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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures

ABSTRACT The development of synthetic microbial consortia in recent years has revealed that complex interspecies interactions, notably the exchange of cytoplasmic material, exist even among organisms that originate from different ecological niches. Although morphogenetic characteristics, viable RNA and protein dyes, and fluorescent reporter proteins have played an essential role in exploring such interactions, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to further investigate interactions in synthetic or semisynthetic consortia. Despite its maturity, several challenges exist in using rRNA-FISH as a tool to quantify individual species population dynamics and interspecies interactions using high-throughput instrumentation such as flow cytometry. In this work, we resolve such challenges and apply rRNA-FISH to double and triple co-cultures of Clostridium acetobutylicum, Clostridium ljungdahlii, and Clostridium kluyveri . In pursuing our goal to capture each organism’s population dynamics, we demonstrate dynamic rRNA, and thus ribosome, exchange between the three species leading to the formation of hybrid cells. We also characterize the localization patterns of the translation machinery in the three species, identifying distinct, dynamic localization patterns among them. Our data also support the use of rRNA-FISH to assess the culture’s health and expansion potential, and, here again, our data find surprising differences among the three species examined. Taken together, our study argues for rRNA-FISH as a valuable and accessible tool for quantitative exploration of interspecies interactions, especially in organisms which cannot be genetically engineered or in consortia where selective pressures to maintain recombinant species cannot be used. IMPORTANCE Though dyes and fluorescent reporter proteins have played an essential role in identifying microbial species in co-cultures, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to quantitatively probe complex interactions between organisms in synthetic consortia. Despite its maturity, several challenges existed before rRNA-FISH could be used to study Clostridium co-cultures of interest. First, species-specific probes for Clostridium acetobutylicum and Clostridium ljungdahlii had not been developed. Second, “state-of-the-art” labeling protocols were tedious and often resulted in sample loss. Third, it was unclear if FISH was compatible with existing fluorescent reporter proteins. We resolved these key challenges and applied the technique to co-cultures of C. acetobutylicum , C. ljungdahlii , and Clostridium kluyveri . We demonstrate that rRNA-FISH is capable of identifying rRNA/ribosome exchange between the three organisms and characterized rRNA localization patterns in each. In combination with flow cytometry, rRNA-FISH can capture sub-population dynamics in co-cultures.

Hill, John D.↗
DOE OSTI2019

PV Cyber Security Research (Final Report)

Extensive deployment of interoperable distributed energy resources (DER) on power systems is increasing the power system cyber security attack surface. National and jurisdictional interconnection standards require DER to include a range of autonomous and commanded grid support functions which can drastically influence power quality, voltage, and bulk system frequency. This project was split into two phases. The first provided a survey and roadmap of the cybersecurity for the solar industry. The second investigated multiple PV cybersecurity research and development (R&D) concepts identified in the first phase. In the first year, the team created a roadmap for improving cybersecurity for distributed solar energy resources. This roadmap was intended to provide direction for the nation over the next five years and focused on the intersection of industry and government and recommends activities in four related areas: stakeholder engagement, cyber security research and development, standards development, and industry best practices. At the same time, the team produced a primer for DER vendors, aggregators, and grid operators to establish a common taxonomy and describe basic principles of cyber security, encryption, communication protocols, DER cyber security recommendations and requirements, and device-, aggregator-, and utility-level security best practices to ensure data confidentiality, integrity, and availability. This material was motivated by the need to assist the broader PV industry with cybersecurity resilience and describe the state-of-the-art for securing DER communications. Lastly, an adversary-based assessment of multiple PV devices was completed at the Distributed Energy Technologies Laboratory at Sandia National Laboratories to determine the status of industry cybersecurity practices. The team found multiple deficiencies in the security features of the assessed devices. In the second year, a set of recommendations was created for DER communication protocols— especially with respect to the state-of-the-art requirements in IEEE 2030.5. Additionally, several cybersecurity R&D technologies related to communications-enabled photovoltaic systems were studied to harden DER communication networks. Specifically, the team investigated (a) using software defined networking to create a moving target defense system for DER communications, and (b) engineering controls that prevent misprogramming or adversary action on DER devices/networks by disallowing setpoints that will generate unstable power system operations.

