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At least 865 records · Page 48

Design and feasibility of a novel program of cervical screening in Nigeria: self-sampled HPV testing paired with visual triage

Background: Accelerated global control of cervical cancer would require primary prevention with human papillomavirus (HPV) vaccination in addition to novel screening program strategies that are simple, inexpensive, and effective. We present the feasibility and outcome of a community-based HPV self-sampled screening program. Methods: In Ile Ife, Nigeria, 9406 women aged 30–49 years collected vaginal self-samples, which were tested for HPV in the local study laboratory using Hybrid Capture-2 (HC2) (Qiagen). HPV-positive women were referred to the colposcopy clinic. Gynecologist colposcopic impression dictated immediate management; biopsies were taken when definite acetowhitening was present to produce a histopathologic reference standard of precancer (and to determine final clinical management). Retrospective linkage to the medical records identified 442 of 9406 women living with HIV (WLWH). Results: With self-sampling, it was possible to screen more than 100 women per day per clinic. Following an audio-visual presentation and in-person instructions, overall acceptability of self-sampling was very high (81.2% women preferring self-sampling over clinician collection). HPV positivity was found in 17.3% of women. Intensive follow-up contributed to 85.9% attendance at the colposcopy clinic. Of those referred, 8.2% were initially treated with thermal ablation and 5.6% with large loop excision of transformation zone (LLETZ). Full visibility of the squamocolumnar junction, necessary for optimal visual triage and ablation, declined from 68.5% at age 30 to 35.4% at age 49. CIN2+ and CIN3+ (CIN- Cervical intraepithelial neoplasia), including five cancers, were identified by histology in 5.9 and 3.2% of the HPV-positive women, respectively (0.9 and 0.5% of the total screening population), leading to additional treatment as indicated. The prevalences of HPV infection and CIN2+ were substantially higher (40.5 and 2.5%, respectively) among WLWH. Colposcopic impression led to over- and under-treatment compared to the histopathology reference standard. Conclusion: A cervical cancer screening program using self-sampled HPV testing, with colposcopic immediate management of women positive for HPV, proved feasible in Nigeria. Based on the collected specimens and images, we are now evaluating the use of a combination of partial HPV typing and automated visual evaluation (AVE) of cervical images to improve the accuracy of the screening program.

59 BASIC BIOLOGICAL SCIENCES↗

Development and Testing of Harpoon-Based Approaches for Collecting Comet Samples (Video Supplement)

This video supplement contains a set of videos created during the approximately 10-year-long course of developing and testing the Goddard Space Flight Center (GSFC) harpoon-based approach for collecting comet samples. The purpose of the videos is to illustrate various design concepts used in this method of acquiring samples of comet material, the testing used to verify the concepts, and the evolution of designs and testing. To play the videos this PDF needs to be opened in the freeware Adobe Reader. They do not seem to play while within a browser. While this supplement can be used as a stand-alone document, it is intended to augment its parent document of the same title, Development and Testing of Harpoon-Based Approaches for Collecting Comet Samples (NASA/CR-2017-219018; this document is accessible from the website: https://ssed.gsfc.nasa.gov/harpoon/SAS_Paper-V1.pdf). The parent document, which only contains text and figures, describes the overall development and testing effort and contains references to each of the videos in this supplement. Thus, the videos are primarily intended to augment the information provided by the text and figures in the parent document. This approach was followed to allow the file size of the parent document to remain small enough to facilitate downloading and storage. Some of the videos were created by other organizations, Johns Hopkins University Applied Physics Laboratory (JHU APL) and the German Aerospace Center called, the Deutsches Zentrum für Luft- und Raumfahrt (DLR), who are partnering with GSFC on developing this technology. Each video is accompanied by text that provides a summary description of its nature and purpose, as well as the identity of the authors. All videos have been edited to only show key parts of the testing. Although not all videos have sound, the sound has been retained in those that have it. Also, each video has been given one or more title screens to clarify what is going in different phases of the video.

