Temporal data classification using linear classifiers

Data classification is usually based on measurements recorded at the same time. This paper considers temporal data classification where the input is a temporal database that describes measurements over a period of time in history while the predicted class is expected to occur in the future. We describe a new temporal classification method that improves the accuracy of standard classification methods. The benefits of the method are tested on weather forecasting using the meteorological database from the Texas Commission on Environmental Quality

The EnzymeTracker: an open-source laboratory information management system for sample tracking

<p>Abstract</p> <p>Background</p> <p>In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems.</p> <p>Results</p> <p>In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking.</p> <p>Conclusions</p> <p>The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at <url>http://cubique.fungalgenomics.ca/enzymedb/index.html</url> under the GNU GPLv3 license.</p

Utilizing Visualization Mechanisms to Improve User Performance during Cyber Defense Competitions

This paper describes the development of a visualization system used by students participating in a collegiate cyber defense competition and a first-pass exploratory analysis of the system. Feedback was gathered from first-time users of the system through open-ended field interviews. This initial contextual analysis examined user attitudes about appropriating a new technology in their overall competition strategy. While challenges in the data display and user interface were reported, the interviewees reported that the team and network views offered by the new visualization system enabled them to improve their performance during the competition activities

Alignment and Aperture Scan at the Fermilab Booster

The Fermilab booster has an intensity upgrade plan called the Proton Improvement plan (PIP). The flux throughput goal is 2E17 protons/hour, which is almost double the current operation at 1.1E17 protons/hour. The beam loss in the machine is going to be the source of issues. The booster accelerates beam from 400 MeV to 8 GeV and extracts to the Main Injector. Several percent of the beam is lost within 3 msec after the injection. The aperture at injection energy was measured and compared with the survey data. The magnets are going to be realigned in March 2012 in order to increase the aperture. The beam studies, analysis of the scan and alignment data, and the result of the magnet moves will be discussed in this paper.Comment: 3 pp. 3rd International Particle Accelerator Conference (IPAC 2012) 20-25 May 2012, New Orleans, Louisian

HENRY A MURRAY AND THE HARVARD PSYCHOLOGICAL CLINIC, 1926-1938: A STRUGGLE TO EXPAND THE DISCIPLINARY BOUNDARIES OF ACADEMIC PSYCHOLOGY

The work of Henry A. Murray at the Harvard Psychological Clinic played a major role in shaping the face of modern American academic psychology. Prior to 1930, proponents of pure and applied psychological research debated the inclusion of personality and psychotherapy in the curriculum. Today, it is generally accepted that Murray was instrumental in broadening academic psychology\u27s boundaries to include these topics. This dissertation details how the controversy surrounding Murray\u27s promotion to Associate Professor in 1937 encapsulated the interplay between the intradisciplinary and extradisciplinary forces involved in psychology\u27s efforts to define its intellectual, methodological, and institutional boundaries. Initially, Murray\u27s work was on the fringes of disciplinary and institutional acceptability. Murray was not trained in academic psychology, but rather in medicine and biochemistry. The Clinic\u27s operations were subsidized by external grants and not from Harvard\u27s own funds. Murray was also constantly in conflict with E. G. Boring, chairman of the Department of Psychology, concerning the administration of the Clinic. Furthermore, Murray rejected psychological reductionism, instead promoting research methods derived from medicine and a theory of personality influenced by psychoanalysis and L. J. Henderson\u27s biological systems theory. These factors made the outcome of Murray\u27s 1936-1937 promotion and tenure review highly doubtful. However, the Rockefeller Foundation intervened and used its financial influence to secure Murray\u27s promotion and ultimately to further the development of research on personality. This served to allow academic psychology to develop as a broadly defined field that would remain open to interdisciplinary influences

Bacterial Protein Structures Reveal Phylum Dependent Divergence

Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against each other to establish their relatedness. As expected, the analysis demonstrates a sharp structural divergence between the bacterial phyla Firmicutes and Proteobacteria. Additionally, each COG had a distinct sequence/structure relationship, indicating that different evolutionary pressures affect the degree of structural divergence. However, our analysis also shows the relative drift rate between sequence identity and structure divergence remains constant

PROFESS: a PROtein Function, Evolution, Structure and Sequence database

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are ∼1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein–protein interaction networks

Depletion of the mitotic kinase Cdc5p in Candida albicans results in the formation of elongated buds that switch to the hyphal fate over time in a Ume6p and Hgc1p-dependent manner

The fungal pathogen Candida albicans differentiates between yeast, hyphae and pseudohyphae in order to enhance survival in the human host. Environmental cues induce hyphal development and expression of hyphal-specific genes. Filaments also result from yeast cell cycle arrest, but the nature of these cells and their mechanisms of formation are less clear. We previously demonstrated that depletion of the mitotic polo-like kinase Cdc5p resulted in the production of filaments under yeast growth conditions that were distinct from hyphae with respect to several criteria, yet expressed hyphal-specific genes at later stages of development. In order to clarify the identity of these growth forms and their relationship to true hyphae, we conducted time course-based investigations of aspects of the polar growth machinery, which can distinguish cell types. During later stages of Cdc5p depletion, the myosin light chain Mlc1p demonstrated a Spitzenkörper-like localization in the tips of some filaments, and the Cdc42p GAP Rga2p became hyper-phosphorylated, as in true hyphae. Hyphal-specific genes HWP1, UME6 and HGC1 were strongly expressed at approximately the same time. HWP1 expression was dependent on Ume6p, and absence of Ume6p or Hgc1p influenced late-stage filament morphology and integrity. Finally, polarized growth and UME6 expression in Cdc5p-depleted cells were independent of the transcription factor Hms1p. Thus, depleting Cdc5p generates elongated buds that switch to a hyphal fate over time through a mechanism that involves UME6 and HGC1 induction, possibly in response to maintenance of polarized growth. The results expand on the multiple strategies with which C. albicans can modulate growth mode and expression of virulence determinants

Kleptoparasitic melees--modelling food stealing featuring contests with multiple individuals

Kleptoparasitism is the stealing of food by one animal from another. This has been modelled in various ways before, but all previous models have only allowed contests between two individuals. We investigate a model of kleptoparasitism where individuals are allowed to fight in groups of more than two, as often occurs in real populations. We find the equilibrium distribution of the population amongst various behavioural states, conditional upon the strategies played and environmental parameters, and then find evolutionarily stable challenging strategies. We find that there is always at least one ESS, but sometimes there are two or more, and discuss the circumstances when particular ESSs occur, and when there are likely to be multiple ESSs