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At least 1,567 records · Page 87

The microbiologist's guide to metaproteomics

Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.

bioinformatics↗

A multimodel intercomparison of resolution effects on precipitation: simulations and theory

An ensemble of six pairs of RCM experiments performed at 25 and 50 km for the period 1961–2000 over a large European domain is examined in order to evaluate the effects of resolution on the simulation of daily precipitation statistics. Application of the non-parametric two-sample Kolmorgorov–Smirnov test, which tests for differences in the location and shape of the probability distributions of two samples, shows that the distribution of daily precipitation differs between the pairs of simulations over most land areas in both summer and winter, with the strongest signal over southern Europe. Two-dimensional histograms reveal that precipitation intensity increases with resolution over almost the entire domain in both winter and summer. In addition, the 25 km simulations have more dry days than the 50 km simulations. The increase in dry days with resolution is indicative of an improvement in model performance at higher resolution, while the more intense precipitation exceeds observed values. The systematic increase in precipitation extremes with resolution across all models suggests that this response is fundamental to model formulation. Simple theoretical arguments suggest that fluid continuity, combined with the emergent scaling properties of the horizontal wind field, results in an increase in resolved vertical transport as grid spacing decreases. This increase in resolution-dependent vertical mass flux then drives an intensification of convergence and resolvable-scale precipitation as grid spacing decreases. In conclusion, this theoretical result could help explain the increasingly, and often anomalously, large stratiform contribution to total rainfall observed with increasing resolution in many regional and global models.

54 ENVIRONMENTAL SCIENCES↗

Scalar excursions in large-eddy simulations

Here, the range of values of scalar fields in turbulent flows is bounded by their boundary values, for passive scalars, and by a combination of boundary values, reaction rates, phase changes, etc., for active scalars. The current investigation focuses on the local conservation of passive scalar concentration fields and the ability of the large-eddy simulation (LES) method to observe the boundedness of passive scalar concentrations. In practice, as a result of numerical artifacts, this fundamental constraint is often violated with scalars exhibiting unphysical excursions. The present study characterizes passive-scalar excursions in LES of a shear flow and examines methods for diagnosis and assesment of the problem. The analysis of scalar-excursion statistics provides support of the main hypothesis of the current study that unphysical scalar excursions in LES result from dispersive errors of the convection-term discretization where the subgrid-scale model (SGS) provides insufficient dissipation to produce a sufficiently smooth scalar field. In the LES runs three parameters are varied: the discretization of the convection terms, the SGS model, and grid resolution. Unphysical scalar excursions decrease as the order of accuracy of non-dissipative schemes is increased, but the improvement rate decreases with increasing order of accuracy. Two SGS models are examined, the stretched-vortex and a constant-coefficient Smagorinsky. Scalar excursions strongly depend on the SGS model. The excursions are significantly reduced when the characteristic SGS scale is set to double the grid spacing in runs with the stretched-vortex model. The maximum excursion and volume fraction of excursions outside boundary values show opposite trends with respect to resolution. The maximum unphysical excursions increase as resolution increases, whereas the volume fraction decreases. The reason for the increase in the maximum excursion is statistical and traceable to the number of grid points (sample size) which increases with resolution. In contrast, the volume fraction of unphysical excursions decreases with resolution because the SGS models explored perform better at higher grid resolution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Robust verification of stochastic simulation codes

We introduce a robust verification tool for computational codes, which we call Stochastic Robust Extrapolation based Error Quantification (StREEQ). Unlike the prevalent Grid Convergence Index (GCI) [1] method, our approach is suitable for both stochastic and deterministic computational codes and is generalizable to any number of discretization variables. Building on ideas introduced in the Robust Verification [2] approach, we estimate the converged solution and orders of convergence with uncertainty using multiple fits of a discretization error model. In contrast to Robust Verification, we perform these fits to many bootstrap samples yielding a larger set of predictions with smoother statistics. Here, bootstrap resampling is performed on the lack-of-fit errors for deterministic code responses, and directly on the noisy data set for stochastic responses. This approach lends a degree of robustness to the overall results, capable of yielding precise verification results for sufficiently resolved data sets, and appropriately expanding the uncertainty when the data set does not support a precise result. For stochastic responses, a credibility assessment is also performed to give the analyst an indication of the trustworthiness of the results. Furthermore, this approach is suitable for both code and solution verification, and is particularly useful for solution verification of high-consequence simulations..

