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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.

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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

An update to the Sandia method for creating Typical Meteorological Years from a limited pool of calendar years

Typical Meteorological Years (TMYs) are essential for the efficient evaluation of energy system performance. Ideally, 30 years of weather data are required to generate TMYs, but significantly fewer years are typically available due to practical limitations. To address this issue, an update to the Sandia method was developed, referred to as the Argonne method, to create TMYs from a limited number of years. Furthermore, this method enhances candidate diversity by systematically shifting original candidate months forward or backward by specific days, creating an expanded pool of candidates. The effectiveness of the Argonne method was validated through statistical testing, comparison of monthly average weather parameters, and numerical simulations. The results demonstrate a high probability of identifying at least one shifted month whose cumulative distribution functions of weather parameters closely align with long-term distributions. In 67 % of all comparisons, the monthly average weather parameters in TMYs generated using the Argonne method exhibit better agreement with long-term averages than TMY3. Moreover, in 74 % of the 318 building simulation cases, the Argonne method outperforms TMY3 in estimating long-term average building heating and cooling demands. Therefore, the Argonne method effectively diversifies the candidate pool and produces typical years that provide more accurate estimations of long-term averages compared to TMY3 when only a limited pool of calendar years (10 years or fewer) is available.

Building energy modeling↗
DOE OSTI2015

Health and vitality assessment of two common pine species in the context of climate change in southern Europe

The Mediterranean Basin is expected to be more strongly affected by ongoing climate change than most other regions of the earth. The South-eastern France can be considered as case study for assessing global change impacts on forests. Based on non-parametric statistical tests, the climatic parameters (temperature, relative humidity, rainfall, global radiation) and forest-response indicators (crown defoliation, discoloration and visible foliar ozone injury) of two pine species (Pinus halepensis and Pinus cembra) were analyzed. In the last 20 years, the trend analyses reveal a clear hotter and drier climate along the coastline and slightly rainier inland. In the current climate change context, a reduction in ground-level ozone (O{sub 3}) was found at remote sites and the visible foliar O{sub 3} injury decreased while deterioration of the crown conditions was observed likely due to a drier and warmer climate. Clearly, if such climatic and ecological changes are now being detected when the climate, in South-eastern France, has warmed in the last 20 years (+0.46–1.08 °C), it can be expected that many more impacts on tree species will occur in response to predicted temperature changes by 2100 (+1.95–4.59 °C). Climate change is projected to reduce the benefits of O{sub 3} precursor emissions controls leading to a higher O{sub 3} uptake. However, the drier and warmer climate should induce a soil drought leading to a lower O{sub 3} uptake. These two effects, acting together in an opposite way, could mitigate the harmful impacts of O{sub 3} on forests. The development of coordinated emission abatement strategies is useful to reduce both climate change and O{sub 3} pollution. Climate change will create additional challenges for forest management with substantial socio-economic and biological diversity impacts. However, the development of future sustainable and adaptive forest management strategies has the potential to reduce the vulnerability of forest species to climate change. - Highlights: • We assess climate change impacts on forests: South-eastern France as case study in the last 20 years. • We detect and estimate trends for O{sub 3} concentrations, climatic parameters and visible injury. • We establish a state-of-the-art of the health of 2 common pine species in a context of climate change. • We use two valuable bio-indicator species for O{sub 3} stress: Pinus halepensis and Pinus cembra. • Deterioration of crown conditions: climate change creates additional challenges for forest.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

The composition of gases from a diffusion flame above longleaf pine needle fuel beds

The gas and tar composition of a diffusion flame from longleaf pine needles is currently poorly understood and more data are needed to fill in the gap between pyrolysis data and smoke plume data, thus improving physical and chemical modeling of wildland smoke formation. A pilot experiment to measure light gas and tar composition of such a flame is described for three flame regions: persistent flame (flame base), intermittent flame, and smoke plume. Flame gases from 24 experimental fires were collected in canisters and analyzed using EPA method TO-14A for CO 2 , CO, H 2 , CH 4 , and C 2 to C 7 hydrocarbon gases. Condensed gas (tar) samples were collected and analyzed using GC/MS. Other light gases were measured using FTIR spectroscopy. Results from compositional data analysis suggest significant differences in (relative) concentration of compounds detected in the three regions of the flame. Statistical tests for differences in flame zones were performed using the canister data: Concentration of hydrocarbons relative to CO and CO 2 decreased from the persistent flame zone above the pyrolyzing needles through the intermittent flame region into the flame-free plume. This was likely due to both chemical reactions (oxidation) occurring in the flame as well as the introduction of air into the flame/plume by entrainment.

