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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response of an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

From multivariate to functional data analysis: Fundamentals, recent developments, and emerging areas

Functional data analysis (FDA), which is a branch of statistics on modeling infinite dimensional random vectors resided in functional spaces, has become a major research area for Journal of Multivariate Analysis. We review some fundamental concepts of FDA, their origins and connections from multivariate analysis, and some of its recent developments, including multi-level functional data analysis, high-dimensional functional regression, and dependent functional data analysis. Here, we also discuss the impact of these new methodology developments on genetics, plant science, wearable device data analysis, image data analysis, and business analytics. Two real data examples are provided to motivate our discussions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Modern analogs for understanding pollen-vegetation dynamics in a Mediterranean mosaic landscape (Balearic Islands, Western Mediterranean)

This paper presents the study of modern pollen analogs from the Balearic Islands. While similar studies have been largely applied to mainland areas, research focused on modern vegetation dynamics on Mediterranean islands remains very rare. In this research, we combine vegetation surveys, pollen analysis and multivariate statistics to understand landscape composition. The main objectives of are: (1) to examine pollen-vegetation relationships in relation to environmental and land-use variables; (2) to understand modern pollen representation in a mosaic landscape structure; and (3) to propose pollen indicators that characterize the primary vegetation types from the Balearic Islands to better interpret past pollen records in Mediterranean island environments. Pollen results and Redundancy Analysis (RDA) distinguish three major groups: (a) Holm oak and box formations; (b) maquis and garrigues; and (c) anthropogenic and open habitats. Landscape form, mean decadal rainfall, mean decadal temperature, fire activity, trampling, slope percentage, wet/flooded soil, saline soil, distance to agropastoral cells, gHM index, domestic herbivory presence, agropastoral use, and soil type are the major variables explaining modern pollen assemblage variation in our research. Poaceae undiff., Plantago sp., Apiaceae undiff., Cerealia-t, and Cichorieae are highly correlated to human activities but should be interpreted cautiously when occurring in low values. Quercus ilex-t, Hypericum, and Buxus are correlated to humid locations while Pistacia, Pinus, Juniperus-t, and Olea to high mean decadal temperatures. Our study indicates how pollen analysis and multivariate analysis are powerful tools for characterizing the mosaic landscape, with special focus on the main vegetation types of the Balearic Islands.

Geology↗
DOE OSTI2012

Improved Outcomes of Breast-Conserving Therapy for Patients With Ductal Carcinoma in Situ

Purpose: Patients treated for ductal carcinoma in situ (DCIS) with breast-conserving surgery (BCS) and radiation therapy (RT) at our center from 1976 to 1990 had a 15% actuarial 10-year local recurrence (LR) rate. Since then, improved mammographic and pathologic evaluation and greater attention to achieving negative margins may have resulted in a lower risk of LR. In addition, clinical implications of hormone receptor and HER-2 status in DCIS remain unclear. We sought to determine the following: LR rates with this more modern approach; the relation between LR and HER-2 status; and clinical and pathologic factors associated with HER-2{sup +} DCIS. Methods and Materials: We studied 246 consecutive patients who underwent BCS and RT for DCIS from 2001 to 2007. Of the patients, 96 (39%) were Grade III and the median number of involved tissue blocks was 3. Half underwent re-excision and 222 (90%) had negative margins (>2 mm). All received whole-breast RT (40-52 Gy) and 99% (244) received a tumor bed boost (8-18 Gy). Routine estrogen receptor (ER), progesterone receptor (PR), and HER-2 immunohistochemistry was instituted in 2003. Results: With median follow-up of 58 months, there were no LRs. Seven patients (3%) developed contralateral breast cancer (4 invasive and 3 in situ). Among 163 patients with immunohistochemistry, 124 were ER/PR{sup +}HER-2{sup -}, 27 were ER/PR{sup +}HER-2{sup +}, 6 were ER{sup -}/PR{sup -}HER-2{sup +}, and 6 were ER{sup -}/PR{sup -}HER-2{sup -}. On univariable analysis, HER-2{sup +}was significantly associated with Grade III, ER{sup -}/PR{sup -}, central necrosis, comedo subtype, more extensive DCIS, and postmenopausal status. On multivariable analysis, Grade III and postmenopausal status remained significantly associated with HER-2{sup +}. Conclusions: In an era of mammographically identified DCIS, larger excisions, widely negative margins and the use of a tumor bed boost, we observed no LR regardless of ER/PR/HER-2 status. Factors associated with HER-2{sup +}DCIS included more extensive DCIS, Grade III, ER{sup -}/PR{sup -}, central necrosis, comedo subtype, and postmenopausal status. Further follow-up and additional studies are required to confirm these results.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Do Angiotensin-Converting Enzyme Inhibitors Reduce the Risk of Symptomatic Radiation Pneumonitis in Patients With Non-Small Cell Lung Cancer After Definitive Radiation Therapy? Analysis of a Single-Institution Database