97 MATHEMATICS AND COMPUTING↗

Process-structure-property considerations for wire-based directed energy deposition of Ti-6Al-4V

Directed energy deposition (DED) is an attractive additive manufacturing (AM) process for large structural components. The rapid solidification and layer-by-layer process associated with DED results in non-ideal microstructures, such as large grains with strong crystallographic textures. These non-ideal microstructures can lead to severe anisotropy in the mechanical properties. Despite these challenges, DED has been identified as a potential solution for the manufacturing of near net shape Ti-6Al-4V preforms, replacing lost casting and forging capabilities. Two popular wire-based directed energy deposition (W-DED) processes were considered for the manufacturing of Ti-6Al-4V with assessments on their respective metallurgical and mechanical properties, as compared to a conventionally processed material. The two W-DED processes explored were wire arc additive manufacturing (WAAM) and electron beam additive manufacturing (EBAM). High throughput inspection and tensile testing procedures were utilized to generate statistically relevant data sets related to each process and sample orientation. The 2 AM technologies produced material with remarkably different microstructures and mechanical properties. Importantly, results revealed key differences in strength and ductility for the two disparate processes which were found to be related to differences in the metallurgical properties.

36 MATERIALS SCIENCE↗

Evaluating and modeling the effects of surface sampling factors on the recovery of organic chemical attribution signatures using the accelerated diffusion sampler and solvent extraction

In this study, an experimental design matrix was created and executed in order to test the effects of various real-world factors on the ability of the (1) accelerated diffusion sampler with solid phase micro-extraction (ADS-SPME) and (2) solvent extraction to capture organic chemical attribution signatures (CAS) from dimethyl methylphosphonate (DMMP) spiked onto painted wall board (PWB) surfaces. The DMMP CAS organic impurities sampled by ADS-SPME and solvent extraction were analyzed by gas chromatography/mass spectrometry (GC/MS). The number of detected DMMP CAS impurities and their respective GC/MS peak areas were determined as a function of DMMP stock, DMMP spiked volume, exposure time, SPME sampling time, and ADS headspace pressure. Based on the statistical analysis of experimental results, several general conclusions are made: (1) ADS-SPME with vacuum (i.e., reduced pressure) increased the amount of detected CAS impurity, as measured by GC/MS peak area, by a factor of 1.7 to 1.9 for PWB under certain experimental conditions, (2) the amount of detected CAS impurity was most influenced by spiked volume, stock, and ADS headspace pressure, (3) the ADS had no measurable effect on the number of detected DMMP impurities, that is, the ADS (with and without reduced pressure) had no practical effect on the DMMP impurity profile collected from spiked PWB, and (4) solvent extraction out performed ADS-SPME in terms of consistently capturing all or most of the targeted DMMP impurities from spiked PWB.

36 MATERIALS SCIENCE↗

Hydrated Anions: From Clusters to Bulk Solution with Quasi-Chemical Theory

The interactions of hydrated ions with molecular and macromolecular solution and interface partners are strong on a chemical energy scale. Here we recount the foremost ab initio theory for the evaluation of the hydration free energies of ions, namely, quasi-chemical theory (QCT). We focus on anions, particularly halides but also the hydroxide anion, because they have been outstanding challenges for all theories. For example, this work supports understanding the high selectivity for F – over Cl – in fluoride-selective ion channels despite the identical charge and the size similarity of these ions. QCT is built by the identification of inner-shell clusters, separate treatment of those clusters, and then the integration of those results into the broader-scale solution environment. Recent work has focused on a close comparison with mass-spectrometric measurements of ion-hydration equilibria. We delineate how ab initio molecular dynamics (AIMD) calculations on ion-hydration clusters, elementary statistical thermodynamics, and electronic structure calculations on cluster structures sampled from the AIMD calculations obtain just the free energies extracted from the cluster experiments. That theory–experiment comparison has not been attempted before the work discussed here, but the agreement is excellent with moderate computational effort. This agreement reinforces both theory and experiment and provides a numerically accurate inner-shell contribution to QCT. The inner-shell complexes involving heavier halides display strikingly asymmetric hydration clusters. Asymmetric hydration structures can be problematic for the evaluation of the QCT outer-shell contribution with the polarizable continuum model (PCM). Nevertheless, QCT provides a favorable setting for the exploitation of PCM when the inner-shell material shields the ion from the outer solution environment. For the more asymmetrically hydrated, and thus less effectively shielded, heavier halide ions clustered with waters, the PCM is less satisfactory. We therefore investigate an inverse procedure in which the inner-shell structures are sampled from readily available AIMD calculations on the bulk solutions. This inverse procedure is a remarkable improvement; our final results are in close agreement with a standard tabulation of hydration free energies, and the final composite results are independent of the coordination number on the chemical energy scale of relevance, as they should be. Finally, a comparison of anion hydration structure in clusters and bulk solutions from AIMD simulations emphasize some differences: the asymmetries of bulk solution inner-shell structures are moderated compared with clusters but are still present, and inner hydration shells fill to slightly higher average coordination numbers in bulk solution than in clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Planck intermediate results. XX. Comparison of polarized thermal emission from Galactic dust with simulations of MHD turbulence

