Avaliação da eficiência de remoção do contaminante de origem farmacêutica atenolol pela planta phragmites australis em leitos construídos de macrófitas

O atenolol é um fármaco β-bloqueador normalmente encontrado em águas residuais devido à incapacidade que os processos convencionais de tratamento destas águas têm em removê-lo. Neste trabalho foram utilizados microcosmos de leitos construídos de macrófitas de fluxo sub-superficial utilizando uma matriz de argila expandida (LECA) e plantados com Phragmites australis para avaliar a sua capacidade em remover atenolol das águas residuais. Para a detecção e quantificação do atenolol em soluções aquosas (águas e efluentes) desenvolveu-se e optimizou-se uma metodologia analítica usando separação cromatográfica por HPLC e detecção espectrofotométrica por diode array (HPLC-DAD) ou por ultravioleta visível (HPLC-UV-Vis). Desenvolveu-se também um procedimento de limpeza e concentração de amostra por extracção em fase sólida (SPE), o qual foi utilizado sempre que as concentrações do analito se encontraram abaixo dos limites de quantificação do equipamento. A utilização desta metodologia de HPLC, combinada com uma eficaz pré-concentração por SPE, resultou num método analítico com um limite de quantificação muito reduzido (9 ngmL-1) e elevada reprodutibilidade (RSD<4%). A eficiência de remoção de atenolol pelos sistemas de macrófitas estudados foi de 93% após um tempo de retenção de 4 dias. Foram testados leitos só com LECA e com LECA e plantas para remoção do atenolol. Nos leitos só com LECA, a cinética de remoção foi caracterizada por um rápido passo inicial (uma remoção de aproximadamente 75% após apenas 24 h), o qual é frequentemente atribuído à adsorção na matriz de LECA. A remoção de atenolol nos leitos de LECA continuou a aumentar de forma constante até ao final do ensaio (8 dias), sendo, contudo cerca de 5-10% mais baixo do que o valor observado nos leitos das plantas após os 4 primeiros dias. Para o tempo de retenção de 4 dias a maioria do atenolol é removido pela matriz de LECA, porém um acréscimo de cerca de 12-14% relativamente à eficiência de remoção global pode ser atribuído às plantas (Phragmites australis), o que está de acordo com trabalhos anteriormente publicados. Apesar de ser necessário realizar mais testes utilizando sistemas em larga escala, de modo a conseguir avaliar totalmente o comportamento do atenolol num sistema de leitos construídos de macrófitas, o presente estudo apresenta a possibilidade de aplicar este tipo de sistemas, relativamente baratos, no tratamento de águas residuais contaminadas com atenolol. ABSTRACT: Atenolol is a β-blocker drug commonly found in wastewaters due to the inability of the conventional wastewater treatment processes to remove it. ln this study, subsurface flow constructed wetland microscosm systems have been established with a matrix of light expanded clay aggregates (LECA) and planted with Phragmites australis in order to evaluate their ability to remove atenolol from wastewater. For the detection and quantification of atenolol in aqueous solutions (water and wastewater), an adequate analytical methodology was developed and optimized using chromatographic separation by HPLC and diode array (DAD) or UV-Vis spectrophotometric detection. A sample clean-up and preconcentration procedure by solid phase extraction (SPE) was also developed for use whenever the concentration levels of the analyte were below the instrument's limit of quantification. Combined with an efficient SPE concentration step, the use of HPLC yielded an analytical method for atenolol quantification with very low LOQ (9 ngmL-1) and high reproducibility (RSD< 4%). Overall atenolol removal efficiency of 93% was achieved after a retention time of only 4 days with the microcosm systems planted with Phragmites australis. The removal kinetics was characterized by an initial fast step (removal of about 75% after just 24h) which is mainly attributable to adsorption on the LECA matrix. Atenolol removal in LECA beds continues to increase in a steady pace up to the end of the assay (8 days) being nevertheless about 5-l 0% lower than those observed in the planted beds after the first 4 days. For the retention time of 4 days most of the atenolol is removed by the LECA matrix but an additional 12-14% to the overall removal efficiency can be attributed to the Phragmites plants, which comes in agreement with other published reports. Despite the fact that further tests using larger­ scale systems are required to fully evaluate the atenolol behavior in a constructed wetland system, this study points out to the possible application of these low-cost wastewater systems to treat atenolol contaminated wastewater.

