Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “LOCALITY”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Local positional and spin symmetry breaking as a source of magnetism and insulation in paramagnetic EuTi O 3

Here we consider theoretically the paramagnetic phases of EuTiO 3 that represent configurations created by two sets of microscopic degrees of freedom (m-DOFs): positional symmetry breaking due to octahedral rotations and magnetic symmetry breaking due to spin disorder. The effect of these sets of m-DOFs on the electronic structure and properties of the para phases is assessed by considering sufficiently large (super) cells with the required nominal global average symmetry, allowing, however, the $\mathcal{local}$ positional and magnetic symmetries to be lowered. We find that tendencies for local symmetry breaking can be monitored by following total energy lowering in mean-fieldlike density-functional theory, without recourse for strong correlation effects. While most nominally cubic ABO 3 perovskites are known for their symmetry breaking due to the B-atom sublattice, the case of f-electron magnetism in EuTiO 3 is associated with A-sublattice symmetry breaking and its coupling to structural distortions. We find that (i) paramagnetic $\mathcal{cubic}$ EuTiO 3 has an intrinsic tendency for both magnetic and positional symmetry breaking, while paramagnetic $\mathcal{tetragonal}$ EuTiO 3 has only magnetic symmetry lowering and no noticeable positional symmetry lowering with respect to low-temperature antiferromagnetic tetragonal phase. (ii) Properly modeled paramagnetic tetragonal and cubic EuTiO 3 have a nonzero local magnetic moment on each Eu ion, consistent with the experimental observations of local magnetism in the para phases of EuTiO 3 significantly above the Néel temperature. Interestingly, (iii) the local positional distortion modes in the short-range ordered para phases are inherited from the long-range ordered low-temperature antiferromagnetic ground-state phase.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Local Feature Sufficiency Exploration for Predicting Security-constrained Generation Dispatch in Multi-Area Power Systems

Deriving generation dispatch is essential for efficient and secure operation of electric power systems. This is usually achieved by solving a security-constrained optimal power flow(SCOPF) problem, which is by nature non-convex, nonlinear and thus computational intensive. The state-of-the-art optimization approaches are not able to solve this problem for large-scale power systems within power system operation time window (usually 5 minutes). In this work, we developed supervised learning approaches to determine security-constrained generation dispatch within much shorter time window. More importantly, the physical constrain of only accessing to local measurements and other information in most utilities’ real-time operation can not be ignored for the predictive models.The feasibility and accuracy of utilizing only local features(measurements and grid information in one area) to predict optimal local generation dispatch (dispatch of all generators in the corresponding area) in multi-area power systems has been explored. The results showed optimal local generation dispatch can be predicted with local features with high accuracy, which is comparable to the results obtained with global features.

Sun, Yixuan↗
DOE OSTI2025

The Persistent Challenge of Data Locality in the Post-Exascale Era

The era of exascale computing, exemplified by systems like Frontier achieving exaflop-level performance, marks a milestone. However, the quest for sheer compute power leads to strong imbalance in system design. Hence, scaling advancements in memory, network bandwidth, and storage are also necessary and pose challenges, with a crucial need to address data locality issues. This article underscores the fundamental importance of data locality as a key abstraction for optimizing application performance. Despite notable software solutions, the growing complexity of parallelism and memory hierarchy demands performance-portable data locality solutions across diverse computing platforms. Additionally, the article revisits data locality aspects, covering hardware considerations, application perspectives, software stack abstractions, and tool support. It concludes with insights into data locality challenges and opportunities, emphasizing the ongoing significance of collaborative research for progress in this critical issue.

Unat, Didem [Koc University, Istanbul (Turkey)] (O↗
DOE OSTI2017

Asynchrony among local communities stabilises ecosystem function of metacommunities

Temporal stability of ecosystem functioning increases the predictability and reliability of ecosystem services, and understanding the drivers of stability across spatial scales is important for land management and policy decisions. We used species-level abundance data from 62 plant communities across five continents to assess mechanisms of temporal stability across spatial scales. We assessed how asynchrony (i.e. different units responding dissimilarly through time) of species and local communities stabilised metacommunity ecosystem function. Asynchrony of species increased stability of local communities, and asynchrony among local communities enhanced metacommunity stability by a wide range of magnitudes (1–315%); this range was positively correlated with the size of the metacommunity. Additionally, asynchronous responses among local communities were linked with species’ populations fluctuating asynchronously across space, perhaps stemming from physical and/or competitive differences among local communities. Accordingly, we suggest spatial heterogeneity should be a major focus for maintaining the stability of ecosystem services at larger spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Local Equilibrium and Retardation Revisited

