Efficient incorporation of channel cross-section geometry uncertainty into regional and global scale flood inundation models

This paper investigates the challenge of representing structural differences in river channel cross-section geometry for regional to global scale river hydraulic models and the effect this can have on simulations of wave dynamics. Classically, channel geometry is defined using data, yet at larger scales the necessary information and model structures do not exist to take this approach. We therefore propose a fundamentally different approach where the structural uncertainty in channel geometry is represented using a simple parameterization, which could then be estimated through calibration or data assimilation. This paper first outlines the development of a computationally efficient numerical scheme to represent generalised channel shapes using a single parameter, which is then validated using a simple straight channel test case and shown to predict wetted perimeter to within 2% for the channels tested. An application to the River Severn, UK is also presented, along with an analysis of model sensitivity to channel shape, depth and friction. The channel shape parameter was shown to improve model simulations of river level, particularly for more physically plausible channel roughness and depth parameter ranges. Calibrating channel Manning’s coefficient in a rectangular channel provided similar water level simulation accuracy in terms of Nash-Sutcliffe efficiency to a model where friction and shape or depth were calibrated. However, the calibrated Manning coefficient in the rectangular channel model was ~2/3 greater than the likely physically realistic value for this reach and this erroneously slowed wave propagation times through the reach by several hours. Therefore, for large scale models applied in data sparse areas, calibrating channel depth and/or shape may be preferable to assuming a rectangular geometry and calibrating friction alone.

The Genetics of Alzheimer`s Disease in Brazil: 10 Years of Analysis in a Unique Population

Alzheimer`s Disease (AD) is the most common type of dementia among the elderly, with devastating consequences for the patient, their relatives, and caregivers. More than 300 genetic polymorphisms have been involved with AD, demonstrating that this condition is polygenic and with a complex pattern of inheritance. This paper aims to report and compare the results of AD genetics studies in case-control and familial analysis performed in Brazil since our first publication, 10 years ago. They include the following genes/markers: Apolipoprotein E (APOE), 5-hidroxytryptamine transporter length polymorphic region (5-HTTLPR), brain-derived neurotrophin factor (BDNF), monoamine oxidase A (MAO-A), and two simple-sequence tandem repeat polymorphisms (DXS1047 and D10S1423). Previously unpublished data of the interleukin-1 alpha (IL-1 alpha) and interleukin-1 beta (IL-1 beta) genes are reported here briefly. Results from others Brazilian studies with AD patients are also reported at this short review. Four local families studied with various markers at the chromosome 21, 19, 14, and 1 are briefly reported for the first time. The importance of studying DNA samples from Brazil is highlighted because of the uniqueness of its population, which presents both intense ethnical miscegenation, mainly at the east coast, but also clusters with high inbreeding rates in rural areas at the countryside. We discuss the current stage of extending these studies using high-throughput methods of large-scale genotyping, such as single nucleotide polymorphism microarrays, associated with bioinformatics tools that allow the analysis of such extensive number of genetics variables, with different levels of penetrance. There is still a long way between the huge amount of data gathered so far and the actual application toward the full understanding of AD, but the final goal is to develop precise tools for diagnosis and prognosis, creating new strategies for better treatments based on genetic profile.

Monodisperse lignin fractions as standards in size-exclusion analysis Comparison with polystyrene standards

The difficulty of preparing monodisperse lignin fractions on a large scale is a limiting factor in many applications. The present paper addresses this problem by examining the properties and size-exclusion behavior of lignin isolated by the acetosolv pulping process from post-extraction crushed sugarcane bagasse. The isolated lignin was subjected to a solvent pretreatment, followed by preparative gel permeation chromatography fractionation. The fractions were analyzed by high-performance size-exclusion chromatography (HPSEC) and these samples showed a great decrease in polydispersity, compared to the original acetosolv lignin. Several fractions of very low polydispersity, close to unity, were employed as calibration curve standards in HPSEC analysis. This original analytical approach allowed calibration with these lignin fractions to be compared with the polystyrene standards that are universally employed for lignin molecular mass determination. This led to a noteworthy result, namely that the lignin fractions and polystyrene standards showed very similar behavior over a large range of molecular masses in a typical HPSEC analysis of acetosolv lignin. (C) 2009 Elsevier B.V. All rights reserved.