Remoção de ibuprofeno de águas por oxidação catalítica

A ocorrência e destino de fármacos no ambiente aquático tem vindo a ser reconhecido como um problema emergente em química ambiental. Alguns compostos são resistentes à degradação nas estações de tratamento de águas residuais, ETARs, enquanto que outros, ainda que sofram degradação parcial, continuam a ser lançados nos meios aquáticos em quantidades apreciáveis. O Ibuprofeno, IB, um dos anti­ inflamatórios mais consumidos por todo o mundo, é um dos fármacos mais detectados no meio hídrico. Apesar dos sistemas de tratamento convencionais utilizados nas ETARs removerem até 90% do IB das águas residuais, é frequente o efluente descarregado conter ainda quantidades significativas deste poluente. A presença destes compostos no ambiente deve ser avaliada dado que possuem actividade biológica, mesmo a baixas concentrações. Os processos avançados de oxidação com peróxido de hidrogénio, na presença de catalisadores heterogéneos, permitem melhorar significativamente a remoção deste tipo de compostos em águas. Assim, foi objectivo deste trabalho o estudo da utilização de peróxido de hidrogénio como agente oxidante na remoção de IB em soluções aquosas, na presença de complexo de acetilacetonato de Ni (II) disperso em PDMS ou encapsulado em zeólitos NaY. Para o doseamento do fármaco em solução foi necessário desenvolver um método analítico consistindo de separação cromatográfica por HPLC e detecção e quantificação por UV-Vis. Não houve necessidade de recorrer a um passo de pré­ concentração de amostras por extracção em fase sólida (SPE) devido ao facto das concentrações de IB medidas ao longo do trabalho se terem sempre encontrado acima do LOQ (811 g L-1) do método analítico por injecção directa. Deste estudo pode concluir-se que o catalisador que apresentou melhor actividade catalítica e consequentemente maior remoção do IB em solução, foi o complexo de acetilacetonato de Ni (II), disperso em PDMS. Foi avaliada a influência, na conversão do IB, de diferentes parâmetros como a concentração inicial de peróxido de hidrogénio adicionada, quantidade de catalisador utilizada na mistura reaccional e temperatura. Os resultados permitiram concluir que os aumentos destes parâmetros conduzem a um aumento da actividade catalítica da reacção. A estabilidade catalítica do acetilacetonato de Ni (II)/PDMS, foi avaliada em ensaios consecutivos com a mesma amostra e nas mesmas condições, tendo-se observado que, após 8 utilizações, o catalisador perde ligeiramente a actividade (cerca de 11% do seu valor inicial). ABSTRACT: The presence and fate of pharmaceuticals in the aquatic environment is an emergent issue in environmental chemistry. Some compounds are poorly removed in wastewater treatment plants (WWTPs) while others, in spite of being partially removed, are still present in the WWTPs effluents and discharged in the receiving water bodies. Ibuprofen, IB, a non-steroid anti-inflammatory drug, is one of the most used and also one of the most frequently detected pharmaceutical contaminants in aquifers worldwide. Its removal by conventional wastewater treatment processes used in most WWTPs is usually high (up to 90% of incoming IB may be removed), but duet the high loads present in the influents, still significant amounts of IB usually leave the WWTPs in the treated effluents. The presence of these compounds in the environment must be evaluated considering that they may have some biological activity even at low concentrations. Advanced oxidation processes using hydrogen peroxide, in the presence of heterogeneous catalysts, provide a significantly improved removal of this type of substances from waters. Therefore, it was the aim of this work to study the use of hydrogen peroxide as an oxidizing agent in the removal of IB from aqueous solutions, in the presence of the catalyst nickel (II) acetylacetonate dispersed in PDMS or encapsulated in the NaY zeolite. For the quantification of the pharmaceutical in aqueous solution it was necessary to develop an analytical methodology based in chromatographic separation by HPLC and with UV-Vis detection and quantification. There was no need for a pre­concentration step of the samples by solid phase extraction (SPE) as the IB concentrations measured were always above the limit of quantification (811 bL1 of) the analytical method. The results from this study have shown that the catalyst which presented the best catalytic activity and the highest IB removal in solution was nickel (II) acetylacetonate dispersed in PDMS.

