Terahertz Computed Tomography of NASA Thermal Protection System Materials

A terahertz axial computed tomography system has been developed that uses time domain measurements in order to form cross-sectional image slices and three-dimensional volume renderings of terahertz-transparent materials. The system can inspect samples as large as 0.0283 cubic meters (1 cubic foot) with no safety concerns as for x-ray computed tomography. In this study, the system is evaluated for its ability to detect and characterize flat bottom holes, drilled holes, and embedded voids in foam materials utilized as thermal protection on the external fuel tanks for the Space Shuttle. X-ray micro-computed tomography was also performed on the samples to compare against the terahertz computed tomography results and better define embedded voids. Limits of detectability based on depth and size for the samples used in this study are loosely defined. Image sharpness and morphology characterization ability for terahertz computed tomography are qualitatively described

Diseño y caracterización de gomitas miel-menta y miel-eucalipto.

A La comercialización de los productos y subproductos de la colmena en cosmetología, farmacéutica y alimentos han aumentado en el mercado nacional, se observa en diferentes ferias apícolas en México. Este artículo describe el diseño de formulaciones de goma conmiel adicionado con esencias de menta y eucalipto, modificados con sabor-color artificial. Evaluación sensorial, Análisis Fisicoquímico y Análisis microbiológico son determinados al producto obtenido, la cual se valora sensorialmente en comparación con gomitas comerciales. Es necesario estandarizar los ingredientes y la miel para el producto obtenido posea las mismas características sensoriales, predominando el sabor miel-menta y miel eucalipto enriquecido con esencia de fresa, considerando a personas que no consumen productos de miel a través de una evaluación sensorial. Las gomitas con esencia de fresa, fisicoquímicamente tiene humedad adecuada para el almacenamiento es ligeramente ácido y un rango de 58-62 grados Brix. Se obtuvo la gomita de miel-eucalipto y miel-menta, poseen un color rojo, sabor a miel y suave textura elástica, con buena aceptación sensorial. Fisicoquímicamente y microbiológicamente los productos obtenidos miel-eucalipto-fresa, miel-menta-fresa cumplen con las Normas Mexicanas además no presentan ningún riesgo para la salud en caso de ingestión

An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB

Motivation: Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases and annotators, making assessment of annotation reliability problematic for users. The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this article. Specifically we investigate word reuse within bulk textual annotations and relate this to Zipf's Principle of Least Effort. We use UniProt Knowledge Base (UniProtKB) as a case study to demonstrate this approach since it allows us to compare annotation change, both over time and between automated and manually curated annotations. Results: By applying power-law distributions to word reuse in annotation, we show clear trends in UniProtKB over time, which are consistent with existing studies of quality on free text English. Further, we show a clear distinction between manual and automated analysis and investigate cohorts of protein records as they mature. These results suggest that this approach holds distinct promise as a mechanism for judging annotation quality. Availability: Source code is available at the authors website: http://homepages.cs.ncl.ac.uk/m.j.bell1/annotation. Contact: [email protected]: Paper accepted at The European Conference on Computational Biology 2012 (ECCB'12). Subsequently will be published in a special issue of the journal Bioinformatics. Paper consists of 8 pages, made up of 5 figure

Toxoplasma, Toxocara and Tuberculosis co-infection in a four year old child

<p>Abstract</p> <p>Background</p> <p>Tuberculosis. toxocariasis and toxoplasmosis are among the common infectious causes of lymphadenitis in children. Cases of <it>Toxoplasma gondii </it>and <it>Toxocara spp </it>co-infection have been reported.</p> <p>Case Presentation</p> <p>This case report describes a co-infection of <it>Toxoplasma gondii</it>, <it>Toxocara </it>spp and tuberculosis in a child with chronic lymphadenopathy and eosinophilia.</p> <p>Conclusion</p> <p>The case report highlights two important points. First is the diagnostic challenges that are encountered by clinicians in tropical countries such as Sri Lanka, where lymphadenopathy and eosinophilia with a positive serology commonly point towards a parasitic infection. Secondly the importance of proper history taking and performing the Mantoux test as a first line investigation in a country where the incidence of tuberculosis is low, even in the absence of a positive contact history.</p

