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At least 1,693 records · Page 94

Smectite phase separation is driven by hydration-mediated interfacial charge

Smectite clay minerals have an outsize impact on the response of clay-rich media to common stimuli, such as hydration and ion exchange, motivating extensive effort to understand behaviors resulting from these processes such as swelling and exfoliation. Smectites are common and historic systems for investigating colloidal and interfacial phenomena, with two swelling regimes commonly identified across myriad clays: osmotic swelling at high water activity and crystalline swelling at low water activity. However, no current swelling model seamlessly spans the full ranges of water, salt and clay content encountered in natural or engineered settings. Here, we show that structures previously rationalized as either osmotic or crystalline coexist as a rich array of distinct colloidal phases that differ by water content, layer stacking thickness, and curvature. We present an analytical model for intermolecular potentials among water, salt and clay in both mono- and divalent electrolytes that predicts swelling pressures across high and low water activities. Our results indicate that all clay swelling is osmotic swelling, but that the osmotic pressure of charged mineral interfaces becomes attractive and dominates that of the electrolyte at high clay activities. Global energy minima are often not reached on experimental timescales due to many local energy minima that promote long-lived intermediate states with vast differences in clay, ion, and water mobilities, leading to hyperdiffusive layer dynamics driven by variable hydration-mediated interfacial charge.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

A census of fish passage facilities at US hydropower developments across the conterminous United States

Hydropower provides reliable and secure electricity and contributes significantly to the flexibility and stability of the US electricity grid. Hydropower dams generally are aquatic barriers and hazards to migratory fish in rivers. Fish passage facilities mitigate risks from hydropower to migratory fish, but information on these facilities is incomplete for the conterminous United States (CONUS). Here, we present the first CONUS-scale dataset of fish passage facilities at US hydropower developments in over 30 years. The existence of fish passage facilities (presence or absence) was specified for 1909 hydropower features, 390 of which had at least one facility. Most features had a single passage facility that provided passage in only one direction, with downstream being more common than upstream passage. Bypasses and ladders accounted for 60 % of the fish passage facility types. While we documented 659 fish passage facilities across CONUS, facilities were most common in the New England, Pacific Northwest, Mid-Atlantic, and Great Lakes regions. In general, fish passage facilities were more common at features that were closer to the ocean, at lower elevations, and at shorter dams, but not related to installed electrical generation capacity. Hydrologic sub-basins containing salmonids also contained the largest number of hydropower features, but the proportion of features with passage was generally higher in sub-basins containing multiple migratory taxa. This census provides valuable information on existing fish passage mitigation and is a benchmark to gauge progress toward a modernized hydropower fleet that provides affordable, reliable energy while protecting fishery resources and river ecosystems.

13 HYDRO ENERGY↗

Direct comparison of Fe-Cr unmixing characterization by atom probe tomography and small angle scattering

The fine microstructure obtained by unmixing of a solid solution either by classical precipitation or spinodal decomposition is often characterized either by small angle scattering or atom probe tomography. This article shows that a common data analysis framework can be used to analyze data obtained from these two techniques. An example of the application of this common analysis is given for characterization of the unmixing of the Fe-Cr matrix of a 15-5 PH stainless steel during long-term ageing at 350 °C and 400 °C. A direct comparison of the Cr composition fluctuations amplitudes and characteristic lengths obtained with both techniques is made showing a quantitative agreement for the fluctuation amplitudes. The origin of the discrepancy remaining for the characteristic lengths is discussed. - Highlights: •Common analysis framework for atom probe tomography and small angle scattering •Comparison of same microstructural characteristics obtained using both techniques •Good correlation of Cr composition fluctuations amplitudes from both techniques •Good correlation of Cr composition fluctuations amplitudes with classic V parameter.

36 MATERIALS SCIENCE↗

Conspicuous variation of the lattice unit cell in the pavonite homologous series and its relation with cation/anion occupational modulations

