Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “NORMAL”

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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Quota management in dCache or making a perfectly normal file system normal

dCache (https://dcache.org) is a highly scalable storage system providing location-independent access to data. The data are stored across multiple data servers as complete files presented to the end-user via a single-rooted namespace. From its inception, dCache has been designed as a caching disk buffer to a tertiary tape storage system with the assumption that the latter has virtually unlimited capacity. dCache can also be configured as a disk-only storage system with no tape backend. Owing to the idea that a tape resource is infinite, or purely physically limited by budget considerations, the system has never provided for any restrictions on how much data can be stored on tape. Likewise, in the disk-only configuration, the capacity of the system is only limited by the aggregate disk capacity of the data servers. In a multi-user environment, however, this has become problematic. This presentation will describe the design and implementation of a user- and group-based quota system, that allows to manage tape and disk space allocations, as part of dCache namespace.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) peak intensity normalization for complex mixture analyses

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a preferred technique for analyzing complex organic mixtures. Currently, there is no consensus normalization approach, nor an objective method for selecting one, for quantitative analyses of FT-ICR-MS data. We investigate a method to evaluate and score the amount of bias various normalization approaches introduce into the data. We evaluate the ability of the Statistical Procedure for the Analysis of Normalization Strategies (SPANS) to guide selection of appropriate normalization approaches for two different FT-ICR-MS datasets. Further, we test the robustness of SPANS results to changes in SPANS parameter values and assess the impact of using various normalization approaches on downstream statistical analyses. The normalization approach identified by SPANS differed for the two datasets. Normalization methods impacted the statistical significance of peaks differently, underscoring the importance of carefully evaluating potential methods. More consistent SPANS scores resulted when at least 120 significant peaks are used, where larger sets of peaks were obtained by increasing the p-value threshold. Interestingly, we show that Total Sum Scaling and highest peak normalization, used in previous studies, underperformed relative to SPANS-recommended normalization approaches. While there is no single, best normalization method for all datasets, SPANS provides a mechanism to identify an appropriate normalization method for analyzing FT-ICR-MS data quantitatively. As a result, the number of peaks used in the background distributions of SPANS contributes more significantly to the reproducibility of results than the p-value thresholds used to obtain those peaks.

47 OTHER INSTRUMENTATION↗
DOE OSTI2016

SU-F-R-31: Identification of Robust Normal Lung CT Texture Features for the Prediction of Radiation-Induced Lung Disease

Purpose: Normal lung CT texture features have been used for the prediction of radiation-induced lung disease (radiation pneumonitis and radiation fibrosis). For these features to be clinically useful, they need to be relatively invariant (robust) to tumor size and not correlated with normal lung volume. Methods: The free-breathing CTs of 14 lung SBRT patients were studied. Different sizes of GTVs were simulated with spheres placed at the upper lobe and lower lobe respectively in the normal lung (contralateral to tumor). 27 texture features (9 from intensity histogram, 8 from grey-level co-occurrence matrix [GLCM] and 10 from grey-level run-length matrix [GLRM]) were extracted from [normal lung-GTV]. To measure the variability of a feature F, the relative difference D=|Fref -Fsim|/Fref*100% was calculated, where Fref was for the entire normal lung and Fsim was for [normal lung-GTV]. A feature was considered as robust if the largest non-outlier (Q3+1.5*IQR) D was less than 5%, and considered as not correlated with normal lung volume when their Pearson correlation was lower than 0.50. Results: Only 11 features were robust. All first-order intensity-histogram features (mean, max, etc.) were robust, while most higher-order features (skewness, kurtosis, etc.) were unrobust. Only two of the GLCM and four of the GLRM features were robust. Larger GTV resulted greater feature variation, this was particularly true for unrobust features. All robust features were not correlated with normal lung volume while three unrobust features showed high correlation. Excessive variations were observed in two low grey-level run features and were later identified to be from one patient with local lung diseases (atelectasis) in the normal lung. There was no dependence on GTV location. Conclusion: We identified 11 robust normal lung CT texture features that can be further examined for the prediction of radiation-induced lung disease. Interestingly, low grey-level run features identified normal lung diseases. This work was supported in part by the National Cancer Institute Grants R01CA172638.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Evaluation of normalization strategies for mass spectrometry-based multi-omics datasets

