Fabrication of GaN nanorods by focused ion beam

Ordered arrays of III-Nitride nanocolumns are excellent candidates for the fabrication of nano-optoelectronic devices. Different technologies such as e-beam lithography or colloidal lithography, have been used to obtain ordered arrays. All these technologies have in common several processing steps that can affect the crystalline growth of the nanocolumns. In this work, we present a single lithographic step that permits to grow ordered GaN nanocolumns with different geometries. The patterning is based in the use of a focusedionbeam with different doses. With this method has been possible to create GaN nanopillars and nanocylinders

Fabrication of GaN nanorods by focused ion beam

Ordered arrays of III-Nitride nanocolumns are excellent candidates for the fabrication of nano-optoelectronic devices. Different technologies such as e-beam lithography or colloidal lithography, have been used to obtain ordered arrays. All these technologies have in common several processing steps that can affect the crystalline growth of the nanocolumns. In this work, we present a single lithographic step that permits to grow ordered GaN nanocolumns with different geometries. The patterning is based in the use of a focused ion beam with different doses. With this method has been possible to create GaN nanopillars and nanocylinders.

Plasmodium falciparum subtilisin-like protease 2, a merozoite candidate for the merozoite surface protein 1–42 maturase

The process of human erythrocyte invasion by Plasmodium falciparum parasites involves a calcium-dependent serine protease with properties consistent with a subtilisin-like activity. This enzyme achieves the last crucial maturation step of merozoite surface protein 1 (MSP1) necessary for parasite entry into the host erythrocyte. In eukaryotic cells, such processing steps are performed by subtilisin-like maturases, known as proprotein convertases. In an attempt to characterize the MSP1 maturase, we have identified a gene that encodes a P. falciparum subtilisin-like protease (PfSUB2) whose deduced active site sequence resembles more bacterial subtilisins. Therefore, we propose that PfSUB2 belongs to a subclass of eukaryotic subtilisins different from proprotein convertases. Pfsub2 is expressed during merozoite differentiation and encodes an integral membrane protein localized in the merozoite dense granules, a secretory organelle whose contents are believed to participate in a late step of the erythrocyte invasion. PfSUB2’s subcellular localization, together with its predicted enzymatic properties, leads us to propose that PfSUB2 could be responsible for the late MSP1 maturation step and thus is an attractive target for the development of new antimalarial drugs.

Isolation and characterization of pokeweed antiviral protein mutations in Saccharomyces cerevisiae: identification of residues important for toxicity.

Pokeweed antiviral protein (PAP), a 29-kDa protein isolated from Phytolacca americana inhibits translation by catalytically removing a specific adenine residue from the 28S rRNA of eukaryotic ribosomes. PAP has potent antiviral activity against many plant and animal viruses, including human immunodeficiency virus. We describe here development of a positive selection system to isolate PAP mutants with reduced toxicity. In vitro translation in the presence or absence of microsomal membranes shows that PAP is synthesized as a precursor and undergoes at least two different proteolytic processing steps to generate mature PAP. The PAP cDNA was placed under control of the galactose-inducible GAL1 promoter and transformed into Saccharomyces cerevisiae. Induction of PAP expression was lethal to yeast. The PAP expression plasmid was mutagenized and plasmids encoding mutant PAP genes were identified by their failure to kill S. cerevisiae. A number of mutant alleles were sequenced. In one mutant, a point mutation at Glu-177 inactivated enzymatic function in vitro, suggesting that this glutamic acid residue is located at or near the catalytic site. Mutants with either point mutations near the N terminus or a nonsense mutation at residue 237 produced protein that was enzymatically active in vitro, suggesting that the toxicity of PAP is not due solely to enzymatic activity. Toxicity of PAP appears to be a multistep process that involves possibly different domains of the protein.

Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE.

