Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A reservoir presents different environmental traits as a function of the flooded area, water circulation pattern, residence time and nutrients entrance. This situation define the aquatic compartments. The objective was use limnological parameter dynamic and spectral data to identify aquatic compartments in the Rodolfo Costa e Silva reservoir, located on central region of the State of Rio Grande do Sul, on southern region of Brazil. The methodology was based on the measure of water transparence with Secchi disc, Total of Suspended Solids (TSS) and chlorophyll a, b and c. These data were monthly collected in 21 sampling points, distributed over the reservoir during hydrologic year (Oct. 2005 to Sept. 2006). However, chlorophyll samples were collected only two times in autumn season. Satellites images from China-Brazil Earth Resources Satellite 2 (CBERS 2 CCD) and Landsat 5 (TM) were used to make a comparison with limnological and field spectral data. The spatial distribution of limnological parameters was done after data interpolation (weighted average) and its analyses allowed the discrimination of aquatic compartments. During the hydrologic year the transparence changed between 100 and 315 cm and could be divided in two periods: a period with low transparences, from August to November (marked by land tillage for summer crop) and; period with high transparence, from December to June. Based on this variable, the reservoir presented three compartments: a) upstream, with lower transparence; b) downstream, with higher transparence; c) central region, even with high transparence. The TSS ranged from 0.17 to 14.16 mg/L in the hydrologic year. Its behavior was inversely to the water transparence but presented the same three compartments than transparence. The chlorophyll concentration varied from 0.63 to 24.19 μg/L and defined two compartments: upstream and downstream. A larger input of nutrients in upstream let the development of phytoplankton (chlorophylls). Results from CCD and TM images were better when TSS concentration was greater and transparence smaller, associated to the highest data variance. Concentrations of TSS up to 4 mg/L periods with low transparence allowed identify aquatic compartments with blue band (centered on 450 nm) and the red band (centered on 661 nm). The chlorophylls a and c showed absorption bands on the field spectrum of reflectance, making possible establish correlations with limnological parameters (TSS and transparence). Finally, the aquatic compartments that were found out are specially related to the entrance of organic and inorganic matter from terrestrial environment. TSS and chlorophyll decreases into downstream. / Normalmente, um reservatório apresenta diferentes características ambientais em função das áreas alagadas, dos diferentes padrões de circulação, do tempo de residência e entrada de nutrientes, que definem diferentes compartimentos aquáticos. A caracterização limnológica e espectral, com a identificação da dinâmica dos compartimentos aquáticos, foram realizadas no reservatório Rodolfo Costa e Silva RS (Brasil). A metodologia baseou-se na coleta de dados de transparência da água medida pelo disco de Secchi, Totais de Sólidos em Suspensão (TSS) e clorofila a, b e c em 21 pontos amostrais, distribuídos em todo o reservatório e obtidos mensalmente para compor um ano hidrológico (Out. 2005 a Set. 2006); com exceção da clorofila, que foi medida em duas datas durante o outono. Imagens dos satélites CBERS 2 CCD e Landsat 5 TM foram utilizadas para relacionar com os dados limnológicos de campo. A distribuição espacial desses dados limnológicos foi identificada por interpolação por média ponderada, para posterior discriminação dos compartimentos aquáticos. A transparência da água apresentou uma variação no ano hidrológico de 100 a 315 cm e pode ser dividida em dois períodos: das baixas transparências, compreendendo o período de agosto a novembro (período de preparo de solo para a safra agrícola de verão); e de altas transparências, compreendendo o período de dezembro a junho. Essa variável forma três compartimentos: a) o de montante, com menor transparência; b) o de jusante, com maior transparência; c) junto ao dique, de elevada transparência. O TSS apresentou uma amplitude de 0,17 a 14,16 mg/L no ano hidrológico, com comportamento inversamente proporcional ao da transparência definindo compartimentos aquáticos semelhantes. As clorofilas com variação de 0,53 a 24,19 μg/L apresentaram os dois compartimentos aquáticos: o de montante e o de jusante. O maior aporte de nutrientes, à montante do reservatório, proporcionaram o desenvolvimento do fitoplâncton (clorofilas). Os resultados obtidos com imagens CCD e TM foram melhores, quando as concentrações de TSS foram maiores e as transparências foram menores, acompanhados de maior variância. As baixas transparências e as concentrações de TSS maiores que 4 mg/L permitiram identificar compartimentos aquáticos nas bandas azul (450 nm) e vermelha (661 nm). As clorofilas a e c apresentaram bandas de absorção nos espectros de reflectância, permitindo estabelecer correlações. Por fim, os compartimentos aquáticos encontrados estão relacionados, principalmente, ao fornecimento de matéria orgânica e inorgânica oriundas do ambiente terrestre para o sistema aquático, verificado no setor montante, e sua concentração diminui no sentido jusante do reservatório.

