Audio-Visual Feedback: Student Attainment and Student and Staff Perceptions

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Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. Conclusions: By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. There is a pressing need for visualization and analysis tools for 5-D live cell image data. We combine accurate unsupervised processes with an intuitive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc

Determination of Cobalt in Cobalt(III) Complexes - A Comparative Study

Cobalt in cobalt(III) complexes was determined by a gravimetric method, weighing cobalt as cobalt(II) sulfate after heating the complexes with concentrated sulfuric acid; by a spectrophotometric method, measuring the color of cobalt(II)-thiocyanate complex in water-acetone mixture after reducing cobalt(III) to cobalt(II) with chromium(II), and by atomic absorption. The three methods were compared for accuracy of results and for convenience in routine analysis

Diagnosing and Responding to Violations in the Positivity Assumption

The assumption of positivity or experimental treatment assignment requires that observed treatment levels vary within confounder strata. This article discusses the positivity assumption in the context of assessing model and parameter-specific identifiability of causal effects. Positivity violations occur when certain subgroups in a sample rarely or never receive some treatments of interest. The resulting sparsity in the data may increase bias with or without an increase in variance and can threaten valid inference. The parametric bootstrap is presented as a tool to assess the severity of such threats and its utility as a diagnostic is explored using simulated data. Several approaches for improving the identifiability of parameters in the presence of positivity violations are reviewed. Potential responses to data sparsity include restriction of the covariate adjustment set, use of an alternative pro jection function to define the target parameter within a non-parametric marginal structural model, restriction of the sample, and modification of the target intervention. All of these approaches can be understood as trading off proximity to the initial target of inference for identifiability; we advocate approaching this tradeoff systematically

Geologic CO2 storage using pre-injection brine production in tandem reservoirs: A strategy for improved storage performance and enhanced water recovery

Deployment barriers for CO2 capture, utilization, and storage (CCUS) in saline reservoirs can be grouped under three categories: (1) net cost (after accounting for utilization benefits); (2) water intensity of CO2 capture, and (3) uncertainty about storage capacity and permanence. The third category is often considered to be the most challenging. Overpressure, which is fluid pressure that exceeds the original reservoir pressure due to CO2 injection, is the limiting metric for storage capacity and permanence because it drives key physical risks: induced seismicity, caprock fracture, and CO2 leakage. Variables that control overpressure include: (1) the quantity of CO2 and the rate at which it is injected, (2) the size of the reservoir storage compartment, and (3) reservoir permeability. Geologic surveys, geologic logs, and core data from exploration wells provide information that can be used to estimate the size and permeability of the reservoir compartment, but large uncertainties will only be narrowed after there is operational experience with moving large quantities of fluid to move into and/or out of the reservoir. Unlike CCUS applied to CO2 Enhanced Oil Recovery (CO2-EOR) in mature oil fields, CCUS in a saline reservoir will typically (a) have less geologic information and little or no production and injection history to estimate how much CO2 can be safely and permanently stored and (b) not have the advantage of depleted reservoir pressure prior to CO2 injection. Numerous studies have evaluated strategies for managing CO2 storage reservoirs by producing brine to reduce the pressure buildup due to CO2 injection. Most of these studies assume that separate injection and production wells will be used and that brine production will begin during or after the CO2 injection phase. We present a strategy where brine production begins prior to the CO2 injection phase, using the wells that will subsequently be used for CO2 injection. In this strategy, all wells are initially used for exploration and monitoring and then to produce brine prior to injecting CO2. Our strategy also includes the option of using reservoirs in tandem, including: CO2-storage reservoirs: due to their high seal integrity, these are preferred for CO2 storage. Brine produced from these reservoirs may or may not be directly used for water generation. Brine-storage reservoirs: these are used to store brine and/or residual brine and, with treatable brine composition, to produce brine for water generation. For zero net injection, high seal integrity is not required. This strategy has several advantages. First, pressure drawdown observed during brine production mirrors the pressure buildup during CO2 injection, providing necessary data to directly estimate reservoir storage capacity before any CO2 is injected. Second, pressure drawdown is greatest where CO2 will be injected, which is more efficient both on a per well basis and per mass of removed brine basis. Pre-injection brine production in saline reservoirs shares two key advantages of CO2-EOR: (a) greater knowledge about reservoir properties and storage capacity and (b) depleted reservoir pressure, which increases storage capacity. A third advantage is that the flexibility of our tandem-reservoir approach can be used to improve the economics of Enhanced Water Recovery (EWR). The primary metric for selecting a brine-storage reservoir is for its brine composition to be more amenable for treatment for beneficial uses, such as saline cooling water or water generated through desalination. Where applicable, EWR will reduce the water intensity of CCUS, which is particularly valuable in water-stressed regions. For a range of tandem-reservoir scenarios, we assess the influence of CO2-storage and brine-storage reservoir properties (e.g., reservoir compartment size, seal permeability, and salinity) on reservoir pressure management and EWR. We also illustrate how pre-injection brine production can be used as a tool for site selection and characterization, including assessments of CO2 storage capacity and permanence. This work was sponsored by the USDOE Fossil Energy, National Energy Technology Laboratory, managed by Traci Rodosta and Andrea McNemar. This work was performed under the auspices of the USDOE by LLNL under contract DE-AC52-07NA27344

