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At least 721 records · Page 40

Application-Specific Graph Sampling for Frequent Subgraph Mining and Community Detection

Graph mining is an important data analysis methodology, but struggles as the input graph size increases. The scalability and usability challenges posed by such large graphs make it imperative to sample the input graph and reduce its size. The critical challenge in sampling is to identify the appropriate algorithm to insure the resulting analysis does not suffer heavily from the data reduction. Predicting the expected performance degradation for a given graph and sampling algorithm is also useful. In this paper, we present different sampling approaches for graph mining applications such as Frequent Subgrpah Mining (FSM), and Community Detection (CD). We explore graph metrics such as PageRank, Triangles, and Diversity to sample a graph and conclude that for heterogeneous graphs Triangles and Diversity perform better than degree based metrics. We also present two new sampling variations for targeted graph mining applications. We present empirical results to show that knowledge of the target application, along with input graph properties can be used to select the best sampling algorithm. We also conclude that performance degradation is an abrupt, rather than gradual phenomena, as the sample size decreases. We present the empirical results to show that the performance degradation follows a logistic function.

Purohit, Sumit↗

Design and Validation of In-Source Atmospheric Pressure Photoionization Hydrogen/Deuterium Exchange Mass Spectrometry with Continuous Feeding of D{sub 2}O

In this study, continuous in-source hydrogen/deuterium exchange (HDX) atmospheric pressure photoionization (APPI) mass spectrometry (MS) with continuous feeding of D{sub 2}O was developed and validated. D{sub 2}O was continuously fed using a capillary line placed on the center of a metal plate positioned between the UV lamp and nebulizer. The proposed system overcomes the limitations of previously reported APPI HDX-MS approaches where deuterated solvents were premixed with sample solutions before ionization. This is particularly important for APPI because solvent composition can greatly influence ionization efficiency as well as the solubility of analytes. The experimental parameters for APPI HDX-MS with continuous feeding of D{sub 2}O were optimized, and the optimized conditions were applied for the analysis of nitrogen-, oxygen-, and sulfur-containing compounds. The developed method was also applied for the analysis of the polar fraction of a petroleum sample. Thus, the data presented in this study clearly show that the proposed HDX approach can serve as an effective analytical tool for the structural analysis of complex mixtures. .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Manipulation of Samples at Extreme Temperatures for Fast in-situ Synchrotron Measurements

An aerodynamic sample levitation system with laser beam heating was integrated with the APS beamlines 6 ID-D, 11 ID-C and 20 BM-B. The new capability enables in-situ measurements of structure and XANES at extreme temperatures (300-3500 °C) and in conditions that completely avoid contact with container surfaces. In addition to maintaining a high degree of sample purity, the use of aerodynamic levitation enables deep supercooling and greatly enhanced glass formation from a wide variety of melts and liquids. Development and integration of controlled extreme sample environments and new measurement techniques is an important aspect of beamline operations and user support. Processing and solidifying liquids is a critical value-adding step in manufacturing semiconductors, optical materials, metals and in the operation of many energy conversion devices. Understanding structural evolution is of fundamental importance in condensed materials, geology, and biology. The new capability provides unique possibilities for materials research and helps to develop and maintain a competitive materials manufacturing and energy utilization industry. Test samples were used to demonstrate key features of the capability including experiments on hot crystalline materials, liquids at temperatures from about 500 to 3500 °C. The use of controlled atmospheres using redox gas mixtures enabled in-situ changes in the oxidation states of cations in melts. Significant innovations in this work were: (i) Use of redox gas mixtures to adjust the oxidation state of cations in-situ (ii) Operation with a fully enclosed system suitable for work with nuclear fuel materials (iii) Making high quality high energy in-situ x-ray diffraction measurements (iv) Making high quality in-situ XANES measurements (v) Publishing high impact results (vi) Developing independent funding for the research on nuclear materials This SBIR project work led to a commercial instrument product for the niche market of processing and studying materials in extreme conditions. MDI registered the trademark “Instruments for Innovation®” and sells products under this trademark. SBIR is the ideal vehicle for funding developments such as this since the total market size is relatively small meaning that venture investments to develop products cannot typically be obtained. The sale of niche market instruments for work in extreme conditions has been several million dollars over the last decade. The work to develop and build and sell this instrument has created stable high paying jobs in the technology manufacturing sector. Outreach enabled by this research helped with PhD thesis research, supported three undergraduate interns and one local high school student. In addition, several scientific articles were published, papers were presented at international conferences, and a workshop was held.