We present that in modeling solute transport with mobile-immobile mass transfer (MIMT), it is common to use an advection-dispersion equation (ADE) with a retardation factor, or retarded ADE. This is commonly referred to as making the local equilibrium assumption (LEA). Assuming local equilibrium, Eulerian textbook treatments derive the retarded ADE, ostensibly exactly. However, other authors have presented rigorous mathematical derivations of the dispersive effect of MIMT, applicable even in the case of arbitrarily fast mass transfer. We resolve the apparent contradiction between these seemingly exact derivations by adopting a Lagrangian point of view. We show that local equilibrium constrains the expected time immobile, whereas the retarded ADE actually embeds a stronger, nonphysical, constraint: that all particles spend the same amount of every time increment immobile. Eulerian derivations of the retarded ADE thus silently commit the gambler's fallacy, leading them to ignore dispersion due to mass transfer that is correctly modeled by other approaches. We then present a particle tracking simulation illustrating how poor an approximation the retarded ADE may be, even when mobile and immobile plumes are continually near local equilibrium. Finally, we note that classic “LEA” (actually, retarded ADE validity) criteria test for insignificance of MIMT-driven dispersion relative to hydrodynamic dispersion, rather than for local equilibrium.

58 GEOSCIENCES↗
DOE OSTI2015

Optical eye tracking system for real-time noninvasive tumor localization in external beam radiotherapy

Purpose: External beam radiotherapy currently represents an important therapeutic strategy for the treatment of intraocular tumors. Accurate target localization and efficient compensation of involuntary eye movements are crucial to avoid deviations in dose distribution with respect to the treatment plan. This paper describes an eye tracking system (ETS) based on noninvasive infrared video imaging. The system was designed for capturing the tridimensional (3D) ocular motion and provides an on-line estimation of intraocular lesions position based on a priori knowledge coming from volumetric imaging. Methods: Eye tracking is performed by localizing cornea and pupil centers on stereo images captured by two calibrated video cameras, exploiting eye reflections produced by infrared illumination. Additionally, torsional eye movements are detected by template matching in the iris region of eye images. This information allows estimating the 3D position and orientation of the eye by means of an eye local reference system. By combining ETS measurements with volumetric imaging for treatment planning [computed tomography (CT) and magnetic resonance (MR)], one is able to map the position of the lesion to be treated in local eye coordinates, thus enabling real-time tumor referencing during treatment setup and irradiation. Experimental tests on an eye phantom and seven healthy subjects were performed to assess ETS tracking accuracy. Results: Measurements on phantom showed an overall median accuracy within 0.16 mm and 0.40° for translations and rotations, respectively. Torsional movements were affected by 0.28° median uncertainty. On healthy subjects, the gaze direction error ranged between 0.19° and 0.82° at a median working distance of 29 cm. The median processing time of the eye tracking algorithm was 18.60 ms, thus allowing eye monitoring up to 50 Hz. Conclusions: A noninvasive ETS prototype was designed to perform real-time target localization and eye movement monitoring during ocular radiotherapy treatments. The device aims at improving state-of-the-art invasive procedures based on surgical implantation of radiopaque clips and repeated acquisition of X-ray images, with expected positive effects on treatment quality and patient outcome.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

TU-AB-201-03: A Robot for the Automated Delivery of An Electromagnetic Tracking Sensor for the Localization of Brachytherapy Catheters

Purpose: To present a programmable robotic system for the accurate and fast deployment of an electromagnetic (EM) sensor for brachytherapy catheter localization. Methods: A robotic system for deployment of an EM sensor was designed and built. The system was programmed to increment the sensor position at specified time and space intervals. Sensor delivery accuracy was measured in a phantom using the localization of the EM sensor and tested in different environmental conditions. Accuracy was tested by measuring the distance between the physical locations reached by the sensor (measured by the EM tracker) and the intended programmed locations. Results: The system consisted of a stepper motor connected to drive wheels (that grip the cable to move the sensor) and a series of guides to connect to a brachytherapy transfer tube, all controlled by a programmable Arduino microprocessor. The total cost for parts was <$300. The positional accuracy of the sensor location was within 1 mm of the expected position provided by the motorized guide system. Acquisition speed to localize a brachytherapy catheter with 20 cm of active length was 10 seconds. The current design showed some cable slip and warping depending on environment temperature. Conclusion: The use of EM tracking for the localization of brachytherapy catheters has been previously demonstrated. Efficient data acquisition and artifact reduction requires fast and accurate deployment of an EM sensor in consistent, repeatable patterns, which cannot practically be achieved manually. The design of an inexpensive, programmable robot allowing for the precise deployment of stepping patterns was presented, and a prototype was built. Further engineering is necessary to ensure that the device provides efficient independent localization of brachytherapy catheters. This research was funded by the Kaye Family Award.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