Purves, Lloyd↗

Dark Energy Survey Year 3 Results: clustering redshifts – calibration of the weak lensing source redshift distributions with redMaGiC and BOSS/eBOSS

ABSTRACT We present the calibration of the Dark Energy Survey Year 3 (DES Y3) weak lensing (WL) source galaxy redshift distributions n(z) from clustering measurements. In particular, we cross-correlate the WL source galaxies sample with redMaGiC galaxies (luminous red galaxies with secure photometric redshifts) and a spectroscopic sample from BOSS/eBOSS to estimate the redshift distribution of the DES sources sample. Two distinct methods for using the clustering statistics are described. The first uses the clustering information independently to estimate the mean redshift of the source galaxies within a redshift window, as done in the DES Y1 analysis. The second method establishes a likelihood of the clustering data as a function of n(z), which can be incorporated into schemes for generating samples of n(z) subject to combined clustering and photometric constraints. Both methods incorporate marginalization over various astrophysical systematics, including magnification and redshift-dependent galaxy-matter bias. We characterize the uncertainties of the methods in simulations; the first method recovers the mean z of tomographic bins to RMS (precision) of ∼0.014. Use of the second method is shown to vastly improve the accuracy of the shape of n(z) derived from photometric data. The two methods are then applied to the DES Y3 data.

79 ASTRONOMY AND ASTROPHYSICS↗

Applying laboratory methods for durability assessment of vitrified material to archaeological samples

Abstract Laboratory testing used to assess the long-term chemical durability of nuclear waste forms may not be applicable to disposal because the accelerated conditions may not represent disposal conditions. To address this, we examine the corrosion of vitrified archeological materials excavated from the near surface of a ~1500-year old Iron Age Swedish hillfort, Broborg, as an analog for the disposal of vitrified nuclear waste. We compare characterized site samples with corrosion characteristics generated by standard laboratory durability test methods including the product consistency test (PCT), the vapor hydration test (VHT), and the EPA Method 1313 test. Results show that the surficial layer of the Broborg samples resulting from VHT displays some similarities to the morphology of the surficial layer formed over longer timescales in the environment. This work provides improved understanding of long-term glass corrosion behavior in terms of the thickness, morphology, and chemistry of the surficial features that are formed.

36 MATERIALS SCIENCE↗

Computing equilibrium free energies through a nonequilibrium quench

Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using reweighting or through Monte Carlo exchanges between replicas at higher temperatures. A recent paper [G. M. Rotskoff and E. Vanden-Eijnden, Phys. Rev. Lett. 122, 150602 (2019)] demonstrated that accurate equilibrium densities of states can also be computed through a nonequilibrium “quench” process, where sampling is performed at a higher temperature to encourage rapid mixing and then quenched to lower energy states with dissipative dynamics. Here, we provide an implementation of the quench dynamics in LAMMPS and evaluate a new formulation of nonequilibrium estimators for the computation of partition functions or free energy surfaces (FESs) of molecular systems. We show that the method is exact for a minimal model of N-independent harmonic springs and use these analytical results to develop heuristics for the amount of quenching required to obtain accurate sampling. We then test the quench approach on alanine dipeptide, where we show that it gives an FES that is accurate near the most stable configurations using the quench approach but disagrees with a reference umbrella sampling calculation in high FE regions. We then show that combining quenching with umbrella sampling allows the efficient calculation of the free energy in all regions. Moreover, by using this combined scheme, we obtain the FES across a range of temperatures at no additional cost, making it much more efficient than standard umbrella sampling if this information is required. Finally, we discuss how this approach can be extended to solute tempering and demonstrate that it is highly accurate for the case of solvated alanine dipeptide without any additional modifications.

