Determining the grain composition of the interstellar medium with high resolution X-ray spectroscopy

We investigate the ability of high resolution X-ray spectroscopy to directly probe the grain composition of the interstellar medium. Using iron K-edge experimental data of likely ISM dust candidates taken at the National Synchrotron Light Source at Brookhaven National Laboratory and the Advanced Photon Source at Argonne National Laboratory, we explore the prospects for determining the chemical composition of astrophysical dust and discuss a technique for doing so. Focusing on the capabilities of the AstroE2 XRS micro-calorimeters, we assess the limiting effects of spectral resolution and noise for detecting significant X-ray absorption fine structure signal in astrophysical environments containing dust. We find that given sufficient signal, the resolution of the XRS will allow us to definitively distinguish gas from dust phase absorption, and certain chemical compositions.Comment: 6 pages, 10 figures - XAFS spectra of Fe compounds; accepted for publication in Ap

Fitting EXAFS data using molecular dynamics outputs and a histogram approach

The estimation of metal nanoparticle diameter by analysis of extended x-ray absorption fine structure (EXAFS) data from coordination numbers is nontrivial, particularly for particles <5 nm in diameter, for which the undercoordination of surface atoms becomes an increasingly significant contribution to the average coordination number. These undercoordinated atoms have increased degrees of freedom over those within the core of the particle, which results in an increase in the degree of structural disorder with decreasing particle size. This increase in disorder, however, is not accounted for by the standard means of EXAFS analysis, where each coordination shell is fitted with a single bond length and disorder term. In addition, the surface atoms of nanoparticles have been observed to undergo a greater contraction than those in the core, further increasing the range of bond distances. Failure to account for this structural change results in an increased disorder being measured, and therefore, a lower apparent coordination number and corresponding particle size are found. Here, we employ molecular dynamics (MD) simulations for a range of nanoparticle sizes to determine each of the nearest neighbor bond lengths, which were then binned into a histogram to construct a radial distribution function (RDF). Each bin from the histogram was considered to be a single scattering path and subsequently used in fitting the EXAFS data obtained for a series of carbon-supported platinum nanoparticles. These MD-based fits are compared with those obtained using a standard fitting model using Artemis and the standard model with the inclusion of higher cumulants, which has previously been used to account for the non-Gaussian distribution of neighboring atoms around the absorber. The results from all three fitting methods were converted to particle sizes and compared with those obtained from transmission electron microscopy (TEM) and x-ray diffraction (XRD) measurements. We find that the use of molecular dynamics simulations resulted in an improved fit over both the standard and cumulant models, in terms of both quality of fit and correlation with the known average particle size

Probing Plasmodium falciparum sexual commitment at the single-cell level

Background: Malaria parasites go through major transitions during their complex life cycle, yet the underlying differentiation pathways remain obscure. Here we apply single cell transcriptomics to unravel the program inducing sexual differentiation in Plasmodium falciparum. Parasites have to make this essential life-cycle decision in preparation for human-to-mosquito transmission. Methods: By combining transcriptional profiling with quantitative imaging and genetics, we defined a transcriptional signature in sexually committed cells. Results: We found this transcriptional signature to be distinct from general changes in parasite metabolism that can be observed in response to commitment-inducing conditions. Conclusions: This proof-of-concept study provides a template to capture transcriptional diversity in parasite populations containing complex mixtures of different life-cycle stages and developmental programs, with important implications for our understanding of parasite biology and the ongoing malaria elimination campaign

Nature of the Ferroelectric Phase Transition in PbTiO₃

We have measured quantitatively the temperature dependence of the local distortions of PbTiO3 crystals below and above the structural ferroelectric phase transition, using x-ray absorption fine-structure (XAFS) measurements. Two probe atoms, Pb and Ti, were used. The results were analyzed by fitting parametrized theoretical XAFS spectra to the experimental results. These measurements provide quantitative distortion parameters defined as the difference between the distance of the probe to its nearest neighbor measured in the actual structure and that in a centrosymmetric structure with the same unit cell dimensions. At low temperatures the Pb-edge spectra were fit using four shells and included single, double, and triple scattering configurations. The high-temperature fits included only two shells. The Ti-edge spectra were fitted with the first shell only. The Pb and Ti distortions vary relatively little with temperature below the transition and decrease faster near the transition temperature. Above the transition temperature, the Pb and Ti distortions at the peaks of their distortion distribution function (DDFs) are both more than 70% of the corresponding low-temperature values. These results show that an essential element of order-disorder is present even in this nominally pure ferroelectric crystal which displays a soft mode and a dielectric constant typical of displacive-type ferroelectrics. The presence of the local distortions suggests that the displacements should have at least two correlation length scales, one associated with the local distortions, the other with the order parameter

