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At least 1,711 records · Page 95
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Profile of Twenty-Three Human Milk Oligosaccharides in Han Chinese Mothers throughout Postpartum 1 year

Human milk oligosaccharides (HMOs) are multifunctional carbohydrates in breast milk, which are composed by a variety of structures. This study aimed to identified HMOs concentration profile, milk microbiota composition, and the associations with major maternal characteristics in Han Chinese mothers in the one-year lactation period. Seventeen healthy mothers aged from 28 to 36 years, who gave birth to healthy term infants, were recruited. Carbohydrates were detected using the MIRIS human milk analyzer (HMA), and twenty-three HMOs were quantified using ultra-performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-MS). Results showed that carbohydrates were relatively stable, while total HMO concentrations ranged from 1.74 to 9.72 g/L and decreased gradually over lactation in breast milk. Based on the structure, seven sialylated HMOs concentration showed the significant decline ( p < 0.05 ) after three months in lactation. In addition, the relationships between maternal factors, containing the lactation period, genetic status, delivery mode, parity, and milk microbiota profile, and the HMO composition in healthy women, which still need further investigations, were observed.

Xun, Yiping↗
DOE OSTI2020

Columnar Vertical Profile (CVP) Methodology for Validating Polarimetric Radar Retrievals in Ice Using In Situ Aircraft Measurements

Abstract A novel way to process polarimetric radar data collected via plan position indicator (PPI) scans and display those data in a time–height format is introduced. The columnar vertical profile (CVP) methodology uses radar data collected via multiple elevation scans, limited to data within a set region in range and azimuth relative to the radar, to create vertical profiles of polarimetric radar data representative of that limited region in space. This technique is compared to others existing in the literature, and various applications are discussed. Polarimetric ice microphysical retrievals are performed on CVPs created within the stratiform rain region of two mesoscale convective systems sampled during two field campaigns, where CVPs follow the track of research aircraft. Aircraft in situ data are collocated to microphysical retrieval data, and the accuracy of these retrievals is tested against other retrieval techniques in the literature.

Engineering↗
DOE OSTI2014

A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

Background: Effective improvement in sorghum crop development necessitates a genomics-based approach to identify functional genes and QTLs. Sequenced in 2009, a comprehensive annotation of the sorghum genome and the development of functional genomics resources is key to enable the discovery and deployment of regulatory and metabolic genes and gene networks for crop improvement. Results: This study utilizes the first commercially available whole-transcriptome sorghum microarray (Sorgh-WTa520972F) to identify tissue and genotype-specific expression patterns for all identified Sorghum bicolor exons and UTRs. The genechip contains 1,026,373 probes covering 149,182 exons (27,577 genes) across the Sorghum bicolor nuclear, chloroplast, and mitochondrial genomes. Specific probesets were also included for putative non-coding RNAs that may play a role in gene regulation (e. g., microRNAs), and confirmed functional small RNAs in related species (maize and sugarcane) were also included in our array design. We generated expression data for 78 samples with a combination of four different tissue types (shoot, root, leaf and stem), two dissected stem tissues (pith and rind) and six diverse genotypes, which included 6 public sorghum lines (R159, Atlas, Fremont, PI152611, AR2400 and PI455230) representing grain, sweet, forage, and high biomass ideotypes. Conclusions: Here we present a summary of the microarray dataset, including analysis of tissue-specific gene expression profiles and associated expression profiles of relevant metabolic pathways. With an aim to enable identification and functional characterization of genes in sorghum, this expression atlas presents a new and valuable resource to the research community.

