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At least 865 records · Page 48

Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction–modification systems

A major barrier to both metabolic engineering and fundamental biological studies is the lack of genetic tools in most microorganisms. One example is Clostridium thermocellum ATCC 27405 T , where genetic tools are not available to help validate decades of hypotheses. A crucial barrier to DNA transformation is restriction–modification systems, which defend against foreign DNA methylated differently than the host. To determine the active restriction–modification systems in this strain, we performed complete methylome analysis via single-molecule, real-time sequencing to detect 6-methyladenine and 4-methylcytosine and the rarely used whole-genome bisulfite sequencing to detect 5-methylcytosine. Multiple active systems were identified, and corresponding DNA methyltransferases were expressed from the Escherichia coli chromosome to mimic the C. thermocellum methylome. Plasmid methylation was experimentally validated and successfully electroporated into C. thermocellum ATCC 27405. This combined method enabled genetic modification of the C. thermocellum -type strain and acts as a blueprint for transformation of other non-model microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗

Testing and Performance Validation of a Shielded Waste Segregation and Clearance Monitor Designed for the Measurement of Low Level Waste-13043

This paper describes the development, testing and validation of a shielded waste segregation and clearance monitor designed for the measurement of low-density low-level waste (LLW). The monitor is made of a measurement chamber surrounded by detectors and a shielded outer frame. The shielded chamber consists of a steel frame, which contains typically 1.5 inches (3.81 cm) of lead and 0.5 inches (1.27 cm) of steel shielding. Inside the shielding are plastic scintillator panels, which serve as gross gamma ray detectors. The detector panels, with embedded photomultipliers, completely surround the internal measurement chamber on all 6 sides. Care has been taken to distribute the plastic scintillator detectors in order to optimise both the efficiency for gamma ray detection and at the same time achieve a volumetric sensitivity, which is as uniform as possible. A common high voltage power supply provides the bias voltage for each of the six photomultipliers. The voltage signals arising from the detectors and photomultipliers are amplified by six sensitive amplifiers. Each amplifier incorporates a single channel analyser with both upper and lower thresholds and the digitised counts from each detector are recorded on six scalars. Operation of the device is by means of a microprocessor from which the scalars are controlled. An internal load cell linked to the microprocessor determines the weight of the waste object, and this information is used to calculate the specific activity of the waste. The monitor makes background measurements when the shielded door is closed and a sample, usually a bag of low-density waste, is not present in the measurement chamber. Measurements of the minimum detectable activity (MDA) of an earlier large volume prototype instrument are reported as part of the development of the Waste Segregation and Clearance Monitor (WSCM) described in the paper. For the optimised WSCM a detection efficiency of greater than 32% was measured using a small Cs-137 source placed in the centre of the measurement chamber. Small sources have also been used to determine the spatial variation of the detection efficiency for various positions within the measurement chamber. The data have been used to establish sentencing limits and different 'fingerprints' for specific waste streams including waste streams containing fission products and others based on other radionuclides including Am-241. Some of the test data that are presented have been used to validate the instrument performance. The monitor is currently in routine use at a nuclear facility for the measurement and sentencing of low-density low activity radioactive waste. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

TeV gamma rays from millisecond pulsars and the detectability of globular clusters

I investigate the detectability of TeV gamma rays from millisecond pulsars, assuming the energy source that powers this emission is the loss of rotational energy of the spinning neutron star. I show that although individual sources may be too weak to detect, the contribution of many (about 1000) active millisecond pulsars may lead to currently detectable TeV gamma-ray emissions from globular clusters, provided the average pulsar converts about 0.1 percent of its spin-down energy into TeV gamma rays. Future detections of TeV gamma rays from globular clusters (or more restrictive upper limits on the fluxes) will lead to better estimates of the number of active millisecond pulsars the clusters contain, and to a better understanding of the pulsar emission mechanism. I also derive flux estimates for the following sources: (1) the Crab Nebula, (2) PSR 19374-21, PSR 1953 4-29, and PSR 1855 4-09, and (3) nearby millisecond pulsars in the galactic disk.