36 MATERIALS SCIENCE↗

Jiangsu Nanjing – Lawrence Berkeley Life Sciences Center for Translational Medicine (CRADA AWD00000392)

Project 1: Our previous work demonstrated that the CES biomarker can be an approximate measure for the levels of chromosomal instability (CIN) in cancer, and that the CES (for Centromere and kinetochore gene Expression Score) biomarker effectively predicts which cancer patients benefit from adjuvant chemotherapies in lung and other cancer types. Such a utility can potentially reduce overtreatment that is common in lung cancer treatment. We determined performance of the multiplex Quantigene RNA assay platform for measuring mRNA levels of CES genes using clinical tumor samples. These experiments determined sensitivity, specificity and detection limit of 12 CES genes and 5 control genes using clinical tumor samples with paired normal tissue samples. We determined how sample concentration and storage conditions affect measurement sensitivity and specificity, and whether sample storage over time affects result reproducibility. Importantly, we confirmed that early stage lung cancer CES values are significantly higher than those of paired normal tissues in all cases. This result greatly extended our bioinformatic data mining by confirming that we can measure CES values directly from patient tumor tissue, and that tumors have higher CES values than normal tissues. Unfortunately, our CRADA partner in China did not finish measuring CES expression levels for a larger group of ~100 tumor samples, due to the long period time required for human subject review in China. This delay prevented us from generating enough additional data to generate a significant statistical model. We finished analyzing all the data acquired during the CRADA, and are trying to work collaboratively with the Shanghai University Lung Cancer Hospital to complete the analysis of more tumor samples. Although no publications have resulted from this research, the findings are crucial for ongoing efforts to obtain funding to develop the technology to address problems in deciding on appropriate treatment regimens for individual patients, in clinical settings. Project 2: The overarching milestones of CRADA Project 2 were to investigate the role of FAM83 family members in cancer progression. Two publications resulted from this work which are highlighted below. The first major goal of the CRADA was to broadly assess the role of FAM83 family oncogenes in human cancer using a multi-omic bioinformatic approach (Snijders et al 2017 Mol. Oncol 11). The second major goal was to specifically assess the role of FAM83D in a cancer progression and metastasis (Yin et al 2019 Cell Oncol; in revision). Role of FAM83 family oncogenes in human cancers Recent studies from our laboratory as well as other groups have demonstrated that FAM83 family members have oncogenic properties and have significantly elevated expression levels in multiple human tumor types, including breast cancers (BC). We performed an integrative multi-omics bio-informatic analysis of the role of FAM83 family oncogenes in human cancers. Our findings were published in the journal Molecular Oncology (Snijders et al; Mol Oncol. 2017 Feb;11(2):167-179). Highlights from this manuscript are: • Transcriptional levels of FAM83 family members are frequently and dramatically elevated across tumor types in human • DNA copy number increase appears to be a potential mechanism for increased expression of FAM83 genes • FAM83 family gene signature is associated with poor survival across human tumor types • FAM83 gene alterations are significantly correlated with TP53, PIK3CA and Ecadherin mutations. In conclusion, this analysis of FAM83 family members opened up a new horizon for further understanding the significance of FAM83 genes in cancer and clinical applications in diagnosis, prognosis and therapy. Role of FAM83D in human non-small cell lung cancer (NSCLC) metastasis and its impact on chemotherapy. Lung cancer is one of the most common malignant tumors in the world and non-small cell lung cancer (NSCLC) accounts for 80~85% of all diagnosed lung cancer cases, one of the deadliest cancers worldwide. FAM83D has been proposed as an oncoprotein in several types of human cancer, yet its role and molecular mechanism in human non-small cell lung cancer (NSCLC) metastasis and its impact on chemotherapy are poorly understood. We evaluated the expression of FAM83D in NSCLC cells and cancerous tissues and its prognostic significance, then investigated the effect of FAM83D on tumorigenic phenotypes such as cell proliferation, EMT and invasive capability, and finally assessed impact of FAM83D on NSCLC chemo-drug resistance. The results of this study are currently in revision at the journal Cellular Oncology. Highlights from this manuscript are: • FAM83D expression is elevated in NSCLC cells and tissues and associated with poor prognosis • FAM83D promotes NSCLC cell proliferation • FAM83D induces EMT in NSCLC cells • FAM83D promotes NSCLC cell migration and invasion • FAM83D promotes EMT and invasive capability of NSCLC cells by regulating AKT/mTOR pathway • FAM83D silencing increases cisplatin sensitivity of NSCLC cells In summary, this second study demonstrated for the first time that FAM83D promoted EMT and metastasis of NSCLC cells through AKT/mTOR signal pathway as well as increased the sensitivity of NSCLC to cisplatin. This study may provide potential targets for advanced NSCLC treatment and personalized therapy.

