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At least 271 records · Page 15

Understanding mutagenesis through delineation of mutational signatures in human cancer

Each individual cell within a human body acquires a certain number of somatic mutations during a course of its lifetime. These mutations originate from a wide spectra of both endogenous and exogenous mutational processes that leave distinct patterns of mutations, termed mutational signatures, embedded within the genomes of all cells. In recent years, the vast amount of data produced by sequencing of cancer genomes was coupled with novel mathematical models and computational tools to generate the first comprehensive map of mutational signatures in human cancer. Up to date, >30 distinct mutational signatures have been identified, and etiologies have been proposed for many of them. This paper provides a brief historical background on examination of mutational patterns in human cancer, summarizes the knowledge accumulated since introducing the concept of mutational signatures and discusses their future potential applications and perspectives within the field.

59 BASIC BIOLOGICAL SCIENCES↗

Time- and momentum-resolved tunneling spectroscopy of pump-driven nonthermal excitations in Mott insulators

We present a computational technique to calculate time- and momentum-resolved nonequilibrium spectral density of correlated systems using a tunneling approach akin to scanning tunneling spectroscopy. The important difference is that our probe is extended, basically a copy of the sample, allowing one to extract the momentum information of the excitations. We illustrate the method by measuring the spectrum of a Mott-insulating extended Hubbard chain after a sudden quench with the aid of time-dependent density-matrix renormalization-group calculations. In this work, we demonstrate that the system realizes a nonthermal state that is an admixture of spin and charge density wave states, with corresponding signatures that are recognizable as in-gap subbands. In particular, we identify a band of excitons and one of stable antibound states at high energies that gains enhanced visibility after the pump. We do not appreciate noticeable relaxation within the time scales considered, which is attributed to the lack of decay channels due to spin-charge separation. These ideas can be readily applied to study transient dynamics and spectral signatures of correlation-driven nonequilibrium processes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Gate-tunable heavy fermion quantum criticality in a moiré Kondo lattice

We propose a realization of Kondo lattice physics in moiré superlattices at the interface between a WX 2 homobilayer and MoX 2 monolayer (X = S,Se). Under appropriate gating conditions, the interface WX 2 layer forms a triangular lattice of local moments that couple to itinerant electrons in the other WX 2 layer via a gate-tunable Kondo exchange interaction. Using a parton mean-field approach, we identify a range of twist angles which support a gate-tuned quantum phase transition between a heavy Fermi liquid with large anomalous Hall conductance and a chiral spin liquid coexisting with a light Fermi liquid and describe experimental signatures to distinguish among competing theoretical scenarios.

36 MATERIALS SCIENCE↗

A Methodology for Calculating Radiation Signatures

A rigorous formalism is presented for calculating radiation signatures from both Special Nuclear Material (SNM) as well as radiological sources. The use of MCNP6 in conjunction with CINDER/ORIGEN is described to allow for the determination of both neutron and photon leakages from objects of interest. In addition, a description of the use of MCNP6 to properly model the background neutron and photon sources is also presented. Examinations of the physics issues encountered in the modeling are investigated so as to allow for guidance in the user discerning the relevant physics to incorporate into general radiation signature calculations. Furthermore, examples are provided to assist in delineating the pertinent physics that must be accounted for. Finally, examples of detector modeling utilizing MCNP are provided along with a discussion on the generation of Receiver Operating Curves, which are the suggested means by which to determine detectability radiation signatures emanating from objects.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Utica Shale Energy and Environment Laboratory Final Scientific/Technical Report