Chemistry↗

Computing Reaction Kinetics with MC-PDFT–OPESf: Combining Multireference Electronic Structure Theory and Enhanced Sampling

Accurate rate constants are crucial for understanding and optimizing catalytic reactions mediated by enzymes, metalloproteins, and heterogeneous catalysts. These systems frequently present a dual computational challenge. Multiconfigurational reaction sites require multireference techniques for the accurate treatment of the electronic structure, and high activation barriers prevent efficient sampling of unbiased reactive transitions. In this work, we combine multiconfiguration pair-density functional theory (MC-PDFT) as an accurate and efficient multireference electronic structure method with on-the-fly probability-enhanced sampling flooding (OPESf) as an enhanced sampling method capable of accelerating reactive transitions. We demonstrate the approach on the Diels–Alder [4+2] cycloaddition between cis-butadiene and ethene as a reaction characterized by a large activation barrier and multireference character. MC-PDFT–OPESf provides reaction rates in agreement with experiments at a fraction of the computational cost required by conventional unbiased ab initio calculations. Here, we propose MC-PDFT–OPESf as an efficient approach for computing kinetics in strongly correlated molecular systems.

Chemical calculations↗

Computational methods for probability of instability calculations

This paper summarizes the development of the methods and a computer program to compute the probability of instability of a dynamic system than can be represented by a system of second-order ordinary linear differential equations. Two instability criteria based upon the roots of the characteristics equation or Routh-Hurwitz test functions are investigated. Computational methods based on system reliability analysis methods and importance sampling concepts are proposed to perform efficient probabilistic analysis. Numerical examples are provided to demonstrate the methods.

Wu, Y.-T.↗

Front Delineation and Tracking with Multiple Underwater Vehicles

This work describes a method for detecting and tracking ocean fronts using multiple autonomous underwater vehicles. Multiple vehicles — equally-spaced along the expected frontal boundary — complete near parallel transects orthogonal to the front. Lateral gradients are used to determine the location of the front crossing from each individual vehicle transect by detecting a change in the observed water property. Adaptive control of the vehicles ensure they remain perpendicular to the estimated front boundary as it evolves over time. This method was demonstrated in and around Monterey Bay, California in May of 2017. We compare the front detection method to previously used methods. We introduce a metric in order to evaluate the adaptive control techniques presented. We show the capability of this method for repeated sampling across a dynamic two-dimensional ocean front using short-range Iver AUVs. This method extends to tracking gradients of different properties using a variety of vehicles.

Chavez, Francisco P.↗

Measurement of Seebeck coefficient using a large thermal gradient

The integral method of measuring the Seebeck voltage, V(T), has been applied to short rod-shaped samples. In the present method, one end of the sample is held at a fixed temperature and the other end is automatically varied through a temperature T range of interest, up to a maximum temperature of 1000 C. The Seebeck coefficient is then obtained from the slope of the V(T) vs T curve. The method offers simplicity of sample handling and minimal operator involvement.