59 BASIC BIOLOGICAL SCIENCES↗

Near-edge x-ray absorption fine structure spectroscopy at atmospheric pressure with a table-top laser-induced soft x-ray source

The authors present a table-top soft x-ray absorption spectrometer, accomplishing investigations of the near-edge x-ray absorption fine structure (NEXAFS) in a laboratory environment. The system is based on a low debris plasma ignited by a picosecond laser in a pulsed krypton gas jet, emitting soft x-ray radiation in the range from 1 to 5 nm. For absorption spectroscopy in and around the “water window” (2.3–4.4 nm), a compact helium purged sample compartment for experiments at atmospheric pressure has been constructed and tested. NEXAFS measurements on CaCl{sub 2} and KMnO{sub 4} samples were conducted at the calcium and manganese L-edges, as well as at the oxygen K-edge in air, atmospheric helium, and under vacuum, respectively. The results indicate the importance of atmospheric conditions for an investigation of sample hydration processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Mg 2 h and k lines in a sample of dMe and dM stars

Both Mg II h and k line fluxes are presented for a sample of 4 dMe and 3 dM stars obtained with the IUE satellite in the long wavelength, low dispersion mode. The observed fluxes are converted to stellar surface flux units and the importance of chromospheric non radiative heating in this sample of M dwarf stars is intercompared. In addition, the net chromospheric radiative losses due to the Ca II H and K lines in those stars in the sample for which calibrated Ca II H and K line data exist are compared. Active region filling factors which likely give rise to the observed optical and ultraviolet chromospheric emission are estimated. The implications of the results for homogeneous, single component stellar model chromospheres analyses are discussed.

Giampapa, M. S.↗

In situ X-ray and IR probes relevant to Earth science at the Advanced Light Source at Lawrence Berkeley Laboratory

Access to synchrotron X-ray facilities has become an important aspect for many disciplines in experimental Earth science. This is especially important for studies that rely on probing samples in situ under natural conditions different from the ones found at the surface of the Earth. The non-ambient condition Earth science program at the Advanced Light Source (ALS), Lawrence Berkeley National Laboratory, offers a variety of tools utilizing the infra-red and hard X-ray spectrum that allow Earth scientists to probe Earth and environmental materials at variable conditions of pressure, stress, temperature, atmospheric composition, and humidity. These facilities are important tools for the user community in that they offer not only considerable capacity (non-ambient condition diffraction) but also complementary (IR spectroscopy, microtomography), and in some cases unique (Laue microdiffraction) instruments. The availability of the ALS’ in situ probes to the Earth science community grows especially critical during the ongoing dark time of the Advanced Photon Source in Chicago, which massively reduces available in situ synchrotron user time in North America.