Development and chemo-mechanical characterization of eco-compatible extenders containing REOB and recycled tyres’ rubber for the production of greener bituminous binders

The concepts of circular economy and sustainability are the basis of the present experimental research that seeks to reduce the environmental impact of traditional road construction materials. This study mainly focuses on the development and the chemo-mechanical characterization of bitumen extenders containing rubber (R) from end-of-life tyres (ELTs) and re-refined engine oil bottoms (REOBs) for the production of innovative and eco-friendly extended bitumens (i.e. bituminous binders containing 25%wt. of recycled products) and asphalt mixtures. In order to create more sustainable asphalt mixes, also recycled aggregates are used for partial replacement of virgin natural aggregates in the aggregate skeleton. The experimental program encompassed five successive steps: (i) the evaluation of physicochemical properties of R and REOB, (ii) the definition of the optimal extenders by the development of a new protocol and their characterizations, (iii) the realization and investigation of the chemo-rheological responses of the extended bitumens at different boundary conditions, (iv) the assessment of the effectiveness of analytical method to predict the rheological parameters of extended bitumens and, finally, (v) the analysis of the mechanical performances of the corresponding asphalt mixtures. A standard 50/70 penetration grade bitumen was chosen as a reference material and the main constituent of the innovative bituminous products. The results of this study underlined the importance of material characterization. The incorporation of R-REOB extenders strongly affects the chemo-rheological responses of the resulting extended bitumens and asphalt mixtures overall the boundary conditions. While the presence of R and the consequent formation of a polymer network improves the elasticity of the final products, especially at high test temperatures; the addition of REOB, softens the bituminous binders and asphalt mixes increasing their response at low test temperatures. Nonetheless, the use of recycled products increased the susceptibility of bituminous material under damaging conditions, which would need further investigations.

The mesophotic zone of the Mediterranean Sea: spatial definition, biodiversity, and predictive models

The mesophotic zone is frequently defined as ranging between 30-40 and 150 m depth. However, these borders are necessarily imprecise due to variations in the penetration of light along the water column related to local factors. Moreover, density of data on mesophotic ecosystems vary along geographical distance, with temperate latitudes largely less explored than tropical situations. This is the case of the Mediterranean Sea, where information on mesophotic ecosystems is largely lower with respect to tropical situations. The lack of a clear definition of the borders of the mesophotic zone may represent a problem when information must be transferred to the policy that requires a coherent spatial definition to plan proper management and conservation measures. The present thesis aims at providing information on the spatial definition of the mesophotic zone in the Mediterranean Sea, its biodiversity and distribution of its ecosystems. The first chapter analyzes information on mesophotic ecosystems in the Mediterranean Sea to identify gaps in the literature and map the mesophotic zone in the Mediterranean Sea using light penetration estimated from satellite data. In the second chapter, different visual techniques to study mesophotic ecosystems are compared to identify the best analytical method to estimate diversity and habitat extension. In the third chapter, a set of Remotely Operated vehicles (ROV) surveys performed on mesophotic assemblages in the Mediterranean Sea are analyzed to describe their taxonomic and functional diversity and environmental factors influencing their structure. A Habitat Suitability Model is run in the fourth chapter to map the distribution of areas suitable for the presence of deep-water oyster reefs in the Adriatic-Ionian area. The fifth chapter explores the mesophotic zone in the northern Gulf of Mexico providing its spatial and vertical extension of the mesophotic zone and information on the diversity associated with mesophotic ecosystems.