14 SOLAR ENERGY↗
DOE OSTI2023

Geochemistry and metagenomics analyses of bacterial community structure in selected waste dumpsites in Lagos Metropolis, Nigeria

Dumpsites are reservoirs of persistent organic pollutants (POPs) and heavy metals (HMs), constituting environmental hazards to humanity. Autochthonous microorganisms in dumpsites exhibit various degrees of responses to contaminants. Unfortunately, there is a dearth of information on the types and concentration of pollutants and the array of microorganisms in these dumpsites which may play important roles in the metabolism of such pollutants or other community processes. Therefore, determining the microbial community structure in such contaminated sites across a municipality is essential for profiling the taxa that would serve as consensus degraders of the pollutants. In this study, soil samples from three dumpsites (Cele, CS; Solous, SS; and Computer Village, CVS) were characterized for geochemical properties using GC-MS, MP-AES, and other analytical protocols, while the dynamics of bacterial communities were evaluated based on their 16S rRNA gene barcodes. A significant difference in the bacterial communities was observed among the dumpsites in relation to the extent of pollution caused by POPs and HMs. CVS, with the highest HM contamination, was rich in Actinobacteria (41.7%) and Acidobacteria (10.2%), in contrast to CS and SS. Proteobacteria (34.1%) and Firmicutes (20%) were the dominant phyla in CS (highest POP contamination), while Bacteroidetes (45.5%) and Proteobacteria (39.9%) were dominant in SS soil.Bacilluswas the dominant genus in the most polluted dumpsite. Canonical correspondence analysis revealed that polycyclic aromatic hydrocarbons (PAHs) and HMs shaped the structure of the bacterial operational taxonomic units (OTUs) in the most polluted dumpsite. Out of a total of 706 OTUs, 628 OTUs exhibited a significant correlation (>50%) with benzo(b)fluoranthene, azobenzene, dibenzofurans, pyrene, dibenzo(a,l)pyrene, Cu, and Zn. In particular, Proteobacteria (Achromobactersp. andSerratiasp.), Bacteroidetes (Zhouiasp.), and Firmicutes (Bacillussp.) were suggested to be pivotal to the ecophysiology of dumpsite soils contaminated with POPs and HMs. The results generally underscored the importance of metagenomic and physicochemical analyses of polluted systems in enabling correlations for useful prediction of drivers of such ecosystems. This will further improve our understanding of the metabolic potential and adaptation of organisms in such systems.

Environmental Sciences & Ecology↗
DOE OSTI2013

Chemoradiation With Paclitaxel and Carboplatin in High-Risk Cervical Cancer Patients After Radical Hysterectomy: A Korean Gynecologic Oncology Group Study

Purpose: To evaluate the efficacy and toxicity of concurrent chemoradiation with paclitaxel and carboplatin in patients with high-risk cervical cancer. Methods and Materials: Patients after radical hysterectomy for cervical cancer, with at least 1 high-risk characteristic, were administered paclitaxel 135 mg/m{sup 2}, carboplatin area under the curve = 5 every 3 weeks for 3 cycles concomitant with radiation therapy as adjuvant treatment. Results: This prospective study enrolled 71 consecutive patients. Sixty-six patients (93%) completed the planned treatment. The majority of grade 3/4 neutropenia or nonhematologic toxicities were usually self-limited. Diarrhea grades 3/4 were observed in 4 patients (5.6%). One patient developed anaphylactic shock after infusion of paclitaxel. With a median follow-up of 57 months, recurrences occurred in 16 patients. Multivariable analysis indicated that common iliac lymph node involvement is an independent risk factor for disease recurrence (odds ratio 13.48; 95% confidence interval 2.93-62.03). In the intent-to-treat population (n=71), the estimated 5-year disease-free survival and overall survival rates were 77.3% and 80.3% respectively. In the per-protocol population (n=62), disease-free survival was 78.9% and overall survival was 83.9%. Conclusions: Concurrent chemoradiation with paclitaxel/carboplatin is well tolerated and seems to be effective for patients who undergo radical hysterectomy. Therefore, a prospective, randomized controlled study should be designed to evaluate efficacy of this approach for patients with high-risk cervical cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
NASA NTRS2006