Polarized emission observed by Planck HFI at 353 GHz towards a sample of nearby fields is presented, focusing on the statistics of polarization fractions p and angles ψ. The polarization fractions and column densities in these nearby fields are representative of the range of values obtained over the whole sky. We find that: (i) the largest polarization fractions are reached in the most diffuse fields; (ii) the maximum polarization fraction p max decreases with column density N H in the more opaque fields with N H > 10 21 cm -2 ; and (iii) the polarization fraction along a given line of sight is correlated with the local spatial coherence of the polarization angle. These observations are compared to polarized emission maps computed in simulations of anisotropic magnetohydrodynamical turbulence in which we assume a uniform intrinsic polarization fraction of the dust grains. We find that an estimate of this parameter may be recovered from the maximum polarization fraction p max in diffuse regions where the magnetic field is ordered on large scales and perpendicular to the line of sight. This emphasizes the impact of anisotropies of the magnetic field on the emerging polarization signal. The decrease of the maximum polarization fraction with column density in nearby molecular clouds is well reproduced in the simulations, indicating that it is essentially due to the turbulent structure of the magnetic field: an accumulation of variously polarized structures along the line of sight leads to such an anti-correlation. In the simulations, polarization fractions are also found to anti-correlate with the angle dispersion function S. However, the dispersion of the polarization angle for a given polarization fraction is found to be larger in the simulations than in the observations, suggesting a shortcoming in the physical content of these numerical models. In summary, we find that the turbulent structure of the magnetic field is able to reproduce the main statistical properties of the dust polarization as observed in a variety of nearby clouds, dense cores excluded, and that the large-scale field orientation with respect to the line of sight plays a major role in the quantitative analysis of these statistical properties.

79 ASTRONOMY AND ASTROPHYSICS↗

The cosmic web of X-ray active galactic nuclei seen through the eROSITA Final Equatorial Depth Survey (eFEDS)

Which galaxies in the general population turn into active galactic nuclei (AGNs) is a keystone of galaxy formation and evolution. Thanks to SRG/eROSITA’s contiguous 140 square degree pilot survey field, we constructed a large, complete, and unbiased soft X-ray flux-limited (FX > 6.5 × 10 -15 erg s -1 cm -2 ) AGN sample at low redshift, 0.05 < z < 0.55. Two summary statistics, the clustering using spectra from SDSS-V and galaxy-galaxy lensing with imaging from HSC, are measured and interpreted with halo occupation distribution and abundance matching models. Both models successfully account for the observations. We obtain an exceptionally complete view of the AGN halo occupation distribution. The population of AGNs is broadly distributed among halos with a mean mass of 3.9 -2.4 +2.0 × 10 12 M ⊙ . This corresponds to a large-scale halo bias of b(z = 0.34) = 0.99 -0.10 +0.08 . The central occupation has a large transition parameter, σ log 10 (M) = 1.28 ± 0.2. The satellite occupation distribution is characterized by a shallow slope, α sat = 0.73 ± 0.38. We find that AGNs in satellites are rare, with f sat < 20%. Most soft X-ray-selected AGNs are hosted by central galaxies in their dark matter halo. A weak correlation between soft X-ray luminosity and large-scale halo bias is confirmed (3.3σ). We discuss the implications of environmental-dependent AGN triggering. This study paves the way toward fully charting, in the coming decade, the coevolution of X-ray AGNs, their host galaxies, and dark matter halos by combining eROSITA with SDSS-V, 4MOST, DESI, LSST, and Euclid data.

79 ASTRONOMY AND ASTROPHYSICS↗

ARE DECAYING MAGNETIC FIELDS ABOVE ACTIVE REGIONS RELATED TO CORONAL MASS EJECTION ONSET?