Shakoor, N↗
DOE OSTI2026

Transplatformer: translating toxicogenomic profiles between generations of platforms

Background Transcriptomic profiling technologies have advanced the analysis of biological and toxicological responses. However, substantial differences in probe design, dynamic range, gene coverage, and preprocessing pipelines across platforms introduce artifacts that limit cross-study integration and hinder the reuse of historical datasets. We aim to develop computational methods for accurate cross-platform translation to maximize the value of legacy resources. Results We present TransPlatformer a deep learning framework for translating gene expression profiles across heterogeneous toxicogenomics platforms. TransPlatformer employs a novel attention-based architecture to map high-dimensional fold-change vectors from legacy microarray technologies to current platforms. Models are trained and evaluated using DrugMatrix, spanning three technological generations. We investigate mixed-tissue, single-tissue, and cross-tissue training paradigms and benchmark performance against multilayer perceptron and matrix-completion baselines. In mixed-tissue training, TransPlatformer achieves a greater than 50% reduction in mean absolute error (0.043 vs. 0.09) and nearly doubles Pearson correlation ( ≈ 0.71 vs. 0.37) relative to baseline methods. Importantly, TransPlatformer preserves rare but biologically meaningful over- and under-expressed signals, with mean absolute error below 0.22. Single-tissue models yield further improvements for well-represented organs, such as a 10% reduction in liver mean absolute error, while underscoring the need for data augmentation strategies in low-sample tissues.ra Conclusions TransPlatformer provides an effective and scalable computational solution for cross-platform transcriptomic translation. By enabling biologically faithful harmonization of gene expression data, the proposed approach facilitates the reuse of legacy toxicogenomics datasets, enhances downstream biomarker discovery, and supports more reproducible predictive modeling in toxicology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Global transcriptome profile of the developmental principles of in vitro iPSC-to-motor neuron differentiation

Abstract Background Human induced pluripotent stem cells (iPSC) have opened new avenues for regenerative medicine. Consequently, iPSC-derived motor neurons have emerged as potentially viable therapies for spinal cord injuries and neurodegenerative disorders including Amyotrophic Lateral Sclerosis. However, direct clinical application of iPSC bears in itself the risk of tumorigenesis and other unforeseeable genetic or epigenetic abnormalities. Results Employing RNA-seq technology, we identified and characterized gene regulatory networks triggered by in vitro chemical reprogramming of iPSC into cells with the molecular features of motor neurons (MNs) whose function in vivo is to innervate effector organs. We present meta-transcriptome signatures of 5 cell types: iPSCs, neural stem cells, motor neuron progenitors, early motor neurons, and mature motor neurons. In strict response to the chemical stimuli, along the MN differentiation axis we observed temporal downregulation of tumor growth factor-β signaling pathway and consistent activation of sonic hedgehog, Wnt/β-catenin, and Notch signaling. Together with gene networks defining neuronal differentiation (neurogenin 2, microtubule-associated protein 2, Pax6, and neuropilin-1), we observed steady accumulation of motor neuron-specific regulatory genes, including Islet-1 and homeobox protein HB9. Interestingly, transcriptome profiling of the differentiation process showed that Ca 2+ signaling through cAMP and LPC was downregulated during the conversion of the iPSC to neural stem cells and key regulatory gene activity of the pathway remained inhibited until later stages of motor neuron formation. Pathways shaping the neuronal development and function were well-represented in the early motor neuron cells including, neuroactive ligand-receptor interactions, axon guidance, and the cholinergic synapse formation. A notable hallmark of our in vitro motor neuron maturation in monoculture was the activation of genes encoding G-coupled muscarinic acetylcholine receptors and downregulation of the ionotropic nicotinic acetylcholine receptors expression. We observed the formation of functional neuronal networks as spontaneous oscillations in the extracellular action potentials recorded on multi-electrode array chip after 20 days of differentiation. Conclusions Detailed transcriptome profile of each developmental step from iPSC to motor neuron driven by chemical induction provides the guidelines to novel therapeutic approaches in the re-construction efforts of muscle innervation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Linear sine wave profiling to machine instability targets

Specialized machining processes and programming have been developed to deliver thin tin and copper Richtmyer-Meshkov instability targets that have different amplitude perturbations across the face of one 4-in.-diameter target. Typical targets have anywhere from two to five different regions of sine waves that have different amplitudes varying from 4 to 200 μm across the face of the target. The puck is composed of multiple rings that are zero press fit together and diamond turned to create a flat platform with a tolerance of 2 μm for the shock experiment. A custom software program was written in Labview to write the point-to-point program for the diamond-turning profiler through the X-Y-Z movements to cut the pure planar straight sine wave geometry. As a result, the software is optimized to push the profile of the whole part into the face while eliminating any unneeded passes that do not cut any material.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Fabrication of engineered dopant profiles in Er/Lu:YAG transparent laser ceramics via additive manufacturing

