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At least 289 records · Page 16

spammR: an R package designed for analysis and integration of spatial multi-omic measurements

Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics. To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with (1) smaller sample sizes and spatial sparsity of samples, (2) considerable missingness, and (3) no a-priori knowledge about proteins or genes of interest, relying on a fully data-driven approach.

spammR↗

BCG alignment with the locations of cluster members and the large-scale structure out to 10 R 200

Using a sample of >200 clusters, each with typically 100–200 spectroscopically confirmed cluster members, we search for a signal of alignment between the position angle (PA) of the Brightest Cluster Galaxy (BCG) and the distribution of cluster members on the sky about the cluster centre out to projected distances of 3 R 200 . The deep spectroscopy, combined with corrections for spectroscopic incompleteness, makes our sample ideal to determine alignment signal strengths. We also use an SDSS based skeleton of the filamentary large-scale structure (LSS), and measure BCG alignment with the location of the LSS skeleton segments on the sky out to projected distances of 10 R 200 . The alignment signal is measured using three separate statistical measures; Rao’s spacing test (U), Kuiper’s V parameter (V), and the Binomial probability test (P). The significance of the BCG alignment signal with both cluster members and LSS segments is extremely high (1 in a million chance or less to be drawn randomly from a uniform distribution). We investigate a wide set of parameters that may influence the strength of the alignment signal. Clusters with more elliptical-shaped BCGs show stronger alignment with both their cluster members and LSS segments. Also, selecting clusters with closely connected filaments, or using a luminosity-weighted LSS skeleton, increases the alignment signal significantly. Alignment strength decreases with increasing projected distance. Combined, these results provide strong evidence for the growth of clusters and their BCGs by preferential feeding along the direction of the filaments in which they are embedded.

79 ASTRONOMY AND ASTROPHYSICS↗

Renormalization group for nonminimal Φ 2 R couplings and gravitational contact interactions

Theories of scalars and gravity, with an Einstein-Hilbert term and nonminimal interactions, M 2 R / 2 - α Φ 2 R / 12 , have graviton exchange-induced contact interactions. These modify the renormalization group, leading to a discrepancy between the conventional calculations in the Jordan frame that ignore this effect (and are found to be incorrect), and the Einstein frame in which α does not exist. Thus, the calculation of quantum effects in the Jordan and Einstein frames does not generally commute with the transition from the Jordan to the Einstein frame. In the Einstein frame, though α is absent, for small steps in scale δ μ / μ infinitesimal contact terms ~ δ α are induced, that are then absorbed back into other couplings by the contact terms. This modifies the β -functions in the Einstein frame. In conclusion, we show how correct results can be obtained in a simple model by including this effect.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Emergent Sp(3,$\mathbb{R}$) Dynamical Symmetry in the Nuclear Many-Body System from an Ab Initio Description

Ab initio nuclear theory provides not only a microscopic framework for quantitative description of the nuclear many-body system, but also a foundation for deeper understanding of emergent collective correlations. In this work, a symplectic Sp(3, $\mathbb{R}$) $\supset$ U(3) dynamical symmetry is identified in ab initio predictions, from a no-core configuration interaction approach, and found to provide a qualitative understanding of the spectrum of 7 Be. Low-lying states form an Elliott SU(3) spectrum, while an Sp(3, $\mathbb{R}$) excitation gives rise to an excited rotational band with strong quadrupole connections to the ground state band.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Hybridized kagome bands and induced Ti magnetism in RTi3Bi4 (R = Nd, Sm, Gd) kagome metals studied using angle-resolved photoemission spectroscopy and x-ray magnetic circular dichroism

Kagome materials are known for hosting emergent quantum phenomena driven by the interaction between different lattice, charge and spin orders. Here, we present a detailed angle resolved photoemission (ARPES), density functional theory (DFT) and x-ray magnetic circular dichroism (XMCD) study of the electronic and magnetic structure of RTi3Bi4 (R = Nd, Sm, Gd). ARPES and DFT demonstrate that the bulk electronic band structure is dominated by the hybridization of the Ti bands, and the weak electron-like pocket at Γ is identified as a surface state. The isotropic XAS profile of the M 4,5-edge of the rare earth is consistent with the presence of R 3+ oxidation state. Using the XMCD sum rules, backed by the atomic multiplet theory calculations, we obtain the spin and orbital magnetic moments. The Ti L2,3-edge XMCD reveals the presence of a small magnetic moment in GdTi3Bi4, presumably driven by the proximity of the Ti kagome layers to the zigzag chains of Gd, while the total magnetic moment of Gd is shared by the f and d electrons. Our combined XMCD, ARPES and DFT study brings an important piece of information to understand the spin flip transitions and anomalous Hall effect observed in the RTi3Bi4 kagome metals.

