The time dimension of neural network models

This review attempts to provide an insightful perspective on the role of time within neural network models and the use of neural networks for problems involving time. The most commonly used neural network models are defined and explained giving mention to important technical issues but avoiding great detail. The relationship between recurrent and feedforward networks is emphasised, along with the distinctions in their practical and theoretical abilities. Some practical examples are discussed to illustrate the major issues concerning the application of neural networks to data with various types of temporal structure, and finally some highlights of current research on the more difficult types of problems are presented

Improvements to the Indiana Geological Survey’s Petroleum Database Management System

This poster was presented at the 2011 Annual Meeting of the American Association of Petroleum Geologists, Eastern Section, in Arlington, Virginia, in September 2011.The Indiana Geological Survey’s Petroleum Database Management System (PDMS) is a web application that provides online access to petroleum-related geological information. Since its debut in 2004, the application has been widely used by the petroleum industry, academia, government agencies, and the general public. On June 6, 2011, a significantly enhanced version of the PDMS went online. New features include a robust search menu that permits elaborate queries of more than 74,000 petroleum wells, rapid and convenient online viewing and downloading of PDF-file well reports and both PDF- and TIFF-file geophysical and other well logs, and streamlined menus for easily accessing extensive well data. An interactive, context-driven web help explains every concept or term used. The PDMS is organized in three main sections. The Well Tables Section includes such information as well location descriptions, completion zones, logs, operators, lease names, tests, reports, hydrocarbon shows, samples, cores, geologic formations and tops, and directional survey data. The Map Viewer Section contains many user-selectable layer options for showing well locations, petroleum fields, producing formations, aerial photographs, and topographic maps. Wells shown in the Map Viewer are hyperlinked to the Well Tables for easy access to the well data. The Fields and Production Section summarizes oil, natural gas, and gas storage field data, including historical oil production volumes in both tables and charts

Tracking Cooper Pairs in a Cuprate Superconductor by Ultrafast Angle-Resolved Photoemission

In high-temperature superconductivity, the process that leads to the formation of Cooper pairs, the fundamental charge carriers in any superconductor, remains mysterious. We use a femtosecond laser pump pulse to perturb superconducting Bi2Sr2CaCu2O8+{\delta}, and study subsequent dynamics using time- and angle-resolved photoemission and infrared reflectivity probes. Gap and quasiparticle population dynamics reveal marked dependencies on both excitation density and crystal momentum. Close to the d-wave nodes, the superconducting gap is sensitive to the pump intensity and Cooper pairs recombine slowly. Far from the nodes pumping affects the gap only weakly and recombination processes are faster. These results demonstrate a new window into the dynamical processes that govern quasiparticle recombination and gap formation in cuprates.Comment: 22 pages, 9 figure

Web-Based Geologic Maps, Databases, and HTML Pages for Marion County, Indiana

This poster was presented at the 2011 meeting of the Indiana Academy of Science, 126th Annual Academy Meeting, March 4-5, 2011, Indianapolis, Indiana.The Indiana Geological Survey (IGS) has created an internet map server for Marion County in central Indiana. The site provides detailed geologic information needed to address environmental issues, resource management issues, and land-use conflicts related to a growing population. Marion County is the location of Indianapolis, the state capital and largest city. The IGS anticipates that the Web site will be widely used by the general public, industry, and government entities concerned about the geology, groundwater, and other natural resources. The Marion County Web site links an Internet map server (IMS) and database to provide a portal to the IGS‘s enterprise geodatabases, which allow users to efficiently create, manage, update, and distribute maps and data. The IMS site retrieves maps of bedrock and surficial geology completed during earlier IGS mapping projects. Hydrogeology, infrastructure, and imagery map layers are also included. Database information includes lithologic information (iLITH) compiled from water-well records stored in the Indiana Department of Natural Resources, Division of Water archives and natural gamma-ray geophysical log data, stratigraphic test hole data, and petroleum well-record data from the IGS. Currently, the following products are being prepared: (1) illustrated Web pages discussing the surficial geology, bedrock geology, and bedrock topography; (2) illustrated Web pages discussing digital elevation model terrain, gamma-ray log, iLITH, and clay thickness data sets; (3) online glossary; and (4) metadata for the map layers. The development of the Web site is funded by the IGS and the Great Lakes Geologic Mapping Coalition.Great Lakes Geologic Mapping Coalitio

