SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Molecular classification of cutaneous malignant melanoma by gene expression profiling

The most common human cancers are malignant neoplasms of the skin. Incidence of cutaneous melanoma is rising especially steeply, with minimal progress in non-surgical treatment of advanced disease. Despite significant effort to identify independent predictors of melanoma outcome, no accepted histopathological, molecular or immunohistochemical marker defines subsets of this neoplasm. Accordingly, though melanoma is thought to present with different 'taxonomic' forms, these are considered part of a continuous spectrum rather than discrete entities. Here we report the discovery of a subset of melanomas identified by mathematical analysis of gene expression in a series of samples. Remarkably, many genes underlying the classification of this subset are differentially regulated in invasive melanomas that form primitive tubular networks in vitro, a feature of some highly aggressive metastatic melanomas. Global transcript analysis can identify unrecognized subtypes of cutaneous melanoma and predict experimentally verifiable phenotypic characteristics that may be of importance to disease progression.

On a Syntactic Characterization of Classification with a Mind Change Bound

Most learning paradigms impose a particular syntax on the class of concepts to be learned; the chosen syntax can dramatically affect whether the class is learnable or not. For classification paradigms, where the task is to determine whether the underlying world does or does not have a particular property, how that property is represented has no implication on the power of a classifier that just outputs 1’s or 0’s. But is it possible to give a canonical syntactic representation of the class of concepts that are classifiable according to the particular criteria of a given paradigm? We provide a positive answer to this question for classification in the limit paradigms in a logical setting, with ordinal mind change bounds as a measure of complexity. The syntactic characterization that emerges enables to derive that if a possibly noncomputable classifier can perform the task assigned to it by the paradigm, then a computable classifier can also perform the same task. The syntactic characterization is strongly related to the difference hierarchy over the class of open sets of some topological space; this space is naturally defined from the class of possible worlds and possible data of the learning paradigm.

Automated recognition of drunk driving on highways from video sequences

A new method for the detection of abnormal vehicle trajectories is proposed. It couples optical flow extraction of vehicle velocities with a neural network classifier. Abnormal trajectories are indicative of drunk or sleepy drivers. A single feature of the vehicle, eg., a tail light, is isolated and the optical flow computed only around this feature rather than at each pixel in the image.

Simple classification of walking activities using commodity smart phones

People interact with mobile computing devices everywhere, while sitting, walking, running or even driving. Adapting the interface to suit these contexts is important, thus this paper proposes a simple human activity classification system. Our approach uses a vector magnitude recognition technique to detect and classify when a person is stationary (or not walking), casually walking, or jogging, without any prior training. The user study has confirmed the accuracy.

Rethinking regulatory design : The Australian National Classification Scheme review

This paper considers issues of methodological innovation in communication, media and cultural studies, that arise out of the extent to which we now live in a media environment characterised by an digital media abundance, the convergence of media platforms, content and services, and the globalisation of media content through ubiquitous computing and high-speed broadband networks. These developments have also entailed a shift in the producer-consumer relationships that characterised the 20th century mass communications paradigm, with the rapid proliferation of user-created content, accelerated innovation, the growing empowerment of media users themselves, and the blurring of distinctions between public and private, as well as age-based distinctions in terms of what media can be accessed by whom and for what purpose. It considers these issues through a case study of the Australian Law Reform Commission's National Classification Scheme Review.

Tool-supported dataflow analysis of a security-critical embedded device

Defence organisations perform information security evaluations to confirm that electronic communications devices are safe to use in security-critical situations. Such evaluations include tracing all possible dataflow paths through the device, but this process is tedious and error-prone, so automated reachability analysis tools are needed to make security evaluations faster and more accurate. Previous research has produced a tool, SIFA, for dataflow analysis of basic digital circuitry, but it cannot analyse dataflow through microprocessors embedded within the circuit since this depends on the software they run. We have developed a static analysis tool that produces SIFA compatible dataflow graphs from embedded microcontroller programs written in C. In this paper we present a case study which shows how this new capability supports combined hardware and software dataflow analyses of a security critical communications device.

The child, the text and the teacher : reading primers and reading instruction

From the late sixteenth century, in response to the problem of how best to teach children to read, a variety of texts such as primers, spellers and readers were produced in England for vernacular instruction. This paper describes how these materials were used by teachers to develop first, a specific religious understanding according to the stricture of the time and second, a moral reading practice that provided the child with a guide to secular conduct. The analysis focuses on the use of these texts as a productive means for shaping the child-reader in the context of newly emerging educational spaces which fostered a particular, morally formative relation among teacher, child and text.

Operations research for mining : a classification and literature review

In this paper, we describe the main processes and operations in mining industries and present a comprehensive survey of operations research methodologies that have been applied over the last several decades. The literature review is classified into four main categories: mine design; mine production; mine transportation; and mine evaluation. Mining design models are further separated according to two main mining methods: open-pit and underground. Moreover, mine production models are subcategorised into two groups: ore mining and coal mining. Mine transportation models are further partitioned in accordance with fleet management, truck haulage and train scheduling. Mine evaluation models are further subdivided into four clusters in terms of mining method selection, quality control, financial risks and environmental protection. The main characteristics of four Australian commercial mining software are addressed and compared. This paper bridges the gaps in the literature and motivates researchers to develop more applicable, realistic and comprehensive operations research models and solution techniques that are directly linked with mining industries.