We report a general mass spectrometric approach for the rapid identification and characterization of proteins isolated by preparative two-dimensional polyacrylamide gel electrophoresis. This method possesses the inherent power to detect and structurally characterize covalent modifications. Absolute sensitivities of matrix-assisted laser desorption ionization and high-energy collision-induced dissociation tandem mass spectrometry are exploited to determine the mass and sequence of subpicomole sample quantities of tryptic peptides. These data permit mass matching and sequence homology searching of computerized peptide mass and protein sequence data bases for known proteins and design of oligonucleotide probes for cloning unknown proteins. We have identified 11 proteins in lysates of human A375 melanoma cells, including: alpha-enolase, cytokeratin, stathmin, protein disulfide isomerase, tropomyosin, Cu/Zn superoxide dismutase, nucleoside diphosphate kinase A, galaptin, and triosephosphate isomerase. We have characterized several posttranslational modifications and chemical modifications that may result from electrophoresis or subsequent sample processing steps. Detection of comigrating and covalently modified proteins illustrates the necessity of peptide sequencing and the advantages of tandem mass spectrometry to reliably and unambiguously establish the identity of each protein. This technology paves the way for studies of cell-type dependent gene expression and studies of large suites of cellular proteins with unprecedented speed and rigor to provide information complementary to the ongoing Human Genome Project.

Pressure and processed water levels from the Time Series Station Spiekeroog, 2005-2011

The quality of water level time series data strongly varies with periods of high and low quality sensor data. In this paper we are presenting the processing steps which were used to generate high quality water level data from water pressure measured at the Time Series Station (TSS) Spiekeroog. The TSS is positioned in a tidal inlet between the islands of Spiekeroog and Langeoog in the East Frisian Wadden Sea (southern North Sea). The processing steps will cover sensor drift, outlier identification, interpolation of data gaps and quality control. A central step is the removal of outliers. For this process an absolute threshold of 0.25m/10min was selected which still keeps the water level increase and decrease during extreme events as shown during the quality control process. A second important feature of data processing is the interpolation of gappy data which is accomplished with a high certainty of generating trustworthy data. Applying these methods a 10 years dataset (December 2002-December 2012) of water level information at the TSS was processed resulting in a seven year time series (2005-2011).

Mechanism of α-defensin HD5 Inhibition of Human Papillomavirus-16

Thesis (Ph.D.)--University of Washington, 2016-06

Sparsity and "something else": an approach to encrypted image folding

A property of sparse representations in relation to their capacity for information storage is discussed. It is shown that this feature can be used for an application that we term Encrypted Image Folding. The proposed procedure is realizable through any suitable transformation. In particular, in this paper we illustrate the approach by recourse to the Discrete Cosine Transform and a combination of redundant Cosine and Dirac dictionaries. The main advantage of the proposed technique is that both storage and encryption can be achieved simultaneously using simple processing steps.

Issues in learning an ontology from text

Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. This paper describes an experiment in ontology construction from text for the animal behaviour domain. Our objective was to see how much could be done in a simple and relatively rapid manner using a corpus of journal papers. We used a sequence of pre-existing text processing steps, and here describe the different choices made to clean the input, to derive a set of terms and to structure those terms in a number of hierarchies. We describe some of the challenges, especially that of focusing the ontology appropriately given a starting point of a heterogeneous corpus. Results - Using mainly automated techniques, we were able to construct an 18055 term ontology-like structure with 73% recall of animal behaviour terms, but a precision of only 26%. We were able to clean unwanted terms from the nascent ontology using lexico-syntactic patterns that tested the validity of term inclusion within the ontology. We used the same technique to test for subsumption relationships between the remaining terms to add structure to the initially broad and shallow structure we generated. All outputs are available at http://thirlmere.aston.ac.uk/~kiffer/animalbehaviour/ webcite. Conclusion - We present a systematic method for the initial steps of ontology or structured vocabulary construction for scientific domains that requires limited human effort and can make a contribution both to ontology learning and maintenance. The method is useful both for the exploration of a scientific domain and as a stepping stone towards formally rigourous ontologies. The filtering of recognised terms from a heterogeneous corpus to focus upon those that are the topic of the ontology is identified to be one of the main challenges for research in ontology learning.