Domestic wastewater is one of the most interested environmental issues in Vietnam, especially in big cities and suburban residential areas. Most of the wastewater was not treated in the right way before discharging to environment. In this research, the author used water hyacinth as a main aquatic plant in aquatic pond model to treat wastewater. The experiment was operated continuously in 1 year with hydraulic retention time (HRT) is 11 and 18 days. Hydraulic loading rate (HRL) is 300 and 500 m3/ha/day, respectively. Treatment efficiency of the model for TSS is 90% (remaining 6 -12mg/l); COD, BOD5 is 63 - 81% (remaining 10 - 48mg/l); TP is 48 – 50% (remaining 3.5 - 9.8mg/l); TKN is 63 - 75% (remaining 8 - 17mg/l). Polluted parameters in effluent were lower than A and B levels of Vietnam standard QCVN 14: 2008/BTNMT and QCVN 40: 2011/BTNMT. The doubling time of water hyacinth in summer is 18days, and in autumn and winter is 28.5 days. Experiment results showed that we can use water hyacinth in aquatic pond to treat domestic wastewater with medium scale. We can apply this natural treatment method for residential areas by utilizing existing natural ponds and abandoned agricultural land with capacity up to 500m3/ha day. However, to get better efficiency we should combine with other aquatic plant species to treat wastewater and improve environmental landscape. / Nước thải – xử lý nước thải sinh hoạt hiện đang là một trong những vấn đề môi trường được quan tâm tại Việt Nam nhất là tại các thành phố lớn và các khu dân cư. Hầu hết lượng nước thải chưa được xử lý đúng cách trước khi thải ra môi trường. Trong nghiên cứu này, tác giả sử dụng mô hình hồ thủy sinh và sử dụng cây Bèo lục bình để xử lý nước thải sinh hoạt của một khu dân thuộc huyện Từ Liêm, tại khu vực này nước thải bị thải trực tiếp vào sông Nhuệ. Thực nghiệm đã được tiến hành trong khoảng thời gian một năm, trải qua các mùa của khu vực miền Bắc với hai chế độ vận hành HRT là 18 và 11 ngày, tương ứng với tải trọng thủy lực HRL là 300 và 500 m3/ha/ngày. Kết quả cho thấy mô hình thủy sinh sử dụng cây bèo lục bình cho kết quả tốt, hiệu suất xử lý với các chất ô nhiễm đạt được như sau: chất rắn lơ lửng đạt 90%, COD, BOD5 đạt 63 - 81%, Phốt pho tổng giảm tới 48 -50%, Nitơ tổng giảm tới 63 - 75%. Hàm lượng các chất ô nhiễm trong nước thải đầu ra của mô hình đều thấp hơn ngưỡng A và B của các tiêu chuẩn QCVN 14: 2008/BTNMT và QCVN 40: 2011/BTNMT. Bên cạnh đó tác giả cũng đã xác định định được tốc độ sinh trưởng của cây bèo tại khu vực miền Bắc là 18 ngày vào mùa hè và 28.5 ngày vào mùa thu đông. Kết quả nghiên cứu cho thấy có thể sử dụng bèo lục bình để xử lý nước thải sinh hoạt, với qui mô vừa và nhỏ và nên áp dụng cho các khu vực ven đô, nông thôn nơi có diện tích đất rộng hoặc tại các hồ sinh thái của các khu đô thị. Tuy nhiên, để hiệu quả tốt hơn ta cần kết hợp với nhiều loại thực vật thủy sinh khác để ngoài tác dụng xử lý nước thải mà còn tạo cảnh quan môi trường xung quanh.

