Planning for execution monitoring on a planetary rover

A planetary rover will be traversing largely unknown and often unknowable terrain. In addition to geometric obstacles such as cliffs, rocks, and holes, it may also have to deal with non-geometric hazards such as soft soil and surface breakthroughs which often cannot be detected until rover is in imminent danger. Therefore, the rover must monitor its progress throughout a traverse, making sure to stay on course and to detect and act on any previously unseen hazards. Its onboard planning system must decide what sensors to monitor, what landmarks to take position readings from, and what actions to take if something should go wrong. The planning systems being developed for the Pathfinder Planetary Rover to perform these execution monitoring tasks are discussed. This system includes a network of planners to perform path planning, expectation generation, path analysis, sensor and reaction selection, and resource allocation

Complex Event Recognition Architecture

Complex Event Recognition Architecture (CERA) is the name of a computational architecture, and software that implements the architecture, for recognizing complex event patterns that may be spread across multiple streams of input data. One of the main components of CERA is an intuitive event pattern language that simplifies what would otherwise be the complex, difficult tasks of creating logical descriptions of combinations of temporal events and defining rules for combining information from different sources over time. In this language, recognition patterns are defined in simple, declarative statements that combine point events from given input streams with those from other streams, using conjunction, disjunction, and negation. Patterns can be built on one another recursively to describe very rich, temporally extended combinations of events. Thereafter, a run-time matching algorithm in CERA efficiently matches these patterns against input data and signals when patterns are recognized. CERA can be used to monitor complex systems and to signal operators or initiate corrective actions when anomalous conditions are recognized. CERA can be run as a stand-alone monitoring system, or it can be integrated into a larger system to automatically trigger responses to changing environments or problematic situations

The dynamic exponent of the Ising model on negatively curved surfaces

We investigate the dynamic critical exponent of the two-dimensional Ising model defined on a curved surface with constant negative curvature. By using the short-time relaxation method, we find a quantitative alteration of the dynamic exponent from the known value for the planar Ising model. This phenomenon is attributed to the fact that the Ising lattices embedded on negatively curved surfaces act as ones in infinite dimensions, thus yielding the dynamic exponent deduced from mean field theory. We further demonstrate that the static critical exponent for the correlation length exhibits the mean field exponent, which agrees with the existing results obtained from canonical Monte Carlo simulations.Comment: 14 pages, 3 figures. to appear in J. Stat. Mec

Novel scaling behavior of the Ising model on curved surfaces

We demonstrate the nontrivial scaling behavior of Ising models defined on (i) a donut-shaped surface and (ii) a curved surface with a constant negative curvature. By performing Monte Carlo simulations, we find that the former model has two distinct critical temperatures at which both the specific heat $C(T)$ and magnetic susceptibility $\chi(T)$ show sharp peaks.The critical exponents associated with the two critical temperatures are evaluated by the finite-size scaling analysis; the result reveals that the values of these exponents vary depending on the temperature range under consideration. In the case of the latter model, it is found that static and dynamic critical exponents deviate from those of the Ising model on a flat plane; this is a direct consequence of the constant negative curvature of the underlying surface.Comment: 11 pages 5 figure

Geometric effects on critical behaviours of the Ising model

We investigate the critical behaviour of the two-dimensional Ising model defined on a curved surface with a constant negative curvature. Finite-size scaling analysis reveals that the critical exponents for the zero-field magnetic susceptibility and the correlation length deviate from those for the Ising lattice model on a flat plane. Furthermore, when reducing the effects of boundary spins, the values of the critical exponents tend to those derived from the mean field theory. These findings evidence that the underlying geometric character is responsible for the critical properties the Ising model when the lattice is embedded on negatively curved surfaces.Comment: 16 pages, 6 figures, to appear in J. Phys. A: Math. Ge