Biomass↗
DOE OSTI2012

Influence of Lymphatic Invasion on Locoregional Recurrence Following Mastectomy: Indication for Postmastectomy Radiotherapy for Breast Cancer Patients With One to Three Positive Nodes

Purpose: The indication for postmastectomy radiotherapy (PMRT) in breast cancer patients with one to three positive lymph nodes has been in discussion. The purpose of this study was to identify patient groups for whom PMRT may be indicated, focusing on varied locoregional recurrence rates depending on lymphatic invasion (ly) status. Methods and Materials: Retrospective analysis of 1,994 node-positive patients who had undergone mastectomy without postoperative radiotherapy between January 1990 and December 2000 at our hospital was performed. Patient groups for whom PMRT should be indicated were assessed using statistical tests based on the relationship between locoregional recurrence rate and ly status. Results: Multivariate analysis showed that the ly status affected the locoregional recurrence rate to as great a degree as the number of positive lymph nodes (p < 0.001). Especially for patients with one to three positive nodes, extensive ly was a more significant factor than stage T3 in the TNM staging system for locoregional recurrence (p < 0.001 vs. p = 0.295). Conclusion: Among postmastectomy patients with one to three positive lymph nodes, patients with extensive ly seem to require local therapy regimens similar to those used for patients with four or more positive nodes and also seem to require consideration of the use of PMRT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

A Prospective Study of {sup 18}FDG-PET With CT Coregistration for Radiation Treatment Planning of Lymphomas and Other Hematologic Malignancies

Purpose: This prospective single-institution study examined the impact of positron emission tomography (PET) with the use of 2-[{sup 18}F] fluoro-2-deoxyglucose and computed tomography (CT) scan radiation treatment planning (TP) on target volume definition in lymphoma. Methods and Materials: 118 patients underwent PET/CT TP during June 2007 to May 2009. Gross tumor volume (GTV) was contoured on CT-only and PET/CT studies by radiation oncologists (ROs) and nuclear medicine physicians (NMPs) for 95 patients with positive PET scans. Treatment plans and dose-volume histograms were generated for CT-only and PET/CT for 95 evaluable sites. Paired t test statistics and Pearson correlation coefficients were used for analysis. Results: 70 (74%) patients had non-Hodgkin lymphoma, 10 (11%) had Hodgkin lymphoma, 12 (10%) had plasma-cell neoplasm, and 3 (3%) had other hematologic malignancies. Forty-three (45%) presented with relapsed/refractory disease. Forty-five (47%) received no prior chemotherapy. The addition of PET increased GTV as defined by ROs in 38 patients (median, 27%; range, 5%-70%) and decreased GTV in 41 (median, 39.5%; range, 5%-80%). The addition of PET increased GTV as defined by NMPs in 27 patients (median, 26.5%; range, 5%-95%) and decreased GTV in 52 (median, 70%; range, 5%-99%). The intraobserver correlation between CT-GTV and PET-GTV was higher for ROs than for NMPs (0.94, P<.01 vs 0.89, P<.01). On the basis of Bland-Altman plots, the PET-GTVs defined by ROs were larger than those defined by NMPs. On evaluation of clinical TPs, only 4 (4%) patients had inadequate target coverage (D95 <95%) of the PET-GTV defined by NMPs. Conclusions: Significant differences between the RO and NMP volumes were identified when PET was coregistered to CT for radiation planning. Despite this, the PET-GTV defined by ROs and NMPs received acceptable prescription dose in nearly all patients. However, given the potential for a marginal miss, consultation with an experienced PET reader is highly encouraged when PET/CT volumes are delineated, particularly for questionable lesions and to assure complete and accurate target volume coverage.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Serum Transforming Growth Factor-β1 Change After Neoadjuvant Chemoradiation Therapy Is Associated With Postoperative Pulmonary Complications in Esophageal Cancer Patients Undergoing Combined Modality Therapy