Transparent ceramic Er:YAG laser rods were fabricated via the direct ink write (DIW) method with engineered doping profiles featuring an Er-doped core with endcaps and core-clad structures. Laser rods up to 11 cm in length were produced which required development of a scalable process. To achieve this, multiple improvements were implemented, including printing the rods horizontally on a substrate, rather than vertically, eliminating the need for an external support structure and using a sacrificial drying layer to mitigate warping and defects. Highly transparent rods were achieved with optical scatter levels as low as 0.5%/cm (at 543 nm). A small refractive index difference of 5.7 ppm was measured at the interface between the Er-doped core and the Lu-doped endcaps and cladding. These results demonstrate DIW as a straightforward method for making good optical quality laser rods with engineered doping profiles to improve laser performance.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Pollen Lipidomics: Lipid Profiling Exposes a Notable Diversity in 22 Allergenic Pollen and Potential Biomarkers of the Allergic Immune Response

Pollen grains are the male gametophytes that deliver sperm cells to female gametophytes during sexual reproduction of higher plants. Pollen is a major source of aeroallergens and environmental antigens. The pollen coat harbors a plethora of lipids that are required for pollen hydration, germination, and penetration of the stigma by pollen tubes. In addition to proteins, pollen displays a wide array of lipids that interact with the human immune system. Prior searches for pollen allergens have focused on the identification of intracellular allergenic proteins, but have largely overlooked much of the extracellular pollen matrix, a region where the majority of lipid molecules reside. Lipid antigens have attracted attention for their potent immunoregulatory effects. By being in close proximity to allergenic proteins on the pollen surface when they interact with host cells, lipids could modify the antigenic properties of proteins. We performed a comparative pollen lipid profiling of 22 commonly allergenic plant species by the use of gas chromatography-mass spectroscopy, followed by detailed data mining and statistical analysis. Three experiments compared pollen lipid profiles. We built a database library of the pollen lipids by matching acquired pollen-lipid mass spectra and retention times with the NIST/EPA/NIH mass-spectral library. We detected, identified, and relatively quantified more than 106 lipid molecular species including fatty acids, n-alkanes, fatty alcohols, and sterols. Pollen derived lipids stimulation up-regulate cytokines expression of dendritic and natural killer T cells co-culture. Here we report on a lipidomic analysis of pollen lipids that can serve as a database for identifying potential lipid antigens and/or novel candidate molecules involved in allergy. The database provides a resource that facilitates studies on the role of lipids in the immunopathogenesis of allergy. Pollen lipids vary greatly among allergenic species and contain many molecules that have stimulatory or regulatory effects on immune responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Fallon FORGE: Seismic Reflection Profiles

Newly reprocessed Naval Air Station Fallon (1994) seismic lines: pre-stack depth migrations, with interpretations to support the Fallon FORGE (Phase 2B) 3D Geologic model. Data along seven profiles (>100 km of total profile length) through and adjacent to the Fallon site were re-processed. The most up-to-date, industry-tested seismic processing techniques were utilized to improve the signal strength and coherency in the sedimentary, volcanic, and Mesozoic crystalline basement sections, in conjunction with fault diffractions in order to improve the identification and definition of faults within the study area.

15 GEOTHERMAL ENERGY↗
DOE OSTI2018

Marine Corps Base Camp Lejeune New River Estuary (NRE) - Autonomous Vertical Profiler (AVP) Stone's Bay Data 2008-2013