Purpose: Preclinical studies have suggested that angiotensin-converting enzyme inhibitors (ACEIs) can mitigate radiation-induced lung injury. We sought here to investigate possible associations between ACEI use and the risk of symptomatic radiation pneumonitis (RP) among patients undergoing radiation therapy (RT) for non–small cell lung cancer (NSCLC). Methods and Materials: We retrospectively identified patients who received definitive radiation therapy for stages I to III NSCLC between 2004 and 2010 at a single tertiary cancer center. Patients must have received a radiation dose of at least 60 Gy for a single primary lung tumor and have had imaging and dosimetric data available for analysis. RP was quantified according to Common Terminology Criteria for Adverse Events, version 3.0. A Cox proportional hazard model was used to assess potential associations between ACEI use and risk of symptomatic RP. Results: Of 413 patients analyzed, 65 were using ACEIs during RT. In univariate analysis, the rate of RP grade ≥2 seemed lower in ACEI users than in nonusers (34% vs 46%), but this apparent difference was not statistically significant (P=.06). In multivariate analysis of all patients, ACEI use was not associated with the risk of symptomatic RP (hazard ratio [HR] = 0.66; P=.07) after adjustment for sex, smoking status, mean lung dose (MLD), and concurrent carboplatin and paclitaxel chemotherapy. Subgroup analysis showed that ACEI use did have a protective effect from RP grade ≥2 among patients who received a low (≤20-Gy) MLD (P<.01) or were male (P=.04). Conclusions: A trend toward reduction in symptomatic RP among patients taking ACEIs during RT for NSCLC was not statistically significant on univariate or multivariate analyses, although certain subgroups may benefit from use (ie, male patients and those receiving low MLD). The evidence at this point is insufficient to establish whether the use of ACEIs does or does not reduce the risk of RP.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Predicting Esophagitis After Chemoradiation Therapy for Non-Small Cell Lung Cancer: An Individual Patient Data Meta-Analysis

Purpose: Concurrent chemoradiation therapy (CCRT) improves survival compared with sequential treatment for locally advanced non-small cell lung cancer, but it increases toxicity, particularly radiation esophagitis (RE). Validated predictors of RE for clinical use are lacking. We performed an individual-patient-data meta-analysis to determine factors predictive of clinically significant RE. Methods and Materials: After a systematic review of the literature, data were obtained on 1082 patients who underwent CCRT, including patients from Europe, North America, Asia, and Australia. Patients were randomly divided into training and validation sets (2/3 vs 1/3 of patients). Factors predictive of RE (grade ≥2 and grade ≥3) were assessed using logistic modeling, with the concordance statistic (c statistic) used to evaluate the performance of each model. Results: The median radiation therapy dose delivered was 65 Gy, and the median follow-up time was 2.1 years. Most patients (91%) received platinum-containing CCRT regimens. The development of RE was common, scored as grade 2 in 348 patients (32.2%), grade 3 in 185 (17.1%), and grade 4 in 10 (0.9%). There were no RE-related deaths. On univariable analysis using the training set, several baseline factors were statistically predictive of RE (P<.05), but only dosimetric factors had good discrimination scores (c > .60). On multivariable analysis, the esophageal volume receiving ≥60 Gy (V60) alone emerged as the best predictor of grade ≥2 and grade ≥3 RE, with good calibration and discrimination. Recursive partitioning identified 3 risk groups: low (V60 <0.07%), intermediate (V60 0.07% to 16.99%), and high (V60 ≥17%). With use of the validation set, the predictive model performed inferiorly for the grade ≥2 endpoint (c = .58) but performed well for the grade ≥3 endpoint (c = .66). Conclusions: Clinically significant RE is common, but life-threatening complications occur in <1% of patients. Although several factors are statistically predictive of RE, the V60 alone provides the best predictive ability. Efforts to reduce the V60 should be prioritized, with further research needed to identify and validate new predictive factors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Interactions between myocardial sympathetic denervation and left ventricular mechanical dyssynchrony: A CZT analysis