Smith, I. A.↗

Energy-efficient Mott activation neuron for full-hardware implementation of neural networks

To circumvent the von Neumann bottleneck, substantial progress has been made towards in-memory computing with synaptic devices. However, compact nanodevices implementing non-linear activation functions are required for efficient full-hardware implementation of deep neural networks. Here, in this work, we present an energy-efficient and compact Mott activation neuron based on vanadium dioxide and its successful integration with a conductive bridge random access memory (CBRAM) crossbar array in hardware. The Mott activation neuron implements the rectified linear unit function in the analogue domain. The neuron devices consume substantially less energy and occupy two orders of magnitude smaller area than those of analogue complementary metal–oxide semiconductor implementations. The LeNet-5 network with Mott activation neurons achieves 98.38% accuracy on the MNIST dataset, close to the ideal software accuracy. We perform large-scale image edge detection using the Mott activation neurons integrated with a CBRAM crossbar array. Our findings provide a solution towards large-scale, highly parallel and energy-efficient in-memory computing systems for neural networks.

electrical and electronic engineering↗

Detection Thresholds of Falling Snow from Satellite-Borne Active and Passive Sensors

Precipitation, including rain and snow, is a critical part of the Earth's energy and hydrology cycles. Precipitation impacts latent heating profiles locally while global circulation patterns distribute precipitation and energy from the equator to the poles. For the hydrological cycle, falling snow is a primary contributor in northern latitudes during the winter seasons. Falling snow is the source of snow pack accumulations that provide fresh water resources for many communities in the world. Furthermore, falling snow impacts society by causing transportation disruptions during severe snow events. In order to collect information on the complete global precipitation cycle, both liquid and frozen precipitation must be collected. The challenges of estimating falling snow from space still exist though progress is being made. These challenges include weak falling snow signatures with respect to background (surface, water vapor) signatures for passive sensors over land surfaces, unknowns about the spherical and non-spherical shapes of the snowflakes, their particle size distributions (PSDs) and how the assumptions about the unknowns impact observed brightness temperatures or radar reflectivities, differences in near surface snowfall and total column snow amounts, and limited ground truth to validate against. While these challenges remain, knowledge of their impact on expected retrieval results is an important key for understanding falling snow retrieval estimations. Since falling snow from space is the next precipitation measurement challenge from space, information must be determined in order to guide retrieval algorithm development for these current and future missions. This information includes thresholds of detection for various sensor channel configurations, snow event system characteristics, snowflake particle assumptions, and surface types. For example, can a lake effect snow system with low (approx 2.5 km) cloud tops having an ice water content (IWC) at the surface of 0.25 g / cubic m and dendrite snowflakes be detected? If this information is known, we can focus retrieval efforts on detectable storms and concentrate advances on achievable results. Here, the focus is to determine thresholds of detection for falling snow for various snow conditions over land and lake surfaces. The results rely on simulated Weather Research Forecasting (WRF) simulations of falling snow cases since simulations provide all the information to determine the measurements from space and the ground truth. Sensitivity analyses were performed to better ascertain the relationships between multifrequency microwave and millimeter-wave sensor observations and the falling snow/underlying field of view. In addition, thresholds of detection for various sensor channel configurations, snow event system characteristics, snowflake particle assumptions, and surface types were studied. Results will be presented for active radar at Ku, Ka, and W-band and for passive radiometer channels from 10 to 183 GHz.

Gail Skofronick-Jackson↗

A Novel Experimental Setup for Rare Events Selection and Its Potential Application to Super-heavy Elements Search

The paper presents a novel instrumentation for rare events selection which was tested in our research of short lived super heavy elements production and detection. The instrumentation includes an active catcher multi elements system and dedicated electronics. The active catcher located in the forward hemisphere is composed of 63 scintillator detection modules. Reaction products of damped collisions between heavy ion projectiles and heavy target nuclei are implanted in the fast plastic scintillators of the active catcher modules. The acquisition system trigger delivered by logical branch of the electronics allows to record the reaction products which decay via the alpha particle emissions or spontaneous fission which take place between beam bursts. One microsecond wave form signal from FADCs contains information on heavy implanted nucleus as well as its decays.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Preliminary analysis of the JAPE ground vehicle test data with an artificial neural network classifier