58 GEOSCIENCES↗

Improvements in the Sample Space for the Backscattering Silicon Spectrometer (BASIS)

The increase in neutron flux at the Oak Ridge National Laboratory (ORNL) Spallation Neutron Source (SNS), currently operating at 2.0 MW proton beam power, has created new opportunities for higher-throughput neutron scattering experiments while also increasing the importance of minimizing background scattering and optimizing sample-environment operations. To address these challenges on the Backscattering Silicon Spectrometer (BA-SIS), several upgrades were developed and evaluated, including boron carbide (B₄C) masking for flat-plate sample containers, multi-cell sample holders used with a vertically translating sample stick, and an automated helium pump and purge (HPP) system for closed-cycle refrigerators. Neutron diffraction measurements demonstrate that B₄C masks reduce background scattering by 49–67%, outperforming both borated aluminum and boron nitride masks while introducing no additional Bragg reflections within the instrument’s accessible Q-range. Commissioning tests of a double-cell flat-plate sample contain-er showed no measurable crosstalk between adjacent sample compartments and con-firmed stable thermal performance, enabling multiple samples to be measured without re-peated temperature cycling. In addition, the automated HPP system provided reproducible sample-space gas handling with approximately ±1 mbar precision while reducing the need for operator intervention and supporting remote operation. Together, these developments improve signal-to-noise performance, increase experimental throughput, and enhance operational efficiency at BASIS, supporting the instrument’s continued operation under higher neutron flux conditions.

Jalarvo, Niina [ORNL] (ORCID:0000000306446866)↗

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US

Soil microbial communities are structured by biogeochemical processes that occur at many different spatial scales, which makes soil sampling difficult. Because soil microbial communities are important in nutrient cycling and soil fertility, it is important to understand how microbial communities function within the heterogeneous soil landscape. In this study, a self-organizing map was used to determine whether landscape data can be used to characterize the distribution of microbial biomass and activity in order to provide an improved understanding of soil microbial community function. Points within a row crop field in south-central Iowa were clustered via a self-organizing map using six landscape properties into three separate landscape clusters. Twelve sampling locations per cluster were chosen for a total of 36 locations. After the soil samples were collected, the samples were then analysed for various metabolic indicators, such as nitrogen and carbon mineralization, extractable organic carbon, microbial biomass, etc. It was found that sampling locations located in the potholes and toe slope positions had significantly greater microbial biomass nitrogen and carbon, total carbon, total nitrogen and extractable organic carbon than the other two landscape position clusters, while locations located on the upslope did not differ significantly from the other landscape clusters. However, factors such as nitrate, ammonia, and nitrogen and carbon mineralization did not differ significantly across the landscape. Altogether, this research demonstrates the effectiveness of a terrain-based clustering method for guiding soil sampling of microbial communities.

54 ENVIRONMENTAL SCIENCES↗

Data Correction of Intensity Modulated Small Angle Scattering

Abstract To investigate long length scale structures using neutron scattering, real space techniques have shown certain advantages over the conventional methods working in reciprocal space. As one of the real space measurement techniques, spin echo modulated small angle neutron scattering (SEMSANS) has attracted attention, due to its relaxed constraints on sample environment and the possibility to combine SEMSANS and a conventional small angle neutron scattering instrument. In this report, we present the first implementation of SEMSANS at a pulsed neutron source and discuss important corrections to the data due to the sample absorption. These corrections allow measurements made with different neutron wavelengths and SEMSANS configurations to be overlaid and give confidence that the measurements provide an accurate representation of the density correlations in the sample.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fission gas trapped in Chornobyl fuel microparticles reveals details of reactor operations

The isotopic ratios of fission gas would provide important source information of a nuclear fuel sample found in the environment. However, it is believed that during a reactor accident like Chornobyl all fission gas is lost and that the radioactive particles found in the Chornobyl Exclusion Zone today are depleted in gases by the initial explosion and subsequent fire. We disprove this hypothesis by detection and analysis of trapped krypton and xenon in these particles. Our analysis of krypton and xenon isotopes by noble gas mass spectroscopy in combination with resonance ionization mass spectrometry establishes that important information about reactor operations like age, neutron flux and plutonium fission fraction can still be reconstructed from individual micrometer-sized particles even after decades of weathering in the environment.