The Ohio State University (OSU) was awarded a contract on October 1, 2014, from the Department of Energy National Energy Technology Laboratory (DOE-NETL) to develop the Utica Shale Energy and Environment Laboratory (USEEL) in the Utica-Point Pleasant shale play of the Appalachian Basin. It was designed to be an environmental and technology development lab that would enable the academic, industry, government, and non-governmental organization (NGO) research communities to better understand unconventional oil and gas (UOG) engineering practices and technology to increase production and safety, and decrease environmental effects. Political and economic consequences necessitated changes in project site location and design, from the Ohio State Eastern Agricultural Research Station (EARS) and the Muskingum Watershed Conservancy District (MWCD) in east-central Ohio to a site located at an Energy Corporation of America (ECA) Marcellus drill pad in Greene County, Pennsylvania. Although the overall project progressed little beyond planning and administration before termination on September 18, 2017, significant research and MS or PhD investigations were completed or continue today. An experimental study design for site specific and regional baseline assessments was developed utilizing ecoregions, United States Geological Survey (USGS) Hydraulic Unit Code watersheds, and GIS technology and databases. This can be utilized to build a defensible and scalable management and research framework for UOG investigations that can be extrapolated for predictive and comparative analyses. The most commonly mentioned perceived risks of shale energy development identified in a socioeconomic analysis included impacts to the environment and water resources, traffic and road deterioration, and crime. Economic benefits, such as the windfall wealth to residents, job opportunities, and the demand for hotels and restaurants emerged, as the main positive impact to the community. Preliminary results of an analysis of the location and mechanisms for extremely high pore pressures of the deep Utica-Point Pleasant formations of southwestern Pennsylvania and their possible relationship to high initial production rates indicate that the overpressure is caused by a combination disequilibrium compaction and fluid expansion. Drilling fluids research designed a proof-of-concept device to evaluate desalination and solvent separation in hydraulic fracturing flowback water that could facilitate water recycling and potentially mitigate deep-well injection. A groundwater study was devised to characterize the subsurface aquifers in terms of the geological framework and groundwater chemistry, including the chemistry of dissolved gases and salts. Brines and gases associated with hydrocarbon migration in groundwater (including noble gases and hydrocarbons) were to be specifically fingerprinted for use as tracers of fluid migration. Trace element analysis of fish otoliths, using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), is being utilized to assess surface water quality. This methodology will be used to reconstruct the exposure histories of fish from watersheds and discriminate between the signatures associated with hydraulic fracturing and coal mining activities.

03 NATURAL GAS↗

Microflaring in Low-Lying Core Fields and Extended Coronal Heating in the Quiet Sun

We have previously reported analyses of Yohkoh SXT data examining the relationship between the heating of extended coronal loops (both within and stemming from active regions) and microflaring in core fields lying along neutral lines near their footpoints (J. G. Porter, D. A. Falconer, and R. L. Moore 1998, in Solar Jets and Coronal Plumes, ed. T. Guyenne, ESA SP-421, and references therein). We found a surprisingly poor correlation of intensity variations in the extended loops with individual microflares in the compact heated areas at their feet, despite considerable circumstancial evidence linking the heating processes in these regions. Now, a study of Fe XII image sequences from SOHO EIT show that similar associations of core field structures with the footpoints of very extended coronal features can be found in the quiet Sun. The morphology is consistent with the finding of Wang et al. (1997, ApJ 484, L75) that polar plumes are rooted at sites of mixed polarity in the magnetic network. We find that the upstairs/downstairs intensity variations often follow the trend, identified in the active region observations, of a weak correspondence. Apparently much of the coronal heating in the extended loops is driven by a type of core field magnetic activity that is "cooler" than the events having the coronal signature of microflares, i.e., activity that results in little heating within the core fields themselves. This work was funded by the Solar Physics Branch of NASA's Office of Space Science through the SR&T Program and the SEC Guest Investigator Program.

Porter, Jason G.↗

Compounds for neutron radiation detectors and systems thereof

A composition of matter includes an organic molecule having a composition different than stilbene. The organic molecule is embodied as a crystal, and exhibits: an optical response signature for neutrons; an optical response signature for gamma rays, and performance comparable to or superior to stilbene in terms of distinguishing neutrons from gamma rays. The optical response signature for neutrons is different than the optical response signature for gamma rays.