Analysis and Evaluation of EndpointSecurity Solutions

The main objective for this degree project was to analyze the Endpoint Security Solutions developed by Cisco, Microsoft and a third minor company solution represented by InfoExpress. The different solutions proposed are Cisco Network Admission Control, Microsoft Network Access Protection and InfoExpress CyberGatekeeper. An explanation of each solution functioning is proposed as well as an analysis of the differences between those solutions. This thesis work also proposes a tutorial for the installation of Cisco Network Admission Control for an easier implementation. The research was done by reading articles on the internet and by experimenting the Cisco Network Admission Control solution. My background knowledge about Cisco routing and ACL was also used. Based on the actual analysis done in this thesis, a conclusion was drawn that all existing solutions are not yet ready for large-scale use in corporate networks. Moreover all solutions are proprietary and incompatible. The future possible standard for Endpoint solution might be driven by Cisco and Microsoft and a rude competition begins between those two giants.

The effects of Ikea and external shopping centers on regional trade and retail growth : A comparative analysis of Ikea’s establishment in Kalmar and Karlstad

This paper examines the effects of Ikea store establishment in Kalmar and Karlstad on the trade and retail inside the two cities, and as well on the trade and retail in the close neighboring municipalities and in further peripheral municipalities in both regions. After the establishment of Ikea store, Kalmar and Karlstad have experienced significant growth in trade and retail. The question, however, is how big this growth is in both cities? And how different locations on different distances from Ikea have been affected? What impact there was on different segments of the retail? How different business branches have been affected? How large the catchment area for the emerging new large-scale retail locations is? These questions, in addition to few others, are investigated in this paper. The thesis starts with an introduction chapter containing a background of the topic, problem description, the investigated questions, the purpose, and the outline of the paper. The next chapter includes the frame of reference which consists of literature review and theoretical framework about the external shopping centers and their impact on retail and regional trade development. It includes also information gathered from previous studies technical reports and other available sources about the subject. The third chapter includes description for the methods used to collect the primary and secondary data needed for the purpose of this study. Then the empirical framework which demonstrates the results of the conducted research followed by analysis and concluded in discussion and conclusion. Mixed methods are used as research strategy in this thesis, and the method to conduct the research is based on telephone interviews for the primary (qualitative) data, and documents and desk research for the secondary (quantitative) data. The gathered data is analyzed and designed in a way that allows the usage of comparative analysis technique to present the findings and draw conclusions. The results showed that new established Ikea retail store outside the city boundaries results with many effects on the city center and on the neighboring municipalities as well. The city center seems not to be affected negatively, but on the contrary positive effects were witnessed in both regions, these positive effects are linked to the increase inflow of customers from the external retail area which is known as spillover effect. III On the other hand, the neighboring towns and municipalities are more negatively affected especially with the trade of con-convenience goods as the consumers in these towns and municipalities start to go to the area of Ikea and the large external retail center to do their purchasing, the substitution effect is then said to be occurred. Moreover, the further far municipalities do not seem to be significantly affected by the establishment of Ikea. These effects whether positive or negative could be monitored by looking to few trade parameters such as the turnover, the sales index, and the consumers’ expenditure, these parameters can be very useful to measure the developments and changes in the trade and retail in a given place. 

Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane

To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST),program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.