Purpose: Our aim was to investigate the association of clinical factors, dosimetric parameters, and biomarkers with postoperative pulmonary complications (PPCs) in patients with locally advanced esophageal squamous cell carcinoma (ESCC) treated by neoadjuvant concurrent chemoradiation therapy (CCRT) under strict pulmonary dose constraints and esophagectomy. Methods and Materials: We prospectively enrolled 112 patients undergoing trimodality treatment (including radiation therapy [40 Gy], concurrent taxane-/5-fluorouracil-based regimens, and radical esophagectomy) for ESCC. A PPC was defined as pneumonia or acute respiratory distress syndrome within 30 days after surgery. Serum samples were collected before and within 1 month after CCRT. The association of serum biomarkers with PPCs was detected by proximity ligation assay (PLA) and verified by enzyme-linked immunosorbent assay. Associations of clinical factors, lung dosimetric parameters, and biomarkers with PPC were tested statistically. Results: Thirty-three patients (29.5%) had PPCs. None of the dosimetric parameters was associated with PPCs. Preoperative functional vital capacity (FVC) was significantly associated with PPCs (P=.004). Of the 15 PLA-screened biomarkers, posttreatment transforming growth factor-β1 (TGF-β1) was borderline significantly associated with PPCs (P=.087). Patients with PPCs had significantly larger pre-CCRT to post-CCRT decrease in serum TGF-β1 concentration (−11,310 vs −5332 pg/mL, P=.005) and higher pre-CCRT to post-CCRT percent decline in serum TGF-β1 concentration (−37.4% vs −25.0%, P=.009) than patients without PPCs. On multivariate analysis, preoperative FVC (P=.003) and decrease in TGF-β1 >7040 pg/mL (P=.014) were independent factors associated with PPCs. Conclusions: Preoperative FVC and decrease in serum TGF-β1 level after dose-limited CCRT to the lung are associated with the development of PPCs.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

On the transferability of residence time distributions in two 10-km long river sections with similar hydromorphic units

Quantifying hydrologic exchange fluxes (HEFs) at the stream-groundwater interface and their residence time distributions (RTDs) in the subsurface are important for managing the water quality and ecosystem health in dynamic river corridors. However, direct simulating high-spatial resolution HEFs and RTDs can be time-consuming, especially for watershed-scale modeling. Efficient surrogate models linking RTDs to hydromorphic units (HUs) can be alternatives for simulating RTDs in large-scale models. A common concern of these surrogate models, though, is the transferability of the relationship between the RTDs and HUs from one river corridor to another. To address this issue, this work evaluates the HEFs and resulting RTD-HU relationships for two 10-km long river corridors along the Columbia River leveraging a one-way coupled three-dimensional transient surface-subsurface water transport modeling framework we previously developed. Applying such a framework at the two river corridors with similar HUs allows for quantitative comparisons of HEFs and RTDs using both statistical tests and machine learning classification models. Finally, our comparison shows that the similarity and transferability of the RTD-HU relationship is very low for the two investigated river sections, which suggests that devising a general algorithm to estimate RTDs based solely on surface water hydrodynamics and short-distance river channel topography data, as well as HU classification, might be nearly impossible.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Irradiation creep measurement and microstructural analysis of chromium nitride–coated zirconium alloy using pressurized tubes