Critical military training and testing on lands along the nation’s coastal and estuarine shorelines are increasingly placed at risk because of encroachment pressures in surrounding areas, impairments due to other anthropogenic disturbances, and changes in climate and sea level. The U.S. Department of Defense (DoD) intends to enhance and sustain its training and testing assets and also optimize its stewardship of natural resources through the development and application of an ecosystem-based management approach on DoD installations. To accomplish this goal, particularly for installations in estuarine/coastal environments, the Strategic Environmental Research and Development Program (SERDP) launched the Defense Coastal/Estuarine Research Program (DCERP) as a 10-year effort at Marine Corps Base Camp Lejeune (MCBCL) in North Carolina. The results of the second 5 years of the program (DCERP2) are presented in the DCERP2 Final Report.There were four overarching objectives of DCERP2. The first objective was to understand the effects of climate change impacts, including warming temperatures, variability in the hydrological cycle, storm events, and sea level rise on the coastal ecosystems at MCBCL from observations and measurements made over the 10-year program. The second objective was to understand the carbon cycle of the coastal and terrestrial ecosystems at MCBCL through a highly integrated sampling program. The third objective was to develop models, tools, and indicators to evaluate current and projected future ecosystem state changes and translate scientific findings into actionable information for installation managers. The last objective was to recommend adaptive management strategies to sustain ecosystem natural resources within the context of an active military installation.This data package includes a zipfile containing the results of continuous (30 minute interval) water quality samples and wind speed and direction anemometer (MET) data from Stone's Bay at Station 3 (AVP1). Description from Monitoring Report: Autonomous vertical profilers (AVPs) were deployed from June 2008 through October 2016 in central Stones Bay at Station 3, and in Morgan Bay upstream of Station 5 and were used to continuously monitor key water quality parameters. The AVPs consist of a moored floating platform housing a computer controlled winch mechanism that lowers and raises a YSI Model 6600 multi-parameter water quality datasonde at programmable time intervals (Reynolds-Fleming et al., 2002). Winch speed and sampling frequency of the AVP system and datasonde were configured to produce full water column profiles of temperature, salinity, DO concentration, chl concentration (by fluorescence), and turbidity every 30 minutes and achieve vertical depth resolution of approximately 10 cm. An anemometer (RM Young) affixed to the mast of the AVP measured six minute averages of wind speed and direction every 30 minutes. Data were stored locally on the AVP computers, and telemetered back to the laboratory each night. Datasondes were exchanged with freshly cleaned and calibrated datasondes as necessary but at least on a monthly basis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Marine Corps Base Camp Lejeune New River Estuary (NRE) - Autonomous Vertical Profiler (AVP) Morgan Bay Data 2008-2016

Critical military training and testing on lands along the nation’s coastal and estuarine shorelines are increasingly placed at risk because of encroachment pressures in surrounding areas, impairments due to other anthropogenic disturbances, and changes in climate and sea level. The U.S. Department of Defense (DoD) intends to enhance and sustain its training and testing assets and also optimize its stewardship of natural resources through the development and application of an ecosystem-based management approach on DoD installations. To accomplish this goal, particularly for installations in estuarine/coastal environments, the Strategic Environmental Research and Development Program (SERDP) launched the Defense Coastal/Estuarine Research Program (DCERP) as a 10-year effort at Marine Corps Base Camp Lejeune (MCBCL) in North Carolina. The results of the second 5 years of the program (DCERP2) are presented in the DCERP2 Final Report.There were four overarching objectives of DCERP2. The first objective was to understand the effects of climate change impacts, including warming temperatures, variability in the hydrological cycle, storm events, and sea level rise on the coastal ecosystems at MCBCL from observations and measurements made over the 10-year program. The second objective was to understand the carbon cycle of the coastal and terrestrial ecosystems at MCBCL through a highly integrated sampling program. The third objective was to develop models, tools, and indicators to evaluate current and projected future ecosystem state changes and translate scientific findings into actionable information for installation managers. The last objective was to recommend adaptive management strategies to sustain ecosystem natural resources within the context of an active military installation.This data package includes a zipfile containing the results of continuous (30 minute interval) water quality samples and wind speed and direction anemometer (MET) data from Morgan Bay upstream of Station 5 (AVP2): Autonomous vertical profilers (AVPs) were deployed from June 2008 through October 2016 in central Stones Bay at Station 3, and in Morgan Bay upstream of Station 5 and were used to continuously monitor key water quality parameters. The AVPs consist of a moored floating platform housing a computer controlled winch mechanism that lowers and raises a YSI Model 6600 multi-parameter water quality datasonde at programmable time intervals (Reynolds-Fleming et al., 2002). Winch speed and sampling frequency of the AVP system and datasonde were configured to produce full water column profiles of temperature, salinity, DO concentration, chl concentration (by fluorescence), and turbidity every 30 minutes and achieve vertical depth resolution of approximately 10 cm. An anemometer (RM Young) affixed to the mast of the AVP measured six minute averages of wind speed and direction every 30 minutes. Data were stored locally on the AVP computers, and telemetered back to the laboratory each night. Datasondes were exchanged with freshly cleaned and calibrated datasondes as necessary but at least on a monthly basis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Root-soil depth profile in Luquillo Experimental Forest, Puerto Rico, February, 2019