36 MATERIALS SCIENCE↗

Global Geospace Science (GGS)/POLAR Thermal Ion Dynamics Experiments (TIDE) Co-Investigator Program: Mission Operations and Data Analysis (MO/DA)

We have pursued several investigations using the Polar/TIDE data set. The first was a comparison of TIDE high-altitude observations with similar ion flux signatures in the Los Alamos National Laboratory (LANL) magnetospheric plasma analyzer (MPA) data. There are several geosynchronously orbiting satellites with LANL MPA instruments onboard. When the satellite is immersed in fresh plasma sheet electrons, the spacecraft voltage drops to several hundred volts negative, and cold ions are accelerated in to the detector. In the LANL MPA spectrograms, the accelerated cold ions appear as a bright, narrow line, following the voltage of the spacecraft. This "ion line" is seen regularly on the nightside, but has not received much attention. The Polar TIDE observations indicated a ubiquitous "lobal wind" in the near-- magnetotail, a field-aligned stream of approx. 100 eV ions flowing out of both polar ionospheres. The interesting result of this research is that the MPA ion line is also peaked in the field-aligned direction, even though the potential well should be uniform in all directions. It is believed that this is evidence that the lobal winds not only populate the high-latitude lobes, but fill the lobes all the way in to the near-Earth plasma sheet (the location of geosynchronous orbit). This activity developed into a full-scale survey of the lobal wind observations in the TIDE database. The universality of these observations with respect to local time and solar wind conditions implies that the ionospheric outflow is supplying the near-Earth plasma sheet at all times, regardless of magnetic activity. We have conducted a statistical study of the characteristics of the lobal wind in these two data sets FIDE and LANL MPA), finding much similarity between them. Using these characteristics as input conditions to our inner magnetosphere ion transport model, we have conducted simulations of the flow of these particles inside of geosynchronous orbit to show the impact these particles will have on the near-Earth space environment. As the study has progressed, these results have been presented several times to the TIDE team during teleconferences. It is planned to present this survey at the GEM 2004 Summer Workshop, and hopefully at additional conferences in the near future. We are presently writing a paper on the lobal wind occurrence statistics, which should be submitted in April or May to the Journal of Geophysical Research for publication. An undergraduate student at the University of Alabama in Huntsville, Will Maddox, working at NASA MSFC with Dr. Paul Craven, is presently creating a database of the values TIDE moments for the lobal wind (under Dr. Liemohn's guidance), and this will be the focus of a follow-on paper.

Nagy, Andrew↗

Testing the Standard Model with the Primordial Inflation Explorer

The Primordial Inflation Explorer is an Explorer-class mission to measure the gravity-wave signature of primordial inflation through its distinctive imprint on the linear polarization of the cosmic microwave background. PIXIE uses an innovative optical design to achieve background-limited sensitivity in 400 spectral channels spanning 2.5 decades in frequency from 30 GHz to 6 THz (1 cm to 50 micron wavelength). The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r < 10A{-3) at 5 standard deviations. The rich PIXIE data set will also constrain physical processes ranging from Big Bang cosmology to the nature of the first stars to physical conditions within the interstellar medium of the Galaxy. I describe the PIXIE instrument and mission architecture needed to detect the inflationary signature using only 4 semiconductor bolometers.

Kogut, Alan J.↗

P-ACTIVE (PCM-Based Actively Tunable Filter) Project at NASA

Phase change material (PCM)-based actively tunable mid-wave IR filters have broad imaging and sensing applications—from probing molecular vibrations in chemical species to detecting radiant thermal signatures. We introduce the Phase-change actively tunable filter (P-ACTIVE) project lead by NASA Langley Research Center with collaborators MIT and the University of Cambridge. It covers background science, experimental and theoretical device performance, as well as recent results obtained from a MISSE-14 mission for space qualification of active metasurface optics and constituent PCM. We conclude with a prospective view of the technology and discuss the potential for these filters to serve multiple NASA missions.