Immunoassays for pesticide analysis in environmental and food matrices

Immunochemical methods have increased considerably in the past years, and many examples of small and large scale studies have demonstrated the reliability of the immunotechniques for control and monitoring gf contaminant residues in different kinds of samples. Application of the immunoassay (IA) methods in pesticide residue control is an area with enormous potential for growth. The most extensively studied IA is the enzyme-linked absorbent assay (ELISA), but several other approaches, that include radioimmunoassay and immunoaffinity chromatography, have been also developed recently. In comparison with classical analytical methods, IA methods offer the possibility of highly sensitive, relatively vapid, and cost-effective measurements. This paper introduces the general IAs used until now, focusing on their use in pesticide analysis, and discussing briefly the effects of interferences from solvent residues or matrix components on the IA performance. Numerous immunochemical methods commonly used for pesticide determination in different samples such as food, crop and environmental samples are presented.

Analysis of the Nicotiana tabacum Stigma/Style Transcriptome Reveals Gene Expression Differences between Wet and Dry Stigma Species

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Economical analysis of ethanol steam reformer for hydrogen production associated with a sugarcane industry

An expressive amount of produced hydrogen is generated by customers in-situ such as petrochemical, fertilizer and sugarcane industries. However, the most utilized feedstock is natural gas, a non-renewable and fossil fuel. The introduction of biohydrogen production process associated in a sugarcane industry is an alternative to diminish emissions and contribute to create a CO2 cycle, where the plants capture this gas by photosynthesis process and produces sucrose for ethanol production. The cost of production of ethanol has dramatically decreased (from about US$ 700/m3 in 1970s to US$ 200/m3 today), becoming this a good option at near term, inclusively for its utilization by customers localized in main regions (localized especially in regions such as Southeastern Brazil) Also in near future, it will possible the utilization of fuel cells as form of distributed generation. Its utilization could occur specially in peak hours, diminishing the cost of investments in newer transmission systems. A technical and economic analysis of steam reformer of ethanol to hydrogen production associated with sugarcane industry was recently performed. This technique will also allow the use of ethanol when its price is relatively low. This study was based on a previous R&D study (sponsored by CEMIG - State of Minas Gerais Electricity Company) where thermodynamic and economic analyses were developed, based in the development of two ethanol steam reformers prototypes.x In this study an analysis was performed considering the use of bagasse as source of heat in the steam reforming process. Its use could to diminish the costs of hydrogen production, especially at large scale, obtaining cost-competitive production and permitting that sugarcane industry produces hydrogen in large scale beyond ethylic alcohol, anhydrous alcohol (or ethanol) and sugar.

Local and regional features of surface radiation fluxes over the tropical Atlantic ocean near Sao Pedro and Sao Paulo archipelago: Evidence of small scale upwelling

To properly describe the interactions between the ocean and atmosphere, it is necessary to assess a variety of time and spatial scales phenomena. Here, high resolution oceanographic and meteorological data collected during an observational campaign carried out aboard a ship in the tropical Atlantic Ocean, on May 15-24, 2002, is used to describe the radiation balance at the ocean interface. Data collected by two PIRATA buoys, along the equator at 23°W and 35°W and satellite and climate data are compared with the data obtained during the observational campaign. Comparison indicates remarkable similarity for daily and hourly values of radiation fluxes components as consequence of the temporal and spatial consistence presented by the air and water temperatures measured in situ and estimated from large scale information. The discrepancy, mainly in the Sao Pedro and Sao Paulo Archipelago area, seems to be associated to the local upwelling of cold water, which is not detected in all other estimates investigated here. More in situ data are necessary to clarify whether this upwelling flow has a larger scale effect and what are the meteorological and oceanographic implications of the local upwelling area on the tropical waters at the Brazilian coast.

Why is it so difficult to identify a single indicator of water stress in plants? A proposal for a multivariate analysis to assess emergent properties

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Automatic Orientation of Multi-Scale Terrestrial Images for 3D Reconstruction

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Strategic planning for dairy cattle: SWOT analysis applied to a property of a farmers' association in Dracena, São Paulo state, Brazil

The sector of milk production in Brazil is very heterogeneous (high-tech in large scale X family properties). This study aimed to develop a diagnostic as a basis for a strategic plan to face the challenges inherent in operating a dairy farm in property of a farmers' association in Dracena, São Paulo, Brazil. It was observed that the association needs a more efficient guidance in the marketing, production and finance areas, not to compromise the search for new markets and continued growth in activity.