Chornobyl↗

Improving Quantitative Laboratory Analysis of Phycobiliproteins to Provide High Quality Validation Data for Ocean Color Remote Sensing Algorithm

Identification and characterization of phytoplankton communities and their physiology is a primary aim of NASA's PACE satellite mission. The concentration and composition of phytoplankton pigments modulate the spectral distribution of light emanating from the ocean, which is measured by ocean color satellites, and thus provide critical information on phytoplankton community composition and physiological parameters. One diagnostic class of pigments not routinely well-characterized is the phycobiliproteins (PBPs), and NASA has a requirement to collect and distribute high quality in situ data in support of data product validation activities for ocean color missions. Phycobiliproteins are light-harvesting proteins that are the predominant photosynthetic pigments in some classes of phytoplankton including cyanobacteria, such as Synechococcus, Trichodesmium, and Microcystis. With the advance of hyperspectral ocean color sensors such as on PACE (expected to launch in late 2022), it is essential that we implement routine analysis of PBPs that satisfies several considerations: reproducible, high extraction efficiency for a variety of environments, and Suitable for large scale analysis. Published techniques for PBP analysis vary in recommendations for: collection, extraction, disruption mode, and analysis; evidence suggests the variation in results may depend at least in part on the species and even strain(s) of interest. Experiments that tested variations in these parameters have drawn very different conclusions regarding extraction efficiency and reproducibility. Cyanobacteria are more difficult to extract than other PBP-containing algae such as cryptophytes, but can be important primary producers. We used a cryptophyte (Rhodomonas salina) and cyanobacterium (Synechococcus sp.) to compare extraction efficiencies of water samples concentrated via centrifugation to filtered samples using two different extraction buffers (phosphate and asolectin-CHAPS). Samples were analyzed on a fluorometer configured for PC and PE detection. The results have important implications for collection and storage of samples for routine analysis; some previous studies (although not all) have suggested that filtered samples have a much lower extraction efficiency than whole water samples.

Kenemer, Christopher↗

Single-shot X-ray absorption spectroscopy at X-ray free electron lasers

X-ray Absorption Spectroscopy (XAS) is a widely used X-ray diagnostic method for studying electronic and structural properties of matter. At first glance, the relatively narrow bandwidth and the highly fluctuating spectral structure of X-ray Free Electron Lasers (XFEL) sources seem to require accumulation over many shots to achieve high data quality. To date the best approach to implementing XAS at XFEL facilities has been using monochromators to scan the photon energy across the desired spectral range. While this is possible for easily reproducible samples such as liquids, it is incompatible with many important systems. Here, we demonstrate collection of single-shot XAS spectra over 10s of eV using an XFEL source, with error bars of only a few percent. We additionally show how to extend this technique over wider spectral ranges towards Extended X-ray Absorption Fine Structure measurements, by concatenating a few tens of single-shot measurements. Our results pave the way for future XAS studies at XFELs, in particular those in the femtosecond regime. This advance is envisioned to be especially important for many transient processes that can only be initiated at lower repetition rates, for difficult to reproduce excitation conditions, or for rare samples, such as those encountered in high-energy density physics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Direct and rapid uranium isotopic analysis of environmental sample swipes via microextraction – LS-APGD/Orbitrap mass spectrometry

Accurate and precise isotopic analysis of actinides collected on environmental sample swipes from within nuclear facilities is an important safeguarding measure for detecting undeclared materials and activities. Traditional isotope ratio (IR) analysis of actinides using a bulk digestion approach can be laborious and time-consuming. Recently, direct analysis of environmental swipe samples using a microextraction approach has been explored as an alternative to conventional bulk digestion methods. The present study further evaluates this approach for accurate and precise isotopic analysis of uranium (U) in cotton swipe samples using the liquid sampling-atmospheric pressure glow discharge (LS-APGD)/Orbitrap-FTMS Booster detection system. The instrumental parameters were optimized, and quantitative capabilities were demonstrated through excellent linearity (R2 = 0.99) across a deposited mass range of 1 to 500 ng, with a limit of detection of 90 pg (in a 2 × 4 mm region) for total U; well below typical U concentrations (ng–mg range) in environmental sample swipes. The 235U/238U ratio showed excellent accuracy (−0.3% relative difference from the certificate value), with ∼20× improvement over previous microextraction-Orbitrap methods. Precision (∼1% relative standard deviation) was also greatly enhanced by ∼5×. This study also demonstrates that figures of merit achieved with neat U solution were not highly degraded when various external interfering elements/matrices were introduced. Finally, the developed method was successfully applied to analyze practical swipe samples representative of laboratory and outdoor environments. The presented figures of merit and applicability to practical samples further validate the capability of the platform for rapid analysis (<7 minutes) of environmental swipe samples.