Environmental barrier coatings for Zr-based materials are currently under development to reduce oxidation and embrittlement in light-water reactors. Chromium nitride is one such candidate for this application, particularly as accident-tolerant fuel cladding. However, quantifying the impact of coatings on the irradiation-induced creep of zircaloy (Zry) is critical as this mechanism often exceeds thermal creep rates under light-water reactor operating conditions and can be a limiting design characteristic. Additionally, examining irradiation effects in the microstructure at the coating interface is key to understanding the compatibility of the material system. Here, to accelerate the experimental measurement of irradiation creep and microstructure evolution in CrN-Zry, compact, pressurized creep tubes were fabricated and irradiated in the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. Miniature, thin-walled rodlets fabricated from annealed Zr-Sn barstock were coated with CrN using physical vapor deposition (PVD) to nominal thicknesses of 4 and 8 μm. Coated and uncoated rodlet specimens were internally pressurized and welded, generating nominal circumferential hoop stresses of 0, 90, or 180 MPa under 300°C irradiation conditions. Twelve specimens were measured diametrically prior to irradiation using a low-cost, automated, contactless laser profilometer developed for this work. Specimens were irradiated in sealed capsules for one 25-day HFIR cycle, accumulating approximately 1.8 $\times$ 10 21 n/cm 2 fast fluence (E n > 10 MeV). The irradiated samples were retrieved and remeasured using the same profilometry system in a shielded hot cell facility. Irradiation creep between specimens was compared using standard statistical tests and showed that both thicknesses of CrN coating had a negligible effect on the irradiation creep strain of the Zry material. Microstructure characterization of pre- and post-irradiated CrN-Zry specimens showed minimal changes due to irradiation but did show a substantial O-rich region at the Zry-CrN interface.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Shared micromobility as a first- and last-mile transit solution? Spatiotemporal insights from a novel dataset

The first- and last-mile (FM/LM) problem is a major deterrent to public transit use. With the rise of shared micromobility options such as shared e-scooters in recent years, there is a growing interest in understanding their potential to serve as a last-mile transit solution. However, empirical data regarding the integrated use of shared micromobility and public transit have been limited so far. As a result, much is unknown regarding the spatiotemporal patterns and characteristics of shared micromobility trips serving as an FM/LM connection to transit. Here, this paper addresses these knowledge gaps by leveraging a novel dataset (i.e., the Spin post-ride survey dataset) that records thousands of transit-connecting shared e-scooter trips in Washington DC. Specifically, we used the dataset to reveal the spatiotemporal patterns of transit-connecting shared e-scooter trips in Washington DC, resulting in some major policy insights regarding the integral use of shared e-scooters and public transit. We further leveraged the dataset to validate if and to what extent a commonly applied buffer-zone approach can infer FM/LM micromobility trips accurately. Statistical tests showed that the actual FM/LM Spin e-scooter trips differ from inferred FM/LM Spin e-scooter trips in both spatial and temporal dimensions. This indicates that the common practice of inferring FM/LM micromobility trips with a buffer-zone approach can lead to inaccurate estimates of transit-connecting micromobility trips.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2014

Dosimetric difference amongst 3 techniques: TomoTherapy, sliding-window intensity-modulated radiotherapy (IMRT), and RapidArc radiotherapy in the treatment of late-stage nasopharyngeal carcinoma (NPC)

To investigate the dosimetric difference amongst TomoTherapy, sliding-window intensity-modulated radiotherapy (IMRT), and RapidArc radiotherapy in the treatment of late-stage nasopharyngeal carcinoma (NPC). Ten patients with late-stage (Stage III or IV) NPC treated with TomoTherapy or IMRT were selected for the study. Treatment plans with these 3 techniques were devised according to departmental protocol. Dosimetric parameters for organ at risk and treatment targets were compared between TomoTherapy and IMRT, TomoTherapy and RapidArc, and IMRT and RapidArc. Comparison amongst the techniques was done by statistical tests on the dosimetric parameters, total monitor unit (MU), and expected delivery time. All 3 techniques achieved similar target dose coverage. TomoTherapy achieved significantly lower doses in lens and mandible amongst the techniques. It also achieved significantly better dose conformity to the treatment targets. RapidArc achieved significantly lower dose to the eye and normal tissue, lower total MU, and less delivery time. The dosimetric advantages of the 3 techniques were identified in the treatment of late-stage NPC. This may serve as a guideline for selection of the proper technique for different clinical cases.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Linear models to perform treaty verification tasks for enhanced information security