phase change material↗

International Safeguards and the Pacific Northwest National Laboratory

Established in 1965, Pacific Northwest National Laboratory’s (PNNL) strong technical ties and shared heritage with the nearby U.S. Department of Energy Hanford Site were central to the early development of expertise in nuclear fuel cycle signatures, separations chemistry, plutonium chemistry, environmental monitoring, modeling and analysis of reactor systems, and nuclear material safeguards and security. From these Hanford origins, PNNL has grown into a multi-program science and engineering enterprise that utilizes this diversity to strengthen the international safeguards regime. Today, PNNL supports the International Atomic Energy Agency (IAEA) in its mission to provide assurances to the international community that nations do not use nuclear materials and equipment outside of peaceful uses. PNNL also serves in the IAEA’s Network of Analytical Laboratories (NWAL) by providing analysis of environmental samples gathered around the world. PNNL is involved in safeguards research and development activities in support of many U.S. Government programs such as the National Nuclear Security Administration’s (NNSA) Office of Research and Development, NNSA Office of Nonproliferation and Arms Control, and the U.S. Support Program to IAEA Safeguards. In addition to these programs, PNNL invests internal resources including safeguards-specific training opportunities for staff, and laboratory-directed research and development funding to further ideas that may grow into new capabilities. This paper and accompanying presentation highlight some of PNNL’s contributions in technology development, implementation concepts and approaches, policy, capacity building, and human capital development, in the field of international safeguards.

Olsen, Khris B.↗

Inflation, Reionization, and All That: The Primordial Inflation Explorer

The Primordial Inflation Explorer is an Explorer-class mission to measure the gravity-wave signature of primordial inflation through its distinctive imprint on the linear polarization of the cosmic microwave background. PIXIE uses an innovative optical design to achieve background-limited sensitivity in 400 spectral channels spanning 2.5 decades in frequency from 30 GHz to 6 THz (1 cm to 50 micron wavelength). The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r < 10(exp -3) at 5 standard deviations. The rich PIXIE data set will also constrain physical processes ranging from Big Bang cosmology to the nature of the first stars to physical conditions within the interstellar medium of the Galaxy. I describe the PIXIE instrument and mission architecture needed to detect the inflationary signature using only 4 semiconductor bolometers.

Kogut, Alan J.↗

The Primordial Inflation Explorer

The Primordial Inflation Explorer is an Explorer-class mission to measure the gravity-wave signature of primordial inflation through its distinctive imprint on the linear polarization of the cosmic microwave background. PIXIE uses an innovative optical design to achieve background-limited sensitivity in 400 spectral channels spanning 2.5 decades in frequency from 30 GHz to 6 THz (1 cm to 50 micron wavelength). The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r < 10(exp -3) at 5 standard deviations. The rich PIXIE data set will also constrain physical processes ranging from Big Bang cosmology to the nature of the first stars to physical conditions within the interstellar medium of the Galaxy. I describe the PIXIE instrument and mission architecture needed to detect the inflationary signature using only 4 semiconductor bolometers.

Kogut, Alan J.↗

Inflation, Reionization, and All That: The Primordial Inflation Explorer

The Primordial Inflation Explorer is an Explorer-class mission to measure the gravity-wave signature of primordial inflation through its distinctive imprint on the linear polarization of the cosmic microwave background. PIXIE uses an innovative optical design to achieve background-limited sensitivity in 400 spectral channels spanning 2.5 decades in frequency from 30 GHz to 6 THz (1 cm to 50 micron wavelength). The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r less than l0^{-3) at 5 standard deviations. The rich PIXIE data set will also constrain physical processes ranging from Big Bang cosmology to the nature of the first stars to physical conditions within the interstellar medium of the Galaxy. I describe the PIXIE instrument and mission architecture needed to detect the inflationary signature using only 4 semiconductor bolometers.

