WAMM: wiki aided meta modelling

All over the world, organizations are becoming more and more complex, and there’s a need to capture its complexity, so this is when the DEMO methodology (Design and Engineering Methodology for Organizations), created and developed by Jan L. G. Dietz, reaches its potential, which is to capture the structure of business processes in a coherent and consistent form of diagrams with their respective grammatical rules. The creation of WAMM (Wiki Aided Meta Modeling) platform was the main focus of this thesis, and had like principal precursor the idea to create a Meta-Editor that supports semantic data and uses MediaWiki. This prototype Meta-Editor uses MediaWiki as a receptor of data, and uses the ideas created in the Universal Enterprise Adaptive Object Model and the concept of Semantic Web, to create a platform that suits our needs, through Semantic MediaWiki, which helps the computer interconnect information and people in a more comprehensive, giving meaning to the content of the pages. The proposed Meta-Modeling platform allows the specification of the abstract syntax i.e., the grammar, and concrete syntax, e.g., symbols and connectors, of any language, as well as their model types and diagram types. We use the DEMO language as a proofof-concept and example. All such specifications are done in a coherent and formal way by the creation of semantic wiki pages and semantic properties connecting them.

Comparison of efficiency between two artificial insemination methods using frozen-thawed semen in domestic cat (Felis catus) Artificial insemination in domestic cats

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

Effect of Progesterone and Ionomycin on Domestic Cat Sperm Motility Patterns and Acrosome Reaction

This study was aimed at assessing the changes in sperm motion patterns and the percentage of acrosome reaction (AR) in domestic cat semen after treatment with either ionomycin or progesterone (P(4)). Ten ejaculates were collected from five tomcats using an artificial vagina, and were diluted, centrifuged and resuspended in a capacitation medium. Samples were evaluated and divided into seven equal aliquots and, after 2 h at 25 degrees C, were incubated for 30 min at 38 degrees C in 5% CO(2) and then analyzed. Computer-assisted sperm analysis and a combination of three fluorescent probes were used to assess sperm plasma, acrosomal membrane integrity and mitochondrial transmembrane potential. Thirty minutes after the start of incubation, P(4) was added (10 mu g/ml) to the P1 group. Groups P2 and P3 were supplemented with P(4) (10 and 20 mu g/ml, respectively) only after 2 h of incubation, and groups I1 and I2 were supplemented with ionomycin (4 and 8 mu M, respectively) 2 h after incubation. Group E was supplemented with ethanol (0.6%) at 2 h after incubation and group C received no supplementation. Ionomycin and P(4) treatments led to a hyperactivation-like sperm motion and an increase (p < 0.05) in the percentage of AR. Although a higher (p < 0.05) percentage of AR was obtained in group I2 when compared with all P(4) groups, a decrease (p < 0.05) in total and progressive motility was observed in I2 group. As I1 group was similar to I2 to induce AR without diminishing sperm motility, we can conclude that ionomycin at 4 mu M seems to be more suitable to trigger AR in domestic cat sperm.

Cryoprotective effect of different glycerol concentrations on domestic cat spermatozoa

Cryopreservation of spermatozoa is a pivotal tool in assisted reproduction, and studies aiming to establish optimal freezing/thawing protocols are essential to enhance sperm survival. The objectives of the present study were to (1) compare the cryoprotective efficiency of three different glycerol concentrations (3%, 5%, and 7%) on the basis of post-thaw sperm quality and (2) investigate whether the incidence of morphologically abnormal sperm in fresh samples is related to cryodamage sensitivity. Semen was collected from six tomcats using an artificial vagina (total 18 ejaculates). Each ejaculate was diluted using Tris-egg yolk-based extender (TEY), evaluated, equally divided into three aliquots, and rediluted using TEY with and without glycerol to achieve final concentrations of 3%, 5%, and 7%. Samples were loaded into 0.25 mL straws, equilibrated for 60 minutes at 5 °C, frozen, and then thawed at 46 °C for 12 seconds. Fresh and frozen-thawed samples were evaluated for sperm motion parameters (computer-assisted sperm analysis), plasma membrane integrity (PMI; propidium iodide and carboxyfluorescein diacetate), and DNA integrity (acridine orange). Plasma and acrosomal membrane integrity were assessed by flow cytometry (propidium iodide and fluorescein isothiocyanate-conjugated pea (Pisum sativum) agglutinin) immediately after thawing. Sperm motion parameters were also evaluated at 30 and 60 minutes of postincubation. For all treatment groups, cryopreservation significantly impaired the PMI and sperm motion parameters, except for straightness and amplitude of lateral head displacement. DNA integrity showed a slight reduction (P < 0.05) when 3% glycerol was used. The percentage of total motility, progressive motility, and rapid spermatozoa were significantly lower immediately after thawing and up to 60 minutes of incubation for the 3% glycerol group when compared with 5% and 7%. No difference (P > 0.05) was found for PMI, acrosome integrity, and DNA integrity among post-thaw groups. However, higher (P < 0.05) incidence of viable cells with reacted acrosome and dead cells with intact acrosome were observed with 7% and 3% glycerol, respectively. Percentage of morphologically abnormal spermatozoa in fresh sample was positively correlated with PMI only in the 3% glycerol group and negatively correlated with sperm motility in the 5% and 7% groups. In conclusion, the final concentration of 5% glycerol offered better cryoprotective effect for ejaculated cat sperm, and the relationship found between prefreezing sperm morphology and post-thaw sperm quality showed to be dependent on final glycerol concentration. © 2013 Elsevier Inc.

