Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler.

BACKGROUND: The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans. There are two bat genome projects currently underway, a circumstance that promises to speed the discovery host factors important in the coevolution of bats with their viruses. These genomes, however, are not yet assembled and one of them will provide only low coverage, making the inference of most genes of immunological interest error-prone. Many more wildlife genome projects are underway and intend to provide only shallow coverage. RESULTS: We have developed a statistical method for the assembly of gene families from partial genomes. The method takes full advantage of the quality scores generated by base-calling software, incorporating them into a complete probabilistic error model, to overcome the limitation inherent in the inference of gene family members from partial sequence information. We validated the method by inferring the human IFNA genes from the genome trace archives, and used it to infer 61 type-I interferon genes, and single type-II interferon genes in the bats Pteropus vampyrus and Myotis lucifugus. We confirmed our inferences by direct cloning and sequencing of IFNA, IFNB, IFND, and IFNK in P. vampyrus, and by demonstrating transcription of some of the inferred genes by known interferon-inducing stimuli. CONCLUSION: The statistical trace assembler described here provides a reliable method for extracting information from the many available and forthcoming partial or shallow genome sequencing projects, thereby facilitating the study of a wider variety of organisms with ecological and biomedical significance to humans than would otherwise be possible.

IBAL manual; the Illiac III basic assembler language,

"Supported in part by contract AT(11-1)-2118 with the United States Atomic Energy Commission."

A generalized assembler.

Issued also as thesis (M.S.) University of Illinois.

A cross-assembler/simulator for a microprocessor-based industrial controller /

Vita: p. 65.

YAQ : a 360 assembler version of the algorithm Aq and comparison with other PL/I programs /

"UILU-ENG 77 1724."

A universal cross-assembler /

Thesis (M. S.)--University of Illinois at Urbana-Champaign.

An assembler for efficient file manipulation /

Thesis (M. S.)--University of Illinois at Urbana-Champaign.

A macro-assembler for Illiac IV /

"December 1, 1969."

Assembler's guide to diagnostic x-ray equipment under the Federal Performance Standard.

Mode of access: Internet.

Timing analysis of assembler code control-flow paths

Timinganalysis of assembler code is essential to achieve the strongest possible guarantee of correctness for safety-critical, real-time software. Previous work has shown how timingconstrain ts on controlflow paths through high-level language programs can be formalised using the semantics of the statements comprisingthe path. We extend these results to assembler-level code where it becomes possible to not only determine timingconstrain ts, but also to verify them against the known execution times for each instruction. A minimal formal model is developed with both a weakest liberal precondition and a strongest postcondition semantics. However, despite the formalism’s simplicity, it is shown that complex timingb ehaviour associated with instruction pipeliningand iterative code can be modelled accurately.

A partial-correctness semantics for modelling assembler programs

Previous work on formally modelling and analysing program compilation has shown the need for a simple and expressive semantics for assembler level programs. Assembler programs contain unstructured jumps and previous formalisms have modelled these by using continuations, or by embedding the program in an explicit emulator. We propose a simpler approach, which uses techniques from compiler theory in a formal setting. This approach is based on an interpretation of programs as collections of program paths, each of which has a weakest liberal precondition semantics. We then demonstrate, by example, how we can use this formalism to justify the compilation of block-structured high-level language programs into assembler.

A case-control study of ambient heat exposure and urolithiasis among outdoor workers in a shipbuilding company, Guangzhou, China