Power Factor Calculation by the Finite Element Method

The use of finite element analysis (FEA) to design electrical motors has increased significantly in the past few years due the increasingly better performance of modern computers. Even though the analytical software remains the most used tool, the FEA is widely used to refine the analysis and gives the final design to be prototyped. The power factor, a standard data of motor manufactures data sheet is important because it shows how much reactive power is consumed by the motor. This data becomes important when the motor is connected to network. However, the calculation of power factor is not an easy task. Due to the saturation phenomena the input motor current has a high level of harmonics that cannot be neglected. In this work the FEA is used to evaluate a proposed (not limitative) methodology to estimate the power factor or displacement factor of a small single-phase induction motor. Results of simulations and test are compared.

In Vitro Evaluation Of Sun Protection Factor And Stability Of Commercial Sunscreens Using Mass Spectrometry.

Sunlight exposure causes several types of injury to humans, especially on the skin; among the most common harmful effects due to ultraviolet (UV) exposure are erythema, pigmentation and lesions in DNA, which may lead to cancer. These long-term effects are minimized with the use of sunscreens, a class of cosmetic products that contains UV filters as the main component in the formulation; such molecules can absorb, reflect or diffuse UV rays, and can be used alone or as a combination to broaden the protection on different wavelengths. Currently, worldwide regulatory agencies define which ingredients and what quantities must be used in each country, and enforce companies to conduct tests that confirm the Sun Protection Factor (SPF) and the UVA (Ultraviolet A) factor. Standard SPF determination tests are currently conducted in vivo, using human subjects. In an industrial mindset, apart from economic and ethical reasons, the introduction of an in vitro method emerges as an interesting alternative by reducing risks associated to UV exposure on tests, as well as providing assertive analytical results. The present work aims to describe a novel methodology for SPF determination directly from sunscreen formulations using the previously described cosmetomics platform and mass spectrometry as the analytical methods of choice.

Validated method for the quantification of artepillin-C in Brazilian propolis

Brazilian propolis contains several phenolic compounds among which 5 diprenyl-4-hydroxycinnamic acid (artepillin-C) is commonly found in areas where flora is rich in Baccharis species. The quantification of artepillin-C has become an important factor as an indicator of Brazilian propolis quality and the compound may be used as a chemical marker for quality control in exportating green propolis. This work was to validate the method and evaluate the content of artepillin-C from 33 samples collected in different Brazilian regions. The method used was HPLC with UV-vis detection and a reversed-phase C-18 Column. The validation parameters studied were: linearity, accuracy, precision, quantification and detection limits. The results obtained were: detection limit = 0.0036 mu g/mL, quantification limit = 0.012 mu g/mL, accuracy = 0.0064 and 0.078, recovery 98-102%. Artepillin-C content varied from 0 to 11% depending on the geographical origin. Propolis from the southeast region presented the highest level of artepillin-C (5.0-11.0%). Whist that from the northeast region did not show any artepillin-C. Copyright (C) 2008 John Wiley & Sons, Ltd.

Box-Behnken design for the optimization of an enantioselective method for the simultaneous analysis of propranolol and 4-hydroxypropranolol by CE