RNA-Strukturen im Hepatitis-C-Virus und ihre Bedeutung für Translation und Replikation

Das Hepatitis C Virus (HCV) ist ein umhülltes Virus aus der Familie der Flaviviridae. Es besitzt ein Plusstrang-RNA Genom von ca. 9600 Nukleotiden Länge, das nur ein kodierendes Leseraster besitzt. Das Genom wird am 5’ und 3’ Ende von nicht-translatierten Sequenzen (NTRs) flankiert, welche für die Translation und vermutlich auch Replikation von Bedeutung sind. Die 5’ NTR besitzt eine interne Ribosomeneintrittsstelle (IRES), die eine cap-unabhängige Translation des ca. 3000 Aminosäure langen viralen Polyproteins erlaubt. Dieses wird ko- und posttranslational von zellulären und viralen Proteasen in 10 funktionelle Komponenten gespalten. Inwieweit die 5’ NTR auch für die Replikation der HCV RNA benötigt wird, war zu Beginn der Arbeit nicht bekannt. Die 3’ NTR besitzt eine dreigeteilte Struktur, bestehend aus einer variablen Region, dem polyU/UC-Bereich und der sogenannten X-Sequenz, eine hochkonservierte 98 Nukleotide lange Region, die vermutlich für die RNA-Replikation und möglicherweise auch für die Translation benötigt wird. Die genuae Rolle der 3’ NTR für diese beiden Prozesse war zu Beginn der Arbeit jedoch nicht bekannt. Ziel der Dissertation war deshalb eine detaillierte genetische Untersuchung der NTRs hinsichtlich ihrer Bedeutung für die RNA-Translation und -Replikation. In die Analyse mit einbezogen wurden auch RNA-Strukturen innerhalb der kodierenden Region, die zwischen verschiedenen HCV-Genotypen hoch konserviert sind und die mit verschiedenen computer-basierten Modellen vorhergesagt wurden. Zur Kartierung der für RNA-Replikation benötigten Minimallänge der 5’ NTR wurde eine Reihe von Chimären hergestellt, in denen unterschiedlich lange Bereiche der HCV 5’ NTR 3’ terminal mit der IRES des Poliovirus fusioniert wurden. Mit diesem Ansatz konnten wir zeigen, dass die ersten 120 Nukleotide der HCV 5’ NTR als Minimaldomäne für Replikation ausreichen. Weiterhin ergab sich eine klare Korrelation zwischen der Länge der HCV 5’ NTR und der Replikationseffizienz. Mit steigender Länge der 5’ NTR nahm auch die Replikationseffizienz zu, die dann maximal war, wenn das vollständige 5’ Element mit der Poliovirus-IRES fusioniert wurde. Die hier gefundene Kopplung von Translation und Replikation in der HCV 5’ NTR könnte auf einen Mechanismus zur Regulation beider Funktionen hindeuten. Es konnte allerdings noch nicht geklärt werden, welche Bereiche innerhalb der Grenzen des IRES-Elements genau für die RNA-Replikation benötigt werden. Untersuchungen im Bereich der 3’ NTR ergaben, dass die variable Region für die Replikation entbehrlich, die X-Sequenz jedoch essentiell ist. Der polyU/UC-Bereich musste eine Länge von mindestens 11-30 Uridinen besitzen, wobei maximale Replikation ab einer Länge von 30-50 Uridinen beobachtet wurde. Die Addition von heterologen Sequenzen an das 3’ Ende der HCV-RNA führte zu einer starken Reduktion der Replikation. In den hier durchgeführten Untersuchungen zeigte keines der Elemente in der 3’ NTR einen signifikanten Einfluss auf die Translation. Ein weiteres cis aktives RNA-Element wurde im 3’ kodierenden Bereich für das NS5B Protein beschrieben. Wir fanden, dass Veränderungen dieser Struktur durch stille Punktmutationen die Replikation hemmten, welche durch die Insertion einer intakten Version dieses RNA-Elements in die variable Region der 3’ NTR wieder hergestellt werden konnte. Dieser Versuchsansatz erlaubte die genaue Untersuchung der für die Replikation kritischen Strukturelemente. Dadurch konnte gezeigt werden, dass die Struktur und die Primärsequenz der Loopbereiche essentiell sind. Darüber hinaus wurde eine Sequenzkomplementarität zwischen dem Element in der NS5B-kodierenden Region und einem RNA-Bereich in der X-Sequenz der 3’ NTR gefunden, die eine sog. „kissing loop“ Interaktion eingehen kann. Mit Hilfe von gezielten Mutationen konnten wir zeigen, dass diese RNA:RNA Interaktion zumindest transient stattfindet und für die Replikation des HCV essentiell ist.