Domestic wastewater is one of the most interested environmental issues in Vietnam, especially in big cities and suburban residential areas. Most of the wastewater was not treated in the right way before discharging to environment. In this research, the author used water hyacinth as a main aquatic plant in aquatic pond model to treat wastewater. The experiment was operated continuously in 1 year with hydraulic retention time (HRT) is 11 and 18 days. Hydraulic loading rate (HRL) is 300 and 500 m3/ha/day, respectively. Treatment efficiency of the model for TSS is 90% (remaining 6 -12mg/l); COD, BOD5 is 63 - 81% (remaining 10 - 48mg/l); TP is 48 – 50% (remaining 3.5 - 9.8mg/l); TKN is 63 - 75% (remaining 8 - 17mg/l). Polluted parameters in effluent were lower than A and B levels of Vietnam standard QCVN 14: 2008/BTNMT and QCVN 40: 2011/BTNMT. The doubling time of water hyacinth in summer is 18days, and in autumn and winter is 28.5 days. Experiment results showed that we can use water hyacinth in aquatic pond to treat domestic wastewater with medium scale. We can apply this natural treatment method for residential areas by utilizing existing natural ponds and abandoned agricultural land with capacity up to 500m3/ha day. However, to get better efficiency we should combine with other aquatic plant species to treat wastewater and improve environmental landscape. / Nước thải – xử lý nước thải sinh hoạt hiện đang là một trong những vấn đề môi trường được quan tâm tại Việt Nam nhất là tại các thành phố lớn và các khu dân cư. Hầu hết lượng nước thải chưa được xử lý đúng cách trước khi thải ra môi trường. Trong nghiên cứu này, tác giả sử dụng mô hình hồ thủy sinh và sử dụng cây Bèo lục bình để xử lý nước thải sinh hoạt của một khu dân thuộc huyện Từ Liêm, tại khu vực này nước thải bị thải trực tiếp vào sông Nhuệ. Thực nghiệm đã được tiến hành trong khoảng thời gian một năm, trải qua các mùa của khu vực miền Bắc với hai chế độ vận hành HRT là 18 và 11 ngày, tương ứng với tải trọng thủy lực HRL là 300 và 500 m3/ha/ngày. Kết quả cho thấy mô hình thủy sinh sử dụng cây bèo lục bình cho kết quả tốt, hiệu suất xử lý với các chất ô nhiễm đạt được như sau: chất rắn lơ lửng đạt 90%, COD, BOD5 đạt 63 - 81%, Phốt pho tổng giảm tới 48 -50%, Nitơ tổng giảm tới 63 - 75%. Hàm lượng các chất ô nhiễm trong nước thải đầu ra của mô hình đều thấp hơn ngưỡng A và B của các tiêu chuẩn QCVN 14: 2008/BTNMT và QCVN 40: 2011/BTNMT. Bên cạnh đó tác giả cũng đã xác định định được tốc độ sinh trưởng của cây bèo tại khu vực miền Bắc là 18 ngày vào mùa hè và 28.5 ngày vào mùa thu đông. Kết quả nghiên cứu cho thấy có thể sử dụng bèo lục bình để xử lý nước thải sinh hoạt, với qui mô vừa và nhỏ và nên áp dụng cho các khu vực ven đô, nông thôn nơi có diện tích đất rộng hoặc tại các hồ sinh thái của các khu đô thị. Tuy nhiên, để hiệu quả tốt hơn ta cần kết hợp với nhiều loại thực vật thủy sinh khác để ngoài tác dụng xử lý nước thải mà còn tạo cảnh quan môi trường xung quanh.

