tutela. Isto porque, como a principal função da responsabilidade civil é remover o dano, naquelas hipóteses, não fosse a utilização de um remédio alternativo, o interventor faria seu o lucro da intervenção, no primeiro caso integralmente e, no segundo, no valor equivalente ao saldo entre o lucro obtido e a indenização que tiver que pagar à vítima. A tese pretende demonstrar que o problema do lucro da intervenção não deve ser solucionado por intermédio das regras da responsabilidade civil, devendo, portanto, ser rejeitadas as propostas de solução neste campo, como a interpretação extensiva do parágrafo único, do artigo 944, do Código Civil, as indenizações punitivas e o chamado terceiro método de cálculo da indenização. Como alternativa, propõe-se o enquadramento dogmático do lucro da intervenção no enriquecimento sem causa, outorgando ao titular do direito uma pretensão de restituição do lucro obtido pelo ofensor em razão da indevida ingerência em seus bens ou direitos. Defende-se que a transferência do lucro da intervenção para o titular do direito tem por fundamento a ponderação dos interesses em jogo à luz da Constituição Federal, com especial atenção ao princípio da solidariedade, e da teoria da destinação jurídica dos bens. A tese procura demonstrar, ainda, que o ordenamento jurídico brasileiro não exige um efetivo empobrecimento do titular do direito para a configuração do enriquecimento sem causa e que a regra da subsidiariedade não impede a cumulação de ações, de responsabilidade civil para eliminar o dano (e no limite do dano), e de enriquecimento sem causa, para forçar a restituição do saldo positivo que permanecer no patrimônio do ofensor após o pagamento da indenização, se houver. Finalmente, a tese pretende provocar a discussão acerca da quantificação do objeto da restituição, propondo alguns critérios que deverão orientar o aplicador do direito. / The present study aims to demonstrate that when someone profits by interfering In: another persons rights without causing damage to the victim, or when the act does cause damage but the benefits so obtained are greater than the damage caused, tort rules alone are not enough, under Brazilian Law, as an efficient sanction for violation of an interest or right that deserves protection. Since the maIn: function of civil liability rules is to redress the damage, or make the victim whole, without an alternative remedy the wrongdoer would keep the benefits wrongfully obtained, fully In: the first case and In: the second case to the extent of the difference between the profits obtained and damages paid to the victim. I aim to show that the problem of benefits wrongfully obtained cannot be solved through tort rules alone, and some proposed measures In: this area, such as expansive interpretation of Article 944, sole paragraph, of the Civil Code, punitive damages and the so-called third method of quantifying damages should be rejected. As an alternative, I propose framing the question of benefits wrongfully obtained withIn: the rules on unjust enrichment, granting the victim the right to claim restitution of benefits obtained by the wrongdoer by interference In: the victims assets or rights. I argue that the transfer of the benefits wrongfully obtained to the victim should be based on a balance of conflicting interests In: light of the Federal Constitution, with special attention to the solidarity principle and on the theory of the juridical allocation of assets. Besides this, I argue that Brazilian law does not require the victim to suffer any kind of damage In: order to apply unjust enrichment rules and that the subsidiarity rule does not prohibit the filing of joint claims, a tort one to remedy the damage (limited to the actual damage caused) and an unjust enrichment one to force restitution of any positive balance that remains with the wrongdoer after payment of damages. Finally, I intend to stimulate discussions on how to quantify the amount of restitution In: these cases and offer some criteria that can guide judges.

Environmental enrichment, for more than fifty years, has shown to increase learning in behaviors and to alter some brain structures (Renner and Rosenzweig). Some brain changes that occur when environmental enrichment is implemented include the following: increases in cortical thickness, especially the occipital cortex, increases in size of neuronal cell bodies, number of dendrites and dendritic spines, increases in astrocyte branching, increases in the number of brain blood capillaries, and increases in mitochondria (an indication of higher metabolic activity) (Stairs and Bard). It has been shown in research studies that rats in the environmental enrichment group are less sensitive to nicotine effects, both repeated and acute, than rats in isolated situations (Green et al). This is so because enrichment changes the intensity of the acute administration of drugs of abuse. Rats are stimulated by the environment, rather than a particular stimulant.

No description available.

Salvia hispanica L. (commonly known as chia) is gaining popularity worldwide and specially in US as a healthy oil and food supplement for human and animal consumption due to its favorable oil composition, and high protein, fiber, and antioxidant contents. Despite these benefits and its growing public demand, very limited gene sequence information is currently available in public databases. In this project, we generated 90 million high quality 150 bp paired-end sequences from the chia leaf and root tissues. The sequences were de novo assembled into 103,367 contigs with average length of 1,445 bp. The resulted assembly represented 92.2% transcriptome completeness. Around 69% of the assembled contigs were annotated against the uniprot database and represented a diverse array of functional and biological categories. A total of 14,267 contigs showed significant expression difference between the leaf and root tissues, with 6,151 and 8,116 contigs upregulated in the leaf and root, respectively. The sequence data generated in this project will provide valuable resources for future functional genomic research in chia. With the availability of transcriptome sequences, it would be possible to identify genes involved in the important metabolic pathways that give chia its unique nutritional and medicinal properties. Finally, the generated data will contribute to the genetic improvement efforts of chia to better serve the public demand.