Background: A correlation between left ventricular (LV) dyssynchrony (LVD) and impaired myocardial sympathetic tone has been hypothesized. We sought to assess the interactions between regional LV sympathetic innervation, perfusion, and mechanical dyssynchrony. Methods: Eighty-three patients underwent evaluation of LV perfusion and sympathetic innervation on {sup 99m}Tc-tetrofosmin/{sup 123}I-metaiodobenzylguanidine ({sup 123}I-MIBG) imaging. The summed rest score and summed {sup 123}I-MIBG score (SS-MIBG) were computed. The extent of “innervation/perfusion” mismatch was defined as the number of denervated LV segments with relatively preserved perfusion. LVD was evaluated on phase analysis and the wall with latest mechanical activation identified. Results: LVD was revealed in 36 (43%) patients. Patients with LVD had more abnormal values of SRS (21 ± 9 vs 10 ± 8, P < 0.001) and SS-MIBG (29 ± 9 vs 17 ± 11, P < 0.001) than those without LVD. The presence of LVD also clustered with a higher burden of “innervation/perfusion” mismatch (P = 0.019). On per-wall analysis, LV walls with delayed mechanical activation showed a higher burden of “innervation/perfusion” mismatch (2.3 ± 1.4 segments) than normally contracting walls (1.3 ± 1.2 segments; P < 0.001). On multivariate analysis, the extent of “innervation/perfusion” mismatch was the only predictor of delayed mechanical activation (P = 0.029). Conclusions: Patients with LVD show an elevated burden of “innervation/perfusion” mismatch that is concentrated at the level of the most dyssynchronous walls.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Volume-Based Parameters of {sup 18}F-Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography Improve Disease Recurrence Prediction in Postmastectomy Breast Cancer Patients With 1 to 3 Positive Axillary Lymph Nodes

Purpose: To determine whether volume-based parameters on pretreatment {sup 18}F-fluorodeoxyglucose positron emission tomography/computed tomography in breast cancer patients treated with mastectomy without adjuvant radiation therapy are predictive of recurrence. Methods and Materials: We retrospectively analyzed 93 patients with 1 to 3 positive axillary nodes after surgery, who were studied with {sup 18}F-fluorodeoxyglucose positron emission tomography/computed tomography for initial staging. We evaluated the relationship between positron emission tomography parameters, including the maximum standardized uptake value, metabolic tumor volume (MTV), and total lesion glycolysis (TLG), and clinical outcomes. Results: The median follow-up duration was 45 months. Recurrence was observed in 11 patients. Metabolic tumor volume and TLG were significantly related to tumor size, number of involved nodes, nodal ratio, nuclear grade, estrogen receptor (ER) status, and triple negativity (TN) (all P values were <.05). In receiver operating characteristic curve analysis, MTV and TLG showed better predictive performance than tumor size, ER status, or TN (area under the curve: 0.85, 0.86, 0.79, 0.74, and 0.74, respectively). On multivariate analysis, MTV was an independent prognostic factor of locoregional recurrence-free survival (hazard ratio 34.42, 95% confidence interval 3.94-882.71, P=.0008) and disease-free survival (DFS) (hazard ratio 13.92, 95% confidence interval 2.65-103.78, P=.0018). The 3-year DFS rate was 93.8% for the lower MTV group (<53.1; n=85) and 25.0% for the higher MTV group (≥53.1; n=8; P<.0001, log–rank test). The 3-year DFS rate for patients with both ER-positive status and MTV <53.1 was 98.2%; and for those with ER-negative status and MTV ≥53.1 it was 25.0% (P<.0001). Conclusions: Volume-based parameters improve recurrence prediction in postmastectomy breast cancer patients with 1 to 3 positive nodes. The addition of MTV to ER status or TN has potential benefits to identify a subgroup at higher risk for recurrence.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Choosing Wisely? Patterns and Correlates of the Use of Hypofractionated Whole-Breast Radiation Therapy in the State of Michigan