Coronal mass ejections (CMEs) are powered by magnetic energy stored in non-potential (current-carrying) coronal magnetic fields, with the pre-CME field in balance between outward magnetic pressure of the proto-ejecta and inward magnetic tension from overlying fields that confine the proto-ejecta. In studies of global potential (current-free) models of coronal magnetic fields-Potential Field Source Surface (PFSS) models-it has been reported that model field strengths above flare sites tend to be weaker when CMEs occur than when eruptions fail to occur. This suggests that potential field models might be useful to quantify magnetic confinement. One straightforward implication of this idea is that a decrease in model field strength overlying a possible eruption site should correspond to diminished confinement, implying an eruption is more likely. We have searched for such an effect by post facto investigation of the time evolution of model field strengths above a sample of 10 eruption sites. To check if the strengths of overlying fields were relevant only in relatively slow CMEs, we included both slow and fast CMEs in our sample. In most events we study, we find no statistically significant evolution in either (1) the rate of magnetic field decay with height, (2) the strength of overlying magnetic fields near 50 Mm, or (3) the ratio of fluxes at low and high altitudes (below 1.1 R{sub Sun }, and between 1.1 and 1.5 R{sub Sun }, respectively). We did observe a tendency for overlying field strengths and overlying flux to increase slightly, and their rates of decay with height to become slightly more gradual, consistent with increased confinement. The fact that CMEs occur regardless of whether the parameters we use to quantify confinement are increasing or decreasing suggests that either (1) the parameters that we derive from PFSS models do not accurately characterize the actual large-scale field in CME source regions, (2) systematic evolution in the large-scale magnetic environment of CME source regions is not, by itself, a necessary condition for CMEs to occur, or both.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Protoplanetary disk masses in the young NGC 2024 cluster

We present the results from a Submillimeter Array survey of the 887 μm continuum emission from the protoplanetary disks around 95 young stars in the young cluster NGC 2024. Emission was detected from 22 infrared sources, with flux densities from ∼5 to 330 mJy; upper limits (at 3σ) for the other 73 sources range from 3 to 24 mJy. For standard assumptions, the corresponding disk masses range from ∼0.003 to 0.2 M{sub ⊙}, with upper limits at 0.002–0.01 M{sub ⊙}. The NGC 2024 sample has a slightly more populated tail at the high end of its disk mass distribution compared to other clusters, but without more information on the nature of the sample hosts it remains unclear if this difference is statistically significant or a superficial selection effect. Unlike in the Orion Trapezium, there is no evidence for a disk mass dependence on the (projected) separation from the massive star IRS 2b in the NGC 2024 cluster. We suggest that this is due to either the cluster youth or a comparatively weaker photoionizing radiation field.

79 ASTRONOMY AND ASTROPHYSICS↗

Stellar velocity dispersion and anisotropy of the Milky Way inner halo

We measure the three components of velocity dispersion, σ{sub R}, σ{sub θ}, σ{sub ϕ}, for stars within 6 < R < 30 kpc of the Milky Way using a new radial velocity sample from the MMT telescope. We combine our measurements with previously published data so that we can more finely sample the stellar halo. We use a maximum likelihood statistical method for estimating mean velocities, dispersions, and covariances assuming only that velocities are normally distributed. The alignment of the velocity ellipsoid is consistent with a spherically symmetric gravitational potential. From the spherical Jeans equation, the mass of the Milky Way is M(R⩽12 kpc)=1.3×10{sup 11} M{sub ⊙} with an uncertainty of 40%. We also find a region of discontinuity, 15 ≲ R ≲ 25 kpc, where the estimated velocity dispersions and anisotropies diverge from their anticipated values, confirming the break observed by others. We argue that this break in anisotropy is physically explained by coherent stellar velocity structure in the halo, such as the Sgr stream. To significantly improve our understanding of halo kinematics will require combining radial velocities with future Gaia proper motions.

79 ASTRONOMY AND ASTROPHYSICS↗

Polarization observables in few nucleon systems with CLAS

The CEBAF Large Acceptance Spectrometer (CLAS), housed in Hall-B at the Thomas Jefferson National Accelerator Facility provides us with the experimental tools to study strongly-interacting matter and its dynamics in the transition from hadronic to partonic degrees of freedom in nuclear interactions. In this paper we discuss the progress made in understanding the relevant degrees of freedom using polarisation observables of deuteron photodisintegration in the few-GeV photon-energy region. We also address progress made in studying the interaction between Hyperons and Nucleons via polarisation observables, utilising high-statistics experiments that provided us with the large data samples needed to study final-state interactions, as well as perform detailed studies on initial-state effects. The polarisation observables presented here provide us with unique experimental tools to study the underlying dynamics of both initial and final-state interactions, as well as the information needed to disentangle signal from background contributions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Random insights into the complexity of two-dimensional tensor network calculations