Introduction Data normalization is crucial for multi-omics integration, reducing systematic errors and maximizing the likelihood of discovering true biological variation. Most studies assess normalization for a single omics type or use datasets from separate experiments. Few address time-course data, where normalization might bias temporal differentiation. In this study, we compared common normalization methods and a machine learning approach, Systematical Error Removal using Random Forest (SERRF), using multi-omics datasets generated from the same experiment—even from the same cell lysate. Objectives To develop a straightforward process to assess normalization effects and identify the most robust methods across multi-omics datasets. Methods We analyzed metabolomics, lipidomics, and proteomics datasets from primary human cardiomyocytes and motor neurons exposed to acetylcholine-active compounds over time. Normalization effectiveness was evaluated based on improvement in QC features consistency and observing the change in treatment and time-related variance. Results Probabilistic Quotient Normalization (PQN) and Locally Estimated Scatterplot Smoothing (LOESS) QC were identified as optimal for metabolomics and lipidomics, while PQN, Median, and LOESS normalization excelled for proteomics. These methods consistently enhanced QC feature consistency in metabolomics and lipidomics, and preserved time-related variance or treatment-related variance in proteomics, demonstrating their effectiveness and robustness. SERRF normalization, applied only to metabolomics in this study, outperformed other methods in some datasets but inadvertently masked treatment-related variance in others. Conclusion Our evaluation identified PQN and LoessQC as the top methods for metabolomics and lipidomics, and PQN, Median, and Loess normalization for proteomics, in multi-omics integration in a temporal study.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Conditionally reprogrammed human normal bronchial epithelial cells express comparable levels of cytochromes p450 and are sensitive to BaP induction

Highlights: • Conditionally reprogrammed human normal bronchial epithelial cells can be propagated for a long term in vitro. • Conditionally reprogrammed human normal bronchial epithelial cells maintain normal karyotype and differentiation potential. • Conditionally reprogrammed human normal bronchial epithelial cells express comparable levels of Cytochromes p450 enzymes. • Conditionally reprogrammed human normal bronchial epithelial cells are sensitive to BaP induction. Cytochromes p450 (CYPs) metabolize thousands of endogenous and exogenous chemicals, including toxic compounds and drugs. The primary cells have relative short life span and are not able to sustain levels of metabolic enzymes CYPs expression and activity long enough in vitro. The immortalized cell lines are also not ideal for toxicity testing because of their low levels of CYPs expression. In this study, we established human normal bronchial epithelial cells using conditional reprogramming (CR) technique from three human donors (named as CR-HNBE1-3). These CR cells can proliferate continuously in defined culture system over 50 PDs within 2 months. The CR-HNBE cells exhibited the normal diploid karyotype, normal response to DNA damage and normal differentiation potential under the matrigel 3D culture condition. The CR-HNBE cells express the basal epithelial marker cytokeratin 14 (CK14) and epithelial secretory marker Mucin 5AC. Most importantly, CR-HNBE cells express comparable levels of CYP1B1 and CYP2E1 as those in lung tissue. These CR cells also express comparable mRNA of CYP1A1/CYP1A2, CYP2B6/CYP2C9/CYP2D6 and CYP3A4/CYP3A5 compared to the lung tissue. The basal activity of CYP1A1/CYP1B1 in these CR cells was 3–6 folds higher than that of 16HBE cells (an immortalized cell line widely used in toxicology field). Our data also demonstrated that Benzo(a)pyrene (BaP) induced up to 100 folds of mRNA expression of CYP1A1 or CYP1A2 in CR-HNBE cells. The activity of CYP1A1/CYP1B1 was induced by BaP up to 7–8 folds in CR-HNBE cells, while the activity of CYP1A1/CYP1B1 was induced maximum 2.5 folds in 16HBE cells. Taken together, CR-HNBE cells express comparable levels of CYPs and are sensitive to BaP induction, and will serve a sensitive, physiological and valuable in vitro toxicity testing model. This is the first report that normal human airway cells can be propagated for a long time and maintain comparable levels of CYPs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Notes on power of normality tests of error terms in regression models

Normality is one of the basic assumptions in applying statistical procedures. For example in linear regression most of the inferential procedures are based on the assumption of normality, i.e. the disturbance vector is assumed to be normally distributed. Failure to assess non-normality of the error terms may lead to incorrect results of usual statistical inference techniques such as t-test or F-test. Thus, error terms should be normally distributed in order to allow us to make exact inferences. As a consequence, normally distributed stochastic errors are necessary in order to make a not misleading inferences which explains a necessity and importance of robust tests of normality. Therefore, the aim of this contribution is to discuss normality testing of error terms in regression models. In this contribution, we introduce the general RT class of robust tests for normality, and present and discuss the trade-off between power and robustness of selected classical and robust normality tests of error terms in regression models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

SU-E-T-168: Evaluation of Normal Tissue Damage in Head and Neck Cancer Treatments

Purpose: To evaluate normal tissue toxicity in patients with head and neck cancer by calculating average survival fraction (SF) and equivalent uniform dose (EUD) for normal tissue cells. Methods: 20 patients with head and neck cancer were included in this study. IMRT plans were generated using EclipseTM treatment planning system by dosimetrist following clinical radiotherapy treatment guidelines. The average SF for three different normal tissue cells of each concerned structure can be calculated from dose spectrum acquired from differential dose volume histogram (DVH) using linear quadratic model. The three types of normal tissues include radiosensitive, moderately radiosensitive and radio-resistant that represents 70%, 50% and 30% survival fractions, respectively, for a 2-Gy open field. Finally, EUDs for three types of normal tissue of each structure were calculated from average SF. Results: The EUDs of the brainstem, spinal cord, parotid glands, brachial plexus and etc were calculated. Our analysis indicated that the brainstem can absorb as much as 14.3% of prescription dose to the tumor if the cell line is radiosensitive. In addition, as much as 16.1% and 18.3% of prescription dose were absorbed by the brainstem for moderately radiosensitive and radio-resistant cells, respectively. For the spinal cord, the EUDs reached up to 27.6%, 35.0% and 42.9% of prescribed dose for the three types of radiosensitivities respectively. Three types of normal cells for parotid glands can get up to 65.6%, 71.2% and 78.4% of prescription dose, respectively. The maximum EUDs of brachial plexsus were calculated as 75.4%, 76.4% and 76.7% of prescription for three types of normal cell lines. Conclusion: The results indicated that EUD can be used to quantify and evaluate the radiation damage to surrounding normal tissues. Large variation of normal tissue EUDs may come from variation of target volumes and radiation beam orientations among the patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