Real-Time Multimodal Retinal Image Registration for a Computer Assisted Laser Photocoagulation System

An algorithm for the real-time registration of a retinal video sequence captured with a scanning digital ophthalmoscope (SDO) to a retinal composite image is presented. This method is designed for a computer-assisted retinal laser photocoagulation system to compensate for retinal motion and hence enhance the accuracy, speed, and patient safety of retinal laser treatments. The procedure combines intensity and feature-based registration techniques. For the registration of an individual frame, the translational frame-to-frame motion between preceding and current frame is detected by normalized cross correlation. Next, vessel points on the current video frame are identified and an initial transformation estimate is constructed from the calculated translation vector and the quadratic registration matrix of the previous frame. The vessel points are then iteratively matched to the segmented vessel centerline of the composite image to refine the initial transformation and register the video frame to the composite image. Criteria for image quality and algorithm convergence are introduced, which assess the exclusion of single frames from the registration process and enable a loss of tracking signal if necessary. The algorithm was successfully applied to ten different video sequences recorded from patients. It revealed an average accuracy of 2.47 ± 2.0 pixels (∼23.2 ± 18.8 μm) for 2764 evaluated video frames and demonstrated that it meets the clinical requirements.

Lost in Translation: Emotion and Expression through Technology

My Thesis study was designed to bring to topic certain issues involved with CMC (computer-mediated communication.) Often we are presented with confusing or misleading situations when it comes to expressing our emotions through technological means. It is important that we are aware of certain issues such as the use of emoticons, expressing sarcasm, and the ongoing trend of Internet slang. These various aspects can create confusion in CMC, leading to a loss in translation. My survey study was designed to probe deeper into these issues by asking general questions and by analyzing sample CMC scenarios.

Automatic Categorization for Improving Spanish into Spanish Sign Language Machine Translation

This paper describes a preprocessing module for improving the performance of a Spanish into Spanish Sign Language (Lengua de Signos Espanola: LSE) translation system when dealing with sparse training data. This preprocessing module replaces Spanish words with associated tags. The list with Spanish words (vocabulary) and associated tags used by this module is computed automatically considering those signs that show the highest probability of being the translation of every Spanish word. This automatic tag extraction has been compared to a manual strategy achieving almost the same improvement. In this analysis, several alternatives for dealing with non-relevant words have been studied. Non-relevant words are Spanish words not assigned to any sign. The preprocessing module has been incorporated into two well-known statistical translation architectures: a phrase-based system and a Statistical Finite State Transducer (SFST). This system has been developed for a specific application domain: the renewal of Identity Documents and Driver's License. In order to evaluate the system a parallel corpus made up of 4080 Spanish sentences and their LSE translation has been used. The evaluation results revealed a significant performance improvement when including this preprocessing module. In the phrase-based system, the proposed module has given rise to an increase in BLEU (Bilingual Evaluation Understudy) from 73.8% to 81.0% and an increase in the human evaluation score from 0.64 to 0.83. In the case of SFST, BLEU increased from 70.6% to 78.4% and the human evaluation score from 0.65 to 0.82.

An automatic translation scheme from prolog to the andorra kernel language

The Andorra family of languages (which includes the Andorra Kernel Language -AKL) is aimed, in principie, at simultaneously supporting the programming styles of Prolog and committed choice languages. On the other hand, AKL requires a somewhat detailed specification of control by the user. This could be avoided by programming in Prolog to run on AKL. However, Prolog programs cannot be executed directly on AKL. This is due to a number of factors, from more or less trivial syntactic differences to more involved issues such as the treatment of cut and making the exploitation of certain types of parallelism possible. This paper provides basic guidelines for constructing an automatic compiler of Prolog programs into AKL, which can bridge those differences. In addition to supporting Prolog, our style of translation achieves independent and-parallel execution where possible, which is relevant since this type of parallel execution preserves, through the translation, the user-perceived "complexity" of the original Prolog program.