Projected entangled pair states (PEPS) offer memory-efficient representations of some quantum many-body states that obey an entanglement area law and are the basis for classical simulations of ground states in two-dimensional (2d) condensed matter systems. However, rigorous results show that exactly computing observables from a 2d PEPS state is generically a computationally hard problem. Yet approximation schemes for computing properties of 2d PEPS are regularly used, and empirically seen to succeed, for a large subclass of (“not too entangled”) condensed matter ground states. Adopting the philosophy of random matrix theory, in this work, we analyze the complexity of approximately contracting a 2d random PEPS by exploiting an analytic mapping to an effective replicated statistical mechanics model that permits a controlled analysis at a large bond dimension. Through this statistical-mechanics lens, we argue that (i) although approximately sampling wave-function amplitudes of random PEPS faces a computational-complexity phase transition above a critical bond dimension, and (ii) one can generically efficiently estimate the norm and correlation functions for any finite bond dimension. Furthermore, these results are supported numerically for various bond-dimension regimes. It is an important open question whether the above results for random PEPS apply more generally also to PEPS representing physically relevant ground states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High-energy-resolution X-ray monochromator calibration using the detailed-balance principle

A new method is presented to calibrate an X-ray energy scale with sub-meV relative accuracy by using the detailed-balance principle of the phonon creation and annihilation. This method is conveniently used to define or verify the energy scale of high-energy-resolution monochromators that are used in inelastic X-ray scattering and nuclear resonant inelastic X-ray scattering instruments at synchrotron radiation facilities. This method does not rely on sample properties and its precision only depends on the statistical data quality. Well calibrated instruments are essential for reliable comparison of data sets obtained at different synchrotron radiation beamlines, of data with theoretical predictions, and of data from other techniques such as neutron or light scattering. The principle of the detailed-balance method is described in this paper and demonstrated experimentally.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Experimental Validation of a Module Cell Cracking Model

The What's Cracking app can predict how changes in crystalline silicon photovoltaic (PV) module materials, design, and mounting affect its susceptibility for cell fracture under uniform loading. This work has experimentally validated the app. A set of commercial crystalline silicon PV modules was obtained for this study. The modules were uniformly loaded at three different mounting points, and their subsequent cell fractures were recorded. A large sample size allowed for the development of an experimental statistical model for cell fracture. Here, the comparison of the experiment to predictions from the app is in excellent agreement. Both experimental and modeling results also elucidate how moving the module mounting points toward the center of the module increases the probability of cell fracture.

14 SOLAR ENERGY↗

Trust Your Gut: Comparing Human and Machine Inference from Noisy Visualizations

People commonly utilize visualizations not only to examine a given dataset, but also to draw generalizable conclusions about the underlying models or phenomena. Prior research has compared human visual inference to that of an optimal Bayesian agent, with deviations from rational analysis viewed as problematic. However, human reliance on non-normative heuristics may prove advantageous in certain circumstances. We investigate scenarios where human intuition might surpass idealized statistical rationality. In two experiments, we examine individuals’ accuracy in characterizing the parameters of known data-generating models from bivariate visualizations. Our findings indicate that, although participants generally exhibited lower accuracy compared to statistical models, they frequently outperformed Bayesian agents, particularly when faced with extreme samples. Participants appeared to rely on their internal models to filter out noisy visualizations, thus improving their resilience against spurious data. However, participants displayed overconfidence and struggled with uncertainty estimation. They also exhibited higher variance than statistical machines. Our findings suggest that analyst gut reactions to visualizations may provide an advantage, even when departing from rationality. These results carry implications for designing visual analytics tools, offering new perspectives on how to integrate statistical models and analyst intuition for improved inference and decision-making. The data and materials for this paper are available at https://osf.io/qmfv6

human-machine collaboration↗

The Automation of Regression Modeling in Osteometric Sorting: An Ordination Approach

Abstract This study compares the original osteometric sorting association method with an ordination approach across all combinations of the humerus, ulna, radius, femur, tibia, and fibula. This includes both the original prediction interval and t ‐statistic approaches. Standard measurements are utilized in the models with full measurements combined and without length measurements. The sample is the osteometric sorting reference from the Defense POW / MIA Accounting Agency. A full set of performance statistics is provided. Results indicate the ordination approach outperforms the original in the majority of bone combinations. Models with length measurements have more exclusion power than those without. It is recommended for the ordination approach to supersede the original when applied to large commingled assemblages.

Lynch, Jeffrey James↗