Wood, C.↗

Dividing the Concentrator Target From the Genesis Mission

The Genesis spacecraft, launched in 2001, traveled to a Lagrangian point between the Earth and Sun to collect particles from the solar wind and return them to Earth. However, during the return of the spacecraft in 2004, the parachute failed to open during descent, and the Genesis spacecraft crashed into the Utah desert. Many of the solar wind collectors were broken into smaller pieces, and the field team rapidly collected the capsule and collector pieces for later assessment. On each of the next few days, the team discovered that various collectors had survived intact, including three of four concentrator targets. Within a month, the team had imaged more than 10,000 fragments and packed them for transport to the Astromaterials Acquisition and Curation Office within the ARES Directorate at JSC. Currently, the Genesis samples are curated along with the other extraterrestrial sample collections within ARES. Although they were broken and dirty, the Genesis solar wind collectors still offered the science community the opportunity to better understand our Sun and the solar system as a whole. One of the more highly prized concentrator collectors survived the crash almost completely intact. The Genesis Concentrator was designed to concentrate the solar wind by a factor of at least 20 so that solar oxygen and nitrogen isotopes could be measured. One of these materials was the Diamond-on-Silicon (DoS) concentrator target. Unfortunately, the DoS concentrator broke on impact. Nevertheless, the scientific value of the DoS concentrator target was high. The Genesis Allocation Committee received a request for approximately 1 cm(sup 2) of the DoS specimen taken near the focal point of the concentrator for the analysis of solar wind nitrogen isotopes. The largest fragment, Genesis sample 60000, was designated for this allocation and needed to be precisely cut. The requirement was to subdivide the designated sample in a manner that prevented contamination of the sample and minimized the risk of losing or breaking the precious requested sample fragment. The Genesis curator determined that the use of laser scribing techniques to "cut" a precise line and subsequently cleave the sample (in a controlled break of the sample along that line) was the best method for accomplishing the sample subdivision. However, there were risks, including excess heating of the sample, that could cause some of the implanted solar wind to be lost via thermal diffusion. Accidentally breaking the sample during the handling and cleaving process was an additional risk. Early in fiscal year 2013, to address this delicate, complicated task, the ARES Directorate assembled its top scientists to develop a cutting plan that would ensure success when applied to the actual concentrator target wafer; i.e., to produce an approximately 1 cm(sup 2) piece from the requested area of the wafer. The team, subsequently referred to as the JSC Genesis Tiger Team, spent months researching and testing parameters and techniques related to scribing, cleaving, transporting, handling, and holding (i.e., mounting) the specimen. The investigation required considerable "thinking outside the box," and many, many trials using nonflight wafer analogs. After all preliminary testing, the following method was adopted as the final cutting plan. It was used in two final end-to-end practice runs before being used on the actual flight target wafer. The wafer was oriented on the laser cutting stage with the 100 and 010 directions of the wafer parallel to the corresponding X and Y directions of the cutting stage. The laser was programed to scribe 31 lines of the appropriate length along the Y stage direction. The programed scribe lines were separated by 5 micron in the X direction. The laser parameters were set as follows: (1) The laser power was 0.5 watts; (2) each line consisted of 50 passes, with the Z position being advanced 5 micron per pass; and (3) 30 s would elapse before the next line was scribed to allow for wafer cool down from any possible heating via the laser. The ablated material that "stuck" in the "scribe-cut" was removed from the "cut" using an ultrasonic micro-tool. After all the ablated silicon was removed from the wafer, the wafer was repositioned in exactly the same orientation on the laser stage. The laser was focused using the bottom of the wafer channel, and the 31-line scribing pattern described above was reprogrammed using the Z position of the groove bottom as the starting Z value instead of the top wafer surface, which was used previously. Upon completion of the second set of scribes, the ultrasonic micro-tool was again used to clean out the cut. The wafer was remounted on the stage in exactly the same orientation as before. The laser was again focused on the bottom of the groove. This time, however, the laser was.programed to scribe only one line down the exact center of the channel. The final scribe line consisted of 100 passes with a Z advance of 5 micron per pass and with the laser power set at 0.5 watts. As mentioned above, the final cutting plan was practiced in two end-to-end trials using non-flight, triangular-shaped silicon wafers similar in size and orientation to the actual DOS 60000 target sample. The actual scribing of the triangular-shaped wafers required scribing two lines and cleaving (i.e. scribe-cleave, then scribe-cleave) to obtain the piece requested for allocation. Early in December 2012, after many months of experiments and practicing and perfecting the techniques and procedures, the team successfully subdivided the Genesis DoS 60000 target sample, one of the most scientifically important samples from the Genesis mission (figure 2). On December 17, 2012, the allocated piece of concentrator target sample was delivered to the requesting principal investigator.The cutting plan developed for the subdivision of this sample will be used as the model for subdividing future requested Genesis flight wafers (appropriately modified for different wafer types).

Lauer, H. V., Jr.↗

XPS guide: Charge neutralization and binding energy referencing for insulating samples

This guide deals with methods to control surface charging during XPS analysis of insulating samples and approaches to extracting useful binding energy information. Furthermore, the guide summarizes the causes of surface charging, how to recognize when it occurs, approaches to minimize charge buildup, and methods used to adjust or correct XPS photoelectron binding energies when charge control systems are used. Additionally, there are multiple ways to control surface charge buildup during XPS measurements and examples of systems on advanced XPS instruments are described. There is no single, simple, and foolproof way to extract binding energies on insulating material, but advantages and limitations of several approaches are described. Because of the variety of approaches and limitations of each it is critical for researchers to accurately describe the procedures that have been applied in research reports and publications.

