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DOE OSTI2024

Two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from field grown transgenic poplar

Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a field grown transgenic poplar engineered with a monolignol 4-O-methyltransferase (MOMT4). The poplar was collected from a 2-year-old rotation trees within a three-year field trial experiment. The poplar was Soxhlet-extracted with toluene/ethanol and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover the lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide for NMR experiments. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (hsqcetgpsisp2.2) on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 220 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the Bruker’s TopSpin 3.6 software. The NMR spectra provides structural characteristics information about lignin in field grown transgenic MOMT4 poplar. Additional meta data is embedded in the raw spectra figures.

Lignin structure, HSQC, poplar, field trial, MOMT4↗

DOE OSTI2023

Comprehensive analysis of common polymers using hyphenated TGA-FTIR-GC/MS and Raman spectroscopy towards a database for micro- and nanoplastics identification, characterization, and quantitation

Environmental contamination by micro- and nanoplastics (MNPs) is well documented with potential for their increased accumulation globally. Growing public concern over environmental, ecological, and human exposure to MNPs has led to exponential increase in publications, news articles, and reports. Significant knowledge gap exists in standardized analytical methods for the identification and quantification of MNPs from real world environmental samples. Here, in this study, we report comprehensive datasets utilizing thermogravimetric analyzer (TGA) coupled to a Fourier transformed infrared spectrometer (FTIR) and a gas chromatography/mass spectrometer (GC/MS) with corresponding Raman spectral data for the most common polymers documented to be present in the environment (35 plastics of 12 polymer types), to serve as a base line reference for the identification and quantitation of MNPs. Various parameters for TGA-FTIR-GC/MS data acquisition were optimized. Commercial consumer plastic product compositions were identified using this analytical database. Case studies to showcase the utility of the method for polymer mixtures analysis is included. This dataset would serve towards the development of a collaborative, global, comprehensive, and curated public database for the identification of various MNPs and mixtures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish

Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studied in vitro and are included in the EPA’s ToxCast program, comprehensive in vivo comparisons using RNA sequencing across structurally diverse agrichemicals, in a single screening platform, are lacking. In this study, we examined structurally diverse agrichemicals found in the U.S. Environmental Protection Agency’s (EPA) Toxcast Phase I and II library by statically exposing early life stage zebrafish at 6 h post fertilization (hpf) until 120 hpf at concentrations ranging from 0.25 to 100 µM. Morphological outcomes were assessed at 120 hpf across 10 endpoints, including yolk sac edema, craniofacial malformations, and axis abnormalities. Chemicals that produced robust concentration-response relationships were selected for transcriptomic profiling. For transcriptomic analysis, zebrafish were statically exposed to each chemical and sampled at 48 hpf, prior to the onset of morphological effects observed at 120 hpf. Differential expression analysis identified between 0 and 4,538 differentially expressed genes (DEGs) per chemical, with no clear correlation to morphological severity. Both DEG and co-expression network analyses revealed chemical-specific expression patterns that converged on shared biological pathways, including neurodevelopment and cytoskeletal organization. Key regulatory genes such as mylpfa and krt4 were identified within co-expression modules, suggesting their potential role in conserved toxicity mechanisms. Semantic similarity analysis of enriched gene ontology (GO) terms, when compared to existing datasets, highlighted gaps in the annotation of neurodevelopmental processes, indicating that some in vivo effects may not be fully captured by current curated resources. The results provide new insights into the modes of action of diverse agrichemicals and establish a framework for understanding how agrichemical structure relates to biological function in a vertebrate model.

agrichemical↗

DOE OSTI2019

A prospective feasibility study evaluating the role of multimodality imaging and liquid biopsy for response assessment in locally advanced rectal carcinoma