Highlights: ► Strong non-uniform variation of unit cell parameters in the pavonite homologous series. ► Conspicuous unit cell variation due to an underlying sub-lattice with cation/anion occupation. ► A modulated model common to the whole series using the superspace formalism proposed. ► Model successfully applied to the {sup 7}P pavonite Ag{sub 3}(Bi,Pb){sub 7}S{sub 12}. ► The model can be applied in a predictive way to other members of the family. - Abstract: The pavonites is a homologous series of sulfosalts with galena-like modules of variable size. A survey of their unit cells reveals that they are severely constrained by the metrics of an underlying common average sublattice. The unit cell of any compound of the series accommodates with high precision an integer number of approximately equal subcells. This explains a peculiar non-uniform variation of the unit cell parameters within the series and evidences that the interface between the galena-like modules, despite having a very different topology, approximately maintains the subperiodicity of the modules, and must therefore be subject to strong steric restrictions. It also implies that cations and anions occupy the nodes of the observed common underlying average sublattice according to a striking alternate cation/anion occupational modulation. This is the starting point for a description of these materials as modulated structures, which can make a proficient use of the approximate atomic positional non-crystallographic correlations caused by their modular character. Under this approach only four parameters suffice to define a realistic approximate model of any member of the series. A full structural characterization of any of the compounds only requires the determination of additional small/smooth modulations. As an example, the case of the {sup 7}P pavonite Ag{sub 3}Bi{sub 6.2}Pb{sub 0.8}S{sub 12}, is analyzed.

36 MATERIALS SCIENCE↗

Immobilization and image-guidance methods for radiation therapy of limb extremity soft tissue sarcomas: Results of a multi-institutional survey

Radiation therapy for limb-extremity soft tissue sarcoma (STS) requires accurate, reproducible dose delivery. However, patient positioning is challenging and there is a lack of existing guidelines to assist institutional standardization. Therefore, we conducted a multi-institutional international survey of STS immobilization, image guidance methods, and treatment protocols to investigate current practice. Seventy-three UK radiotherapy centers and 15 hospitals in 7 other countries completed a questionnaire on STS immobilization and image-guidance procedures. Specifically, the survey collated information on the current usage of immobilization equipment, including custom devices, patient setup tolerances, the use of written protocols, the modality and frequency of image guidance, the method of treatment, allocated treatment times, and the application of surgical clips. Multiple combinations of immobilization devices were reported. In the UK, 12%, 40%, 30%, 12%, and 5% use 1, 2, 3, 4, and 5 types of device for lower limb STS. Vacuum bag plus either foot or ankle support was most common (66%). Of 15 international centers, 27%, 60%, 7%, 0%, 7% use 1, 2, 3, 4, 5 devices, with vacuum bags (73%) and thermoplastic (47%) predominant, similar to UK values of 77% and 52%. For image guidance, in the UK, 37% use kV planar, 34% use MV planar, and 16% use cone-beam CT for the first 3 fractions and then weekly. Internationally, daily imaging was more prevalent with 33% using kV planar, 7% MV planar, and 40% cone-beam CT daily. Custom devices plus combinations of devices, along with 5- and 10-mm set-up tolerances, were most commonly reported. Less than half of centers have written treatment protocols. Conventional treatment is most common in the UK, with only 42% using conformal techniques. Treatment is allocated between 10 and 30 minutes. Twenty-six percent of UK centers and 53% of international centers use surgical clips. Across treatment centers, there is no consistent approach to STS immobilization, image-guidance methods, or treatment protocols assessed by this survey. A wide variety of immobilization devices and configurations are utilized, and the frequency and modality of imaging are similarly diverse. In the absence of guidelines, the creation of an online repository of example immobilization techniques could enable centers to compare a diversity of cases. The availability of a forum for viewing and discussing a range of cases could potentially lead to improved patient setup and reduce the time taken to devise an individual immobilization strategy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Revisiting group contribution theory for estimating fractional free volume of microporous polymer membranes

Fractional free volume (FFV) is a commonly used metric for the development of structure–property relationships for polymer membranes. The most common method to calculate FFV uses Bondi's group contribution method, first introduced in 1964. While updated in 1997, there has not been a significant compilation of new structural motifs since the advent of linear microporous polymers. Here, in this study, we critically examined the assumptions in Bondi's original method and provide four recommendations to streamline and improve the accuracy of calculating van der Waals volume (V W ) for any group. Using these recommendations, we created an updated list of (V W ) values for structural groups commonly present in microporous polymers. The (V W ) and FFV values were then calculated for a database of 123 microporous and high free volume polymers from the literature, showing an average 7% decrease in (V W ) and corresponding increase in FFV by a factor of 24% when compared to prior group contribution correlations in the literature. The significant apparent increase in estimated FFV provides a new perspective to understand and interpret the role of free volume on the separation performance of linear microporous polymers. Additionally, standardization of the group contribution method allows for the direct comparison of FFV values across studies.