Linear mathematical models were applied to binary-discrimination tasks relevant to arms control verification measurements in which a host party wishes to convince a monitoring party that an item is or is not treaty accountable. These models process data in list-mode format and can compensate for the presence of variability in the source, such as uncertain object orientation and location. The Hotelling observer applies an optimal set of weights to binned detector data, yielding a test statistic that is thresholded to make a decision. The channelized Hotelling observer applies a channelizing matrix to the vectorized data, resulting in a lower dimensional vector available to the monitor to make decisions. We demonstrate how incorporating additional terms in this channelizing-matrix optimization offers benefits for treaty verification. We present two methods to increase shared information and trust between the host and monitor. The first method penalizes individual channel performance in order to maximize the information available to the monitor while maintaining optimal performance. Second, we present a method that penalizes predefined sensitive information while maintaining the capability to discriminate between binary choices. Data used in this study was generated using Monte Carlo simulations for fission neutrons, accomplished with the GEANT4 toolkit. Custom models for plutonium inspection objects were measured in simulation by a radiation imaging system. Model performance was evaluated and presented using the area under the receiver operating characteristic curve.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Identifying paleowater in California drinking water wells

Identification of paleowater in aquifers tapped for the public water supply is important both for sound water management, because paleowater is likely to be withdrawn unsustainably in high demand regions in the absence of large scale artificial recharge operations, and for contamination susceptibility assessment, because paleowater is typically isolated from contamination sources. In this study, paleowater, which herein includes pre-Holocene groundwater and also water that recharged well before the onset of significant human alteration of the hydrologic system in California, is identified using three key isotopic indicators of groundwater residence time: tritium ( 3 H), radiocarbon ( 14 C), and radiogenic helium-4 ( 4 He rad ). In this work, we compared results of these three tracers from a unique data set of more than 2000 wells that are predominantly long-screened drinking water production wells. Although considerable uncertainty is associated with calculated apparent ages for individual samples, non-parametric statistical tests indicate that the composite set of isotopic indicators support classification of samples into categories that allow identification of wells most likely to produce paleowater. Approximately 7% of the wells included in the study show strong evidence for producing paleowater, with screens extending greater than 146 m below ground surface, in which 3 H activity is less than 1 pCi/L, 14C activity is less than 40.9 pmC, and 4Herad concentration exceeds 7.4 × 10 –8 cm 3 STP/g water . An additional 22% of wells produce mixed-age water with a component of paleowater, with screens extending greater than 95 m below ground surface, in which 3 H is less than 5 pCi/L, and 14C activity is less than 95.91 pmC. Wells in desert basins of southeastern California and wells in the southwestern quadrant of the Central Valley are most likely to produce paleowater that is pre-Holocene in age. Very few wells in the northwestern portion of the state, the foothills and Sierra Nevada regions, and coastal basins with intensive artificial recharge activities are categorized as producing paleowater. Climate is the primary control on paleowater occurrence, with arid portions of the state that were wetter during the Pleistocene having the largest number of wells categorized as producing paleowater. Secondarily, paleowater is found at the end of very long flow paths in confined aquifers, e.g., in the center of the Northern Sacramento Valley. In contrast, paleowater may be masked in areas where unconfined or semi-confined conditions allow substantial mixing between modern recharge and paleowater. Modern, artificially recharged water has replaced very old groundwater on a large scale in urban coastal basins.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Detecting Thermally Induced Spinodal Decomposition with Picosecond Ultrasonics in Cast Austenitic Stainless Steels