Purpose: Colorectal cancer is a commonly encountered disease that poses several diagnostic and therapeutic challenges. The inherent heterogeneity of tumor biology and propensity to relapse despite “curative” resection pose significant challenges with regard to response assessment. Although MR imaging already plays a key role in primary staging of patients with rectal carcinoma, its reliability in restaging after neoadjuvant therapy is debatable (Van der broek et al. in Dis Colon Rectum 60(3):274–283, 2017). Therefore, there is significant interest in developing additional methods which may improve diagnostic accuracy. This study aims to evaluate the role of multimodality imaging and liquid biopsy in therapeutic response assessment. Methods: Seventeen patients were enrolled into the study over a span of 24 months. All underwent hybrid PET-MRI and CT-perfusion (CT-P), prior to and following neoadjuvant therapy for locally advanced rectal carcinoma. Twelve of the 17 patients also underwent liquid biopsy, which consisted of blood sampling and analysis of circulating tumor cells (CTCs) and extracellular vesicles (EVs), including cell fragments and microparticles (MPs), using the Cell Search System (Menarini Silicon Biosystems). SUV, DWI, and ADC were calculated during PET-MRI, and several parameters were evaluated during CT-perfusion, including average perfusion, blood flow (BF), blood volume (BV), mean transit time (MTT), permeability-surface area product (PS), contrast extraction efficiency (E), and K-trans (K). Changes observed pre- and post-neoadjuvant therapy in each modality were compared to tumor response at histopathology using a modified Ryan tumor regression grading system. Results: Of the 17 patients included in the study, 14 were classified as non-responders, and 3 were classified as responders as determined by the modified Ryan Tumor Regression Grade (TRG) scoring system (Van der broek et al. in Dis Colon Rectum 60(3):274–283, 2017). When combined, blood markers and CT-P parameters (mean transit time (MTT), K-trans, and permeability-surface area product (PS)) produced the strongest models (p < 0.01). PET (SUV measurement) combined with CT-P-derived K-trans produced a marginally significant (p = 0.057) model for predicting response. MRI-derived ADC value did not provide a significant model for response prediction. Conclusion: A model of CT-P parameters plus liquid biopsy more accurately predicts tumor response than PET-MRI, CT-P alone, or liquid biopsy alone. These results suggest that in the evaluation of treatment response, liquid biopsy could provide additional information to functional imaging modalities such as CT-P and should therefore be explored further in a trial with larger sample size.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2024

Carbon-13 NMR spectra of lignin isolated from field grown transgenic poplar

Here we present a curated dataset of a series of 13C nuclear magnetic resonance (NMR) spectra of lignin isolated from transgenic monolignol 4-O-methyltransferase (MOMT4) engineered poplar. The transgenic poplar was collected from a 3-year field trial experiment. The poplar was Soxhlet-extracted with toluene/ethanol and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h. The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover the lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide for NMR characterization. 13C experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (zgpg) on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following conditions: spectra width 229 ppm, 64k data points, 1s pulse delay, and 6k scans. All the data was processed using the Bruker’s TopSpin 3.6 software. Additional meta data is embedded in the raw spectra files.

13C NMR, lignin, poplar, field trial, MOMT4, CBI↗

NASA NTRSDate not supplied

Revisiting the Origin of Macromolecular Carbon (MMC) in Lunar Basalts 15556 & 10044

Volatile elements influence the geo-chemical evolution of planetary bodies and they are in magmas at every stage, from melting within planetary interiors to eruption at the surface. Analyses of lunar mare basalts supported the hypothesis that lunar mag-mas were depleted in volatiles (H-C-F-Cl-S), relative to their terrestrial analogs [1]. Nevertheless, several early studies of samples returned during the Apollo program proposed that the mare basalt eruptions, including the “fire fountain” eruptions, were propelled by the oxidation of magmatic graphite to CO (and/or CO2) gas [2, 3]. Seminal studies during the 1970’s measured the bulk concentration and isotopic compositions of C from Apollo 11 samples, and identified several carbonaceous compounds, including: (a) gaseous (CO, CO2, and traces of CH4), (b) metallic carbide, and (c) potentially elemental carbon [4-6]. These studies reported a relatively broad range of C contents (~100-400 μg/g) and isotopic values (δC13 = -30 to +20), and suggested that these heterogeneities can be explained by contribution from multiple factors, including: (a) indigenous carbon, (b) solar wind implantation, (c) bombardment and/or meteorite impact, and (d) terrestrial contamination [5,6]. However, unequivocal observations of magmatic graphite in lunar basalts have never been made. Macromolecular carbon (MMC)—graphitic carbon varying from nearly amorphous to highly crystalline varieties—was identified as inclusions hosted by igneous pyroxenes from Martian meteorites and were attributed to being indigenous to Mars [8]. The authors carefully considered the textural and mineralogical relationship of the MMC phases, and concluded that the subset of MMC located within and/or adjacent to cracks, or at a disrupted surface (e.g., cut) were most consistent with terrestrial contamination. The near absence of con-firmed instances of lunar magmatic MMC within the literature [9], combined with the wide range of isotopic values and bulk carbon contents measured in lunar bas-alts begs the question as to whether previously measured carbon is of an indigenous origin, or the result of terrestrial contamination. Using Raman spectroscopy, we have observed MMC in lunar basalts subjected to different forms of anthropogenic modification related to sample preparation including polished sections, sawn surfaces, and fractured surfaces adjacent to sawn sur-faces. We have observed MMC of unknown origin in all of these settings. Here we report the preliminary textural and spectroscopic characteristics of MMC hosted within the groundmass of Apollo 15 (15556) and Apollo 11 basalts (10044) as part of our ongoing investigation of the origin of these carbonaceous materials.