Purpose: Given evidence from randomized trials that have established the non-inferiority of more convenient and less costly courses of hypofractionated radiotherapy to the whole breast in selected breast cancer patients who receive lumpectomy, we sought to investigate the use of hypofractionated radiation therapy and factors associated with its use in a consortium of radiation oncology practices in Michigan. We sought to determine the extent to which variation in use occurs at the physician or practice level versus the extent to which use reflects individualization based on potentially relevant patient characteristics (such as habitus, age, chemotherapy receipt, or laterality). Methods and Materials: We evaluated associations between receipt of hypofractionated radiation therapy and various patient, provider, and practice characteristics in a multilevel model. Results: Of 1477 patients who received lumpectomy and whole-breast radiation therapy and were registered by the Michigan Radiation Oncology Quality Consortium (MROQC) from October 2011 to December 2013, 913 had T1-2, N0 breast cancer. Of these 913, 283 (31%) received hypofractionated radiation therapy. Among the 13 practices, hypofractionated radiation therapy use ranged from 2% to 80%. On multilevel analysis, 51% of the variation in the rate of hypofractionation was attributable to the practice level, 21% to the provider level, and 28% to the patient level. On multivariable analysis, hypofractionation was more likely in patients who were older (odds ratio [OR] 2.16 for age ≥50 years, P=.007), less likely in those with larger body habitus (OR 0.52 if separation between tangent entry and exit ≥25 cm, P=.002), and more likely without chemotherapy receipt (OR 3.82, P<.001). Hypofractionation use was not higher in the last 6 months analyzed: 79 of 252 (31%) from June 2013 to December 2013 and 204 of 661 (31%) from October 2011 to May 2013 (P=.9). Conclusions: Hypofractionated regimens of whole-breast radiation therapy have been variably administered in the adjuvant setting in Michigan after the publication of long-term trial results and consensus guidelines. Most of this variability is explained at the practice and provider level rather than by patient-level features, although care is being individualized to some degree.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Prognostic Significance of Tumor Response as Assessed by Sequential {sup 18}F-Fluorodeoxyglucose-Positron Emission Tomography/Computed Tomography During Concurrent Chemoradiation Therapy for Cervical Cancer

Purpose: To investigate the prognostic role of metabolic response by the use of serial sets of positron emission tomography/computed tomography (PET/CT) in patients with cervical cancer who were treated with concurrent chemoradiation therapy (CCRT). Methods and Materials: A total of 60 patients who were treated with CCRT between February 2009 and December 2010 were analyzed. Three sequential PET/CT images were acquired for each patient: pre-CCRT, during-CCRT at 4 weeks of CCRT, and 1 month post-CCRT PET/CT. Metabolic responses were assessed qualitatively. The percentage changes in the maximum values of standardized uptake value (ΔSUV{sub max}%) from the PET/CT images acquired pre-CCRT and during-CCRT were calculated. Receiver operating characteristic (ROC) curve analysis was performed to evaluate whether ΔSUV{sub max}% could predict complete response (CR) on the post-CCRT PET/CT and to identify the best cutoff value. Prognostic factors of progression-free survival (PFS) were analyzed. Results: During-CCRT PET/CT showed that 8 patients (13%) had CR, and the other 52 patients (87%) had partial response (PR). On the post-CCRT PET/CT, 43 patients (73%) had CR, 12 patients (20%) had PR, and 4 patients (7%) had progressive disease. The average SUV{sub max} in primary tumors was 16.3 (range, 6.4-53.0) on the pre-CCRT PET/CT images and 5.3 (range, 0-19.4) on the during-CCRT PET/CT images. According to ROC curve analysis, ΔSUV{sub max}% could predict CR response on post-CCRT PET/CT (P<.001, cutoff value of 59.7%). In all patients, the PFS rate was 71.9% at 2 years. Multivariate analysis showed that ΔSUV{sub max}% ≥60% (P=.045) and CR response on the post-CCRT PET/CT (P=.012) were statistically significant predictors of PFS. Conclusion: Metabolic responses on the during-CCRT images at 4 weeks of treatment and 1-month post-CCRT PET/CT images may predict treatment outcomes in patients with cervical cancer. ΔSUV{sub max}% ≥60% at 4 weeks of CCRT may predict CR response on 1-month post-CCRT PET/CT and also PFS.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2017