Fossil Coleoptera from Florissant, Col.

p. 41-55, 4 leaves of plates : ill. ; 24 cm

Tenthredinoidea of the Florissant shales

p. 521-530 : ill. ; 24 cm.Includes bibliographical references

Patience, Persistence and Pragmatism: Experiences and Lessons Learnt from the Implementation of Clinically Integrated Teaching and Learning of Evidence-Based Health Care - A Qualitative Study

Clinically integrated teaching and learning are regarded as the best options for improving evidence-based healthcare (EBHC) knowledge, skills and attitudes. To inform implementation of such strategies, we assessed experiences and opinions on lessons learnt of those involved in such programmes.We conducted semi-structured interviews with 24 EBHC programme coordinators from around the world, selected through purposive sampling. Following data transcription, a multidisciplinary group of investigators carried out analysis and data interpretation, using thematic content analysis. Successful implementation of clinically integrated teaching and learning of EBHC takes much time. Student learning needs to start in pre-clinical years with consolidation, application and assessment following in clinical years. Learning is supported through partnerships between various types of staff including the core EBHC team, clinical lecturers and clinicians working in the clinical setting. While full integration of EBHC learning into all clinical rotations is considered necessary, this was not always achieved. Critical success factors were pragmatism and readiness to use opportunities for engagement and including EBHC learning in the curriculum; patience; and a critical mass of the right teachers who have EBHC knowledge and skills and are confident in facilitating learning. Role modelling of EBHC within the clinical setting emerged as an important facilitator. The institutional context exerts an important influence; with faculty buy-in, endorsement by institutional leaders, and an EBHC-friendly culture, together with a supportive community of practice, all acting as key enablers. The most common challenges identified were lack of teaching time within the clinical curriculum, misconceptions about EBHC, resistance of staff, lack of confidence of tutors, lack of time, and negative role modelling.Implementing clinically integrated EBHC curricula requires institutional support, a critical mass of the right teachers and role models in the clinical setting combined with patience, persistence and pragmatism on the part of teachers

Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli

Despite extensive study of individual enzymes and their organization into pathways, the means by which enzyme networks control metabolite concentrations and fluxes in cells remains incompletely understood. Here, we examine the integrated regulation of central nitrogen metabolism in Escherichia coli through metabolomics and ordinary-differential-equation-based modeling. Metabolome changes triggered by modulating extracellular ammonium centered around two key intermediates in nitrogen assimilation, α-ketoglutarate and glutamine. Many other compounds retained concentration homeostasis, indicating isolation of concentration changes within a subset of the metabolome closely linked to the nutrient perturbation. In contrast to the view that saturated enzymes are insensitive to substrate concentration, competition for the active sites of saturated enzymes was found to be a key determinant of enzyme fluxes. Combined with covalent modification reactions controlling glutamine synthetase activity, such active-site competition was sufficient to explain and predict the complex dynamic response patterns of central nitrogen metabolites

Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison

(Micro)evolutionary changes and the evolutionary potential of bird migration

Seasonal migration is the yearly long-distance movement of individuals between their breeding and wintering grounds. Individuals from nearly every animal group exhibit this behavior, but probably the most iconic migration is carried out by birds, from the classic V-shape formation of geese on migration to the amazing nonstop long-distance flights undertaken by Arctic Terns Sterna paradisaea. In this chapter, we discuss how seasonal migration has shaped the field of evolution. First, this behavior is known to turn on and off quite rapidly, but controversy remains concerning where this behavior first evolved geographically and whether the ancestral state was sedentary or migratory (Fig. 7.1d, e). We review recent work using new analytical techniques to provide insight into this topic. Second, it is widely accepted that there is a large genetic basis to this trait, especially in groups like songbirds that migrate alone and at night precluding any opportunity for learning. Key hypotheses on this topic include shared genetic variation used by different populations to migrate and only few genes being involved in its control. We summarize recent work using new techniques for both phenotype and genotype characterization to evaluate and challenge these hypotheses. Finally, one topic that has received less attention is the role these differences in migratory phenotype could play in the process of speciation. Specifically, many populations breed next to one another but take drastically different routes on migration (Fig. 7.2). This difference could play an important role in reducing gene flow between populations, but our inability to track most birds on migration has so far precluded evaluations of this hypothesis. The advent of new tracking techniques means we can track many more birds with increasing accuracy on migration, and this work has provided important insight into migration's role in speciation that we will review here