Lim, C.↗

How R Developers explain their Package Choice: A Survey

Background: Contemporary software development relies heavily on reusing already implemented functionality, usually in the form of packages. Aims: We aim to shed light on developers' preferences when selecting packages in R language. Method: To do that, we create and administer a survey to over 1000 developers who have added one of two common dataframe enhancement libraries in R to their projects: data.table or tidyr. We design a questionnaire using the Social Contagion Theory (SCT) following prior work on technology adoption and ensure that key dimensions affecting developer choice are considered. Results: Of the 1085 developers we contacted, 803 completed the survey asking them to prioritize various factors known to affect developer perceptions of package quality and to provide their background. Most developers self-identified as data scientists with two to five years of work experience. We found significant differences between the preferences of developers who chose data.table and tidyr. Surprisingly, package reputation based on easy-to-see measures, such as the number of stars on GitHub, was not an important factor for either group. Conclusions: Our findings demonstrate the inherently social nature of package adoption. They can help design future studies on how different populations of developers make decisions on which software packages to use in their projects. Finally, package developers and maintainers can benefit by better understanding the prime concerns of the users of their packages.

Malviya Thakur, Addi↗

Search for R-parity-violating supersymmetry in a final state containing leptons and many jets with the ATLAS experiment using $\sqrt{s}=13\hbox{TeV}$ proton–proton collision data

A search for R-parity-violating supersymmetry in final states characterized by high jet multiplicity, at least one isolated light lepton and either zero or at least three b-tagged jets is presented. The search uses 139fb –1 of $\sqrt{s}=13\hbox{TeV}$ proton–proton collision data collected by the ATLAS experiment during Run 2 of the Large Hadron Collider. The results are interpreted in the context of R-parity-violating supersymmetry models that feature gluino production, top-squark production, or electroweakino production. The dominant sources of background are estimated using a data-driven model, based on observables at medium jet multiplicity, to predict the b-tagged jet multiplicity distribution at the higher jet multiplicities used in the search. Machine-learning techniques are used to reach sensitivity to electroweakino production, extending the data-driven background estimation to the shape of the machine-learning discriminant. No significant excess over the Standard Model expectation is observed and exclusion limits at the 95% confidence level are extracted, reaching as high as 2.4 TeV in gluino mass, 1.35 TeV in top-squark mass, and 320 (365) GeV in higgsino (wino) mass.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

R-Stream

R-Stream version 3.21.3, including its TensorFlow front-end (TFRCC) and LLVM 9 front-end. This version includes the features developed in the Portacy Phase II contract. R-Stream is a source-to-source automatic parallelization engine. For usage, please refer to the manuals (In particular, user guide and release notes) available in the package.

Meister, Benoit [Reservoir Labs, Inc., Portland, O↗

DeBoinR: Density Boxplots in R

DeBoinR (Density Boxplots in R) takes in a set of Probability Density Functions (PDFs), calculates outliers based on several notions of distance, and visualizes these outliers via functional boxplots. This code is written as a stand-along R package with the hopes of eventually submitting it to CRAN. The package is written in generality; it would be useful to any researching looking to analyze a general ensemble of PDFs.

Murph, Alexander↗

Detailed Simulation Datasets Quantifying U.S. DOE VTO/HFTO R&D Benefits Across Light- to Heavy-Duty Vehicles

For more than 20 years, Argonne National Laboratory’s Vehicle & Mobility Systems Department has assessed how R&D investments by the U.S. Department of Energy’s Transportation Technologies Office and Alternative Fuels and Feedstocks Office affect vehicle energy use and cost. The analyses are performed using Autonomie, Argonne’s full-vehicle simulation tool for energy consumption, performance, and cost. The study covers five time frames ranging from present day through 2050, with more than 30 vehicle classes and applications (10 light duty and >20 medium and heavy duty), as well as six powertrain configurations (conventional, start-stop, hybrid electric vehicle, plug-in hybrid electric vehicle, battery-electric vehicle, and fuel cell electric vehicle) and five fuels (gasoline, diesel, natural gas, hydrogen, and electricity). Low and high technology uncertainty scenarios have been considered to capture a realistic range of outcomes. The resulting datasets include the assumptions used (i.e., efficiency, $/kWh), vehicle-level data (power, energy, weight, and cost), and outputs such as energy consumption, manufacturer’s suggested retail price, and total cost of ownership. These data are critical to stakeholders working in transportation, technology assessment, and long-term R&D planning.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Chiral gauge theories on $R^3 \times S^1$ and SUSY breaking

We study SU(5) S U ( 5 ) chiral gauge theories on R^3\times S^1 R 3 × S 1 . With an unequal number of fundamental and antifundmental matter representations we calculate nontrivial pre-ADS superpotentials generated by composite multi-monopoles. We also point out that the structure of the composite multi-monopoles can be determined simply from the affine Dynkin diagrams of the gauge group and its unbroken subgroup. For the case of one flavor, we find that the superpotential is independent of the composite meson. We show that dynamical 4D SUSY breaking in the simplest chiral SU(5) S U ( 5 ) gauge theory can be demonstrated directly via semi-classical effects on the circle.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

COVID-19 Testing R&D (Final Report)

Eleven Labs within the US Department of Energy (DOE), National Virtual Biotechnology Laboratory (NVBL), came together as a team to address significant R&D gaps in COVID-19 testing. Beginning in March 2020, the NVBL COVID Testing Team developed an R&D agenda, worked with DOE and other agencies to set priorities, and collaborated to deliver timely results. Priority was given to quick implementation as well as development of novel capabilities for immediate and evolving pandemic needs without placing additional burden on operational performers. Priority elements capitalized on DOE National Laboratory strengths and expertise. The Team delivered: testing and evaluation that enabled decisions on testing options, forwardleaning approaches to prepare for future scale-up needs, and models and experiments that supported prioritization of diagnostic and therapeutic candidates.