TU-EF-204-10: A Preliminary Study Evaluating Calculation Variations of Local Noise Power Spectra for CT Simulation in Radiation Therapy

Purpose: Local noise power spectrum (NPS) properties are significantly affected by calculation variables and CT acquisition and reconstruction parameters, but a thoughtful analysis of these effects is absent. In this study, we performed a complete analysis of the effects of calculation and imaging parameters on the NPS. Methods: The uniformity module of a Catphan phantom was scanned with a Philips Brilliance 64-slice CT simulator using various scanning protocols. Images were reconstructed using both FBP and iDose4 reconstruction algorithms. From these images, local NPS were calculated for regions of interest (ROI) of varying locations and sizes, using four image background removal methods. Additionally, using a predetermined ground truth, NPS calculation accuracy for various calculation parameters was compared for computer simulated ROIs. A complete analysis of the effects of calculation, acquisition, and reconstruction parameters on the NPS was conducted. Results: The local NPS varied with ROI size and image background removal method, particularly at low spatial frequencies. The image subtraction method was the most accurate according to the computer simulation study, and was also the most effective at removing low frequency background components in the acquired data. However, first-order polynomial fitting using residual sum of squares and principle component analysis provided comparable accuracy under certain situations. Similar general trends were observed when comparing the NPS for FBP to that of iDose4 while varying other calculation and scanning parameters. However, while iDose4 reduces the noise magnitude compared to FBP, this reduction is spatial-frequency dependent, further affecting NPS variations at low spatial frequencies. Conclusion: The local NPS varies significantly depending on calculation parameters, image acquisition parameters, and reconstruction techniques. Appropriate local NPS calculation should be performed to capture spatial variations of noise; calculation methodology should be selected with consideration of image reconstruction effects and the desired purpose of CT simulation for radiotherapy tasks.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-J-13: Choosing An IMRT Technique in the Treatment of Head and Neck Cancer with Daily Localization Uncertainties

Purpose: Head and Neck cancer treatment with IMRT/VMAT has two choices: split-filed IMRT(SFI), in which the LAN is treated with a separate anterior field and the extended whole-field IMRT(WFI) in which LAN is included with the IMRT/VMAT field. This study shows that under the same dose limit criteria, choosing the technique becomes a critical issue if daily localization and immobilization altered the dose distribution. Methods: Nine common head-and-neck cancer cases were chosen to illustrate how the daily localization and immobilization uncertainties affect to choose between SFI and WFI. Both SFI and WFI at upper target coverage were generated with VMAT. For each case, the same planning criteria were applied to the target and critical structures; therefore, similar target coverage and dose falloff can be observed in both techniques. Thirty days of kV cone beam CT(CBCT) images on each case were also delineated with contralateral and ipsilateral target as well as larynx as critical structure. About 300 CBCT images with daily delivered doses were analyzed and compared in a form of dose-volume histograms. Results: While both plans for SFI and WFI with VMAT planning utilized and meet the criteria of D95>prescription dose and for not-involved larynx with mean dose <35Gy and V55<10%, the daily localization and immobilization has a great contribution to the resulted dose delivery. With WFI, the better daily contralateral and ipsilateral neck target coverage can reflect a simpler or shorter localization; however, a much superior avoidance (WFI: mean dose a 42.5Gy; SFI: mean dose a 18.9Gy) of the non-involved larynx from the SFI is preferred. Conclusion: Dosimetrically, SFI and WFI are equally well for head and Neck cancer treatment with VMAT technique; however, if considering the contribution of daily localization(CBCT) method uncertainties, SFI is better with sparing non-involved larynx and WFI has better target coverage.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-JeP3-01: A Method to Quantify Lung SBRT Target Localization Accuracy Based On Digitally Reconstructed Fluoroscopy