Given the existential climate crisis faced by mankind and the world, the lifetime and sustainability of nuclear reactors as a carbon-free source of renewable energy depend on the susceptibility of their structural components to environmental degradation. In particular, critical components for light water reactors (LWRs) evolve over decades in service, losing ductility and toughness due to thermal and irradiation aging. Techniques to monitor their health cannot be easily applied in the field due to their destructive, expensive, or immobile nature. Thus, non-destructive evaluation (NDE) methods are sought to monitor and evaluate the health of major LWR components such as core barrels, steam generator tubes, or primary coolant pipes and are often required by policy, such as NRC policy #10-CFR-50.65. In this work we demonstrate the use of gigahertz, non-contact ultrasonics to gauge the state of cast austenitic stainless steels (CASS), used in some of the largest components in LWR primary systems. We do so by linking changes in their surface acoustic wave (SAW) characteristics using transient grating spectroscopy (TGS) to transmission electron microscopy (TEM)-verified evidence of spinodal decomposition and G-phase precipitation. In this thesis, thermal aging is shown to induce SAW peak splitting in spinodally decomposed CASS alloys, correlated strongly with lowered toughness and decreased ductility. Furthermore, statistical testing on the number of SAW peak splits observed show that the second SAW peak significantly appears more frequently and is significantly different in frequency in comparison to counts and frequencies measured in unaged specimens. The ability of this technique to non-destructively detect microstructural degradation at a distance in a predictive manner in the case of CASS motivates extending gigahertz ultrasonics to detect other LWR material degradation modes as an in-vessel inspection technique, such as reactor pressure vessel (RPV) embrittlement. This allows for the greater use of NDE techniques for confident monitoring of LWR structural material health to 80 years and beyond, saving costs by minimizing structural replacements until needed and maximizing energy production by preventing early decommission until necessary.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Rechargeable Zinc Alkaline Anodes for Long-Cycle Energy Storage

Zinc alkaline anodes command significant share of consumer battery markets and are a key technology for the emerging grid-scale battery market. Improved understanding of this electrode is required for long-cycle deployments at kWh and MWh scale due to strict requirements on performance, cost, and safety. For this article, we give a modern literature survey of zinc alkaline anodes with levelized performance metrics and also present an experimental assessment of leading formulations. Long-cycle materials characterization, performance metrics, and failure analysis are reported for over 25 unique anode formulations with up to 1500 cycles and ~1.5 years of shelf life per test. Statistical repeatability of these measurements is made for a baseline design (fewest additives) via 15 duplicates. Baseline design capacity density is 38 mAh per mL of anode volume, and lifetime throughput is 72 Ah per mL of anode volume. We then report identical measurements for anodes with improved material properties via additives and other perturbations, some of which achieve capacity density over 192 mAh per mL of anode volume and lifetime throughput of 190 Ah per mL of anode volume. Novel in operando X-ray microscopy of a cycling zinc paste anode reveals the formation of a nanoscale zinc material that cycles electrochemically and replaces the original anode structure over long-cycle life. Ex situ elemental mapping and other materials characterization suggest that the key physical processes are hydrogen evolution reaction (HER), growth of zinc oxide nanoscale material, concentration deficits of OH – and ZnOH 4 2– , and electrodeposition of Zn growths outside and through separator membranes.

25 ENERGY STORAGE↗
DOE OSTI2021

Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss

Proteinaceous aggregates containing ?-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson’s disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights on proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss and controls with no neuronal loss. Using label-free LC-MS/MS approach we quantified the 2,963 most abundant proteins. Statistical testing for differential protein abundance, followed by pathway enrichment and Bayesian learning of the causal network structure were performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of the neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g. TDP-43 and FUS) have strong inverse correlation with Lewy bodies and may reflect alternative mechanism of nigral neurodegeneration.