lunar↗

DOE OSTI2021

Quantile-dependent expressivity of serum C-reactive protein concentrations in family sets

“Quantile-dependent expressivity” occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g., C-reactive protein, CRP) is high or low relative to its distribution. We have previously shown that the heritabilities ( h 2 ) of coffee and alcohol consumption, postprandial lipemia, lipoproteins, leptin, adiponectin, adiposity, and pulmonary function are quantile-specific. Whether CRP heritability is quantile-specific is currently unknown. Methods Serum CRP concentrations from 2,036 sibships and 6,144 offspring-parent pairs were analyzed from the Framingham Heart Study. Quantile-specific heritability from full-sib (β FS , h 2 ={(1 + 8r spouse β FS ) 0.5 - 1}/(2r spouse )) and offspring-parent regression slopes (β OP , h 2 = 2β OP /(1 + r spouse )) were estimated robustly by quantile regression with nonparametric significance determined from 1,000 bootstrap samples. Results Quantile-specific h 2 (±SE) increased with increasing percentiles of the offspring’s age- and sex-adjusted CRP distribution when estimated from β OP ( P trend = 0.0004): 0.02 ± 0.01 at the 10th, 0.04 ± 0.01 at the 25th, 0.10 ± 0.02 at the 50th, 0.20 ± 0.05 at the 75th, and 0.33 ± 0.10 at the 90th percentile, and when estimated from β FS ( P trend = 0.0008): 0.03±0.01 at the 10th, 0.06 ± 0.02 at the 25th, 0.14 ± 0.03 at the 50th, 0.24 ± 0.05 at the 75th, and 0.53 ± 0.21 at the 90th percentile. Conclusion Heritability of serum CRP concentration is quantile-specific, which may explain or contribute to the inflated CRP differences between CRP (rs1130864, rs1205, rs1800947, rs2794521, rs3091244), FGB (rs1800787), IL-6 (rs1800795, rs1800796), IL6R (rs8192284), TNF- α (rs1800629) and APOE genotypes following CABG surgery, stroke, TIA, curative esophagectomy, intensive periodontal therapy, or acute exercise; during acute coronary syndrome or Staphylococcus aureus bacteremia; or in patients with chronic rheumatoid arthritis, diabetes, peripheral arterial disease, ankylosing spondylitis, obesity or inflammatory bowel disease or who smoke.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Abstract Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH 4 and CO 2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Treatment-Related Toxicity in Patients With Early-Stage Non-Small Cell Lung Cancer and Coexisting Interstitial Lung Disease: A Systematic Review