In-beam spectroscopy using the (t,p) reaction: recent results near A = 100

Charged particle spectroscopy using the (t,p) reaction has been employed for more than two decades to study the low-energy structure of nuclei. This reaction has contributed significantly to the elucidation of single-particle and collective phenomena for neutron rich nuclei in virtually every mass region. We have begun to use the (t,p) reaction in conjunctionuclei with in-beam ..gamma..-ray and conversion-electron spectroscopy to bring additional understanding to low-energy nuclear structure. In this report we briefly discuss the experimental considerations in using this reaction for in-beam spectroscopy, and present some results for nuclei with mass near 100

Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?

The genus Pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. The relationship of the Pseudomonas genus to Azotobacter vinelandii is examined using three genomic sequence-based methods. First, using 16S rRNA trees, it is shown that A. vinelandii groups within the Pseudomonas close to Pseudomonas aeruginosa. Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster. Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms. Third, exhaustive BLAST comparisons demonstrate that the fraction of shared genes between A. vinelandii and Pseudomonas genomes is similar to that of Pseudomonas species with each other. The results of these different methods point to a high similarity between A. vinelandii and the Pseudomonas genus, suggesting that Azotobacter might actually be a Pseudomonas

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats

<p>Abstract</p> <p>Background</p> <p>Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes.</p> <p>Results</p> <p>CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT proved to be a huge improvement over Patscan. Both CRT and Pilercr were comparable in speed, however CRT was faster for genomes containing large numbers of repeats.</p> <p>Conclusion</p> <p>In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, showed some important improvements over current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(<it>n</it>) in space and O(<it>nm</it>/<it>l</it>) in time.</p

The Salmonella enterica Pan-genome

Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences). Of these, 35 were found to be of sufficiently good quality to allow a detailed analysis, along with two Escherichia coli strains (K-12 substr. DH10B and the avian pathogenic E. coli (APEC O1) strain). All genomes were subjected to standardized gene finding, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection of variable genomic regions or islands. These include the SPIs but also encompass phage insertion sites and transposable elements. The islands were typically well conserved in several, but not all, isolates—a difference which may have implications in, e.g., host specificity

Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes.

INTRODUCTION: Genomic base composition ranges from less than 25% AT to more than 85% AT in prokaryotes. Since only a small fraction of prokaryotic genomes is not protein coding even a minor change in genomic base composition will induce profound protein changes. We examined how amino acid and codon frequencies were distributed in over 2000 microbial genomes and how these distributions were affected by base compositional changes. In addition, we wanted to know how genome-wide amino acid usage was biased in the different genomes and how changes to base composition and mutations affected this bias. To carry this out, we used a Generalized Additive Mixed-effects Model (GAMM) to explore non-linear associations and strong data dependences in closely related microbes; principal component analysis (PCA) was used to examine genomic amino acid- and codon frequencies, while the concept of relative entropy was used to analyze genomic mutation rates. RESULTS: We found that genomic amino acid frequencies carried a stronger phylogenetic signal than codon frequencies, but that this signal was weak compared to that of genomic %AT. Further, in contrast to codon usage bias (CUB), amino acid usage bias (AAUB) was differently distributed in AT- and GC-rich genomes in the sense that AT-rich genomes did not prefer specific amino acids over others to the same extent as GC-rich genomes. AAUB was also associated with relative entropy; genomes with low AAUB contained more random mutations as a consequence of relaxed purifying selection than genomes with higher AAUB. CONCLUSION: Genomic base composition has a substantial effect on both amino acid- and codon frequencies in bacterial genomes. While phylogeny influenced amino acid usage more in GC-rich genomes, AT-content was driving amino acid usage in AT-rich genomes. We found the GAMM model to be an excellent tool to analyze the genomic data used in this study