Higher ambient temperatures will increase heat stress on workers, leading to impacts upon their individual health and productivity. In particular, research has indicated that higher ambient temperatures can increase the prevalence of urolithiasis. This thesis examines the relationship between ambient heat exposure and urolithiasis among outdoor workers in a shipbuilding company in Guangzhou, China, and makes recommendations for minimising the possible impacts of high ambient temperatures on urolithiasis. A retrospective 1:4 matched case-control study was performed to investigate the association between ambient heat exposure and urolithiasis. Ambient heat exposure was characterised by total exposure time, type of work, department and length of service. The data were obtained from the affiliated hospital of the shipbuilding company under study for the period 2003 to 2010. A conditional logistic regression model was used to estimate the association between heat exposure and urolithiasis. This study found that the odds ratio (OR) of urolithiasis for total exposure time was 1.5 (95% confidence interval (CI): 1.2–1.8). Eight types of work in the shipbuilding company were investigated, including welder, assembler, production security and quality inspector, planing machine operator, spray painter, gas-cutting worker and indoor employee. Five out of eight types of work had significantly higher risks for urolithiasis, and four of the five mainly consisted of outdoors work with ORs of 4.4 (95% CI: 1.7–11.4) for spray painter, 3.8 (95% CI: 1.9–7.2) for welder, 2.7 (95% CI: 1.4–5.0) for production security and quality inspector, and 2.2 (95% CI: 1.1–4.3) for assembler, compared to the reference group (indoor employee). Workers with abnormal blood pressure (hypertension) were more likely to have urolithiasis with an OR of 1.6 (95% CI: 1.0–2.5) compared to those without hypertension. This study contributes to the understanding of the association between ambient heat exposure and urolithiasis among outdoor workers in China. In the context of global climate change, this is particularly important because rising temperatures are expected to increase the prevalence of urolithiasis among outdoor workers, putting greater pressure on productivity, occupational health management and health care systems. The results of this study have clear implications for public health policy and planning, as they indicate that more attention is required to protect outdoor workers from heat-related urolithiasis.

Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana

Background Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assemble all possible transcripts from a transcriptome. Results In an effort to maximise the diversity and completeness of de novo assembled transcripts, we utilised four de novo transcriptome assemblers, TransAbyss, Trinity, SOAPdenovo-Trans, and Oases, using a range of k-mer sizes and different input RNA-seq read counts. We complemented the parameter space biologically by using RNA from 10 plant tissues. We then combined the output of all assemblies into a large super-set of sequences. Using a method from the EvidentialGene pipeline, the combined assembly was reduced from 9.9 million de novo assembled transcripts to about 235,000 of which about 50,000 were classified as primary. Metrics such as average bit-scores, feature response curves and the ability to distinguish paralogous or homeologous transcripts, indicated that the EvidentialGene processed assembly was of high quality. Of 35 RNA silencing gene transcripts, 34 were identified as assembled to full length, whereas in a previous assembly using only one assembler, 9 of these were partially assembled. Conclusions To achieve a high quality transcriptome, it is advantageous to implement and combine the output from as many different de novo assemblers as possible. We have in essence taking the ‘best’ output from each assembler while minimising sequence redundancy. We have also shown that simultaneous assessment of a variety of metrics, not just focused on contig length, is necessary to gauge the quality of assemblies.

Diseño de un sistema para la detección y caracterización de impactos sobre estructuras.

[ES]Este documento pretende describir de manera clara y concisa la creacion de un dispositivo detector de impactos para estructuras de avion durante su transporte de muy bajo consumo, desde su concepcion como idea hasta su montaje, programacion y posterior comprobacion. El objetivo sera la culminacion exitosa del producto para mas adelante exponerlo ante posibles compradores y/o investigadores. Este dispositivo esta compuesto de tres partes, una unidad de adquisicion y adecuacion de la señal, que ser a recogida por un piezoelectrico; la unidad de inteligencia, que sera un microcontrolador programado en ensamblador mediante la herramienta MPLAB y un chip de radio, que se encargara de transmitir los datos a una unidad mas potente, lease un PC, tablet, movil...

Sistema de control multipropósito programable por pulsación de teclas con álgebra RPN.

[ES]Para la elaboración del presente proyecto, primeramente se explicara los requerimientos técnicos y el origen del microprocesador a utilizar para poder situar y centrar el tema del trabajo. Una vez acotado y delimitado el tema objeto de estudio, se planteara una arquitectura de software sobre la posibilidad de generar unas “pseudolibrerias” de mayor nivel de programación que el ensamblador. Posteriormente, se verificara la posible viabilidad o no de tal planteamiento, exponiendo sus resultados y las consideraciones oportunas a las que nos ha llevado su estudio. Para ello se analizara en una primera instancia el microprocesador a utilizar, que será el PIC16F887, centrándonos en el debido al amplio manejo y conocimiento que poseemos sobre este microprocesador. El objeto de este escrito será presentar una oferta económica relativa al desarrollo e instalación de dichos microprocesadores para la mejora en el ámbito industrial. Finalmente, realizaremos un estudio sobre la implementación de este tipo de arquitectura software en diferentes microprocesadores de mayores prestaciones, estudiando si la infraestructura será eficiente, funcional y económica.