42 ENGINEERING↗

Validation and Testing of ENDF/B-VII Decay Data

The nuclear decay library developed for the ORIGEN code was upgraded from ENDF/B-VI.8 to -VII.0 and released in the SCALE nuclear modeling and simulation code system in 2011. Experience with the ENDF/B-VII.0 library identified serious errors and performance issues in the evaluated decay sublibrary. Initially, errors were identified in the decay scheme for the 238U series, leading to large discrepancies in the gamma emission rate for uranium. Further testing of the fission product decay data revealed significant performance issues with ENDF/B-VII.0 relative to the previous release of ENDF/B-VI. To address the performance issues, the decay data library in SCALE was upgraded to ENDF/B-VII.1 and released as an update for users in 2013. This paper describes the practical impact of the ENDF/B-VII.0 decay data performance issues on common code applications, and the validation and testing performed on the updated ORIGEN libraries developed from the ENDF/B-VII.1 sublibrary.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

252 Cf yield calibration method for nuclear material accountancy and safeguards practitioners

Californium-252 is an isotope commonly encapsulated as a physically small but strong spontaneous fission neutron source for applications in industry, academia, and research. Within the nuclear safeguards community, a well-characterized 252 Cf source is often used as an accessible alternative for plutonium in calibrations measurements, which require the absolute source strength. Current methods of source strength quantification can provide an accurate estimate, approximately 1% uncertainty under optimal conditions, but are typically costly and time consuming. An alternative method was developed to determine 252 Cf source strength using passive neutron correlation counting (PNCC). The PNCC method enables institutions and facilities to perform 252 Cf source calibration measurements in-house using detection systems that are common within the nuclear safeguards community. This novel method was previously successfully demonstrated using neutron multiplicity well counters. However, the previous evaluation utilized detection systems with high neutron detection efficiencies, greater than 60%. The purpose of the current study is to extend the previous evaluation and demonstrate the feasibility of the PNCC 252 Cf calibration method for suite of coincidence counters with lower neutron detection efficiencies, between 15% and 35%, which are more commonly encountered in the field, as well as to provide a step-by-step guide to using the method. The neutron source used in this evaluation was previously certified by the National Institutes of Science and Technology (NIST), which provides a reference for the accuracy of the PNCC method. In conclusion, the present source yield calculations demonstrate excellent agreement with a NIST calibration technique and achieve a standard uncertainty below the target 1%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Plant wax and carbon isotope response to heat and drought in the conifer Juniperus monosperma

Plant waxes, including n-alkanes, are commonly used for a wide range of paleo-applications. Several common traits of n-alkanes that are used as paleo-proxies include chain length distribution and average chain length (ACL), as well as plant wax carbon and hydrogen isotopic compositions. The effect of climate on plant wax traits has been the subject of many studies, but a common challenge with modern calibrations is disentangling the effects of species (genetic), temperature, and precipitation from one another. Here, in this study, we explore the effect of temperature and drought, independently and combined, on plant wax composition of the species Juniper monosperma in a large ecosystem-scale field manipulation experiment. We find that n-alkane concentrations significantly increase with temperature, but other parameters (including ACL) are not affected. These results support physiological studies that identify n-alkanes as an important barrier to water loss within the plant cuticle. Combined with prior studies, it appears that changes in ACL within sediments are likely controlled by changes in species composition rather than directly by changes in climate. We find little variation in the carbon isotopic composition (δ 13 C) of n-alkanes across the treatments whereas bulk leaf δ 13 C values are higher in the heat and drought treatment. Because leaf δ 13 C values represent a weighted C assimilation signal, these values reflect differences in leaf gas exchange among treatments, whereas the n-alkanes are synthesized when water availability is higher and differences among treatments are not significant enough to influence their values. These results have important implications for using n-alkane traits, including ACL and δ 13 C values, for paleoenvironmental reconstructions.

Compound-specific isotope analysis↗

Benchmark probabilistic solar forecasts: Characteristics and recommendations

We illustrate and compare commonly used benchmark, or reference, methods for probabilistic solar forecasting that researchers use to measure the performance of their proposed techniques. A thorough review of the literature indicates wide variation in the benchmarks implemented in probabilistic solar forecast studies. To promote consistent and sensible methodological comparisons, we implement and compare ten variants from six common benchmark classes at two temporal scales: intra-hourly forecasts and hourly resolution forecasts. Using open-source Surface Radiation Budget Network (SURFRAD) data from 2018, these benchmark methods are compared using proper probabilistic metrics and common diagnostic tools. Practical implementation issues, such as the impact of missing data and applicability for operational forecasting, are also discussed. Furthermore, we make recommendations for practitioners on the appropriate selection of benchmark methods to properly showcase state-of-the-art improvements in forecast reliability and sharpness. All code and open-source data are available on Github for reproducibility and for other researchers to apply the same benchmark methods to their own data.