47 OTHER INSTRUMENTATION↗

Controllable Thin‐Film Approaches for Doping and Alloying Transition Metal Dichalcogenides Monolayers

Abstract Two‐dimensional (2D) transition metal dichalcogenides (TMDs) exhibit exciting properties and versatile material chemistry that are promising for device miniaturization, energy, quantum information science, and optoelectronics. Their outstanding structural stability permits the introduction of various foreign dopants that can modulate their optical and electronic properties and induce phase transitions, thereby adding new functionalities such as magnetism, ferroelectricity, and quantum states. To accelerate their technological readiness, it is essential to develop controllable synthesis and processing techniques to precisely engineer the compositions and phases of 2D TMDs. While most reviews emphasize properties and applications of doped TMDs, here, recent progress on thin‐film synthesis and processing techniques that show excellent controllability for substitutional doping of 2D TMDs are reported. These techniques are categorized into bottom–up methods that grow doped samples on substrates directly and top–down methods that use energetic sources to implant dopants into existing 2D crystals. The doped and alloyed variants from Group VI TMDs will be at the center of technical discussions, as they are expected to play essential roles in next‐generation optoelectronic applications. Theoretical backgrounds based on first principles calculations will precede the technical discussions to help the reader understand each element's likelihood of substitutional doping and the expected impact on the material properties.

36 MATERIALS SCIENCE↗

Oxygen K -edge X-ray absorption spectra of liquids with minimization of window contamination

We report oxygen K-edge X-ray absorption spectroscopy is used routinely to study a range of solid materials. However, liquid samples are studied less frequently at the oxygen K-edge due to the combined challenges of high-vacuum conditions and oxygen contamination of window materials. A modular sample holder design with a twist-seal sample containment system that provides a simple method to encapsulate liquid samples under high-vacuum conditions is presented. This work shows that pure silicon nitride windows have lower oxygen contamination than both diamond- and silicon-rich nitride windows, that the levels of oxygen contamination are related to the age of the windows, and provides a protocol for minimizing the background oxygen contamination. Acid-washed 100 nm-thick silicon nitride windows were found to give good quality oxygen K-edge data on dilute liquid samples.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Calculation of power spectrums from digital time series with missing data points

Two algorithms are developed for calculating power spectrums from the autocorrelation function when there are missing data points in the time series. Both methods use an average sampling interval to compute lagged products. One method, the correlation function power spectrum, takes the discrete Fourier transform of the lagged products directly to obtain the spectrum, while the other, the modified Blackman-Tukey power spectrum, takes the Fourier transform of the mean lagged products. Both techniques require fewer calculations than other procedures since only 50% to 80% of the maximum lags need be calculated. The algorithms are compared with the Fourier transform power spectrum and two least squares procedures (all for an arbitrary data spacing). Examples are given showing recovery of frequency components from simulated periodic data where portions of the time series are missing and random noise has been added to both the time points and to values of the function. In addition the methods are compared using real data. All procedures performed equally well in detecting periodicities in the data.

Murray, C. W., Jr.↗

Efficient sampling of free energy landscapes with functions in Sobolev spaces

Molecular simulations of biological and physical phenomena generally involve sampling complicated, rough energy landscapes characterized by multiple local minima. In this work, we introduce a new family of methods for advanced sampling that draw inspiration from functional representations used in machine learning and approximation theory. As shown here, such representations are particularly well suited for learning free energies using artificial neural networks. As a system evolves through phase space, the proposed methods gradually build a model for the free energy as a function of one or more collective variables, from both the frequency of visits to distinct states and generalized force estimates corresponding to such states. Implementation of the methods is relatively simple and, more importantly, for the representative examples considered in this work, they provide computational efficiency gains of up to several orders of magnitude over other widely used simulation techniques.