Data Integration Support for Data Served in the OPeNDAP and OGC Environments

NASA is coordinating a technology development project to construct a gateway between system components built upon the Open-source Project for a Network Data AcceSs Protocol (OPeNDAP) and those made available made available via interfaces specified by the Open Geospatial Consortium (OGC). This project is funded though the Advanced Collaborative Connections for Earth-Sun System Science (ACCESS) Program and is a NASA contribution to the Committee on Earth Satellites (CEOS) Working Group on Information Systems and Services (WGISS). The motivation for the project is the set of data integration needs that have been expressed by the Coordinated Enhanced Observing Period (CEOP), an international program that is addressing the study of the global water cycle. CEOP is assembling a large collection in situ and satellite data and mode1 results from a wide variety of sources covering 35 sites around the globe. The data are provided by systems based on either the OPeNDAP or OGC protocols but the research community desires access to the full range of data and associated services from a single client. This presentation will discuss the current status of the OPeNDAP/OGC Gateway Project. The project is building upon an early prototype that illustrated the feasibility of such a gateway and which was demonstrated to the CEOP science community. In its first year as an ACCESS project, the effort has been has focused on the design of the catalog and data services that will be provided by the gateway and the mappings between the metadata and services provided in the two environments.

McDonald, Kenneth R.↗
DOE OSTI2016

Clinical Experience and Evaluation of Patient Treatment Verification With a Transit Dosimeter

Purpose: To prospectively evaluate a protocol for transit dosimetry on a patient population undergoing intensity modulated radiation therapy (IMRT) and to assess the issues in clinical implementation of electronic portal imaging devices (EPIDs) for treatment verification. Methods and Materials: Fifty-eight patients were enrolled in the study. Amorphous silicon EPIDs were calibrated for dose and used to acquire images of delivered fields. Measured EPID dose maps were back-projected using the planning computed tomographic (CT) images to calculate dose at prespecified points within the patient and compared with treatment planning system dose offline using point dose difference and point γ analysis. The deviation of the results was used to inform future action levels. Results: Two hundred twenty-five transit images were analyzed, composed of breast, prostate, and head and neck IMRT fields. Patient measurements demonstrated the potential of the dose verification protocol to model dose well under complex conditions: 83.8% of all delivered beams achieved the initial set tolerance level of Δ{sub D} of 0 ± 5 cGy or %Δ{sub D} of 0% ± 5%. Importantly, the protocol was also sensitive to anatomic changes and spotted that 3 patients from 20 measured prostate patients had undergone anatomic change in comparison with the planning CT. Patient data suggested an EPID-reconstructed versus treatment planning system dose difference action level of 0% ± 7% for breast fields. Asymmetric action levels were more appropriate for inversed IMRT fields, using absolute dose difference (−2 ± 5 cGy) or summed field percentage dose difference (−6% ± 7%). Conclusions: The in vivo dose verification method was easy to use and simple to implement, and it could detect patient anatomic changes that impacted dose delivery. The system required no extra dose to the patient or treatment time delay and so could be used throughout the course of treatment to identify and limit systematic and random errors in dose delivery for patient groups.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2012

Complications of Microwave Ablation for Liver Tumors: Results of a Multicenter Study

Purpose: New technologies for microwave ablation (MWA) have been conceived, designed to achieve larger areas of necrosis compared with radiofrequency ablation (RFA). The purpose of this study was to report complications by using this technique in patients with focal liver cancer. Methods: Members of 14 Italian centers used a 2.45-GMHz generator delivering energy through a cooled miniature-choke MW antenna and a standardized protocol for follow-up. They completed a questionnaire regarding number and type of deaths, major and minor complications and side effects, and likelihood of their relationship to the procedure. Enrollment included 736 patients with 1.037 lesions: 522 had hepatocellular carcinoma with cirrhosis, 187 had metastases predominantly from colorectal cancer, and 27 had cholangiocellular carcinoma. Tumor size ranged from 0.5 to 10 cm. In 13 centers, the approach used was percutaneous, in 4 videolaparoscopic, and in 3 laparotomic. Results: No deaths were reported. Major complications occurred in 22 cases (2.9%), and minor complications in 54 patients (7.3%). Complications of MWA do not differ from those RFA, both being based on the heat damage. Conclusion: Results of this multicenter study confirmed those of single-center experiences, indicating that MWA is a safe procedure, with no mortality and a low rate of major complications. The low rate of complications was probably due to precautions adopted, knowing in advance possible risk conditions, on the basis of prior RFA experience.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Rapid AI-based Dissection of Ashes using Raman and XRF Spectroscopy (RADAR-X)