Penile Microbiota and Female Partner Bacterial Vaginosis in Rakai, Uganda

Bacterial vaginosis (BV) is a common vaginal bacterial imbalance associated with risk for HIV and poor gynecologic and obstetric outcomes. Male circumcision reduces BV-associated bacteria on the penis and decreases BV in female partners, but the link between penile microbiota and female partner BV is not well understood. We tested the hypothesis that having a female partner with BV increases BV-associated bacteria in uncircumcised men. We characterized penile microbiota composition and density (i.e., the quantity of bacteria per swab) by broad-coverage 16S rRNA gene-based sequencing and quantitative PCR (qPCR) in 165 uncircumcised men from Rakai, Uganda. Associations between penile community state types (CSTs) and female partner’s Nugent score were assessed. We found seven distinct penile CSTs of increasing density (CST1 to 7). CST1 to 3 and CST4 to 7 were the two major CST groups. CST4 to 7 had higher prevalence and abundance of BV-associated bacteria, such as Mobiluncus and Dialister, than CST1 to 3. Men with CST4 to 7 were significantly more likely to have a female partner with a high Nugent score (P = 0.03). Men with two or more extramarital partners were significantly more likely to have CST4 to 7 than men with only marital partners (CST4 to 7 prevalence ratio, 1.84; 95% confidence interval [CI], 1.16 to 2.92). Female partner Nugent BV is significantly associated with penile microbiota. Our data support the exchange of BV-associated bacteria through intercourse, which may explain BV recurrence and persistence. IMPORTANCE Bacterial vaginosis (BV) is sexually associated but not considered a sexually transmitted disease. Our findings suggest that the uncircumcised penis is an important niche for BV-associated genital anaerobes. In addition, we found a link between extramarital sexual relationships and BV-associated bacteria in men, which parallels earlier findings of the association between sexual activity and BV in women. This suggests the sexual transmissibility of BV-associated bacteria. Reducing bacterial exchange by barrier methods and managing carriage of BV-associated bacteria in men may decrease BV persistence and recurrence in women

Nonresonant valence-to-core x-ray emission spectroscopy of niobium

The valence-to-core (V2C) portion of x-ray emission spectroscopy (XES) measures the electron states close to the Fermi level. These states are involved in bonding, thus providing a measure of the chemistry of the material. In this article, we show the V2C XES spectra for several niobium compounds. The K β ′′ peak in the V2C XES results from the transition of a ligand 2 s electron into the 1 s core-hole of the niobium, a transition allowed by hybridization with the niobium 4 p . This location in energy of this weak peak shows a strong ligand dependence, thus providing a sensitive probe of the ligand environment about the niobium

Condensed Matter Astrophysics: A Prescription for Determining the Species-Specific Composition and Quantity of Interstellar Dust using X-rays

We present a new technique for determining the *quantity and composition* of dust in astrophysical environments using <6keV X-rays. We argue that high resolution X-ray spectra as enabled by the Chandra and XMM-Newton gratings should be considered a powerful and viable new resource for delving into a relatively unexplored regime for directly determining dust properties: composition, quantity, and distribution. We present initial cross-section measurements of astrophysically likely iron-based dust candidates taken at the Lawrence Berkeley National Laboratory Advanced Light Source synchrotron beamline, as an illustrative tool for the formulation of our methodology. Focused at the 700eV Fe LIII and LII photoelectric edges, we discuss a technique for modeling dust properties in the soft X-rays using L-edge data, to complement K-edge X-ray absorption fine structure analysis techniques discussed in Lee & Ravel 2005. This is intended to be *a techniques paper* of interest and usefulness to both condensed matter experimentalists and astrophysicists. For the experimentalists, we offer a new prescription for normalizing relatively low S/N L-edge cross section measurements. For astrophysics interests, we discuss the use of X-ray absorption spectra for determining dust composition in cold and ionized astrophysical environments, and a new method for determining *species-specific gas-to-dust ratios*. Possible astrophysical applications of interest, are offered. Prospects for improving on this work with future X-ray missions with higher throughput and spectral resolution are presented in the context of spectral resolution goals for gratings and calorimeters, for proposed and planned missions such as Astro-H and the International X-ray Observatory.Comment: 37 pages; 8 figures; accepted for publication in Ap

Self-driving Multimodal Studies at User Facilities

Multimodal characterization is commonly required for understanding materials. User facilities possess the infrastructure to perform these measurements, albeit in serial over days to months. In this paper, we describe a unified multimodal measurement of a single sample library at distant instruments, driven by a concert of distributed agents that use analysis from each modality to inform the direction of the other in real time. Powered by the Bluesky project at the National Synchrotron Light Source II, this experiment is a world's first for beamline science, and provides a blueprint for future approaches to multimodal and multifidelity experiments at user facilities.Comment: 36th Conference on Neural Information Processing Systems (NeurIPS 2022). AI4Mat Worksho

Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria

Male circumcision reduces female-to-male HIV transmission. Hypothesized mechanisms for this protective effect include decreased HIV target cell recruitment and activation due to changes in the penis microbiome. We compared the coronal sulcus microbiota of men from a group of uncircumcised controls (n= 77) and from a circumcised intervention group (n = 79) at enrollment and year 1 follow-up in a randomized circumcision trial in Rakai, Uganda. We characterized microbiota using16S rRNA gene-based quantitative PCR (qPCR) and pyrosequencing, log response ratio (LRR), Bayesian classification, nonmetric multidimensional scaling (nMDS), and permutational multivariate analysis of variance (PerMANOVA). At baseline, men in both study arms had comparable coronal sulcus microbiota; however, by year 1, circumcision decreased the total bacterial load and reduced microbiota biodiversity. Specifically, the prevalence and absolute abundance of 12 anaerobic bacterial taxa decreased significantly in the circumcised men. While aerobic bacterial taxa also increased postcircumcision, these gains were minor. The reduction in anaerobes may partly account for the effects of circumcision on reduced HIV acquisition. IMPORTANCE The bacterial changes identified in this study may play an important role in the HIV risk reduction conferred by male circumcision. Decreasing the load of specific anaerobes could reduce HIV target cell recruitment to the foreskin. Understanding the mechanisms that underlie the benefits of male circumcision could help to identify new intervention strategies for decreasing HIV transmission, applicable to populations with high HIV prevalence where male circumcision is culturally less acceptable