Purpose: To develop a methodology based on digitally-reconstructed-fluoroscopy (DRF) to quantitatively assess target localization accuracy of lung SBRT, and to evaluate using both a dynamic digital phantom and a patient dataset. Methods: For each treatment field, a 10-phase DRF is generated based on the planning 4DCT. Each frame is pre-processed with a morphological top-hat filter, and corresponding beam apertures are projected to each detector plane. A template-matching algorithm based on cross-correlation is used to detect the tumor location in each frame. Tumor motion relative beam aperture is extracted in the superior-inferior direction based on each frame’s impulse response to the template, and the mean tumor position (MTP) is calculated as the average tumor displacement. The DRF template coordinates are then transferred to the corresponding MV-cine dataset, which is retrospectively filtered as above. The treatment MTP is calculated within each field’s projection space, relative to the DRF-defined template. The field’s localization error is defined as the difference between the DRF-derived-MTP (planning) and the MV-cine-derived-MTP (delivery). A dynamic digital phantom was used to assess the algorithm’s ability to detect intra-fractional changes in patient alignment, by simulating different spatial variations in the MV-cine and calculating the corresponding change in MTP. Inter-and-intra-fractional variation, IGRT accuracy, and filtering effects were investigated on a patient dataset. Results: Phantom results demonstrated a high accuracy in detecting both translational and rotational variation. The lowest localization error of the patient dataset was achieved at each fraction’s first field (mean=0.38mm), with Fx3 demonstrating a particularly strong correlation between intra-fractional motion-caused localization error and treatment progress. Filtering significantly improved tracking visibility in both the DRF and MV-cine images. Conclusion: We have developed and evaluated a methodology to quantify lung SBRT target localization accuracy based on digitally-reconstructed-fluoroscopy. Our approach may be useful in potentially reducing treatment margins to optimize lung SBRT outcomes. R01-184173.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-FG-BRA-02: Docetaxel Eluting Brachytherapy Spacers for Local Chemo-Radiation Therapy in Prostate Cancer

Purpose: We propose an innovative combinatorial treatment strategy of Local ChemoRadiation Therapy (LCRT) using a sustained drug delivery platform in the form of a spacer to locally radio-sensitize the prostate with Docetaxel (DTX) enabling a synergistic cure with the use of lower radiation doses. These biodegradable spacers are physically similar to the inert spacers routinely used in prostate brachytherapy but are now loaded with formulations of DTX. Methods: Spacers were loaded with ∼500µg Docetaxel (DTX) for prostate cancer studies. The implants were characterized in vitro using SEM and HPLC. The release kinetic studies were carried out in buffer (pH 6.0) at 37°C. Subcutaneous PC3 tumors were xenografted in nude mice. Prostate cancer studies were done with and without radiation using SARRP at 5Gy, 10Gy, and 15Gy. Drug-loaded implants were injected once intratumorally using an 18G brachytherapy needle. Results: The release study in vitro showed a highly sustained release for multiple weeks at therapeutically relevant doses. The monotherapy with local DTX spacer showed sustained tumor inhibition compared to empty implants and an equivalent DTX dose given systemically. At 40 days, 89% survival was observed for mice treated with DTX implants compared with 0% in all other treatment groups. The combined treatment with local DTX spacer and radiation (10Gy) showed the highest degree of tumor suppression (significant tumor growth inhibition by day 90). The control mice showed continuous tumor growth and were scarified by day 56. Groups of mice treated with DTX-spacer or radiation alone showed initial tumor suppression but growth continued after day 60. A larger experiment is ongoing. Conclusion: This approach provides localized delivery of the chemotherapeutic sensitizer directly to the tumor and avoids the toxicities associated with both brachytherapy and current systemic delivery of docetaxel. Sustained release of DTX is an effective chemotherapy option alone or in combination with radiation therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations

Vibrio cholerae represents both an environmental pathogen and a widely distributed microbial species comprised of closely related strains occurring in the tropical to temperate coastal ocean across the globe (Colwell RR, Science 274:2025-2031, 1996; Griffith DC, Kelly-Hope LA, Miller MA, Am. J. Trop. Med. Hyg. 75:973-977, 2006; Reidl J, Klose KE, FEMS Microbiol. Rev. 26:125-139, 2002). However, although this implies dispersal and growth across diverse environmental conditions, how locally successful populations assemble from a possibly global gene pool, relatively unhindered by geographic boundaries, remains poorly understood. Here, we show that environmental Vibrio cholerae possesses two, largely distinct gene pools: one is vertically inherited and globally well mixed, and the other is local and rapidly transferred across species boundaries to generate an endemic population structure. While phylogeographic analysis of isolates collected from Bangladesh and the U.S. east coast suggested strong panmixis for protein-coding genes, there was geographic structure in integrons, which are the only genomic islands present in all strains of V. cholerae (Chun J, et al., Proc. Natl. Acad. Sci. U. S. A. 106:15442-15447, 2009) and are capable of acquiring and expressing mobile gene cassettes. Geographic differentiation in integrons arises from high gene turnover, with acquisition from a locally co-occurring sister species being up to twice as likely as exchange with conspecific but geographically distant V. cholerae populations. IMPORTANCE Functional predictions of integron genes show the predominance of secondary metabolism and cell surface modification, which is consistent with a role in competition and predation defense. We suggest that the integron gene pool's distinctness and tempo of sharing are adaptive in allowing rapid conversion of genomes to reflect local ecological constraints. Because the integron is frequently the main element differentiating clinical strains (Chun J, et al., Proc. Natl. Acad. Sci. U. S. A. 106:15442-15447, 2009) and its recombinogenic activity is directly stimulated by environmental stresses (Guerin E, et al., Science 324:1034, 2009), these observations are relevant for local emergence and subsequent dispersal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Local polynomial chaos expansion for linear differential equations with high dimensional random inputs

In this paper we present a localized polynomial chaos expansion for partial differential equations (PDE) with random inputs. In particular, we focus on time independent linear stochastic problems with high dimensional random inputs, where the traditional polynomial chaos methods, and most of the existing methods, incur prohibitively high simulation cost. Furthermore, the local polynomial chaos method employs a domain decomposition technique to approximate the stochastic solution locally. In each subdomain, a subdomain problem is solved independently and, more importantly, in a much lower dimensional random space. In a postprocesing stage, accurate samples of the original stochastic problems are obtained from the samples of the local solutions by enforcing the correct stochastic structure of the random inputs and the coupling conditions at the interfaces of the subdomains. Overall, the method is able to solve stochastic PDEs in very large dimensions by solving a collection of low dimensional local problems and can be highly efficient. In our paper we present the general mathematical framework of the methodology and use numerical examples to demonstrate the properties of the method.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

A Molecular View of Plant Local Adaptation: Incorporating Stress-Response Networks

Ecological specialization in plants occurs primarily through local adaptation to different environments. Local adaptation is widely thought to result in costly fitness trade-offs that result in maladaptation to alternative environments. However, recent studies suggest that such trade-offs are not universal. Additionally, there is currently a limited understanding of the molecular mechanisms responsible for fitness trade-offs associated with adaptation. Here, we review the literature on stress responses in plants to identify potential mechanisms underlying local adaptation and ecological specialization. We focus on drought, high and low temperature, flooding, herbivore, and pathogen stresses. We then synthesize our findings with recent advances in the local adaptation and plant molecular biology literature. In the process, we identify mechanisms that could cause fitness trade-offs and outline scenarios where trade-offs are not a necessary consequence of adaptation. Lastly, future studies should aim to explicitly integrate molecular mechanisms into studies of local adaptation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Linking Large-Scale Double-ITCZ Bias to Local-Scale Drizzling Bias in Climate Models

Tropical precipitation in climate models presents significant biases in both the large-scale pattern (i.e., double intertropical convergence zone bias) and local-scale characteristics (i.e., drizzling bias with too frequent drizzle/convection and reduced occurrences of no and heavy precipitation). By untangling the coupled system and analyzing the biases in precipitation, cloud, and radiation, this study shows that local-scale drizzling bias in atmospheric models can lead to large-scale double-ITCZ bias in coupled models by inducing convective-regime-dependent biases in precipitation and cloud radiative effects (CRE). The double-ITCZ bias consists of a hemispherically asymmetric component that arises from the asymmetric SST bias and a nearly symmetric component that exists in atmospheric models without the SST bias. By increasing light rain but reducing heavy rain, local-scale drizzling bias induces positive (negative) precipitation bias in the moderate (strong) convective regime, leading to the nearly symmetric wet bias in atmospheric models. By affecting the cloud profile, local-scale drizzling bias induces positive (negative) CRE bias in the stratocumulus (convective) regime in atmospheric models. Because the stratocumulus (convective) region is climatologically more pronounced in the southern (northern) tropics, the CRE bias is deemed to be hemispherically asymmetric and drives warm and wet (cold and dry) biases in the southern (northern) tropics when coupled to ocean. Our results suggest that correcting local-scale drizzling bias is critical for fixing large-scale double-ITCZ bias. Finally, the drizzling and double-ITCZ biases are not alleviated in models with mesoscale (0.25°–0.5°) or even storm-resolving (~3 km) resolution, implying that either large-eddy simulation or fundamental improvement in small-scale subgrid parameterizations is needed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Response of U.S. West Coast Mountain Snowpack to Local Sea Surface Temperature Perturbations: Insights from Numerical Modeling and Machine Learning