Remotely sensing and classifying military vehicles in a battlefield environment have been the source of much research over the past 20 years. The ability to know where threat vehicles are located is an obvious advantage to military personnel. In the past active methods of ground vehicle detection such as radar have been used, but with the advancement of technology to locate these active sensors, passive sensors are preferred. Passive sensors detect acoustic emissions, seismic movement, electromagnetic radiation, etc., produced by the target and use this information to describe it. Deriving the mathematical models to classify vehicles in this manner has been, and is, quite complex and not always reliable. However, with the resurgence of artificial neural network (ANN) research in the past few years, developing models for this work may be a thing of the past. Preliminary results from an ANN analysis to the tank signatures recorded at the Joint Acoustic Propagation Experiment (JAPE) at the US Army White Sands Missile Range, NM, in July 1991, are presented.

Larsen, Nathan F.↗

Eddy covariance towers as sentinels of abnormal radioactive material releases

Ensuring accurate detection and attribution of abnormal releases of radioactive material is critical for protecting human health and safety. Most commonly, such detection is accomplished via active monitoring approaches involving the collection of physical samples. Further, this is labor intensive and limits the temporal and spatial resolution of any detected events to a relatively coarse level. As an alternative first step towards passive monitoring, we developed an approach using eddy flux tower data records to identify signals from a known abnormal release and quantify the extent to which that signal also occurs at other times in the data record. Through two case studies, one of which targeted the Fukushima nuclear disaster and the other targeting an abnormal release event at a radioisotope production facility in Fleurus, Belgium, we tested our approach and identified several potential heretofore unidentified abnormal events that were consistent with atmospheric circulation patterns and/or wind direction from known release sites. Because our approach is relatively simple and is resistant to systematic errors in the observational record, it has broad applicability beyond specific constituents and ecosystem types to identify a wide variety of limited-duration anomalies in flux tower data to ensure human health and industrial safety.

54 ENVIRONMENTAL SCIENCES↗

New Laboratory and Astrophysical Probes of Physics Beyond the Standard Model (Final Technical Report)

The first of these directions centers on new ideas in dark matter detection. As experimental scrutiny narrows the window for new physics at the weak scale, it has become apparent that the solution to the dark matter mystery may not reside there. Theoretical developments such as the hidden sector/valley paradigm have, at the same time, shown that compelling theories of dark matter reside below the weak scale. Searching for dark matter at lower mass scales requires looking beyond the current paradigm of dark matter direct detection based on nuclear recoils. It is the goal of this project to provide new ideas to guide the experimental program looking for light dark matter. I am actively proposing ideas for detecting dark matter as light as a meV, well beyond the current focus of GeV-TeV scale dark matter. Some of the ideas I have proposed, such as superconducting, superfluid, and polar material targets, are actively being developed into experiments. My group will provide the relevant calculations to determine dark matter reach, providing crucial input to experiment on which targets should be developed. We will also provide an effective field theory framework to understand which types of experiments are most sensitive to each interaction type. The second of these directions is on probes of dark matter substructure as a mean to constrain, or observe, models of dark matter. The standard ΛCDM paradigm assumes that the dark matter density perturbations are adiabatic, scale invariant, and produced during inflation. However, many standard models of dark matter will produce modifications of this prediction, such as axion models with symmetry broken below the inflationary scale. Remarkably, we have limited direct measurements of the dark matter clumpiness at mass scales below dwarf galaxies. This allows for the possibility of observing modifications from vanilla ΛCDM due to particle dynamics. In many cases, simulations of dark matter structure in the presence of non-scale invariant fluctu- ations are understudied or completely lacking. I plan to develop both theoretical predictions for small scale structure in models with additional matter power on small scales, as well as observa- tional probes of small scale halos or clumps. One idea I have been recently focused on is pulsar timing, though my group will pursue a variety of lensing and astrometric probes. Lastly, the most risky direction involves spacetime fluctuations from quantum gravity. I showed that if one assumes that metric fluctuations in the Minkowski vacuum, at a surface separating a region in and out of causal contact (which we call a “horizon”), are determined by standard thermodynamic considerations at horizon, these metric fluctuations are large enough to observe in an interferometer with similar sensitivity to LIGO. In a follow-up paper we showed that these assumption holds for the vacuum in AdS/CFT. In future work, I plan to connect this work to recent soft graviton results, to frame this work in a concrete Randall-Sundrum model, and to work out concrete phenomenological predictions from the model. This work unquestionably takes a less trodden path, and works well as part of a well-rounded portfolio of less and more risky ideas. Particle physics is currently at a juncture which requires bold exploration of qualitatively new directions. This proposal outlines some of my plans over the coming years in these directions, leaving room also for surprises.