The impact of intensity-modulated radiation therapy plan normalization in the postprostatectomy setting—does it matter?

The International Commission on Radiation Units & Measurements -83 recommends prescribing intensity-modulated radiation therapy (IMRT) in a dose-volume manner. Despite this, clinical variation still exists in how prostate IMRT plans are prescribed. This study aims to investigate the impact of different plan normalization methods for postprostatectomy IMRT. IMRT treatment plans were created retrospectively for 20 postprostatectomy patients. These were normalized such that the dose received by 98% (D98) of the planning target volume (PTV) was equal to 100% of the prescribed dose. All plans were individually optimized to achieve target coverage and organ at risk (OAR) dose constraints. Each patient's plan was then copied and normalized such that the mean dose (Dmean) received by the PTV was equal to 100% of the prescribed dose. The International Commission on Radiation Units & Measurements -83 recommended dosimetric end points were extracted for targets and Quantitative Analyses of Normal Tissue Effects in the Clinic or Radiation Therapy Oncology Group 0534 end points extracted for OARs. Statistical analysis using the Wilcoxon signed-rank test to measure the difference between data from plans normalized to D98 and Dmean was conducted. Extracted dosimetric end points of the targets and OARs were significantly higher in plans normalized to D98 than Dmean (p Normalization impacts on dosimetric end points of a plan. Hence, reporting the normalization method used is necessary to allow for meaningful interpretation of IMRT dosimetric studies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Insights into acetone photochemistry on rutile TiO₂(110). 2. new photodesorption channel with CH₃ ejection along the surface normal

Angle-resolved photon stimulated desorption (PSD) combined with infrared reflection-adsorption spectroscopy and temperature programmed desorption reveal two distinct channels in the photochemistry of acetone on rutile TiO₂(110) surface. During UV irradiation of co-adsorbed oxygen and acetone molecules, methyl radicals (CH₃) are ejected in two different directions: i) normal to the surface and ii) off-normal at ~±66° to the surface normal in the azimuth (i.e. perpendicular to the rows of bridging oxygen and Ti atoms). Both components are relatively narrow and non-cosine, indicating non-thermal evolution of CH₃ radicals. The direction of the “off-normal” PSD component is consistent with orientation of the C–CH₃ bonds in the n²-acetone diolate—a photoactive form of acetone chemisorption on the oxidized TiO₂(110) surface proposed earlier from experimental and theoretical studies. The direction of the “normal” PSD component requires an orientation of a C–CH₃ bond which is not consistent with the n²-acetone diolate structure. The angular distribution of the CH₃ PSD depends on the acetone coverage. The “off-normal” PSD component dominates at lower acetone coverage (< 0.2 ML), but does not increase at higher coverages in accord with the acetone diolate peak intensity in the infrared reflection-absorption spectra. The “normal” PSD component grows with the acetone coverage up to 0.6 ML. The newly discovered “normal” PSD channel is tentatively assigned to a photo-produced n²- acetone enolate as a potential precursor based on the H/D exchange experiments

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Calculation of grain boundary normals directly from 3D microstructure images

The determination of grain boundary normals is an integral part of the characterization of grain boundaries in polycrystalline materials. These normal vectors are difficult to quantify due to the discretized nature of available microstructure characterization techniques. The most common method to determine grain boundary normals is by generating a surface mesh from an image of the microstructure, but this process can be slow, and is subject to smoothing issues. A new technique is proposed, utilizing first order Cartesian moments of binary indicator functions, to determine grain boundary normals directly from a voxelized microstructure image. In order to validate the accuracy of this technique, the surface normals obtained by the proposed method are compared to those generated by a surface meshing algorithm. Specifically, the local divergence between the surface normals obtained by different variants of the proposed technique and those generated from a surface mesh of a synthetic microstructure constructed using a marching cubes algorithm followed by Laplacian smoothing is quantified. Next, surface normals obtained with the proposed method from a measured 3D microstructure image of a Ni polycrystal are used to generate grain boundary character distributions (GBCD) for Σ3 and Σ9 boundaries, and compared to the GBCD generated using a surface mesh obtained from the same image. Finally, the results show that the proposed technique is an efficient and accurate method to determine voxelized fields of grain boundary normals.

36 MATERIALS SCIENCE↗