An experimental design optimization (Box-Behnken design, BBD) was used to develop a CE method for the simultaneous resolution of propranolol (Prop) and 4-hydroxypropranolol enantiomers and acetaminophen (internal standard). The method was optimized using an uncoated fused silica capillary, carboxymethyl-beta-cyclodextrin (CM-beta-CD) as chiral selector and triethylamine/phosphoric acid buffer in alkaline conditions. A BBD for four factors was selected to observe the effects of buffer electrolyte concentration, pH, CM-beta-CD concentration and voltage on separation responses. Each factor was studied at three levels: high, central and low, and three center points were added. The buffer electrolyte concentration ranged from 25 to 75 mM, the pH ranged from 8 to 9, the CM-beta-CD concentration ranged from 3.5 to 4.5%w/v, and the applied run voltage ranged from 14 to 20 W. The responses evaluated were resolution and migration time for the last peak. The obtained responses were processed by Minitab (R) to evaluate the significance of the effects and to find the optimum analysis conditions. The best results were obtained using 4%w/v CM-beta-CD in 25 mM triethylamine/H(3)PO(4) buffer at pH 9 as running electrolyte and 17 kV of voltage. Resolution values of 1.98 and 1.95 were obtained for Prop and 4-hydroxypropranolol enantiomers, respectively. The total analysis time was around of 15 min. The BBD showed to be an adequate design for the development of a CE method, resulting in a rapid and efficient optimization of the pH and concentration of the buffer, cyclodextrin concentration and applied voltage.

Effect of the C-factor and Dentin Preparation Method in the Bond Strength of a Mild Self-etch Adhesive

This study evaluated the effect of the C-factor and dentin preparation method (DPM) in the bond strength (BS) of a mild self-etch adhesive; the study also observed the SEM superficial aspects of the corresponding smear layer. For purposes of this study, 25 molars (n=5) were used in a bond strength test. The molars were divided into two parts (buccal and lingual): one part received a Class V cavity (C-factor=3) and the other received a flat surface (C-factor=0) with the same bur type (coarse diamond or carbide bur and fine diamond or carbide bur), both within the same dentin depth. Five teeth were prepared with wet 60-grit and 600-grit SiC papers. After restoration with Clearfil SE Bond, microtensile beans (0.8 mm(2)) were prepared and tested after 24 hours in a universal testing machine (0.5 mm/minute). An additional two teeth for each DPM were prepared for SEM evaluation of the smear layer superficial aspects. The BS values were submitted to one-way ANOVA, considering only the DPM (flat surfaces) and two-way ANOVA (C-Factor x DPM, considering only burs) with p=0.05. Although the DPM in the flat surfaces was not significant, the standard deviations of carbide bur-prepared specimens were markedly lower. The BS was significantly lower in cavities. The fine carbide bur presented the most favorable smear layer aspect. It was concluded that different dentin preparation methods could not prevent the adverse effect in bond strength of a high C-factor. A coarse cut carbide bur should be avoided prior to a mild self-etch adhesive, because it adversely affected bond strength. In contrast, a fine cut carbide bur provided the best combination: high bond strength with low variability, which suggests a more reliable bond strength performance.

Optimization of QuEChERS method for the analysis of organochlorine pesticides in soils with diverse organic matter

A QuEChERS method has been developed for the determination of 14 organochlorine pesticides in 14 soils from different Portuguese regions with wide range composition. The extracts were analysed by GC-ECD (where GC-ECD is gas chromatography-electron-capture detector) and confirmed by GC-MS/MS (where MS/MS is tandem mass spectrometry). The organic matter content is a key factor in the process efficiency. An optimization was carried out according to soils organic carbon level, divided in two groups: HS (organic carbon>2.3%) and LS (organic carbon<2.3%). Themethod was validated through linearity, recovery, precision and accuracy studies. The quantification was carried out using a matrixmatched calibration to minimize the existence of the matrix effect. Acceptable recoveries were obtained (70–120%) with a relative standard deviation of ≤16% for the three levels of contamination. The ranges of the limits of detection and of the limits of quantification in soils HS were from 3.42 to 23.77 μg kg−1 and from 11.41 to 79.23 μg kg−1, respectively. For LS soils, the limits of detection ranged from 6.11 to 14.78 μg kg−1 and the limits of quantification from 20.37 to 49.27 μg kg−1. In the 14 collected soil samples only one showed a residue of dieldrin (45.36 μg kg−1) above the limit of quantification. This methodology combines the advantages of QuEChERS, GC-ECD detection and GC-MS/MS confirmation producing a very rapid, sensitive and reliable procedure which can be applied in routine analytical laboratories.