Sea surface temperature (SST) significantly modulates the precipitation and temperature over land, with important consequences on land surface processes such as snowpack. Compared to the impact of remote SST, the effect of nearshore/local SST is less well understood. In this study, the impact of local SST on the mountain snowpack of the U.S. West Coast is investigated using two 6-km regional climate simulations driven by the same lateral boundary conditions but with time-varying versus time-invariant and warmer local SSTs during 2003–15. Results show that local SST warming leads to warmer winter with more precipitation over the mountains. Meanwhile, the removal of SST temporal variability results in reduced temperature variability but increased precipitation variability. As a result, winter snow accumulation decreases by ~200 mm per season in the Cascade Mountains in the north but increases by ~100 mm per season in the Sierra Nevada in the south. Such a dipole response results from the competing effects of precipitation and temperature change at different elevations and are amplified by the enhanced atmospheric river moisture transport. To further delineate the relative contributions of different meteorological factors to the snowpack response, two neural network models were developed to predict the snow behaviors at seasonal and monthly scales. These models reveal the dominant influence of the total amount and the average temperature of precipitation on the snowpack response. Furthermore, these findings highlight the sensitivity of mountain snowpack to local SST in the western United States and underscore the importance of local SST and atmospheric rives to accurate snowpack estimations for water management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

A Piecewise Local Partial Least Squares (PLS) Method for the Quantitative Analysis of Plutonium Nitrate Solutions

We have developed a piecewise local (PL) partial least squares (PLS) analysis method for total plutonium measurements by absorption spectroscopy in nitric acid-based nuclear material processing streams. Instead of using a single PLS model that covers all expected solution conditions, the method selects one of several local models based on an assessment of solution absorbance, acidity, and Pu oxidation state distribution. The local models match the global model for accuracy against the calibration set, but were observed in several instances to be more robust to variations associated with measurements in the process. The improvements are attributed to the relative parsimony of the local models. Not all of the sources of spectral variation are uniformly present at each part of the calibration range. Thus, the global model is locally overfitting and susceptible to increased variance when presented with new samples. A second set of models quantifies the relative concentrations of Pu(III), (IV), and (VI). Standards containing a mixture of these species were not at equilibrium due to a disproportionation reaction. Therefore, a separate principal component analysis is used to estimate of the concentrations of the individual oxidation states in these standards in the absence of independent confirmatory analysis. The PL analysis approach is generalizable to other systems where the analysis of chemically complicated systems can be aided by rational division of the overall range of solution conditions into simpler sub-regions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2011

Genome-wide protein localization prediction strategies for gram negative bacteria

Genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function. While a variety of computational tools have been developed for this purpose, errors in the gene models and use of protein sorting signals that are not recognized by the more commonly accepted tools can diminish the accuracy of their output. As part of an effort to manually curate the annotations of 19 strains of Shewanella, numerous insights were gained regarding the use of computational tools and proteomics data to predict protein localization. Identification of the suite of secretion systems present in each strain at the start of the process made it possible to tailor-fit the subsequent localization prediction strategies to each strain for improved accuracy. Comparisons of the computational predictions among orthologous proteins revealed inconsistencies in the computational outputs, which could often be resolved by adjusting the gene models or ortholog group memberships. While proteomic data was useful for verifying start site predictions and post-translational proteolytic cleavage, care was needed to distinguish cellular versus sample processing-mediated cleavage events. Searches for lipoprotein signal peptides revealed that neither TatP nor LipoP are designed for identification of lipoprotein substrates of the twin arginine translocation system and that the +2 rule for lipoprotein sorting does not apply to this Genus. Analysis of the relationships between domain occurrence and protein localization prediction enabled identification of numerous location-informative domains which could then be used to refine or increase confidence in location predictions. This collective knowledge was used to develop a general strategy for predicting protein localization that could be adapted to other organisms.

59 BASIC BIOLOGICAL SCIENCES↗