Issues in learning an ontology from text

Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. This paper describes an experiment in ontology construction from text for the Animal Behaviour domain. Our objective was to see how much could be done in a simple and rapid manner using a corpus of journal papers. We used a sequence of text processing steps, and describe the different choices made to clean the input, to derive a set of terms and to structure those terms in a hierarchy. We were able in a very short space of time to construct a 17000 term ontology with a high percentage of suitable terms. We describe some of the challenges, especially that of focusing the ontology appropriately given a starting point of a heterogeneous corpus.

Focused ion beam manufacturing of magnetic nanostructures

A number of patterning methods including conventional photo-lithography and E-beam lithography have been employed to pattern devices with critical dimensions of submicrometer levels. The methods of device fabrication by lithography and multilevel processing are usually specific to the chemical and physical properties of the etchants and materials used, and require a number of processing steps. As an alternative, focused ion beam (FIB) lithography is a unique and straightforward tool to rapidly develop nanomagnetic prototyping devices. This feature of FIB is critical to conduct the basic study necessary to advance the state-of-the-art in magnetic recording. ^ The dissertation develops a specific design of nanodevices and demonstrates FIB-fabricated stable and reproducible magnetic nanostructures with a critical dimension of about 10 nm. The project included the fabrication of a patterned single and multilayer magnetic media with areal densities beyond 10 Terabit/in 2. Each block had perpendicular or longitudinal magnetic anisotropy and a single domain structure. The purpose was to demonstrate how the ability of FIB to directly etch nanoscale patterns allowed exploring (even in the academic environment) the true physics of various types of nanostructures. ^ Another goal of this study was the investigation of FIB patterned magnetic media with a set of characterization tools: e.g. Spinstand Guzik V2002, magnetic force microscopy, scanning electron microscopy with energy dispersive system and wavelength dispersive system. ^ In the course of this work, a unique prototype of a record high density patterned magnetic media device capable of 10 terabit/in 2 was built. The read/write testing was performed by a Guzik spinstand. The readback signals were recorded and analyzed by a digital oscilloscope. A number of different configurations for writing and reading information from a magnetic medium were explored. The prototype transducers for this work were fabricated via FIB trimming of different magnetic recording heads. ^

Standardized geo-referenced catch, fishing effort and length-frequency data for the Indian Ocean Bigeye Tuna, Thunnus obesus (1952-2014)

Geo-referenced catch and fishing effort data of the bigeye tuna fisheries in the Indian Ocean over 1952-2014 were analysed and standardized to facilitate population dynamics modelling studies. During this sixty-two years historical period of exploitation, many changes occurred both in the fishing techniques and the monitoring of activity. This study includes a series of processing steps used for standardization of spatial resolution, conversion and standardization of catch and effort units, raising of geo-referenced catch into nominal catch level, screening and correction of outliers, and detection of major catchability changes over long time series of fishing data, i.e., the Japanese longline fleet operating in the tropical Indian Ocean. A total of thirty fisheries were finally determined from longline, purse seine and other-gears data sets, from which 10 longline and four purse seine fisheries represented 96% of the whole historical catch. The geo-referenced records consists of catch, fishing effort and associated length frequency samples of all fisheries.

Remoção de corantes utilizando tensoativos: extração por ponto de nuvem e floculação iônica

The textile sector is one of the main contributors to the generation of industrial wastewaters due to the use of large volumes of water, which has a high organic load content. In these, it is observed to the presence of dyes, surfactants, starch, alcohols, acetic acid and other constituents, from the various processing steps of the textiles. Hence, the treatment of textile wastewater becomes fundamental before releasing it into water bodies, where they can cause disastrous physical-chemical changes for the environment. Surfactants are substances widely used in separation processes and their use for treating textile wastewaters was evaluated in this research by applying the cloud point extraction and the ionic flocculation. In the cloud point extraction was used as surfactant nonylphenol with 9.5 ethoxylation degree to remove reactive dye. The process evaluation was performed in terms of temperature, surfactant and dye concentrations. The dye removal reached 91%. The ionic flocculation occurs due to the presence of calcium, which reacts with anionic surfactant to form insoluble surfactants capable of attracting the organic matter by adsorption. In this work the ionic flocculation using base soap was applied to the treatment of synthetic wastewater containing dyes belonging to three classes: direct, reactive, and disperse. It was evaluated by the influence of the following parameters: surfactant and electrolyte concentrations, stirring speed, equilibrium time, temperature, and pH. The flocculation of the surfactant was carried out in two ways: forming the floc in the effluent itself and forming the floc before mixing it to the effluent. Removal of reactive and direct dye, when the floc is formed into textile effluent was 97% and 87%, respectively. In the case where the floc is formed prior to adding it to the effluent, the removal to direct and disperse dye reached 92% and 87%, respectively. These results show the efficience of the evaluated processes for dye removal from textile wastewaters.