Purpose: Definitive treatment for patients with early-stage non-small cell lung cancer (ES-NSCLC) is usually well tolerated. Patients with ES-NSCLC and coexisting interstitial lung disease (ILD) are at increased risk of severe treatment-related toxicity after definitive therapy. The main objective of this systematic review is to provide a pooled estimation of treatment-related mortality and ILD-specific toxicity in this population of patients and to identify trends for further study. Methods and Materials: The MEDLINE and Embase databases were queried from respective dates of inception to January 2016. Studies that included patients who underwent definitive treatment for ES-NSCLC not combined with other treatments were included. Patients with oligometastases who were treated with aggressive palliation were included if it did not constitute the majority of patients in a specific study. The results were summarized with weighted proportions according to the sample size of individual studies. Results: Overall, 3056 records were reviewed and 50 journal articles were included in the abstraction. The weighted proportion of treatment-related mortality (and ILD-specific toxicity) in primarily medically inoperable patients was as follows: stereotactic ablative radiation therapy (SABR) 15.6% (25%), particle beam therapy 4.3% (18.2%) and radiofrequency ablation (RFA) 8.7% (25%). The data for medically operable patients who underwent surgery were extracted for reference. Treatment-related mortality and ILD-specific toxicity were 2.2% and 12%, respectively, in the surgical population. On analysis of reported SABR dose parameters, V20 ≤ 6.5% and mean lung dose ≤4.5 Gy were found to be metrics associated with reduced mortality. Conclusion: A consistently high level of treatment-related mortality and ILD-specific toxicity was observed in primarily medically inoperable patients treated with SABR, particle beam therapy, and RFA. For these patients, curative treatment should be considered in the context of the high toxicity rates and overall poor prognosis. Stringent radiation dosimetric parameters may result in reduced toxicity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2024

Cellulose crystallinity index (CrI) of switchgrass measured by solid-state NMR

Here we present a curated dataset of switchgrass cellulose crystallinity index (CrI) measured using solid state nuclear magnetic resonance (NMR) spectroscopy. Seventy-two topline switchgrass lines grown in greenhouse were collected and ground to -20/+80 mesh. The switchgrass was then Soxhlet-extracted with toluene/ethanol for 24 h to remove extractives. The extractives-free switchgrass was holopulped by using peracetic acid at 5 g loading per g biomass and the solution consistency was adjusted to 5% with DI water. Holopulping was conducted at room temperature for 24 h with stirring. The obtained holocellulose was washed excessively with DI water and air-dried at room temperature for 24 h. The dried holocellulose was treated with hydrochloric acid (2.5 M) for 2 h to remove hemicellulose. The isolated cellulose was collected by filtration, rinsed with DI water, and used to analyze cellulose crystallinity by solid-state NMR. The NMR samples were prepared by packing the moisturized cellulose into 4-mm cylindrical Zirconia MAS rotors. Cross polarization/magic angle spinning (CP/MAS) NMR analysis of cellulose was carried out on a Bruker Avance III 400-MHz spectrometer operating at 100.59 MHz for 13C in a Bruker double-resonance MAS probe head at spinning speeds of 8 kHz. The CP/MAS experiments utilized a 5 ms (90°) proton pulse, 1.5 ms contact pulse, 4 s recycle delay and 4000 scans. The cellulose crystallinity index was determined from the areas of the cellulose crystalline C4 signal (δ 86-92 ppm) over the entire C4 regions (δ 79-92 ppm) in the NMR spectra.

Cellulose, crystallinity index, switchgrass, solid↗

DOE OSTI2026

Dark Energy Survey Year 6 Results: Photometric Dataset for Cosmology

We describe the photometric dataset assembled from the full 6 yr of observations by the Dark Energy Survey (DES) in support of static-sky cosmology analyses. DES Y6 Gold is a curated dataset derived from DES Data Release 2 (DR2) that incorporates improved measurement, photometric calibration, object classification and value-added information. Y6 Gold comprises nearly 5000 deg$^{2}$ of grizY imaging in the south Galactic cap and includes 669 million objects with a depth of i$_{AB}$ ∼ 23.4 mag at a signal-to-noise ratio ∼ 10 for extended objects and a top-of-the-atmosphere photometric uniformity <2 mmag. Y6 Gold augments DES DR2 with simultaneous fits to multiepoch photometry for more robust galaxy shapes, colors, and photometric redshift estimates. Y6 Gold features improved morphological star–galaxy classification with an efficiency of 98.6% and a contamination of 0.8% for galaxies with 17.5 < i$_{AB}$ < 22.5. Additionally, it includes per-object quality information, and accompanying maps of the footprint coverage, masked regions, imaging depth, survey conditions, and astrophysical foregrounds that are used for cosmology analyses. After quality selections, benchmark samples contain 448 million galaxies and 120 million stars. This publication is complemented by data access and documentation.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from Populus trichocarpa residues after CELF pretreatment and CBP fermentation

Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a woody energy crop (Populus trichocarpa) residues after co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment and consolidated bioprocessing (CBP) process. The natural poplar variant GW-9947 from the Center for Bioenergy Innovation (CBI) was used. The poplar was knife milled and passed through a 1 mm sieve. The CELF pretreatment was performed in a Parr autoclave reactor with 7.5 wt % solids loading, 0.5 wt% H2SO4 as catalyst at 150°C with 15, 25 and 30 minutes, respectively. Tetrahydrofuran was added in a 1:1 mass ratio with water as the pretreatment solvent. The residues from CELF pretreatment were then subjected to CBP using the bacterium C. thermocellum DSM 1313. CBP fermentations were performed at 60 °C in a shaker at 50 grams/L solids loadings. Lignin was isolated from the pretreated samples after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 580 rpm for 2.5 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The lignin samples were characterized using 13C–1H HSQC experiments which were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus. A standard Bruker pulse sequence was used on a Prodigy platform cryoprobe. The dry lignin samples were dissolved in deuterated dimethylsulfoxide for HSQC experiments. The spectra were acquired under the following acquisition conditions: 210 ppm spectral width in F1 (13C) dimension with 256 data points and 11 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the TopSpin 3.6 software (Bruker BioSpin). The NMR spectra provides structural characteristics information about lignin remaining in solids after CELF (150 °C with 15, 25 and 30 minutes) process and C. thermocellum CBP.

Lignin structure, HSQC, poplar, CELF, CBP, CBI↗

NASA NTRSDate not supplied

Statistical Classification of Biosignature Information using Multiple Instrument Observations

The accurate identification of biosignatures (indications of life) from data taken from remote or in situ planetary exploration is one of the most important challenges in astrobiology, the interdisciplinary field examining habitability and the potential for extraterrestrial life. This study employs machine learning algorithms to optimize the identification of biosignatures, with an emphasis on those which are agnostic to a specific biochemical basis. We exploit the wealth of terrestrial data available from biogenic and abiogenic systems to enhance efficient feature prioritization. Our dataset, pulled from public databases and laboratory recorded measurements, includes elemental abundance, isotopic fractionation, and VNIR/Raman spectra The data curation process included standardization for detection limits and ranges. Subsequent feature extraction yielded detailed inputs for machine learning, including combinations of elemental content, isotopic ratios, and parameters of spectral peaks and troughs. Feature significance was evaluated across diverse machine learning methodologies, such as k-nearest neighbors, logistic regression, Random Forest, support vector machines, and Gaussian Naïve Bayes, along with a combined voting classifier. We utilized Receiver Operating Characteristic Area Under the Curve (ROC AUC) across 2,000 50% test-train splits as a robust metric of model performance. Results revealed a promising ROC AUC of 0.853 for the combined voting classifier. Removing elemental abundance data notably reduced model accuracy (13% decrease in AUC), highlighting its critical role in biosignature detection. Several other individual data features exhibited significance within their respective data types, offering additional granularity. This research fortifies the relevance of machine learning to astrobiology, potentially enhancing life detection missions by allowing algorithmic prioritization of high-interest samples for further investigation. Future work will refine data standardization, expand the dataset to include more terrestrial systems, and incorporate convolutional neural networks for spectral feature extraction. The potential for public data sharing is also under exploration, reinforcing our commitment to collective scientific advancement.

Statistical↗

DOE OSTI2021

Dark Energy Survey Year 3 Results: Photometric Data Set for Cosmology

In this work, we describe the Dark Energy Survey (DES) photometric data set assembled from the first three years of science operations to support DES Year 3 cosmologic analyses, and provide usage notes aimed at the broad astrophysics community. Y3 GOLD improves on previous releases from DES, Y1 GOLD, and Data Release 1 (DES DR1), presenting an expanded and curated data set that incorporates algorithmic developments in image detrending and processing, photometric calibration, and object classification. Y3 GOLD comprises nearly 5000 deg 2 of grizY imaging in the south Galactic cap, including nearly 390 million objects, with depth reaching a signal-to-noise ratio ~10 for extended objects up to iAB ~ 23.0, and top-of-the-atmosphere photometric uniformity <3 mmag. Compared to DR1, photometric residuals with respect to Gaia are reduced by 50%, and per-object chromatic corrections are introduced. Y3 GOLD augments DES DR1 with simultaneous fits to multi-epoch photometry for more robust galactic color measurements and corresponding photometric redshift estimates. Y3 GOLD features improved morphological star–galaxy classification with efficiency >98% and purity >99% for galaxies with 19 < i AB < 22.5. Additionally, it includes per-object quality information, and accompanying maps of the footprint coverage, masked regions, imaging depth, survey conditions, and astrophysical foregrounds that are used to select the cosmologic analysis samples.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS2015