Correlating laser-induced breakdown spectroscopy with neutron activation analysis to determine the elemental concentration in the ionome of the Populus trichocarpa leaf

The black cottonwood poplar (Populus trichocarpa) leaf ionome (inorganic trace elements and mineral nutrients) is an important aspect for determining the physiological and developmental processes contributing to biomass production. A number of techniques are used to measure the ionome, yet characterizing the leaf spatial heterogeneity remains a challenge, especially in solid samples. Laser-induced breakdown spectroscopy (LIBS) has been used to determine the elemental composition of leaves and is able to raster across solid matrixes at 10 μm resolution. Here, we evaluate the use of LIBS for solid sample leaf elemental characterization in relation to neutron activation. In fact, neutron activation analysis is a laboratory-based technique which is used by the National Institute of Standards and Technology (NIST) to certify trace elements in candidate reference materials including plant leaf matrices. Introduction to the techniques used in this research has been presented in this manuscript. Neutron activation analysis (NAA) data has been correlated to the LIBS spectra to achieve quantification of the elements or ions present within poplar leaves. The regression coefficients of calibration and validation using multivariate analysis (MVA) methodology for six out of seven elements have been determined and vary between 0.810 and 0.998. LIBS and NAA data has been presented for the elements such as, calcium, magnesium, manganese, aluminum, copper, and potassium. Chlorine was also detected but it did not show good correlation between the LIBS and NAA techniques. This research shows that LIBS can be used as a fast, high-spatial resolution technique to quantify elements as part of large-scale field phenotyping projects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Prognostic Utility of Cell Cycle Progression Score in Men With Prostate Cancer After Primary External Beam Radiation Therapy

Purpose: To evaluate the prognostic utility of the cell cycle progression (CCP) score, a RNA signature based on the average expression level of 31 CCP genes, for predicting biochemical recurrence (BCR) in men with prostate cancer treated with external beam radiation therapy (EBRT) as their primary curative therapy. Methods and Materials: The CCP score was derived retrospectively from diagnostic biopsy specimens of men diagnosed with prostate cancer from 1991 to 2006 (n=141). All patients were treated with definitive EBRT; approximately half of the cohort was African American. Outcome was time from EBRT to BCR using the Phoenix definition. Median follow-up for patients without BCR was 4.8 years. Association with outcome was evaluated by Cox proportional hazards survival analysis and likelihood ratio tests. Results: Of 141 patients, 19 (13%) had BCR. The median CCP score for patient samples was 0.12. In univariable analysis, CCP score significantly predicted BCR (P=.0017). The hazard ratio for BCR was 2.55 for 1-unit increase in CCP score (equivalent to a doubling of gene expression). In a multivariable analysis that included Gleason score, prostate-specific antigen, percent positive cores, and androgen deprivation therapy, the hazard ratio for CCP changed only marginally and remained significant (P=.034), indicating that CCP provides prognostic information that is not provided by standard clinical parameters. With 10-year censoring, the CCP score was associated with prostate cancer-specific mortality (P=.013). There was no evidence for interaction between CCP and any clinical variable, including ethnicity. Conclusions: Among men treated with EBRT, the CCP score significantly predicted outcome and provided greater prognostic information than was available with clinical parameters. If validated in a larger cohort, CCP score could identify high-risk men undergoing EBRT who may need more aggressive therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