With an objective of associating the distribution of roots in the soil profile with functional attributes related to phosphorus nutrition, 1-m cores were collected from sites in the Luquillo Experimental Forest, Puerto Rico, in February, 2019. The sampled sites were ridge and valley locations at El Verde and Icacos with soils that differ in parent material and phosphorus fertility. Depth profiles of soil physical characteristics (bulk density, moisture content, and particle size distribution), phosphorus content (total phosphorus, organic phosphorus, and resin or available phosphorus), soil and root-associated phosphatase activity, and fine-root traits (biomass, specific root length and area, and phosphorus content) were determined.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Image mapping for multiple charge state beams using a beam induced fluorescence profile monitors

Work continues on a minimally invasive, nitrogen fluorescence gas sheet at the Facility for Rare Isotope Beams (FRIB). A low density gas sheet may be used to observe the 2D transverse beam profile of high intensity, multiple charge state beams with minimal interference. Spatially and temporally correlated profiles are of particular interest in locations where there is significant charge state spread, such as the FRIB linac folding segments. A low-density gas sheet measurement system offers advantages for gas handling in nitrogen sensitive areas, however signal intensity is significantly lower than techniques using higher density gas sheets and jets. This work discusses measurement considerations for photon distributions generated by several spatially separated interaction points and design considerations for a high-sensitivity optics system for handling the expected low signal intensity.

Accelerator Physics↗
DOE OSTI2026

Design of a non-invasive laser-based beam profile monitor system for the new Fermilab PIP-II superconducting H- linac

As part of the new Proton Improvement Plan (PIP-II), Fermilab is undertaking the development of a new 800 MeV, 2 mA H- superconducting RF linac to replace its present normal conducting 400 MeV linac. The PIP-II linac consists of a series of superconducting RF cryomodules from 2.1 MeV to 800 MeV. To limit the potential damage to the superconducting RF cavities, PIP-II will utilize non-invasive laser-based monitors (laserwires) to obtain beam profiles via photoionization. This paper will present the design of this PIP-II laserwire system including the picosecond pulsed laser, optical transport line, 13 individual laserwire stations, laser feedback and timing controls. The paper also describes the signal detection system and operation of the profile measurements.

Scarpine, Victor [Fermilab]↗
DOE OSTI2018

Development of a Gas Sheet Beam Profile Monitor for IOTA

A nitrogen gas sheet will measure the two dimensional transverse profile of the 2.5 MeV proton beam in IOTA. The beam lifetime is limited by the interaction with the gas, thus a minimally invasive instrument is required. To produce a gas sheet with the desired density and thickness, various nozzle types are being investigated, including rectangular capillary tubes for gas injection and skimmers for final shaping of the gas. It is essential to meet vacuum requirements in the interaction chamber while maintaining the precise thickness and density of the gas, without significantly affecting the beam lifetime. The current design of a gas sheet beam profile monitor and present status will be discussed.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Skimmer-Nozzle Configuration Measurements for a Gas Sheet Beam Profile Monitor

Understanding the characteristics of the gas sheet being produced and optimal configuration of the gas injection system is essential to the the performance of a gas sheet beam profile monitor. A gas injection system test stand has been built at Fermilab to test various nozzle and slit configurations. The distance between the nozzle and slit can be changed to find an optimal configuration. Using a moveable cold cathode gauge the gas profile is measured.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Paleotopography controls weathering of Cambrian-age profiles beneath the Great Unconformity, St. Francois Mountains, SE Missouri, U.S.A.