Since their discovery in 1953, adenoviruses have significantly contributed to the understanding of virus-host cell interactions, including mechanistic details of cellular processes such as cell cycle control and alternative RNA splicing. Among the first characterized adenoviral genes were the virus-associated RNAs (VA RNAI/II), which are produced in massive amount during a lytic infection. The VA RNAs perform multiple functions and are required for a successful adenovirus life cycle. More recently, it was shown that the VA RNAs are processed into small viral miRNAs, so-called mivaRNAs, which interfere with the function of the cellular RNAi/miRNA machinery. In papers I and II, we focused on a structural and functional characterization of the mivaRNAs using two approaches. Firstly, we created a model system where the predicted miRNA-like function of mivaRNAI could be investigated, without interfering with other VA RNA functions. This was accomplished by construction of recombinant adenoviruses, in which the seed sequence of mivaRNAI was altered. The results showed that in cell culture experiments the mivaRNAI seed sequence mutants grew as the wild type virus, suggesting that the mivaRNAs are not required during the lytic phase of an adenovirus infection. Secondly, we showed that the VA RNAs from different human adenoviruses (Ad4, Ad5, Ad11 and Ad37) undergo the same type of Dicer-dependent processing into mivaRNAs, which subsequently are loaded onto the RNA induced silencing complex (RISC), albeit with different efficiencies. In paper III, we demonstrated that the promoter proximal region of the adenovirus major late promoter (MLP) produces a novel non-canonical class of small RNAs, which we termed the MLP-TSS-sRNAs. Surprisingly the MLP-TSS-sRNA maintains the m7G-cap structure while bound to Ago2 containing RISC. These complexes are functional suppressing expression of target mRNAs with complementary binding site. Most importantly, the MLP-TSS-sRNA limits the efficiency of viral DNA replication probably through a targeting of the E2B mRNAs, which are transcribed in the antisense orientation. In conclusion, the MLP-TSS-sRNA represents the first viral small RNA, which has been shown to have a function as a regulator of an adenovirus infection.

This proposed research focused on the prediction and identification of dissolved heavy metals in storm water runoff from elevated roadways. Storm water runoff from highways transports a significant load of contaminants, especially heavy metals and particulate matter, to receiving waters. Heavy metals, either in dissolved or particulatebound phases, are unique in the fact that unlike organic compounds, they are not degraded in the environment. The objective of this research was to develop a mathematical model to relate dissolved heavy metal concentration to different measurable parameters which are easily available and routinely measurable for elevated roadways. The reliability of the developed models was then evaluated by comparing the raw data versus data predicted by the models. The test site for this research was selected at the intersection of the Interstate-10 and Interstate-610, Orleans Parish, New Orleans, Louisiana. Subsequently a research test site was developed and highway storm water runoff was collected. Volumetric flow rates were measured with every collected sample by measuring the amount of collected water and the collection time. Storm water runoff from the examined elevated roadway section was sampled for 10 storm events throughout the course of the study from which hydrologic and water quality data were collected. The measurement of different parameters made it possible to determine the percentage of dissolved heavy metal mass loading and the characterization of high runoff flow intensity and low runoff flow intensity storm events. Another very important achievement in this research was the construction of a predictive model for dissolved heavy metal concentrations based on field measurements. Data analysis proceeded by applying different variable selection statistical methods as well as multiple regression analyses in order to evaluate the simultaneous effects of all variables on the concentration of dissolved heavy metals in storm water runoff. The developed model enables the user to predict dissolved heavy metal concentrations with known field measurements within a prediction interval of 95 % confidence. The reliability of the models was verified by carrying out significant-difference tests for both sets of data, observed and predicted, for a 5% of significance level.