79 ASTRONOMY AND ASTROPHYSICS↗

Real-Time, Single-Step Bioassay Using Nanoplasmonic Resonator With Ultra-High Sensitivity

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Zhang, Xiang↗

Real-time, single-step bioassay using nanoplasmonic resonator with ultra-high sensitivity

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

47 OTHER INSTRUMENTATION↗

CLASS Survey Description: Coronal-line Needles in the SDSS Haystack

Coronal lines are a powerful, yet poorly understood, tool to identify and characterize active galactic nuclei. There have been few large-scale surveys of coronal lines in the general galaxy population in the literature so far. Using a novel preselection technique with a flux-to-rms ratio $\mathcal{F}$, followed by Markov Chain Monte Carlo fitting, we searched for the full suite of 20 coronal lines in the optical spectra of almost 1 million galaxies from the Sloan Digital Sky Survey Data Release 8. We present a catalog of the emission-line parameters for the resulting 258 galaxies with detections. The Coronal Line Activity Spectroscopic Survey includes line properties, host-galaxy properties, and selection criteria for all galaxies in which at least one line is detected. This comprehensive study reveals that a significant fraction of coronal-line activity is missed in past surveys based on a more limited set of coronal lines; ~60% of our sample do not display the more widely surveyed [Fe x] λ6374. In addition, we discover a strong correlation between coronal-line and Wide-field Infrared Survey Explorer W2 luminosities, suggesting that the mid-infrared flux can be used to predict coronal-line fluxes. For each line we also provide a confidence level that the line is present, generated by a novel neural network, trained on fully simulated data. We find that after training the network to detect individual lines using 100,000 simulated spectra, we achieve an overall true-positive rate of 75.49% and a false-positive rate of only 3.96%.

79 ASTRONOMY AND ASTROPHYSICS↗

A system for measuring thermal activation energy levels in silicon by thermally stimulated capacitance

One method being used to determine energy level(s) and electrical activity of impurities in silicon is described. The method is called capacitance transient spectroscopy (CTS). It can be classified into three basic categories: the thermally stimulated capacitance method, the voltage-stimulated capacitance method, and the light-stimulated capacitance method; the first two categories are discussed. From the total change in capacitance and the time constant of the capacitance response, emission rates, energy levels, and trap concentrations can be determined. A major advantage of using CTS is its ability to detect the presence of electrically active impurities that are invisible to other techniques, such as Zeeman effect atomic absorption, and the ability to detect more than one electrically active impurity in a sample. Examples of detection of majority and minority carrier traps from gold donor and acceptor centers in silicon using the capacitance transient spectrometer are given to illustrate the method and its sensitivity.

Cockrum, R. H.↗

Low-noise low-jitter 32-pixels CMOS single-photon avalanche diodes array for single-photon counting from 300 nm to 900 nm

We developed a single-photon counting multichannel detection system, based on a monolithic linear array of 32 CMOS SPADs (Complementary Metal-Oxide-Semiconductor Single-Photon Avalanche Diodes). All channels achieve a timing resolution of 100 ps (full-width at half maximum) and a photon detection efficiency of 50% at 400 nm. Dark count rate is very low even at room temperature, being about 125 counts/s for 50 μm active area diameter SPADs. Detection performance and microelectronic compactness of this CMOS SPAD array make it the best candidate for ultra-compact time-resolved spectrometers with single-photon sensitivity from 300 nm to 900 nm.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie

Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.