Comprehensive genome methylation and whole genome expression analysis in penile carcinoma: Uncovering new molecular markers

Background: Penile carcinoma (PeCa) is frequently associated with high morbidity rates. Unlikely of the vast majority of tumors, there is no molecular markers described that are able to assist in diagnosis and prognosis or with potential to be therapeutic targets in PeCa. Patients and methods: DNA methylation status (244K Human DNA Methylation Microarray platform, Agilent Technologies) and large-scale expression analysis (4x44K Whole Human Genome Microarray, Agilent Technologies) were performed in 35 and 37 PeCa, respectively. Quantitative bisulfite pyrosequencing (qBP) and RT-qPCR were used to validate the findings in 93 samples. HPV status was assessed using the Linear Array HPV Genotyping kit (Roche Molecular Diagnostics, CA, USA). Results: Methylome analysis revealed 171 hypermethylated and 449 hypomethylated CpGs sites and the transcriptome profiling showed 2986 down- and 2817 over-expressed genes. HPV positivity was found in 32.7% of the cases, mainly the HPV16. The integrative analysis in 32 PeCa revealed a panel of 96 genes with inverse correlation between methylation and gene expression levels. The CpG hypermetlylation and gene downexpression, was confirmed for TWIST1, RSOP2, SOX3, SOX17, CD133, OTX2, HOXA3 and MEIS. In addition, BIRC5, DNMT1 and DNMT3B presented low levels of methylation and overexpression. The comparison of the results with clinical findings revealed that LIN28A, NKX2.2, NKX2.3, LHX5, BDNF, FOXA1 and CDX2 were associated with poor prognosis features. Conclusion: Putative prognostic markers were detected revealing that DNA methylation modulates the expression of several genes in PeCa. These data may prove instrumental for biomarker discovery in clinics and molecular epidemiology of PeCa.

Automated peritoneal dialysis is associated with better survival rates compared to continuous ambulatory peritoneal dialysis: a propensity score matching analysis

The impact of peritoneal dialysis modality on patient survival and peritonitis rates is not fully understood, and no large-scale randomized clinical trial (RCT) is available. In the absence of a RCT, the use of an advanced matching procedure to reduce selection bias in large cohort studies may be the best approach. The aim of this study is to compare automated peritoneal dialysis (APD) and continuous ambulatory peritoneal dialysis (CAPD) according to peritonitis risk, technique failure and patient survival in a large nation-wide PD cohort. This is a prospective cohort study that included all incident PD patients with at least 90 days of PD recruited in the BRAZPD study. All patients who were treated exclusively with either APD or CAPD were matched for 15 different covariates using a propensity score calculated with the nearest neighbor method. Clinical outcomes analyzed were overall mortality, technique failure and time to first peritonitis. For all analysis we also adjusted the curves for the presence of competing risks with the Fine and Gray analysis. After the matching procedure, 2,890 patients were included in the analysis (1,445 in each group). Baseline characteristics were similar for all covariates including: age, diabetes, BMI, Center-experience, coronary artery disease, cancer, literacy, hypertension, race, previous HD, gender, pre-dialysis care, family income, peripheral artery disease and year of starting PD. Mortality rate was higher in CAPD patients (SHR1.44 CI95%1.21-1.71) compared to APD, but no difference was observed for technique failure (SHR0.83 CI95%0.69-1.02) nor for time till the first peritonitis episode (SHR0.96 CI95%0.93-1.11). In the first large PD cohort study with groups balanced for several covariates using propensity score matching, PD modality was not associated with differences in neither time to first peritonitis nor in technique failure. Nevertheless, patient survival was significantly better in APD patients.