Search for non-resonant Higgs boson pair production in the $2b+2\ell +{E}_{\textrm{T}}^{\textrm{miss}}$ final state in pp collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

A search for non-resonant Higgs boson pair (HH) production is presented, in which one of the Higgs bosons decays to a b-quark pair ($b\bar{b}$) and the other decays to WW * , ZZ * , or τ + τ – , with in each case a final state with ℓ + ℓ – + neutrinos (ℓ = e, μ). The analysis targets separately the gluon-gluon fusion and vector boson fusion production modes. Data recorded by the ATLAS detector in proton-proton collisions at a centre-of-mass energy of 13 TeV at the Large Hadron Collider, corresponding to an integrated luminosity of 140 fb –1 , are used in this analysis. Events are selected to have exactly two b-tagged jets and two leptons with opposite electric charge and missing transverse momentum in the final state. These events are classified using multivariate analysis algorithms to separate the HH events from other Standard Model processes. No evidence of the signal is found. The observed (expected) upper limit on the cross-section for non-resonant Higgs boson pair production is determined to be 9.7 (16.2) times the Standard Model prediction at 95% confidence level. The Higgs boson self-interaction coupling parameter κ λ and the quadrilinear coupling parameter κ 2V are each separately constrained by this analysis to be within the ranges [–6.2, 13.3] and [–0.17, 2.4], respectively, at 95% confidence level, when all other parameters are fixed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2013

Biochemical Response to Androgen Deprivation Therapy Before External Beam Radiation Therapy Predicts Long-term Prostate Cancer Survival Outcomes

Purpose: To determine whether the response to neoadjuvant androgen deprivation therapy (ADT) defined by a decline in prostate-specific antigen (PSA) to nadir values is associated with improved survival outcomes after external beam radiation therapy (EBRT) for prostate cancer. Methods and Materials: One thousand forty-five patients with localized prostate cancer were treated with definitive EBRT in conjunction with neoadjuvant and concurrent ADT. A 6-month course of ADT was used (3 months during the neoadjuvant phase and 2 to 3 months concurrently with EBRT). The median EBRT prescription dose was 81 Gy using a conformal-based technique. The median follow-up time was 8.5 years. Results: The 10-year PSA relapse-free survival outcome among patients with pre-radiation therapy PSA nadirs of ≤0.3 ng/mL was 74.3%, compared with 57.7% for patients with higher PSA nadir values (P<.001). The 10-year distant metastases-free survival outcome among patients with pre-radiation therapy PSA nadirs of ≤0.3 ng/mL was 86.1%, compared with 78.6% for patients with higher PSA nadir values (P=.004). In a competing-risk analysis, prostate cancer-related deaths were also significantly reduced among patients with pre-radiation therapy PSA nadirs of <0.3 ng/mL compared with higher values (7.8% compared with 13.7%; P=.009). Multivariable analysis demonstrated that the pre-EBRT PSA nadir value was a significant predictor of long-term biochemical tumor control, distant metastases-free survival, and cause-specific survival outcomes. Conclusions: Pre-radiation therapy nadir PSA values of ≤0.3 ng/mL after neoadjuvant ADT were associated with improved long-term biochemical tumor control, reduction in distant metastases, and prostate cancer-related death. Patients with higher nadir values may require alternative adjuvant therapies to improve outcomes.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

MAVTgsa: An R Package for Gene Set (Enrichment) Analysis

Gene set analysis methods aim to determine whether an a priori defined set of genes shows statistically significant difference in expression on either categorical or continuous outcomes. Although many methods for gene set analysis have been proposed, a systematic analysis tool for identification of different types of gene set significance modules has not been developed previously. This work presents an R package, called MAVTgsa, which includes three different methods for integrated gene set enrichment analysis. (1) The one-sided OLS (ordinary least squares) test detects coordinated changes of genes in gene set in one direction, either up- or downregulation. (2) The two-sided MANOVA (multivariate analysis variance) detects changes both up- and downregulation for studying two or more experimental conditions. (3) A random forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes. MAVTgsa computes the P values and FDR (false discovery rate) q -value for all gene sets in the study. Furthermore, MAVTgsa provides several visualization outputs to support and interpret the enrichment results. This package is available online.