Desenvolvimento de um cerâmico Al2O3/TI(C,N) para uso em maquinação

O principal objetivo deste trabalho é preparar um cermeto do tipo Al2O3/Ti(C,N) com propriedades mecânicas adequadas à sua utilização na maquinação de materiais do tipo DIN ISO 513:K01-K10 e ISO H01-H10. De forma a incrementar a sinterabilidade do cermeto investigou-se o efeito da adição de dopantes metálicos, nomeadamente alumínio metálico (Al) e hidreto de titânio (TiH2) e o efeito da substituição da moagem convencional por moagem de alta energia. As variáveis das etapas principais de processamento, i.e., da moagem, prensagem e sinterização, foram selecionadas com trabalho realizado quer na Universidade de Aveiro quer na empresa Palbit. Foram preparadas três composições do cermeto Al2O3/Ti(C,N) com adições de 5%TiH2, 1%Al e 5%TiH21%Al através da moagem de alta energia. Os parâmetros de moagem, i.e. a velocidade de rotação, o rácio bolas/pó e o tempo de moagem foram otimizados para os seguintes valores: 350 rpm, 10:1 e 5 h, respetivamente. A utilização da moagem de alta energia permitiu uma redução do tamanho de partícula dos pós até aproximadamente 100 nm e a obtenção de uma boa uniformidade da distribuição das fases (Al2O3+Ti(C,N)). A etapa de conformação foi efetuada por prensagem uniaxial seguida de prensagem isostática. A avaliação da reatividade dos cermetos através de dilatometria em atmosfera de vácuo revelou que a densificação é maioritariamente realizada em estado sólido. A adição de apenas 1%Al é a menos efetiva para a densificação. Os cermetos foram sinterizados através de sinterização convencional em forno de vazio a 1650ºC e prensagem a quente (1650ºC com uma pressão uniaxial de 25 MPa). Os valores de densificação obtidos, aproximadamente 80% e 100%, respetivamente, indicam que a aplicação de pressão durante a sinterização é efetiva para atingir densificações elevadas nos compactos, compatíveis com as suas aplicações tecnológicas. As propriedades mecânicas de dureza e de tenacidade avaliadas nos três cermetos apresentaram valores aproximados de 1800-1900 HV50 para a dureza e entre 5.4 e 7.7 MPa.m1/2 para a tenacidade à fratura.

DopSCAT: A mission concept for simultaneous measurements of marine winds and surface currents

A radar scatterometer operates by transmitting a pulse of microwave energy toward the ocean's surface and measuring the normalized (per-unit-surface) radar backscatter coefficient (σ°). The primary application of scatterometry is the measurement of near-surface ocean winds. By combining σ° measurements from different azimuth angles, the 10 m vector wind can be determined through a Geophysical Model Function (GMF), which relates wind and backscatter. This paper proposes a mission concept for the measurement of both oceanic winds and surface currents, which makes full use of earlier C-band radar remote sensing experience. For the determination of ocean currents, in particular, the novel idea of using two chirps of opposite slope is introduced. The fundamental processing steps required to retrieve surface currents are given together with their associated accuracies. A detailed description of the mission proposal and comparisons between real and retrieved surface currents are presented. The proposed ocean Doppler scatterometer can be used to generate global surface ocean current maps with accuracies better than 0.2 m/s at a spatial resolution better than 25 km (i.e., 12.5 km spatial sampling) on a daily basis. These maps will allow gaining some insights on the upper ocean mesoscale dynamics. The work lies at a frontier, given that the present inability to measure ocean currents from space in a consistent and synoptic manner represents one of the greatest weaknesses in ocean remote sensing.