14 SOLAR ENERGY↗

Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily

Enzyme superfamily members that share common chemical and/or biological functions also share common features. While the role of structure is well characterized, the link between enzyme function and dynamics is not well understood. We present a systematic characterization of intrinsic dynamics of over 20 members of the pancreatic-type RNase superfamily, which share a common structural fold. This study is motivated by the fact that the range of chemical activity as well as molecular motions of RNase homologs spans over 105 folds. Dynamics was characterized using a combination of nuclear magnetic resonance experiments and computer simulations. Phylogenetic clustering led to the grouping of sequences into functionally distinct subfamilies. Detailed characterization of the diverse RNases showed conserved dynamical traits for enzymes within subfamilies. These results suggest that selective pressure for the conservation of dynamical behavior, among other factors, may be linked to the distinct chemical and biological functions in an enzyme superfamily.

Biochemistry & Molecular Biology↗

Transcriptomic analysis in the developing zebrafish embryo after compound exposure: Individual gene expression and pathway regulation

The zebrafish embryotoxicity test is a promising alternative assay for developmental toxicity. Classically, morphological assessment of the embryos is applied to evaluate the effects of compound exposure. However, by applying differential gene expression analysis the sensitivity and predictability of the test may be increased. For defining gene expression signatures of developmental toxicity, we explored the possibility of using gene expression signatures of compound exposures based on commonly expressed individual genes as well as based on regulated gene pathways. Four developmental toxic compounds were tested in concentration-response design, caffeine, carbamazepine, retinoic acid and valproic acid, and two non-embryotoxic compounds, D-mannitol and saccharin, were included. With transcriptomic analyses we were able to identify commonly expressed genes, which were mostly development related, after exposure to the embryotoxicants. We also identified gene pathways regulated by the embryotoxicants, suggestive of their modes of action. Furthermore, whereas pathways may be regulated by all compounds, individual gene expression within these pathways can differ for each compound. Overall, the present study suggests that the use of individual gene expression signatures as well as pathway regulation may be useful starting points for defining gene biomarkers for predicting embryotoxicity. - Highlights: • The zebrafish embryotoxicity test in combination with transcriptomics was used. • We explored two approaches of defining gene biomarkers for developmental toxicity. • Four compounds in concentration-response design were tested. • We identified commonly expressed individual genes as well as regulated gene pathways. • Both approaches seem suitable starting points for defining gene biomarkers.

60 APPLIED LIFE SCIENCES↗

Sex-specific patterns and deregulation of endocrine pathways in the gene expression profiles of Bangladeshi adults exposed to arsenic contaminated drinking water

Arsenic contamination of drinking water occurs globally and is associated with numerous diseases including skin, lung and bladder cancers, and cardiovascular disease. Recent research indicates that arsenic may be an endocrine disruptor. This study was conducted to evaluate the nature of gene expression changes among males and females exposed to arsenic contaminated water in Bangladesh at high and low doses. Twenty-nine (55% male) Bangladeshi adults with water arsenic exposure ranging from 50 to 1000 μg/L were selected from the Folic Acid Creatinine Trial. RNA was extracted from peripheral blood mononuclear cells for gene expression profiling using Affymetrix 1.0 ST arrays. Differentially expressed genes were assessed between high and low exposure groups for males and females separately and findings were validated using quantitative real-time PCR. There were 534 and 645 differentially expressed genes (p < 0.05) in the peripheral blood mononuclear cells of males and females, respectively, when high and low water arsenic exposure groups were compared. Only 43 genes overlapped between the two sexes, with 29 changing in opposite directions. Despite the difference in gene sets both males and females exhibited common biological changes including deregulation of 17β-hydroxysteroid dehydrogenase enzymes, deregulation of genes downstream of Sp1 (specificity protein 1) transcription factor, and prediction of estrogen receptor alpha as a key hub in cardiovascular networks. Arsenic-exposed adults exhibit sex-specific gene expression profiles that implicate involvement of the endocrine system. Due to arsenic's possible role as an endocrine disruptor, exposure thresholds for arsenic may require different parameters for males and females. - Highlights: • Males and females exhibit unique gene expression changes in response to arsenic. • Only 23 genes are common among the differentially expressed genes for the sexes. • Male and female gene lists exhibit common biological implications. • Both sexes exhibit deregulation of cardiovascular and endocrine pathways.