Petyuk, Vladislav A.↗
DOE OSTI2018

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards

Selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), is a data acquisition technique used in targeted analysis of molecules, including targeted proteomic studies. It exploits the unique capability of triple-quadrupole (QQQ) mass spectrometers to monitor the predefined precursor and fragment ion pairs of specific molecules of interest throughout a liquid chromatography (LC) elution profile. Compared to shotgun proteomics, targeted proteomics using SRM has high selectivity, high sensitivity, and a wide linear dynamic range,(1-3) which makes it especially useful in the accurate and reproducible quantification of low-abundance proteins in highly complex biological samples. SRM has been widely used in the fields of biomarker discovery,(4-7) analysis of protein post-translational modifications(8) and characterization of biological protein networks.(4,9) In the recent years, multiple technical advances have greatly improved the throughput of SRM analyses, allowing for the quantification of hundreds of peptides in a single analysis.(6,7,10) For example, a single 800-plex SRM assay (e.g., 400 unlabeled and heavy-labeled peptide pairs and 2400 transitions with retention time scheduling) using ultrahigh-performance liquid chromatography (UHPLC) has been developed to quantify proteins in plasma.(11) Advanced labeling techniques utilizing in vitro proteome-assisted MRM for protein absolute quantification (iMPAQT) demonstrated the capability of SRM in genome-wide protein quantification of over 18?000 human proteins.(12) Moreover, the scan speed of QQQ instrumentation has been greatly improved in recent releases of commercial instrumentation. The newly developed TSQ Altis (released in 2017) can scan more than 600 transitions per second, which is 6 times more than a traditional QQQ scan speed of 100 transitions per second. The breadth of measurement enabled by these technological improvements to QQQ mass spectrometry has increased the feasibility and popularity of large scale targeted proteomics studies,(13) a major application of which will be in clinical studies in which up to hundreds of protein candidates need to be quantified in hundreds of clinical specimens.(14) Quantitative accuracy is a primary motivating factor for utilizing a targeted proteomics protocol. The precise and reproducible absolute quantification produced by SRM assays is essential to many clinical and laboratory experiments.(15,16) Because the abundance of an endogenous peptide is calculated from the measurement of the spiked-in reference standard, it is essential to assess the data quality of these references.(17) In early applications of targeted proteomics, when instrument speed greatly limited the number of transitions that could be monitored, much of this quality assessment was done manually. However, recent improvements in instrument performance and experimental design have enabled a dramatic increase in the number of target peptides and associated SRM transitions, which makes manual quality assessment an untenable and laborious task. A variety of computational tools assist in SRM experiment design and data analysis. The first task in creating an SRM experiment is the choice of proteins and representative peptides to monitor. Achieving a reliable protein abundance requires appropriately choosing peptides that have a strong signal and are free from interferences in the biological matrix. Numerous computational tools exist to facilitate assay design by identifying peptides and refining SRM transitions.(18-21) To help share these assays and eliminate time spent designing the same transitions at multiple institutions, community portals have begun to host well-designed and vetted assays.(22-24) Analyzing the experimental data requires significant computational effort to align files across replicates and experimental conditions, pick peaks and produce quantitative values, normalize data and perform statistical tests, etc.(25-27)

Gibbons, Bryson C.↗
DOE OSTI2012

Sensitivity of Surface Flux Simulations to Hydrologic Parameters Based on an Uncertainty Quantification Framework Applied to the Community Land Model

Uncertainties in hydrologic parameters could have significant impacts on the simulated water and energy fluxes and land surface states, which will in turn affect atmospheric processes and the carbon cycle. Quantifying such uncertainties is an important step toward better understanding and quantification of uncertainty of integrated earth system models. In this paper, we introduce an uncertainty quantification (UQ) framework to analyze sensitivity of simulated surface fluxes to selected hydrologic parameters in the Community Land Model (CLM4) through forward modeling. Thirteen flux tower footprints spanning a wide range of climate and site conditions were selected to perform sensitivity analyses by perturbing the parameters identified. In the UQ framework, prior information about the parameters was used to quantify the input uncertainty using the Minimum-Relative-Entropy approach. The quasi-Monte Carlo approach was applied to generate samples of parameters on the basis of the prior pdfs. Simulations corresponding to sampled parameter sets were used to generate response curves and response surfaces and statistical tests were used to rank the significance of the parameters for output responses including latent (LH) and sensible heat (SH) fluxes. Overall, the CLM4 simulated LH and SH show the largest sensitivity to subsurface runoff generation parameters. However, study sites with deep root vegetation are also affected by surface runoff parameters, while sites with shallow root zones are also sensitive to the vadose zone soil water parameters. Generally, sites with finer soil texture and shallower rooting systems tend to have larger sensitivity of outputs to the parameters. Our results suggest the necessity of and possible ways for parameter inversion/calibration using available measurements of latent/sensible heat fluxes to obtain the optimal parameter set for CLM4. This study also provided guidance on reduction of parameter set dimensionality and parameter calibration framework design for CLM4 and other land surface models under different hydrologic and climatic regimes.

54 ENVIRONMENTAL SCIENCES↗