Enhancement of translation by the epsilon element is independent of the sequence of the 460 region of 16S rRNA

The epsilon enhancer element is a pyrimidine-rich sequence that increases expression of T7 gene 10 and a number of Escherichia coli mRNAs during initiation of translation and inhibits expression of the recF mRNA during elongation. Based on its complementarity to the 460 region of 16S rRNA, it has been proposed that epsilon exerts its enhancer activity by base pairing to this complementary rRNA sequence. We have tested this model of enhancer action by constructing mutations in the 460 region of 16S rRNA and examining expression of epsilon-containing CAT reporter genes and recF–lacZ fusions in strains expressing the mutant rRNAs. Replacement of the 460 E.coli stem–loop with that of Salmonella enterica serovar Typhimurium or a stem–loop containing a reversal of all 8 bp in the helical region produced fully functional rRNAs with no apparent effect on cell growth or expression of any epsilon-containing mRNA. Our experiments confirm the reported effects of the epsilon elements on gene expression but show that these effects are independent of the sequence of the 460 region of 16S rRNA, indicating that epsilon–rRNA base pairing does not occur.

Computer-modeling origin of a simple genetic apparatus

This computer simulation is based on a model of the origin of life proposed by H. Kuhn and J. Waser, where the evolution of short molecular strands is assumed to take place in a distinct spatiotemporal structured environment. In their model, the prebiotic situation is strongly simplified to grasp essential features of the evolution of the genetic apparatus without attempts to trace the historic path. With the tool of computer implementation confining to principle aspects and focused on critical features of the model, a deeper understanding of the model's premises is achieved. Each generation consists of three steps: (i) construction of devices (entities exposed to selection) presently available; (ii) selection; and (iii) multiplication of the isolated strands (R oligomers) by complementary copying with occasional variation by copying mismatch. In the beginning, the devices are single strands with random sequences; later, increasingly complex aggregates of strands form devices such as a hairpin-assembler device which develop in favorable cases. A monomers interlink by binding to the hairpin-assembler device, and a translation machinery, called the hairpin-assembler-enzyme device, emerges, which translates the sequence of R1 and R2 monomers in the assembler strand to the sequence of A1 and A2 monomers in the A oligomer, working as an enzyme.

CNI-1493 inhibits monocyte/macrophage tumor necrosis factor by suppression of translation efficiency.

Tumor necrosis factor (TNF) mediates a wide variety of disease states including septic shock, acute and chronic inflammation, and cachexia. Recently, a multivalent guanylhydrazone (CNI-1493) developed as an inhibitor of macrophage activation was shown to suppress TNF production and protect against tissue inflammation and endotoxin lethality [Bianchi, M., Ulrich, P., Bloom, O., Meistrell, M., Zimmerman, G. A., Schmidtmayerova, H., Bukrinsky, M., Donnelley, T., Bucala, R., Sherry, B., Manogue, K. R., Tortolani, A. J., Cerami, A. & Tracey, K. J. (1995) Mol. Med. 1, 254-266, and Bianchi, M., Bloom, O., Raabe, T., Cohen, P. S., Chesney, J., Sherry, B., Schmidtmayerova, H., Zhang, X., Bukrinsky, M., Ulrich, P., Cerami, A. & Tracey, J. (1996) J. Exp. Med., in press]. We have now elucidated the mechanism by which CNI-1493 inhibits macrophage TNF synthesis and show here that it acts through suppression of TNF translation efficiency. CNI-1493 blocked neither the lipopolysaccharide (LPS)-induced increases in the expression of TNF mRNA nor the translocation of nuclear factor NF-kappa B to the nucleus in macrophages activated by 15 min of LPS stimulation, indicating that CNI-1493 does not interfere with early NF-kappa B-mediated transcriptional regulation of TNF. However, synthesis of the 26-kDa membrane form of TNF was effectively blocked by CNI-1493. Further evidence for the translational suppression of TNF is given by experiments using chloram-phenicol acetyltransferase (CAT) constructs containing elements of the TNF gene that are involved in TNF translational regulation. Both the 5' and 3' untranslated regions of the TNF gene were required to elicit maximal translational suppression by CNI-1493. Identification of the molecular target through which CNI-1493 inhibits TNF translation should provide insight into the regulation of macrophage activation and mechanisms of inflammation.

An extended syntax-directed translation scheme /

Bibliography: p. 36.

A translation of relational database query languages into SIBYL /

Bibliography: p. [77]-78.

The works of Anatole France in an English translation.

Imprint varies slightly.