To minimize coastal land loss and create new land, dredged sediment has been in use in coastal Louisiana during the last several years. Engineering properties and material characteristics of dredged material are input parameters in several mathematical models used to predict the long-term hydrodynamic behavior of the coast. Therefore, proper characterization of the dredged material is of utmost importance in the correct design of coastal restoration and land creation projects. The sedimentation characteristics of the dredged material, among other factors, depends on the (a) grain size distribution of the dredged material, (b) salinity (fresh, brackish, or saltwater environment) of the composite slurry, and (c) concentration of the solid particles in the slurry. In this research, dredged sediments obtained from actual coastal restoration projects were characterized. Furthermore, the effects of grain size distribution, salinity and solid particle concentration on sedimentation characteristics have been evaluated.

Les sites de fixation des facteurs de transcription ou éléments régulateurs sont impliqués dans la régulation de l'expression des gènes. Une meilleure connaissance de l'architecture des promoteurs est aujourd'hui accessible via l'annotation des génomes et les données transcriptomiques. Certains éléments régulateurs sont conservés à une position préférentielle dans les promoteurs. Chez A. thaliana, nous avons mis au point une approche pour caractériser de tels motifs. Ce travail a permis de proposer une cartographie des promoteurs en identifiant 5105 motifs caractérisés par une sur-représentation locale dans les promoteurs proximaux. L'étude du promoteur central où est observée la boîte TATA, élément régulateur conservé entre eucaryotes, a été approfondie. Une liste de 15 variants fonctionnels de la boîte TATA a été identifiée, ainsi qu'une nouvelle classe d'éléments régulateurs qui sont caractérisés par des mêmes contraintes topologiques que la boîte TATA : les motifs-TC. Ils sont conservés chez A. thaliana et le riz, Oryza sativa, mais absents chez les mammifères. Les 18% de gènes d'A. thaliana contenant un motif-TC ont tendance à être exprimés dans des conditions expérimentales spécifiques. Ces éléments pourraient participer à la régulation de l'expression des gènes. L'étude de l'élément initiateur YR chez A. thaliana a mis en évidence une extension de ces 4 dinucléotides dans l'UTR 5'. Des associations entre ces éléments régulateurs peuvent montrer une collaboration fonctionnelle. La recherche de caractéristiques fonctionnelles communes aux gènes possédant une même organisation d'éléments régulateurs pourra permettre de contribuer à l'annotation fonctionnelle de ces éléments.

The present work consists of three parts. In the first part (chapters III and IV), the dynamics of Lorentz lattice gases (LLG) on graphs is analyzed. We study the fixed scatterer model on finite graphs. A tight bound is established on the size of the orbit for arbitrary graphs, and the model is shown to perform a depth-first search on trees. Rigidity models on trees are also considered, and the size of the resulting orbit is established. In the second part (chapter V), we give a complete description of dynamics for LLG on the one-dimensional integer lattice, with a particular interest in showing that these models are not capable of universal computation. Some statistical properties of these models are also analyzed. In the third part (chapter VI) we attempt to partition a pool of workers into teams that will function as independent TSS lines. Such partitioning may be aimed to make sure that all groups work at approximately the same rate. Alternatively, we may seek to maximize the rate of convergence of the corresponding dynamical systems to their fixed points with optimal production at the fastest rate. The first problem is shown to be NP-hard. For the second problem, a solution for splitting into pairs is given, and it is also shown that this solution is not valid for partitioning into teams composed of more than two workers.