Waste-to-energy (WTE) facilities incinerate ~35 million tons of municipal solid waste annually in the United States. The incineration process reduces the mass and the volume of the waste fraction by over 75 and 95%, respectively. The fraction left after incineration remains as ash residues and is referred to as WTE ash, compromising of bottom and fly ash. In the United States, ~10 million tons of WTE ashes are generated annually and predominantly landfilled because of the lack of secondary end-use pathways. This incurs a significant financial burden (landfilling costs) on U.S. WTE facilities and also results in the loss of materials to the landfill. The primary objective of this research is to understand better the elemental and mineralogical composition of WTE ashes from diverse origins and find composition dependent upcycling pathways for diverting these ashes from landfills. This primary objective was addressed through three research tasks –(Task I) An AI-led Multi-Modal Approach for Compositional Analysis, (Task II) Developing a Dissolution-Based Test for Real Time Analysis, and (Task III) Establishing composition-dependent end uses. The chemical composition of WTE ash is dependent on two factors, i.e., the input waste composition and the operational parameters of a WTE facility (combustion conditions). Amongst these two factors, the input waste composition will likely show spatial and temporal variation. As a result, the chemical composition of WTE ash will also fluctuate. To understand the spatial and temporal variation in WTE ash composition, in Task I, we collected 128 ash samples (62 bottom ash and 66 fly ash samples) from 11 WTE facilities located in 11 U.S. states and characterized them via X-ray Fluorescence, powder X-ray Diffraction, and Raman Spectroscopy. The findings from this extensive characterization work indicated that the key elements in WTE fly ashes are Ca, Cl (greater than 10 wt. %), Si, S, K, Zn ( between 1 and 10 wt. %), Mg, Al, P, Ti, Fe, Cu, Br, and Pb (between 0.1 and 1 wt. %). Similarly, the key elements in WTE bottom ash fraction finer than 45μm are Ca (greater than 10 wt. %), Mg, Al, Si, S, Cl, K, Ti, Fe, Zn (between 1 and 10 wt. %), P, V, Cr, Mn, Cu, Br, and Pb (between 0.1 and 1 wt. %). Here, we note that the dominant fraction of WTE bottom ash is the coarse fraction. The coarse WTE bottom ash fraction (rich in silicon) was not characterized in this study because of excessive grinding requirements and their unsuitability as a supplementary cementitious material due to their coarse nature. The elements in WTE bottom ashes are present as calcite, anhydrite, vaterite, hydroxyapatite, quartz, bassanite, gehlenite, akermanite, hydrocalumite, and portlandite. Similarly, the mineralogical species present in WTE fly ashes are calcium chloride hydroxide, halite, calcite, anhydrite, sylvite, hydrocalumite, vaterite, hannebachite, quartz, and bassanite. Temporal variation in ash composition may also result in significant fluctuations in chemical compositions. Therefore, a WTE facility may need to monitor the ash composition (elemental and mineralogical composition) in real time. In Task I, we evaluated the possibility of using a portable X-ray fluorescence (XRF) spectrometer to monitor the elemental composition in real-time. Specifically, we collected XRF data on identical specimens via a portable XRF spectrometer (low-end) and a lab-based benchtop XRF spectrometer (high-end). The collected data was used to train an A.I. algorithm (portable XRF data as an input and benchtop XRF data as an output) to predict accurate elemental composition using portable XRF data. Finally, we developed a 2-minute photobleaching protocol to monitor the mineralogical characteristics of WTE ashes via Raman spectroscopy. Overall, the activities in Task I improved our understanding of ash composition and developed techniques to monitor elemental and mineralogical composition in near real-time. Based on the findings of Task I, we find that WTE ashes exhibit wide variability in mineralogy. For ICP-based elemental analysis, all the mineralogical species in WTE ashes must be brought into solution. This is traditionally accomplished with acid digestion using a combination of multiple acids. However, acid digestion with multiple acids is time-consuming and often fails to ensure complete digestion of the ash matrix. To address this limitation, in Task II, we developed an alkali-fusion-based digestion protocol using a combination of lithium tetraborate, lithium metaborate, and their combinations as possible alkali fluxes for digesting WTE ashes entirely and rapidly. The validity of the developed method was evaluated on two standard ash specimens, i.e., SRM 1633c coal fly ash and BCR-176R incineration fly ash specimen. The findings suggest that the developed protocol can ensure complete digestion of elements such as Al, Ba, Ca, Cr, Cu, Mg, Mn, P, Sr, V, Zn, Be, K, and rare earth elements. The recent changes in the energy market towards renewables and increased metal recycling have resulted in reduced supplies of supplementary cementitious materials (coal fly ash and slag). Therefore, in Task III, we evaluated the possibility of employing WTE ashes as SCMs. As the chemical composition of WTE ashes varies temporally (on an hourly basis), there was also a need to develop tests that can evaluate the suitability of material to act as supplementary cementitious material rapidly, i.e., in a few minutes. Therefore, in Task II, we also developed a rapid test to assess the suitability of a material to act as an SCM in 5 minutes. This represents a significant advance over the state-of-the-art R 3 test, which takes ~144 hours. This test was initially validated on amorphous aluminosilicates, such as calcined clays, and could be extended to evaluate other industrial by-products, such as WTE ashes. In Task III, we evaluated the possibility of employing WTE ashes for two applications, i.e., as an SCM and a lime substitute for clay stabilization. The findings from Task I indicated that WTE ashes are enriched in chlorine and, therefore, cannot be used directly as an SCM due to corrosion-related risks and altered hydration kinetics. Accordingly, we developed an ash treatment protocol to reduce the solubility of chlorine-containing species in WTE ashes. The developed treatment protocol also immobilized lead in certain mineral forms. As a result of the treatment, WTE ashes can be used as SCMs without any corrosion or heavy metal leaching concerns. The second application examined in this study was clay stabilization. WTE ashes are calcium-rich and can be an adequate lime replacement for clay stabilization. Our findings reveal that the sum of the concentrations of Ca(OH) 2 and CaClOH controls the clay stabilization capability of WTE ashes. In summary, in this work, we evaluated the elemental and mineralogical characteristics of U.S. WTE ashes from diverse origins and developed tests to evaluate the chemical characteristics of these ashes in real time through a portable XRF and a benchtop Raman spectrometer. Based on the chemical characteristics of these ashes, we developed an ash treatment process to enable the use of WTE ashes as an SCM and also evaluated the possibility of employing these ashes for clay stabilization. Overall, the findings from this work enables the diversion of WTE ashes from landfills for multiple end-uses, i.e., as an SCM or a lime substitute for clay stabilization.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Development, Validation and Approval of A Planetary Extravehicular Activity Prebreathe Protocol: NASA Exploration Atmosphere Tests 1 & 2