Shrestha, Suraj [Clemson University, SC]↗

Identifying the Effects of X-Ray Computed Tomography on Mars 2020 Tier I Organic Compounds

Mars sample return presents unique challenges for the clean collection, containment, curation and processing of samples. The related issues of life detection and Planetary Protection are of particular importance when developing successful strategies for the acquisition and handling of Mars returned samples. In order to achieve the Mars Sample Return (MSR) science goals, reliable analyses will depend on overcoming some challenging signal/noise-related issues, such that sparse Martian organic compounds will need to be reliably analyzed against the contamination background arising from the complicated MSR campaign. Reliable analyses will depend on clean acquisition, as well as robust documentation of all aspects of both the development and management of the cache.

Weizenbach, L. C.↗

Thermolytic Hydrogen Generation Testing of Tank 22 Material

Savannah River National Laboratory performed hydrogen generation rate (HGR) testing using Tank 22 actual-waste sample material. The main objective of the testing was to determine the thermolysis HGR for Tank 22 material with and without added glycolate. An important use of the data from actual-waste sample testing is to validate equations for the Savannah River Site Concentration, Storage, and Transfer Facility (CSTF) HGR being developed through simulated-waste testing. Not exclusive to providing data for model validation, the desired outcome of this testing was to demonstrate a negligible thermolytic HGR in Tank 22 from the contribution of glycolate from the future Defense Waste Processing Facility (DWPF) Nitric-Glycolic Acid (NGA) flowsheet to Tank 22. Tank 22 is the pathway for glycolate in the DWPF recycle stream to enter the CSTF. Testing with added glycolate used the estimated future concentration of glycolate based on DWPF recycle with limited Sludge Receipt and Adjustment Tank and Slurry Mix Evaporator (SME) material carry-over but without glycolate mitigation in the Recycle Collection Tank. Minor objectives include the determination of the impact of the glycolate source used in testing and the inclusion of sludge solids in testing.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Adventitious Carbon on Primary Sample Containment Metal Surfaces

Future missions that return astromaterials with trace carbonaceous signatures will require strict protocols for reducing and controlling terrestrial carbon contamination. Adventitious carbon (AC) on primary sample containers and related hardware is an important source of that contamination. AC is a thin film layer or heterogeneously dispersed carbonaceous material that naturally accrues from the environment on the surface of atmospheric exposed metal parts. To test basic cleaning techniques for AC control, metal surfaces commonly used for flight hardware and curating astromaterials at JSC were cleaned using a basic cleaning protocol and characterized for AC residue. Two electropolished stainless steel 316L (SS- 316L) and two Al 6061 (Al-6061) test coupons (2.5 cm diameter by 0.3 cm thick) were subjected to precision cleaning in the JSC Genesis ISO class 4 cleanroom Precision Cleaning Laboratory. Afterwards, the samples were analyzed by X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy.

Calaway, M. J.↗

Thematic Mapper Data Quality and Performance Assessment in Renewable Resources/agriculture Remote Sensing

It is believed that the increased spatial resolution will provide solutions to proportion estimation error due to mixed pixels, and the increased spectral resolution will provide for the identification of important agricultural features such as crop stage, and condition. The results of analyses conducted relative to these hypothesis from sample segments extracted from the 4-band Detroit scene and the 7-band Mississippi County, Arkansas engineering test scene are described. Several studies were conducted to evaluate the geometric and radiometric performance of the TM to determine data viability for the more pertinent investigations of TM utility. In most cases this requirement was more than sufficiently satisfied. This allowed the opportunity to take advantage of detailed ground observations for several of the sample segments to assess class separability and detection of other important features with TM. The results presented regarding these TM characteristics show that not only is the increased definition of the within scene variance captured by the increased spatial and spectral resolution, but that the mid-IR bands (5 and 7) are necessary for optimum crop type classification. Both qualitative and quantitative results are presented that describe the improvements gained with the TM both relative to the MSS and on its own merit.

Bizzell, R. M.↗