A Combined Study Investigating the Insoluble and Soluble Organic Compounds in Category 3 Carbonaceous Itokawa Particles Recovered by the Hayabusa Mission

At the 3rd International Announcement of Opportunity (AO), we have been approved for five Category 3 carbonaceous Itokawa particles (RA-QD02-0012, RA-QD02-0078, RB-CV-0029, RB-CV-0080 and RB-QD04-0052) recovered by the first Hayabusa mission of JAXA. In this investigation, we aim to provide a comprehensive study to characterize and account for the presence of carbon-bearing phases as suggested by the initial Scanning Electron Microscopy (SEM) analysis carried out by JAXA at the curation facility, and to describe the mineralogical components of the particles. The insoluble organic content of Itokawa particle has been investigated with the use of micro-Raman spectroscopy by Kitajima and co-workers [1]. The Raman spectra of Itokawa particles show broad G- and D-bands typical of low temperature material which offers an interesting contrast to the high metamorphic grade (LL4-6) of the Itokawa parent body. Amino acid analysis has been conducted by Naraoka et al. [2] to study the soluble organic component of Itokawa particles, but since it was a preliminary study and thus did not have the opportunity to target on Category 3 carbonaceous particles, only terrestrial contaminants were identified. The investigation will be carried out in the following order prioritized according to the progressive damage the analytical techniques can induce: (1) micro-Raman spectrometry, (2) two-step laser mass spectrometry (micro-L2MS), (3) ultra-high performance liquid chromatography with fluorescence detection and time-of-flight mass spectrometry (LC-FD/ToF-MS), and optimally if we can recover the particles after wet chemistry analysis, we will mount the samples and perform (4) electron beam microscopy (SEM, electron back-scattered diffraction [EBSD]) and (5) carbon X-ray absorption near edge structure spectroscopy (C-XANES). We will begin the analytical procedures upon receiving the samples in September/October. This work will provide us with an understanding of the variety and origins of the carbon-bearing phases present in primitive solar system bodies from a direct sample-returned mission, which is less likely hampered by risks of terrestrial contamination as compared to meteorite finds and falls.

Chan, Q. H. S.↗

DOE OSTI2024

Heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from switchgrass residues after fermentation with milling

Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a herbaceous energy crop (Panicum virgatum L.). The lowland variant “Timber” switchgrass from Ernst seeds was used. The switchgrass was knife milled and passed through a 2 mm sieve prior to consolidated bioprocessing (CBP) process. Switchgrass was suspended in Milli-Q water and autoclaved for 90 min on liquid cycles. The residues after autoclaving were then subjected to CBP using coculture of Clostridium thermocellum (C. thermocellum DSM 1313 (LL1004)) and Thermoanaerobacterium thermosaccarolyticum ( T. thermosaccharolyticum HG-8 ATCC 31960 (LL1244)). Once-fermented and twice-fermented (FF) switchgrass were subjected to ball and disc milling in bioreactors at 55 °C and 60, 48 grams/L solids loadings for primary and secondary fermentation respectively. When fermentations were completed, the residual solids were rinsed with milli-Q water. Lignin was isolated from the pretreated residues after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 600 rpm for 2 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and characterized using 13C–1H HSQC in a Bruker Avance III HD 500-MHz NMR spectrometer. A standard Bruker pulse sequence (hsqcetgpsisp.2) was used on a Prodigy platform cryoprobe. The spectra were acquired with the following acquisition conditions: 230 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 2048 data points, a 90° pulse, with a C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin 3.6 software.