INTRODUCTION: Denitrogenation prebreathe protocols used to mitigate DCS risk for Space Shuttle and International Space Station EVAs are validated for the microgravity environment, but the significantly increased risk of DCS during equivalent ambulatory surface EVAs make these protocols inapplicable to planetary/Lunar missions as planned by the Artemis program. Living in an “Exploration Atmosphere” of 56.5 kPa (8.2 psia), 34% O2, 66% N2 has been recommended by NASA for future Moon and Mars missions as a compromise that balances pre-EVA prebreathe duration, hypoxia, and flammability risk, assuming a 29.6 kPa (4.3 psi) spacesuit. A prebreathe validation campaign at NASA’s Johnson Space Center in 2022–2023 has aimed to validate the prebreathe durations and is being operationalized by NASA for use in upcoming Lunar EVAs. METHODS: Twelve volunteers lived in a hyboparic chamber for 11 days with an “exploration atmosphere” of 56.6kPa/34% O2 66% N2. Subjects acclimated to this atmosphere for 48 hrs and thereafter participated in five 6-hour simulated EVAs at 34kPa/85% O2 / 15% N2 over the course of 11 days. Prior to each simulated EVA, subjects underwent a 20-minute prebreathe at 85% O2. The EVA simulation was designed to include tasks that are physically and ergonomically representative of future planetary EVAs, proportionate to the subject’s VO2max. Decompression stress was evaluated during the simulated EVA by serial doppler and echocardiographs alternating every 15 min, as well as clinical monitoring for DCS signs/symptoms. Venous gas emboli (VGE) and DCS outcomes were verified against NASA Standard 3001, which guides allowable prebreathe protocol acceptance criteria. RESULTS AND DISCUSSION: Venous gas emboli (VGE) were identified during EVAs. No Grade IV VGE were observed. Two cases of mild, Type I DCS were identified in the subjects over the course of 50 EVA exposures. Ten planned EVA exposures were eliminated due to mask fit, metabolic rate, or subject safety concerns. One subject was removed from the study due to presence of left ventricular VGE. Additionally, two doppler techs also experienced DCS, and one case of hypoxia was noted. All cases of DCS resolved with treatment. No cases of severe DCS were observed. The observed incidence (4%, 1.1–13.5% at 95% confidence) met the NASA Standard 3001 criteria leading to the transition of this protocol from research to operational use for upcoming Lunar missions.