EXPLORING THE REGULATION OF SECONDARY METABOLITES IN STREPTOMYCES

The genus Streptomyces harbors a wealth of untapped pharmaceutical potential within uncharacterized biosynthetic clusters whose transcription may be silent or their product undetected. Regulation of these clusters is, in part, managed by global transcription factors, nucleoid-associated proteins, and pathway-specific regulatory proteins. Consequently, a complicated interplay of regulatory elements governs secondary metabolite production and a lack of understanding of this has undermined efforts to screen for novel drug candidates. In an effort to better understand this regulation, we have focussed on one highly expressed NAP, and one silent and cryptic biosynthetic cluster. In parallel, we have leveraged our existing knowledge to improve our screening of Streptomyces for novel bioactive compounds. Here, we investigate the nucleoid-associated protein Streptomyces integration host factor (sIHF), which non-specifically binds DNA and impacts development and antibiotic production. Through targeted mutations, we probe the interfaces of sIHF thought responsible for its interactions with DNA and assess the relevance of these interfaces to in vivo activity. Further, we examine the transcriptionally silent SCO6429-SCO6438 biosynthetic cluster and attempt to activate transcription from its promoter by manipulating its potential regulatory proteins. Binding sites for the putative global regulator cAMP-receptor protein (Crp) in close proximity to this cluster and a potential pathway specific regulator are examined. Finally, we overexpress Crp in a library of Streptomyces and assay for novel bioactivity against known clinical pathogens. Collectively, this work establishes a foundation for further exploring the regulatory networks within Streptomyces and how they may be influenced to discover novel pharmaceuticals.ThesisMaster of Science (MSc

On the margins of minority life: Zoroastrians and the state in Safavid Iran

This article looks at the treatment of the Zoroastrians by central and provincial authorities in early modern Yazd, Kirman and Isfahan, emphasizing the institutional weaknesses of the central or khāsṣạ protection they were supposed to benefit from under the Safavids (907–1135/1501– 1722). It is argued that the maltreatment the Zoroastrians endured under the Safavids had little to do with religious bigotry. Rather, it arose from rivalries between the central and the provincial services of the Safavid bureaucracy, putting Zoroastrians in Yazd, Kirman, Sistan and Isfahan at risk of over-taxation, extortion, forced labour and religious persecution. The argument developed in this article pivots on the material interest of the central and the provincial agents of the Safavid bureaucracy in the revenue and labour potentials of the Zoroastrians, and the way in which the conflict of interest between these two sectors led to such acts of persecution as over-taxation, forced labour, extortion and violenc

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

<p>Abstract</p> <p>Background</p> <p>Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a diverse literature. Here we report on the design, implementation and several evaluations of OpenDMAP, an ontology-driven, integrated concept analysis system. It significantly advances the state of the art in information extraction by leveraging knowledge in ontological resources, integrating diverse text processing applications, and using an expanded pattern language that allows the mixing of syntactic and semantic elements and variable ordering.</p> <p>Results</p> <p>OpenDMAP information extraction systems were produced for extracting protein transport assertions (transport), protein-protein interaction assertions (interaction) and assertions that a gene is expressed in a cell type (expression). Evaluations were performed on each system, resulting in F-scores ranging from .26 – .72 (precision .39 – .85, recall .16 – .85). Additionally, each of these systems was run over all abstracts in MEDLINE, producing a total of 72,460 transport instances, 265,795 interaction instances and 176,153 expression instances. </p> <p>Conclusion</p> <p>OpenDMAP advances the performance standards for extracting protein-protein interaction predications from the full texts of biomedical research articles. Furthermore, this level of performance appears to generalize to other information extraction tasks, including extracting information about predicates of more than two arguments. The output of the information extraction system is always constructed from elements of an ontology, ensuring that the knowledge representation is grounded with respect to a carefully constructed model of reality. The results of these efforts can be used to increase the efficiency of manual curation efforts and to provide additional features in systems that integrate multiple sources for information extraction. The open source OpenDMAP code library is freely available at <url>http://bionlp.sourceforge.net/</url></p

The advancement of blood cell research by optical tweezers

Demonstration of the light radiation pressure on a microscopic level by A. Ashkin led to the invention of optical tweezers (OT). Applied in the studies of living systems, OT have become a preferable instrument for the noninvasive study of microobjects, allowing manipulation and measurement of the mechanical properties of molecules, organelles, and cells. In the present paper, we overview OT applications in hemorheological research, placing emphasis on red blood cells but also discussing OT applications for the investigation of the biomechanics of leukocytes and platelets. Blood properties have always served as a primary parameter in medical diagnostics due to the interconnection with the physiological state of an organism. Despite blood testing being a well-established procedure of conventional medicine, there are still many complex processes that must be unraveled to improve our understanding and contribute to future medicine. OT are advancing single-cell research, promising new insights into individual cell characteristics compared to the traditional approaches. We review the fundamental and practical findings revealed in blood research through the optical manipulation, stretching, guiding, immobilization, and inter-/intracellular force measurements of single blood cells