Lignin, HSQC, Switchgrass, CBP , Ball mill, Disc m↗

DOE OSTI2011

Cognitive Functioning After Radiotherapy or Chemoradiotherapy for Head-and-Neck Cancer

Purpose: To perform a comprehensive cognitive function (CF) assessment in patients who were relapse free after curative intent radiotherapy (RT) or chemoradiotherapy for squamous cell carcinoma of the head and neck. Methods and Materials: Patients underwent neuropsychological tests to assess their objective CF; completed questionnaires to assess subjective CF, quality of life, and affect; and underwent blood tests to assess hematologic, biochemical, endocrine, and cytokine status. Retrospectively, the dosimetry of incidental radiation to the brain was determined for all patients, and the dose intensity of cisplatin was determined in those who had undergone chemoradiotherapy. Results: A total of 10 patients were enrolled (5 treated with radiotherapy only and 5 with radiotherapy and cisplatin). The mean time from the end of treatment was 20 months (range, 9-41). All patients were able to complete the assessment protocol. Of the 10 patients, 9 had impaired objective CF, with memory the most severely affected. The severity of memory impairment correlated significantly with the radiation dose to the temporal lobes, and impaired dexterity correlated significantly with the radiation dose to the cerebellum, suggesting that these deficits might be treatment related. Patients receiving cisplatin appeared to have poorer objective CF than patients receiving only RT, although this difference did not achieve statistical significance, likely owing to the small sample size. Consistent with the published data, objective CF did not correlate with subjective CF or quality of life. No association was found between objective CF and patients' affect, hematologic, biochemical, endocrine, and cytokine status. Conclusion: Neuropsychological testing is feasible in squamous cell carcinoma of the head-and-neck survivors. The findings were suggestive of treatment-related cognitive dysfunction. These results warrant additional investigation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

NASA NTRS2015

Carbon and Oxygen Isotope Measurements of Ordinary Chondrite (OC) Meteorites from Antarctica Indicate Distinct Carbonate Species Using a Stepped Acid Extraction Procedure

The purpose of this study is to characterize the stable isotope values of terrestrial, secondary carbonate minerals from five Ordinary Chondrite (OC) meteorites collected in Antarctica. These samples were identified and requested from NASA based upon their size, alteration history, and collection proximity to known Martian meteorites. They are also assumed to be carbonate-free before falling to Earth. This research addresses two questions involving Mars carbonates: 1) characterize terrestrial, secondary carbonate isotope values to apply to Martian meteorites for isolating in-situ carbonates, and 2) increase understanding of carbonates formed in cold and arid environments with Antarctica as an analog for Mars. Two samples from each meteorite, each approximately 0.5 grams, were crushed and dissolved in pure phosphoric acid for 3 sequential reactions: a) R times 0 for 1 hour at 30 degrees Centigrade (fine calcite extraction), b) R times 1 for 18 hours at 30 degrees Centigrade (course calcite extraction), and c) R times 2 for 3 hours at 150 degrees Centigrade (siderite and/or magnesite extraction). CO (sub 2) was distilled by freezing with liquid nitrogen from each sample tube, then separated from organics and sulfides with a TRACE GC using a Restek HayeSep Q 80/100 6 foot 2 millimeter stainless column, and then analyzed on a Thermo MAT 253 Isotope Ratio Mass Spectrometer (IRMS) in Dual Inlet mode. This system was built at NASA/JSC over the past 3 years and proof-tested with known carbonate standards to develop procedures, assess yield, and quantify expected error bands. Two distinct species of carbonates are found: 1) calcite, and 2) non-calcite carbonate (future testing will attempt to differentiate siderite from magnesite). Preliminary results indicate the terrestrial carbonates are formed at approximately sigma (sup 13) C equal to plus 5 per mille, which is consistent with atmospheric CO (sub 2) sigma (sup 13) C equal to minus 7 per mille and fractionation of plus12 per mille based upon polar temperature of -20 degrees Centigrade. The oxygen values fractionate sigma (sup 18) O equal to minus 10-20 per mille lighter between the R times 0 and R times 1 reactions at 30 degrees Centigrade. The carbonate oxygen isotope measurements are consistently heavier than expected with meteoric water and temperatures from Antarctica, perhaps due to secondary carbonate formation during curation in Houston, TX.

Evans, Michael E.↗