A Clinically Relevant Method of Analyzing Continuous Change in Robotic Upper Extremity Chronic Stroke Rehabilitation

Background. Robots designed for rehabilitation of the upper extremity after stroke facilitate high rates of repetition during practice of movements and record precise kinematic data, providing a method to investigate motor recovery profiles over time. Objective. To determine how motor recovery profiles during robotic interventions provide insight into improving clinical gains. Methods. A convenience sample (n = 22), from a larger randomized control trial, was taken of chronic stroke participants completing 12 sessions of arm therapy. One group received 60 minutes of robotic therapy (Robot only) and the other group received 45 minutes on the robot plus 15 minutes of translation-to-task practice (Robot + TTT). Movement time was assessed using the robot without powered assistance. Analyses (ANOVA, random coefficient modeling [RCM] with 2-term exponential function) were completed to investigate changes across the intervention, between sessions, and within a session. Results. Significant improvement (P < .05) in movement time across the intervention (pre vs post) was similar between the groups but there were group differences for changes between and within sessions (P < .05). The 2-term exponential function revealed a fast and slow component of learning that described performance across consecutive blocks. The RCM identified individuals who were above or below the marginal model. Conclusions. The expanded analyses indicated that changes across time can occur in different ways but achieve similar goals and may be influenced by individual factors such as initial movement time. These findings will guide decisions regarding treatment planning based on rates of motor relearning during upper extremity stroke robotic interventions

High-frequency monitoring reveals how hydrochemistry and dissolved carbon respond to rainstorms at a karstic critical zone, Southwestern China

Hydrochemical behavior and dissolved carbon dynamics are highly-sensitive to hydrological variations in the monsoon-influenced karstic critical zone which has high chemical weathering rates and experiences strong anthropogenic impact. Continuous high-frequency monitoring in the spring outlet of a karstic catchment in Southwestern China revealed that most hydrochemical variables changed distinctively in response to hydrologic variations, influenced by mixing of different sources and miscellaneous biogeochemical processes. Na+, K+ and SO42− varied significantly with hydrology, showing weak chemostatic behavior controlled by dilution. The flushing effect and random behavior of NO3− and Cl− likely reflect agricultural inputs from high throughflow. Soil CO2 in infiltrated water supports carbonate weathering, enabling DIC (dissolved inorganic carbon) and weathering products (e.g., Ca2+ and Mg2+) to maintain chemostatic behavior. Biogenic DIC exhibited a stronger chemostatic response than carbonate sources and was the foremost control in DIC behavior. Carbon exchange between DIC and DOC (dissolved organic carbon) did not significantly influence DIC concentration and δ13C due to very low DOC concentration. More DOC was exported by flushing from increasing discharge. Hysteretic analysis indicated that the transport processes were controlled by proximal sources mixing and diverse mobilization in various periods responding to rainstorms. NO3− and Cl− presented different hysteresis behavior as sourced from agricultural activities. DOC increased on the hydrograph rising limb and was controlled by a transport-limited regime. However, the hysteresis behavior of most weathering products and DIC were regulated by a process-limited regime in the karstic critical zone. Overall, biogeochemical processes, hydrogeological properties, storm intensity/magnitude and the timing of storms (antecedent conditions) are main factors influencing the response of hydrochemical variables and dissolved carbon to storm events