Approximation theory↗

Entropy-driven Optimal Sub-sampling of Fluid Dynamics for Developing Machine-learned Surrogates

Optimal sub-sampling of large datasets from fluid dynamics simulations is essential for training reduced-order machine learned models. A method using Shannon entropy was developed to weight flow features according to their level of information content, such that the most informative features can be extracted and used for training a surrogate model. The method is demonstrated in the canonical flow over a cylinder problem simulated with OpenFOAM. Both time-independent predictions and temporal forecasting were investigated as well as two types of prediction targets: local per-grid-point predictions and global per-time-step predictions. When tested on training a surrogate model, results indicate that our entropy-based sampling method typically outperforms random sampling and yields more reproducible results in less iterations. Finally, the method was used to train a surrogate model for modeling turbulence in magnetohydrodynamic flows, which revealed various challenges and opportunities for future research.

Brewer, Wes↗

Identifying crystallographic faces of the fluorites urania and thoria with rotational polarized Raman spectroscopy

Crystallite orientation identification is invaluable, but is often limited to small area identification or requires a large area sample. Nondestructive optical methods such as polarized Raman spectroscopy, in contrast, can be used to completely map a variety of sample sizes, but their potential is not yet fully realized. Here, we report a systematic study of polarized Raman scattering of high-quality, hydrothermally grown, single crystals of urania and thoria. The peak intensity variations for as-grown major crystal planes, post-growth polished crystal planes, and a post-growth polished non-crystallographic plane are directly linked to crystallographic orientation and crystal rotation, and agree with computed models. In particular, the parallel polarized peak intensity results are directly correlated with metal–oxygen–metal chains in the fluorite structure and can be used to determine both orientation and rotational alignment of a given crystal face if sufficiently small rotational steps are applied. These results are structure based, being applicable to the larger fluorite phase space, which is useful for optical, semiconductor, nuclear, and solid oxide fuel cell industries. Further, these results suggest that Raman spectroscopy can identify non-crystallographic orientations that are not discernable by traditional means.

36 MATERIALS SCIENCE↗

Computational Optimization of 133m Xe Production via Neutron Irradiation in a TRIGA Reactor

Here, the Comprehensive Nuclear-Test-Ban Treaty bans all nuclear tests worldwide. As part of treaty compliance, the concentration of radioactive nuclides in the atmosphere is monitored to detect nuclear weapons tests. Radioactive noble gas fission products, specifically radioxenon, can vent into the atmosphere after a nuclear weapons test, even if the test is well contained underground or underwater. Radioxenon thus serves as a signal for nuclear weapons tests. All atmospheric monitoring systems require samples of radioxenon isotopes for detector calibration, quality control, and certification. Here, we present a novel, improved method for creating samples of 133m Xe via neutron irradiation of 132 Xe in the Washington State University TRIGA reactor. 132 Xe neutron absorption results in either 133 Xe or 133m Xe—thermal neutron absorption results in 133m Xe 12% of the time, while fast neutron absorption (above ~1 MeV) results in 133m Xe ~50% of the time. To optimize the production of 133m Xe via neutron absorption in 132 Xe in the thermal TRIGA reactor, spectral tuning using an irradiation chamber is required to maximize the fraction of fast neutrons being absorbed and minimize the number of thermal neutrons interacting with the 132 Xe. We used MCNP to tally 132 Xe absorptions with the isotopic tally function, flux tallies and neutron attenuation to estimate the number of neutrons reaching the 132 Xe through the irradiation chamber, and the adjoint importance function to improve the source strength estimate. Additionally, we performed a heat transfer analysis for safety considerations. It was determined that the use of a 96% enriched 10 B boron carbide chamber, placed next to the fuel elements in reactor position D8, increases the 133m Xe/ 133 Xe activity ratio from a baseline value of 0.3 to 1.0, a 233% increase. Additionally, it was determined that the alpha heating produced in the boron does not become an unmanageable problem in the Washington State University reactor.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