ABSTRACT Precambrian (1.4 to 1.5 Ga) granite and rhyolite in the St. Francois Mountains at the northeast corner of the Ozark Plateau in Missouri has been altered down to a depth up to 8 meters below the Great Unconformity (the contact between Paleozoic sedimentary rock and underlying Precambrian). Petrographic, geochemical, and mineralogic data indicate that at least two events generated this alteration: 1) surficial weathering due to subaerial exposure of the granite before Cambrian burial—this material is preserved as a paleosol; and 2) alteration due to reaction with basinal fluids channeled along the unconformity from nearby sedimentary basins long after burial by Paleozoic strata. To assess the variation between surficial weathering and basinal fluid alteration, we measured and sampled for petrologic, geochemical, and mineralogic data in the rock at and just below the Great Unconformity at three paleoelevations. Whole-rock geochemical oxide and X-ray diffraction data indicate that K-metasomatism and highly crystalline illite occurred in each profile. The K increase reflects crystallization of authigenic feldspar and illite from basinal fluids that were channeled along the Great Unconformity during younger Paleozoic fluid-flow events. Each profile also exhibits an upward increase in altered feldspar crystals and highly crystalline kaolinite, and an upward decrease in Ca and Na. Such changes reflect soil formation due to reaction with meteoric water before Cambrian burial, indicating that the altered granite was a paleosol before Paleozoic basinal fluid-flow events. Notably, the paleosol at the highest paleoelevation displays the least amount of paleoweathering and the paleosol at the lowest displays the greatest amount of paleoweathering. These results demonstrate that not only can characteristics of the paleosol just below the Great Unconformity be recognized in the St. Francois Mountains, despite subsequent alteration, but also it is possible to detect variations in soil thickness that were controlled by slope steepness and, therefore, water availability and/or soil creep or failure. This spatial relationship is compatible with studies of modern soils which indicate that soil character varies with position on a slope.

Geology↗
DOE OSTI2023

Association of Serum Bile Acid and Unsaturated Fatty Acid Profiles with the Risk of Diabetic Retinopathy in Type 2 Diabetic Patients

Aim: We aimed to identify the ability of serum bile acids (BAs) and unsaturated fatty acids (UFAs) profiles to predict the development of diabetic retinopathy (DR) in type 2 diabetes mellitus (T2DM) patients. Methods: We first used univariate and multivariate analysis to compare 15 serum BA and 11 UFA levels in healthy control (HC) group (n = 82), T2DM patients with DR (n = 58) and T2DM patients without DR (n = 60). Forty T2DM patients were considered for validation. Then, the receiver operating characteristic curve (ROC) and decision curve analysis were used to assess the diagnostic value and clinical benefit of serum biomarkers alone, clinical variables alone or in combination, and the area under the curve (AUC), integrated discrimination improvement (IDI), and net reclassification improvement (NRI) were used to further assess whether the addition of biomarkers significantly improved the predictive ability of the model. Results: Orthogonal partial least squares-discriminant analysis (OPLS-DA) of serum BAs and UFAs separated the three cohorts including HC, T2DM patients with or without DR. The difference in serum BA and UFA profiles of T2DM patients with or without DR was mainly manifested in the three metabolites of taurolithocholic acid (TLCA), tauroursodeoxycholic acid (TUDCA) and arachidonic acid (AA). Together, they had an AUC of 0.785 (0.918 for validation cohort) for predicting DR in T2DM patients. After adjusting for numerous confounding factors, TLCA, TUDCA, and AA were independent predictors that differentiated T2DM with or without DR. The results of AUC, IDI, and NRI demonstrated that adding these three biomarkers to a model with clinical variables statistically increased their predictive value and were replicated in our independent validation cohort. Conclusion: These findings highlight the association of three metabolites, TLCA, TUDCA and AA, with DR and may indicate their potential value in the pathogenesis of DR.

60 APPLIED LIFE SCIENCES↗