Transcriptional regulation is a complicated process controlled by numerous factors such as transcription factors (TFs), chromatin remodeling enzymes, nucleosomes, post-transcriptional machineries, and cis-acting DNA sequence. I explored the complex transcriptional regulation in eukaryotes through three distinct studies to comprehensively understand the functional genomics at various steps. Although a variety of high throughput approaches have been developed to understand this complex system on a genome wide scale with high resolution, a lack of accurate and comprehensive annotation transcription start sites (TSS) and polyadenylation sites (PAS) has hindered precise analyses even in Saccharomyces cerevisiae, one of the simplest eukaryotes. We developed Simultaneous Mapping Of RNA Ends by sequencing (SMORE-seq) and identified the strongest TSS and PAS of over 90% of yeast genes with single nucleotide resolution. Owing to the high accuracy of TSS identified by SMORE-seq, we detected possibly mis-annotated 150 genes that have a TSS downstream of the annotated start codon. Furthermore, SMORE-seq showed that 5’-capped non-coding RNAs were highly transcribed divergently from TATA-less promoters in wild-type cells under normal conditions. Mapping of DNA-protein interactions is essential to understanding the role of TFs in transcriptional regulation. ChIP-seq is the most widely used method for this purpose. However, careful attention has not been given to technical bias reflected in final target calling due to many experimental steps of ChIP-seq including fixation and shearing of chromatin, immunoprecipitation, sequencing library construction, and computational analysis. While analyzing large-scale ChIP-seq data, we observed that unrelated proteins appeared to bind to the gene bodies of highly transcribed genes across datasets. Control experiments including input, IgG ChIP in untagged cells, and the Golgi factor Mnn10 ChIP also showed the strong binding at the same loci, indicating that the signals were obviously derived from bias that is devoid of biological meaning. In addition, the appearance of nucleosomal periodicity in ChIP-seq data for proteins localizing to gene bodies is another bias that can be mistaken for false interactions with nucleosomes. We alleviated these biases by correcting data with proper negative controls, but the biases could not be completely removed. Therefore, caution is warranted in interpreting the results from ChIP-seq. Nucleosome positioning is another critical mechanism of transcriptional regulation. Global mapping of nucleosome occupancy in S. cerevisiae strains deleted for chromatin remodeling complexes has elucidated the role of these complexes on a genome wide scale. In this study, loss of chromodomain helicase DNA binding protein 1 (Chd1) resulted in severe disorganization of nucleosome positioning. Despite the difficulties of performing ChIP-seq for chromatin remodeling complexes due to their transient and dynamic localization on chromatin, we successfully mapped the genome-wide occupancy of Chd1 and quantitatively showed that Chd1 co-localizes with early transcription elongation factors, but not late transcription elongation factors. Interestingly, Chd1 occupancy was independent of the methylation levels at H3K36, indicating the necessity of a new working model describing Chd1 localization.

Linux-based Edge Gateways that connects hundreds or maybe thousands of IoT devices, are exposed to various threats and cyber-attacks from the internet. These attacks form a considerable risk targeting the privacy and confidentiality of IoT devices throughout their gateways. Many researches and studies have been conducted to alleviate such a problem. One of the solutions can be achieved by building a root of trust based on a hardware module such as Trusted Platform Module (TPM) or software like Trusted Execution Environment (TEE). In this work, we provide a solution to the problem by enabling Hardware Root of Trust (HRoT) using TPM on a product from HMS Industrial Network AB known as GWen board, a Linux-based embedded system, used as gateway to connect IoT devices. We describe a method that uses the processor of the GWen (i.e. Zynq-7020 FPGA SoC) to enable secure boot. Besides, we provide a method to enable the TPM chip mounted on the GWen (i.e. SLB 9670 TPM 2.0) using TPM Software Stack TSS 2.0. We demonstrated, in detail, various use-cases using the TPM on GWen including cryptographic keys generation, secure key storage and key usage for different cryptographic operations. Furthermore, we conducted an analysis to the adopted solution by inspecting the latency of TPM commands on the GWen gateway. According to the high restrictions of TPM 2.0 specifications and based on our results, adding the TPM 2.0 to the IoT gateway GWen will enhance the security of its Linux distribution and will makes it possible to securely identify and authenticate the gateway on the network based on its secret keys that are stored securely inside its TPM.