Chien, Chih-Yi↗
DOE OSTI2022

Prognostic importance of the preoperative New‐Naples prognostic score for patients with gastric cancer

Abstract Background The wide applicability of the Naples prognostic score (NPS) is still worthy of further study in gastric cancer (GC). This study aimed to construct a New‐NPS based on the differences in immunity and nutrition in patients with upper and lower gastrointestinal tumors to help obtain an individualized prediction of prognosis. Methods This study retrospectively analyzed patients who underwent radical gastrectomy from April 2014 to September 2016. The cutoff values of the preoperative neutrophil‐to‐lymphocyte ratio (NLR), lymphocyte‐to‐monocyte ratio (LMR), serum albumin (Alb), and total cholesterol (TC) were calculated by ROC curve analysis. ROC and t‐ROC were used to evaluate the accuracy of the prognostic markers. The Kaplan–Meier method and log‐rank test were used to analyze the overall survival probability. Univariate and multivariate analyses based on Cox risk regression were used to show the independent predictors. The nomogram was made by R studio. The predictive accuracy of nomogram was assessed using a calibration plot, concordance index (C‐index), and decision curve. Results A total of 737 patients were included in training cohort, 411 patients were included in validation cohort. ROC showed that the New‐NPS was more suitable for predicting the prognosis of GC patients. NPS = 2 indicated a poor prognosis. Multivariate analysis showed that CEA ( P = 0.026), Borrmann type ( P = 0.001), pTNM ( P < 0.001), New‐NPS ( P < 0.001), and nerve infiltration ( P = 0.035) were independent risk factors for prognosis. Conclusion The New‐NPS based on the cutoff values of NLR, LMR, Alb, and TC is not only suitable for predicting prognosis but can also be combined with clinicopathological characteristics to construct a nomogram model for GC patients.

Wang, Hao↗
DOE OSTI2018

Multivariate network traffic analysis using clustered patterns

Traffic analysis is a core element in network operations and management for various purposes including change detection, traffic prediction, and anomaly detection. In this paper, we introduce a new approach to online traffic analysis based on a pattern-based representation for high-level summarization of the traffic measurement data. Unlike the past online analysis techniques limited to a single variable to summarize (e.g., sketch), the focus of this study is on capturing the network state from the multivariate attributes under consideration. To this end, we employ clustering with its benefit of the aggregation of multidimensional variables. The clustered result represents the state of the network with regard to the monitored variables, which can also be compared with the observed patterns from previous time windows enabling intuitive analysis. Finally, we demonstrate the proposed method with two popular use cases, one for estimating state changes and the other for identifying anomalous states, to confirm its feasibility. Our extensive experimental results with public traces and collected monitoring measurements from ESnet traffic traces show that our pattern-based approach is effective for multivariate analysis of online network traffic with visual and quantitative tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Peeking Network States with Clustered Patterns

Network traffic monitoring has long been a core element for effec- tive network management and security. However, it is still a chal- lenging task with a high degree of complexity for comprehensive analysis when considering multiple variables and ever-increasing traffic volumes to monitor. For example, one of the widely con- sidered approaches is to scrutinize probabilistic distributions, but it poses a scalability concern and multivariate analysis is not gen- erally supported due to the exponential increase of the complexity. In this work, we propose a novel method for network traffic moni- toring based on clustering, one of the powerful deep-learning tech- niques. We show that the new approach enables us to recognize clustered results as patterns representing the network states, which can then be utilized to evaluate “similarity” of network states over time. In addition, we define a new quantitative measure for the similarity between two compared network states observed in dif- ferent time windows, as a supportive means for intuitive analysis. Finally, we demonstrate the clustering-based network monitoring with public traffic traces, and show that the proposed approach us- ing the clustering method has a great opportunity for feasible, cost- effective network monitoring.

97 MATHEMATICS AND COMPUTING↗