60 APPLIED LIFE SCIENCES↗

An Investigation of Innovative Energy Technologies Entering the Market between 2009-2015, Enabled by EERE-Funded R&D

This report documents technologies that have been commercialized by the private sector and other partners—such as technology developers in startups, companies, and universities—in part because of R&D funding from EERE. It also documents emerging technologies that have the potential to reach the market within the next three years with the support of EERE R&D investments. Commercial and emerging technology tracking in this manner assists EERE technology managers, analysts, communications staff, and senior management in describing and explaining the benefits of EERE-funded research. Policy- and decision-makers would then have the latest information to guide future program development and direction.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

RF Accelerator Technology R&D: Report of AF7-rf Topical Group to Snowmass 2021

Accelerator radio frequency (RF) technology has been and remains critical for modern high energy physics (HEP) experiments based on particle accelerators. Tremendous progress in advancing this technology has been achieved over the past decade in several areas highlighted in this report. These achievements and new results expected from continued R&D efforts could pave the way for upgrades of existing facilities, improvements to accelerators already under construction (e.g., PIP-II), well-developed proposals (e.g., ILC, CLIC), and/or enable concepts under development, such as FCC-ee, CEPC, C 3 , HELEN, multi-MW Fermilab Proton Intensity Upgrade, future Muon Colloder, etc. Advances in RF technology have impact beyond HEP on accelerators built for nuclear physics, basic energy sciences, and other areas. Recent examples of such accelerators are European XFEL, LCLS-II and LCLS-II-HE, SHINE, SNS, ESS, FRIB, and EIC. To support and enable new accelerator-based applications and even make some of them feasible, we must continue addressing their challenges via a comprehensive RF R&D program that would advance the existing RF technologies and explore the nascent ones.

43 PARTICLE ACCELERATORS↗

Transactive Campus Energy Systems: An R&D Testbed for Renewables, Integration, Efficiency, and Grid Services (CRADA 356 / Amendment 1)

The Clean Energy and Transactive Campus (CETC) work described in this report was done as part of Amendment 1 to Campus Cooperative Research and Development Agreement (CRADA) 356, the Transactive Campus CRADA with the Washington State Department of Commerce (Commerce) between the U.S. Department of Energy’s (DOE’s), Pacific Northwest National Laboratory (PNNL) and the Commerce through the Clean Energy Fund (CEF). The original project team consisted of PNNL, the University of Washington (UW) and Washington State University (WSU), to connect the PNNL, UW, and WSU campuses to construct and operate the testbed as both a regional flexibility resource and as a platform for research and development (R&D) for buildings/grid integration. Building on the foundational transactive system established by the Pacific Northwest Smart Grid Demonstration (PNWSGD), the purpose of the project was to construct the testbed as both a regional flexibility resource and as a platform for R&D on buildings/grid integration and information-based energy efficiency. The testbed supports the integration of renewables and other regional needs, using the flexibility provided by building loads, energy storage, and smart inverters for batteries and photovoltaic (PV) solar systems, at four physical scales: multiple campuses, campus, microgrid and building.

24 POWER TRANSMISSION AND DISTRIBUTION↗

EDA R-Matrix Evaluations Report on n+ 9 Be, n+ 16 O [Slides]

This presentation discusses new developments in light-element R-matrix evaluation and recent light-element work. The presentation also reviewed R-matrix theory, EDAf90 code implementation, including interface EDAf90 with NJOY, ENDFtk, EXFOR/CSISRS, and a new evaluation for n+ 9 Be. The presentation concludes by stating that further development is needed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Progress on the R-matrix Analysis for the n+ 181 Ta Evaluation [Slides]

This presentation discusses how nuclear data evaluations can influence the accuracy of computational nuclear design calculations. It also discusses the motivation for a new evaluation of 181 Ta. The goals of the evaluations are to generate a set of resonance parameters in the Resolved Resonance Region (RRR) that extends up to 2.6 keV, to generate a set of average resonance parameters in the Unresolved Resonance Region (URR) up to 100 keV (derived from the RRR parameters), and to generate covariance information for both RRR and URR. The presentation discusses how several different experimental data sets will be fit simultaneously in the evaluation of 181 Ta. It states that the level density of 181 Ta can make R-matrix fitting a challenge as the width of the levels increase with energy (as well as decreasing experimental resolution) and the measured resonances can overlap. The presentation concludes by discussing R-matrix analysis and covariance information as the latter is important when propagated to quantify the uncertainty on output responses of nuclear design calculations such as the multiplication factor k .

07 ISOTOPE AND RADIATION SOURCES↗