Kogut, Alan J.↗

Linear beam stability in periodic focusing systems: Krein signature and band structure

The general question of how a beam becomes unstable has been one of the fundamental research topics among beam and accelerator physicists for several decades. In this study, we revisited the general problem of linear beam stability in periodic focusing systems by applying the concepts of Krein signature and band structure. We numerically calculated the eigenvalues and other associated characteristics of one-period maps, and discussed the stability properties of single-particle motions with skew quadrupoles and envelope perturbations in high-intensity beams on an equal footing. In particular, an application of the Krein theory to envelope instability analysis was newly attempted in this study. Finally, the appearance of instabilities is interpreted as the result of the collision between eigenmodes of opposite Krein signatures and the formation of a band gap.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Assessing Performance and Tradeoffs of Bioforensic Signature Systems

Chemical and biological forensic programs rely heavily on laboratory measurements to determine how a threat agent may have been produced. In addition to laboratory analyses, it may also be useful to identify institutions where the same threat agent has been produced by the same or a very similar process, since the producer of the agent may have learned methods at a university or similar institution. We developed a Bayesian network framework that combines the results of laboratory measurements with evidence from scientific literature to probabilistically rank institutions that have published papers on the agent of interest. As an example, we consider a network of three laboratory assays that are used to estimate the probabilities that a forensic sample of Yersinia pestis was produced using one of three culture media. We then apply techniques from multi-attribute decision science to assess and compare the performance of the various implementations of the Bayesian network in terms of three attributes: fidelity, document curation intensity, and consumption of the forensic sample. The mathematical approach we use to compare the various implementations is generalizable to the evaluation of other signature systems.

Watkins, Daniel M.↗

Auroral Current and Electrodynamics Structure (ACES) Observations of Ionospheric Feedback in the Alfven Resonator

In 2009, the Auroral Current and Electrodynamics Structure (ACES) High and Low sounding rockets were launched from the Poker Flat Rocket Range (PFRR) in Alaska, with the science objective of gathering in-situ data to quantify current closure in a discrete auroral arc. As ACES High crossed through the return current of an arc (that was monitored using an all sky camera from the ground at Fort Yukon), its instruments recorded clear Alfv nic signatures both poleward and equatorward of the return current region, but not within the main region of the return current itself. These data provide an excellent opportunity to study ionospheric feedback and how it interacts with the Alfv n resonator. We compare the observations with predictions and new results from a model of ionospheric feedback in the ionospheric Alfv n resonator (IAR) and report the significance and impact of these new data for the Magnetosphere-Ionosphere Coupling in the Alfv n Resonator (MICA) rocket mission to launch from PFRR this winter. MICA s primary science objectives specifically focus on better understanding the small-scale structure that the model predicts should exist within the return current region.

Cohen, Ian J.↗

ToF-SIMS evaluation of PEG-related mass peaks and applications in PEG detection in cosmetic products

Polyethylene glycols (PEGs) are used in industrial, medical, health care, and personal care applications. The cycling and disposal of synthetic polymers like PEGs pose significant environmental concerns. Detecting and monitoring PEGs in the real world calls for immediate attention. This study unveils the efficacy of time-of-flight secondary ion mass spectrometry (ToF-SIMS) as a reliable approach for precise analysis and identification of reference PEGs and PEGs used in cosmetic products. By comparing SIMS spectra, we show remarkable sensitivity in pinpointing distinctive ion peaks inherent to various PEG compounds. Moreover, the employment of principal component analysis effectively discriminates compositions among different samples. Notably, the application of SIMS two-dimensional image analysis visually portrays the spatial distribution of various PEGs as reference materials. The same is observed in authentic cosmetic products. The application of ToF-SIMS underscores its potential in distinguishing PEGs within intricate environmental context. ToF-SIMS provides an effective solution to studying emerging environmental challenges, offering straightforward sample preparation and superior detection of synthetic organics in mass spectral analysis. These features show that SIMS can serve as a promising alternative for evaluation and assessment of PEGs in terms of the source, emission, and transport of anthropogenic organics.

36 MATERIALS SCIENCE↗