60 APPLIED LIFE SCIENCES↗

Avoiding Misannotation of In-Source Fragmentation Products as Cellular Metabolites in Liquid Chromatography–Mass Spectrometry-Based Metabolomics

Liquid chromatography–mass spectrometry (LC-MS) technology allows for rapid quantitation of cellular metabolites, with metabolites identified by mass spectrometry and chromatographic retention time. Recently, with the development of rapid scanning high-resolution high accuracy mass spectrometers and the desire for high throughput screening, minimal or no chromatographic separation has become increasingly popular. Furthermore, when analyzing complex cellular extracts, however, the lack of chromatographic separation could potentially result in misannotation of structurally related metabolites. Here, we show that, even using electrospray ionization, a soft ionization method, in-source fragmentation generates unwanted byproducts of identical mass to common metabolites. For example, nucleotide-triphosphates generate nucleotide-diphosphates, and hexose-phosphates generate triose-phosphates. We also evaluated yeast intracellular metabolite extracts and found more than 20 cases of in-source fragments that mimic common metabolites. Finally and accordingly, chromatographic separation is required for accurate quantitation of many common cellular metabolites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Gold Polar Intermetallics: Structural Versatility through Exclusive Bonding Motifs

The design of new materials with desired chemical and physical characteristics requires thorough understanding of the underlying composition–structure–property relationships and the experimental possibility of their modification through the controlled involvement of new components. From this point of view, intermetallic phases, a class of compounds formed by two or more metals, present an endless field of combinations that produce several chemical compound classes ranging from simple alloys to true ionic compounds. Polar intermetallics (PICs) belong to the class that is electronically situated in the middle, between Hume–Rothery phases and Zintl compounds and possessing e/a (valence electron per atom) values around 2. In contrast to the latter, where logical rules of formation and classification systems were developed decades ago, polar intermetallics remain a dark horse with a huge diversity of crystal structures but unclear mechanisms of their formation. Partial incorporation of structural and bonding features from both nonpolar and Zintl compounds is commonly observed here. A decent number of PICs can be described in terms of complex metallic alloys (CMAs) following the Hume–Rothery electron-counting schemes but exhibit electronic structure changes that cannot be explained by the latter. Our research is aimed at the discovery and synthesis of new polar intermetallic compounds, their structural characterization, and investigation of their properties in line with the analysis of the principles connecting all of these components. Understanding of the basic structural tendencies is one of the most anticipated outcomes of this analysis, and systematization of the available knowledge is the initial and most important step. Here in this Account, we focus on a well-represented but rather small section of PICs: ternary intermetallic compounds of gold with electropositive and post-transition metals of groups 12 to 15. The strong influence of relativistic effects in its chemical bonding results in special, frequently unique structural motifs, while at the same time gold participates in common structure types as an ordinary transition element. Enhanced bonding strength leads to the formation and stabilization of complex homo- and heteroatomic clusters and networks that are compositionally restricted to just a few options throughout the periodic table. Because it has the highest absolute electronegativity among metals, comparable to those of some halogens, gold usually plays the role of an anion, even being able to form true salts with the most electropositive metals. We discuss the occurrence of the structure types and show the place of gold intermetallics in the general picture. Among the structures considered are ones as common as AlB 2 or BaAl 4 types, in line with the recently discovered diamond-like homoatomic metal networks, formation of local fivefold symmetry, different types of tunneled structures, and more complex intergrown multicomponent structures.

36 MATERIALS SCIENCE↗

malbacR: A Package for Standardized Implementation of Batch Correction Methods for Omics Data

Mass spectrometry is a powerful tool for identifying and analyzing small molecules, such as metabolites and lipids, in com-plex biological samples. Liquid chromatography and gas chromatography mass spectrometry studies quite commonly in-volve large numbers of samples, which can require significant time for sample preparation and analyses. To accommodate such studies, the samples are commonly split into batches. Inevitably, variations in sample handling, temperature fluctua-tion, imprecise timing, column degradation and other factors result in systematic errors or biases of the measured abundances between the batches. Numerous methods are available via R packages to assist with batch correction for small molecule om-ics data; however, since these methods were developed by different research teams, the algorithms are available in separate R packages, each with different data input and output formats. We introduce the malbacR package which consolidates eleven common batch effect correction methods for small molecule omics data into one place so users can easily implement and compare: pareto scaling, power scaling, range scaling, ComBat, EigenMS, NOMIS, RUV-random, QC-RLSC, WaveI-CA2.0, TIGER, and SERRF. The malbacR package standardizes data input and output formats across these batch correction methods. The package works in conjunction with the pmartR package, allowing users to seamlessly include batch effect cor-rection in a pmartR workflow without needing any additional data manipulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