Numerical simulations of Lamb waves in plates using a semi-analytical finite element method

Magdeburg, Univ., Fak. für Maschinenbau, Diss., 2011

Design and analysis of ChIP-Seq experiments for nuclear factor I DNA-binding proteins

SUMMARY : Eukaryotic DNA interacts with the nuclear proteins using non-covalent ionic interactions. Proteins can recognize specific nucleotide sequences based on the sterical interactions with the DNA and these specific protein-DNA interactions are the basis for many nuclear processes, e.g. gene transcription, chromosomal replication, and recombination. New technology termed ChIP-Seq has been recently developed for the analysis of protein-DNA interactions on a whole genome scale and it is based on immunoprecipitation of chromatin and high-throughput DNA sequencing procedure. ChIP-Seq is a novel technique with a great potential to replace older techniques for mapping of protein-DNA interactions. In this thesis, we bring some new insights into the ChIP-Seq data analysis. First, we point out to some common and so far unknown artifacts of the method. Sequence tag distribution in the genome does not follow uniform distribution and we have found extreme hot-spots of tag accumulation over specific loci in the human and mouse genomes. These artifactual sequence tags accumulations will create false peaks in every ChIP-Seq dataset and we propose different filtering methods to reduce the number of false positives. Next, we propose random sampling as a powerful analytical tool in the ChIP-Seq data analysis that could be used to infer biological knowledge from the massive ChIP-Seq datasets. We created unbiased random sampling algorithm and we used this methodology to reveal some of the important biological properties of Nuclear Factor I DNA binding proteins. Finally, by analyzing the ChIP-Seq data in detail, we revealed that Nuclear Factor I transcription factors mainly act as activators of transcription, and that they are associated with specific chromatin modifications that are markers of open chromatin. We speculate that NFI factors only interact with the DNA wrapped around the nucleosome. We also found multiple loci that indicate possible chromatin barrier activity of NFI proteins, which could suggest the use of NFI binding sequences as chromatin insulators in biotechnology applications. RESUME : L'ADN des eucaryotes interagit avec les protéines nucléaires par des interactions noncovalentes ioniques. Les protéines peuvent reconnaître les séquences nucléotidiques spécifiques basées sur l'interaction stérique avec l'ADN, et des interactions spécifiques contrôlent de nombreux processus nucléaire, p.ex. transcription du gène, la réplication chromosomique, et la recombinaison. Une nouvelle technologie appelée ChIP-Seq a été récemment développée pour l'analyse des interactions protéine-ADN à l'échelle du génome entier et cette approche est basée sur l'immuno-précipitation de la chromatine et sur la procédure de séquençage de l'ADN à haut débit. La nouvelle approche ChIP-Seq a donc un fort potentiel pour remplacer les anciennes techniques de cartographie des interactions protéine-ADN. Dans cette thèse, nous apportons de nouvelles perspectives dans l'analyse des données ChIP-Seq. Tout d'abord, nous avons identifié des artefacts très communs associés à cette méthode qui étaient jusqu'à présent insoupçonnés. La distribution des séquences dans le génome ne suit pas une distribution uniforme et nous avons constaté des positions extrêmes d'accumulation de séquence à des régions spécifiques, des génomes humains et de la souris. Ces accumulations des séquences artéfactuelles créera de faux pics dans toutes les données ChIP-Seq, et nous proposons différentes méthodes de filtrage pour réduire le nombre de faux positifs. Ensuite, nous proposons un nouvel échantillonnage aléatoire comme un outil puissant d'analyse des données ChIP-Seq, ce qui pourraient augmenter l'acquisition de connaissances biologiques à partir des données ChIP-Seq. Nous avons créé un algorithme d'échantillonnage aléatoire et nous avons utilisé cette méthode pour révéler certaines des propriétés biologiques importantes de protéines liant à l'ADN nommés Facteur Nucléaire I (NFI). Enfin, en analysant en détail les données de ChIP-Seq pour la famille de facteurs de transcription nommés Facteur Nucléaire I, nous avons révélé que ces protéines agissent principalement comme des activateurs de transcription, et qu'elles sont associées à des modifications de la chromatine spécifiques qui sont des marqueurs de la chromatine ouverte. Nous pensons que lés facteurs NFI interagir uniquement avec l'ADN enroulé autour du nucléosome. Nous avons également constaté plusieurs régions génomiques qui indiquent une éventuelle activité de barrière chromatinienne des protéines NFI, ce qui pourrait suggérer l'utilisation de séquences de liaison NFI comme séquences isolatrices dans des applications de la biotechnologie.