59 BASIC BIOLOGICAL SCIENCES↗

Swift-XRT Follow-up of Gravitational-wave Triggers in the Second Advanced LIGO/Virgo Observing Run

The Neil Gehrels Swift Observatory carried out prompt searches for gravitational-wave (GW) events detected by the LIGO/Virgo Collaboration (LVC) during the second observing run ("O2"). Swift performed extensive tiling of eight LVC triggers, two of which had very low false-alarm rates (GW170814 and the epochal GW170817), indicating a high confidence of being astrophysical in origin; the latter was the first GW event to have an electromagnetic counterpart detected. In this paper we describe the follow-up performed during O2 and the results of our searches. No GW electromagnetic counterparts were detected; this result is expected, as GW170817 remained the only astrophysical event containing at least one neutron star after LVC's later retraction of some events. A number of X-ray sources were detected, with the majority of identified sources being active galactic nuclei. We discuss the detection rate of transient X-ray sources and their implications in the O2 tiling searches. Finally, we describe the lessons learned during O2 and how these are being used to improve the Swift follow-up of GW events. In particular, we simulate a population of gamma-ray burst afterglows to evaluate our source ranking system's ability to differentiate them from unrelated and uncataloged X-ray sources. We find that ≈60%–70% of afterglows whose jets are oriented toward Earth will be given high rank (i.e., "interesting" designation) by the completion of our second follow-up phase (assuming that their location in the sky was observed), but that this fraction can be increased to nearly 100% by performing a third follow-up observation of sources exhibiting fading behavior.

79 ASTRONOMY AND ASTROPHYSICS↗

Swift-XRT Follow-up of Gravitational-wave Triggers in the Second Advanced LIGO/Virgo Observing Run

The Neil Gehrels Swift Observatory carried out prompt searches for gravitational-wave (GW) events detected by the LIGO/Virgo Collaboration (LVC) during the second observing run ("O2"). Swift performed extensive tiling of eight LVC triggers, two of which had very low false-alarm rates (GW170814 and the epochal GW170817), indicating a high confidence of being astrophysical in origin; the latter was the first GW event to have an electromagnetic counterpart detected. In this paper we describe the follow-up performed during O2 and the results of our searches. No GW electromagnetic counterparts were detected; this result is expected, as GW170817 remained the only astrophysical event containing at least one neutron star after LVC's later retraction of some events. A number of X-ray sources were detected, with the majority of identified sources being active galactic nuclei. We discuss the detection rate of transient X-ray sources and their implications in the O2 tiling searches. Finally, we describe the lessons learned during O2 and how these are being used to improve the Swift follow-up of GW events. In particular, we simulate a population of gamma-ray burst afterglows to evaluate our source ranking system's ability to differentiate them from unrelated and uncataloged X-ray sources. We find that ≈60%–70% of afterglows whose jets are oriented toward Earth will be given high rank (i.e., "interesting" designation) by the completion of our second follow-up phase (assuming that their location in the sky was observed), but that this fraction can be increased to nearly 100% by performing a third follow-up observation of sources exhibiting fading behavior.

N. J. Klingler↗

Hardware Verification and Validation for a Navigation Sensor Software Model in Support of Flight Vehicle Performance Analysis

… or, “It’s in the details, how to make complicated software perform like complicated hardware.” In attempts to minimize development time and quickly build an operational vehicle, NASA’s Space Launch System (SLS) has had to be intentional about integrated testing. Constraints on budget and schedule have required balance between testing needs and the desire for an integrated flight vehicle as soon as possible. To provide key insights early in design and analysis cycles, a large amount of effort has shifted into maturing and validating models at the component level with integrated testing as a means to validate their integration. In terms of SLS Navigation, this, and the model-based design approach have pushed explicit requirements for sensor models to be validated against flight hardware to high precision. This paper covers the approach taken to verify and validate the models for the two key navigation sensors on the SLS vehicle, the Redundant Inertial Navigation Sensor and the Rate Gyro Assembly. These models are used in performance evaluation, fault detection, and operations development extensively. Using a mix of data from hardware vendor documentation and testing reports, limited in-house testing, and integration activities, these models were able to be validated against flight hardware at multiple levels, from the internal software design to statistical behavior at the raw sensor and integrated box levels. The high level of insight into the hardware elements is instrumental to support flight certification activities and building confidence in SLS Navigation capability. Focused testing enabled additional insight and validation that proved invaluable and the resulting insights were used to focus and mature models. Additionally, of having validated performance-based hardware models enables a wide breadth of activities including detailed fault detection studies and integration into future vehicle frameworks, such as an upper stage and provide a valuable asset to continued SLS analysis and design.

Evan J Anzalone↗