Exploration Atmosphere↗
DOE OSTI2015

SU-E-I-31: Differences Observed in Radiation Doses Across 2 Similar CT Scanners From Adult Brain-Neck CT Angiography

Purpose: The aim of this study is to evaluate the difference in radiation doses from adult Brain-Neck CT angiography (CTA) between two CT scanners. Methods: We collected CT dose index data (CTDIvol, DLP) from adult Brain-Neck CTA performed with two CT scanners (Sensation 64 (S64) and Definition AS (AS), Siemens Healthcare) performed at two of our facilities from Jan 1st to Dec 31th, 2014. X-ray dose management software (Radmetrics, Bayer Healthcare) was used to mine these data. All exams were performed with Tube Current Modulation (Care Dose 4D), tube voltage of 120 kVp, quality reference mAs of 300, beam collimation of 64*0.6 mm. The rotation time was set to 0.5 sec for S64 and 1.0 sec for AS. We also scanned an anthropomorphic skull and chest phantom under routine Brain-Neck CTA protocol with the two scanners and extracted the tube current values from the raw projection data. Results: The mean CTDIvol and DLP in Brain-Neck CTA was 72 mGy and 2554 mGy*cm for AS, which was substantially larger than the mean values of 46 mGy and 1699 mGy*cm for S64. The maximum tube current was 583 mA for most cases on the S64 while the maximum was 666 mA for AS even though the rotation time set for AS was 1.0 sec. Measurements obtained with the anthropomorphic phantom showed that the tube current reached 583 mA at the shoulder region for S64 while it reached to 666 mA for AS. Conclusion: The results of this study showed that substantially different CT doses can Result from Brain-Neck CTA protocols even when similar scanners and similar settings are used. Though both scanners have a similar maximum mA rating, differences in mA were observed through the shoulders, resulting in substantially different CTDIvol values.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-R-21: The Stability of Radiomics Features On 4D FDG-PET/CT Images

Purpose: The aim of our study was to perform a stability analysis of 4D PET-derived features in non-small cell lung carcinoma (NSCLC) based on six different respiratory phases. Methods: The 4D FDG-PET/CT respiratory phases were labeled as T0%, T17%, T33%,T50%, T67%, T83% phases, with the T0% phase approximately corresponding to the normal end-inspiration. Lesions were manually delineated based on fused PET-CT, using a standardized clinical delineation protocol. Six texture parameters were analyzed. Results: Results showed that the majority of assessed features had a low stability such as Homogeneity (0.385–0.416), Dissimilarity (3.707–3.861), Angular two moments (0.013–0.019), Contrast (39.782–49.562), Entropy(4.683–5.002) and Inverse differential moment (0.317–0.362) on different respiratory phases. Conclusion: This study suggest that further research of quantitative PET imaging features is warranted with respect to respiratory motion.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

SU-E-J-105: Stromal-Epithelial Responses to Fractionated Radiotherapy

Purpose: The stromal-epithelial-cell interactions that are responsible for directing normal breast-tissue development and maintenance play a central role in the progression of breast cancer. In the present study, we developed three-dimensional (3-D) cell co-cultures used to study cancerous mammary cell responses to fractionated radiotherapy. In particular, we focused on the role of the reactive stroma in determining the therapeutic ratio for postsurgical treatment. Methods: Cancerous human mammary epithelial cells were cultured in a 3-D collagen matrix with human fibroblasts stimulated by various concentrations of transforming growth factor beta 1 (TGF-β1). These culture samples were designed to model the post-lumpectomy mammary stroma in the presence of residual cancer cells. We tracked over time the changes in medium stiffness, fibroblast-cell activation (conversion to cancer activated fibroblasts (CAF)), and proliferation of both cell types under a variety of fractionated radiotherapy protocols. Samples were exposed to 6 MV X-rays from a linear accelerator in daily fraction sizes of 90, 180 and 360 cGy over five days in a manner consistent with irradiation exposure during radiotherapy. Results: We found in fractionation studies with fibroblasts and CAF that higher doses per fraction may be more effective early on in deactivating cancer-harboring cellular environments. Higher-dose fraction schemes inhibit contractility in CAF and prevent differentiation of fibroblasts, thereby metabolically uncoupling tumor cells from their surrounding stroma. Yet, over a longer time period, the higher dose fractions may slow wound healing and increase ECM stiffening that could stimulate proliferation of surviving cancer cells. Conclusion: The findings suggest that dose escalation to the region with residual disease can deactivate the reactive stroma, thus minimizing the cancer promoting features of the cellular environment. Large-fraction irradiation may be used to sterilize residual tumor cells and inhibit activation of intracellular transduction pathways that are promoted during the post-surgical woundhealing period. NIH award R01CA138882.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2

Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Practical Guide to Measuring Wetland Carbon Pools and Fluxes

Abstract Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions.

Bansal, Sheel (ORCID:0000000312331707)↗
DOE OSTI2018

Characterization of the quantumness of unsteerable tripartite correlations

Quantumness for a bipartite unsteerable quantum correlation is operationally characterized by the notion of super-unsteerability. Super-unsteerability refers to the requirement of a larger dimension of the random variable that the steering party has to preshare with the party to be steered in the classical simulation protocol to generate an unsteerable correlation than the local Hilbert space dimension of the quantum states (reproducing the given unsteerable correlation) at the steering party’s side. In the present study, this concept of super-unsteerability is generalized by defining the notion of super-bi-unsteerability for tripartite correlations, which is unsteerable across a bipartite cut. Genuine super-bi-unsteerability is defined as the occurrence of super-bi-unsteerability across all possible bipartite cuts. Specific example of genuine super-bi-unsteerability for tripartite correlations has been presented. This study provides a tool to characterize the genuine quantumness of tripartite quantum correlations which are unsteerable across every bipartite cut.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Observation of current-induced switching in non-collinear antiferromagnetic IrMn 3 by differential voltage measurements

There is accelerating interest in developing memory devices using antiferromagnetic (AFM) materials, motivated by the possibility for electrically controlling AFM order via spin-orbit torques, and its read-out via magnetoresistive effects. Recent studies have shown, however, that high current densities create non-magnetic contributions to resistive switching signals in AFM/heavy metal (AFM/HM) bilayers, complicating their interpretation. Here we introduce an experimental protocol to unambiguously distinguish current-induced magnetic and nonmagnetic switching signals in AFM/HM structures, and demonstrate it in IrMn 3 /Pt devices. A six-terminal double-cross device is constructed, with an IrMn 3 pillar placed on one cross. The differential voltage is measured between the two crosses with and without IrMn 3 after each switching attempt. For a wide range of current densities, reversible switching is observed only when write currents pass through the cross with the IrMn 3 pillar, eliminating any possibility of non-magnetic switching artifacts. Micromagnetic simulations support our findings, indicating a complex domain-mediated switching process.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Phonons and magnetic excitation correlations in weak ferromagnetic YCrO{sub 3}

Here, we report the temperature dependent Raman spectroscopic studies on orthorhombically distorted perovskite YCrO{sub 3} over a temperature range of 20–300 K. Temperature dependence of DC-magnetization measurements under field cooled and zero field cooled protocols confirmed a Néel transition at T{sub N} ∼ 142 K. Magnetization isotherms recorded at 125 K show a clear loop opening without any magnetization saturation up to 20 kOe, indicating a coexistence of antiferromagnetic (AFM) and weak ferromagnetic (WFM) phases. Estimation of exchange constants using mean-field approximation further confirm the presence of a complex magnetic phase below T{sub N}. Temperature evolution of Raman line-shape parameters of the selected modes (associated with the octahedral rotation and A(Y)-shift in the unit-cell) reveal an anomalous phonon shift near T{sub N}. An additional phonon anomaly was identified at T{sup *} ∼ 60 K, which could possibly be attributed to the change in the spin dynamics. Moreover, the positive and negative shifts in Raman frequencies between T{sub N} and T{sup *} suggest competing WFM and AFM interactions. A close match between the phonon frequency of B{sub 3g} (3)-octahedral rotation mode with the square of sublattice magnetization between T{sub N} and T{sup *} is indicative of the presence of spin-phonon coupling in multiferroic YCrO{sub 3}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