Differential outcome of concurrent radiotherapy plus epidermal growth factor receptor inhibitors versus radiotherapy plus cisplatin in patients with human papillomavirus-related head and neck cancer.

BACKGROUND Human papillomavirus (HPV)-related head and neck cancer has been associated with an improved prognosis in patients treated with radiotherapy (RT) +/- chemotherapy (CT); however, RT combined with epidermal growth factor receptor (EGFR) inhibitors has not been fully studied in this group of patients. METHODS Immunohistochemical expression of p16 and PCR of HPV16 DNA were retrospectively analyzed in tumor blocks from 108 stage III/IV head and neck cancer patients treated with RT+CT (56) or RT+EGFR inhibitors (52). Disease-free survival (DFS) and overall survival (OS) were analyzed by the Kaplan-Meier method. RESULTS DNA of HPV16 was found in 12 of 108 tumors (11%) and p16 positivity in 18 tumors (17%), with similar rates in both arms of treatment. After a median follow-up time of 35 months (range 6-135), p16-positive patients treated with RT+EGFR inhibitors showed improved survival compared with those treated with RT+CT (2-year OS 88% vs. 60%, HR 0.18; 95% CI 0.04 to 0.88; p = 0.01; and 2-year DFS 75% vs. 47%, HR 0.17; 95% CI 0.03 to 0.8; p = 0.01). However, no differences were observed in p16-negative patients (2-year OS 56% vs. 53%, HR 0.97; 95% CI 0.55 to 1.7; p = 0.9; and 2-year DFS 43% vs. 45%, HR 0.99; 95% CI 0.57 to 1.7; p = 0.9). CONCLUSIONS This is the first study to show that p16-positive patients may benefit more from RT+EGFR inhibitors than conventional RT+CT. These results are hypothesis-generating and should be confirmed in prospective trials.

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

The ability to determine the location and relative strength of all transcription-factor binding sites in a genome is important both for a comprehensive understanding of gene regulation and for effective promoter engineering in biotechnological applications. Here we present a bioinformatically driven experimental method to accurately define the DNA-binding sequence specificity of transcription factors. A generalized profile was used as a predictive quantitative model for binding sites, and its parameters were estimated from in vitro-selected ligands using standard hidden Markov model training algorithms. Computer simulations showed that several thousand low- to medium-affinity sequences are required to generate a profile of desired accuracy. To produce data on this scale, we applied high-throughput genomics methods to the biochemical problem addressed here. A method combining systematic evolution of ligands by exponential enrichment (SELEX) and serial analysis of gene expression (SAGE) protocols was coupled to an automated quality-controlled sequence extraction procedure based on Phred quality scores. This allowed the sequencing of a database of more than 10,000 potential DNA ligands for the CTF/NFI transcription factor. The resulting binding-site model defines the sequence specificity of this protein with a high degree of accuracy not achieved earlier and thereby makes it possible to identify previously unknown regulatory sequences in genomic DNA. A covariance analysis of the selected sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism.

Extension of the impedance field method to the noise analysis of a semiconductor junction: Analytical approach

We present an analytical procedure to perform the local noise analysis of a semiconductor junction when both the drift and diffusive parts of the current are important. The method takes into account space-inhomogeneous and hot-carriers conditions in the framework of the drift-diffusion model, and it can be effectively applied to the local noise analysis of different devices: n+nn+ diodes, Schottky barrier diodes, field-effect transistors, etc., operating under strongly inhomogeneous distributions of the electric field and charge concentration