Tidal Distortion and Disruption of Rubble-Pile Method and Results
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Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting
Background Although pathogenic Gram-negative bacteria lack their own ubiquitination machinery, they have evolved or acquired virulence effectors that can manipulate the host ubiquitination process through structural and/or functional mimicry of host machinery. Many such effectors have been identified in a wide variety of bacterial pathogens that share little sequence similarity amongst themselves or with eukaryotic ubiquitin E3 ligases. Methods To allow identification of novel bacterial E3 ubiquitin ligase effectors from protein sequences we have developed a machine learning approach, the SVM-based Identification and Evaluation of Virulence Effector Ubiquitin ligases (SIEVE-Ub). We extend the string kernel approach used previously to sequence classification by introducing reduced amino acid (RED) alphabet encoding for protein sequences. Results We found that 14mer peptides with amino acids represented as simply either hydrophobic or hydrophilic provided the best models for discrimination of E3 ligases from other effector proteins with a receiver-operator characteristic area under the curve (AUC) of 0.90. When considering a subset of E3 ubiquitin ligase effectors that do not fall into known sequence based families we found that the AUC was 0.82, demonstrating the effectiveness of our method at identifying novel functional family members. Feature selection was used to identify a parsimonious set of 10 RED peptides that provided good discrimination, and these peptides were found to be located in functionally important regions of the proteins involved in E2 and host target protein binding. Our general approach enables construction of models based on other effector functions. We used SIEVE-Ub to predict nine potential novel E3 ligases from a large set of bacterial genomes. SIEVE-Ub is available for download at https://doi.org/10.6084/m9.figshare.7766984.v1 or https://github.com/biodataganache/SIEVE-Ub for the most current version.
59 BASIC BIOLOGICAL SCIENCES↗
PV O&M Cost Model [SWR-21-14]
This tool presents a method for calculating costs associated with the operation and maintenance (O&M) of photovoltaic (PV) systems. The tool compiles details regarding the cost and frequency of multiple O&M services to estimate annual O&M costs ($/year) for each year of an analysis period, the net present value ($) of life cycle costs accumulated over the analysis period, and the reserve account amount ($) that might be required to fund unexpected repairs. The reserve account includes parts inventory and is important for providing a source of funds to make repairs quickly and avoid lost production. This method allows a detailed selection of services to perform based on system size, market served (e.g., residential, commercial, or utility), type and configuration of system components (e.g., micro-, string, or central inverter), and site and environmental conditions (e.g., pollen, bird populations) which is an improvement over simple per unit valuations of O&M costs ($/kW/year). This model also distinguishes costs that vary from year to year and increase at different rates over time as modeled by heuristic failure distributions (e.g., Weibull or Lognormal distribution) based on actuarial data for many of the services.
Walker, Andy↗
On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
All known terrestrial proteins are coded as continuous strings of ≈20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein sequences using a mathematically precise definition for “repetition”, an efficient algorithmic implementation and a robust scoring system with no adjustable parameters. We show that the sequence patterns can be well-separated into disjoint classes according to their recurrence in nested structures. The statistics of the occurrences of patterns indicate that short repetitions are sufficient to account for the differences between natural families and randomized groups of sequences by more than 10 standard deviations, while contiguous sequence patterns shorter than 5 residues are effectively random in their occurrences. A small subset of patterns is sufficient to account for a robust ”familiarity” definition between arbitrary sets of sequences.
Pablo Turjanski↗
Power supply and method of manufacturing
A multiplier assembly for a power supply and a method of manufacturing the multiplier assembly. The multiplier assembly may be a stack of capacitors and support elements electrically and mechanically coupled together to form a first capacitor string and a second capacitor string. The support elements may electrically and mechanically connect adjacent series capacitors in the first capacitor string. Additionally or alternatively, the support elements may electrically and mechanically connect adjacent series capacitors in the second capacitor string. In one embodiment, the power supply may include drive and feedback circuitry capable of controlling operation of the multiplier assembly.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Beyond AdS 2 /dCFT 1 : insertions in two Wilson loops
We consider two-point correlators of local operator insertions in a system of two Wilson-Maldacena loops in $\mathcal{N}$ = 4 supersymmetric Yang-Mills theory on both sides of the AdS/CFT correspondence. On the holographic side the correlator of two Wilson-Maldacena loops is given by a classical string world-sheet which in one phase connects two asymptotically AdS 2 regions and in the other phase is given by two disconnected AdS 2 caps; this configuration breaks supersymmetry as well as conformal invariance. We present a complete systematic account of the string world-sheet fluctuations, including the fermionic sector, and study the behavior of the holographic two-point correlators. On the field theory side we compute certain two-point correlators of local operator insertions by resumming sets of ladder diagrams. Our results demonstrate the efficacy of previously developed methods in tackling this non-conformal, non-susy regime.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
The disk partition function in string theory
We investigate the disk partition function for the open string. This is a subtle problem because of the presence of a residual gauge group PSL(2, R) on the worldsheet even after fixing the conformal gauge. It naively has infinite volume and leads to a vanishing answer. We use different methods that all demonstrate that PSL(2, R) effectively behaves like a group with finite negative volume in the path integral, which leads to a simple prescription for the computation of the disk partition function. We apply our findings to give a simple rederivation of the D-brane tensions.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Cosmic microwave background constraints for global strings and global monopoles
We present the first cosmic microwave background (CMB) power spectra from numerical simulations of the global O( N ) linear σ-model, with N =2,3, which have global strings and monopoles as topological defects. In order to compute the CMB power spectra we compute the unequal time correlators (UETCs) of the energy-momentum tensor, showing that they fall off at high wave number faster than naive estimates based on the geometry of the defects, indicating non-trivial (anti-)correlations between the defects and the surrounding Goldstone boson field. We obtain source functions for Einstein-Boltzmann solvers from the UETCs, using a recently developed method that improves the modelling at the radiation-matter transition. We show that the interpolation function that mimics the transition is similar to other defect models, but not identical, confirming the non-universality of the interpolation function. The CMB power spectra for global strings and global monopoles have the same overall shape as those obtained using the non-linear σ-model approximation, which is well captured by a large- N calculation. However, the amplitudes are larger than the large- N calculation would naively predict, and in the case of global strings much larger: a factor of 20 at the peak. Finally we compare the CMB power spectra with the latest CMB data in other to put limits on the allowed contribution to the temperature power spectrum at multipole l = 10 of 1.7% for global strings and 2.4% for global monopoles. These limits correspond to symmetry-breaking scales of 2.9× 10{sup 15} GeV (6.3× 10{sup 14} GeV with the expected logarithmic scaling of the effective string tension between the simulation time and decoupling) and 6.4× 10{sup 15} GeV respectively. The bound on global strings is a significant one for the ultra-light axion scenario with axion masses m {sub a} ∼< 10{sup −28} eV . These upper limits indicate that gravitational waves from global topological defects will not be observable at the gravitational wave observatory LISA.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Multiview Incomplete Knowledge Graph Integration with application to cross-institutional EHR data harmonization
Objective: The growing availability of electronic health records (EHR) data opens opportunities for integrative analysis of multi-institutional EHR to produce generalizable knowledge. A key barrier to such integrative analyses is the lack of semantic interoperability across different institutions due to coding differences. We propose a Multiview Incomplete Knowledge Graph Integration (MIKGI) algorithm to integrate information from multiple sources with partially overlapping EHR concept codes to enable translations between healthcare systems. Methods: The MIKGI algorithm combines knowledge graph information from (i) embeddings trained from the co-occurrence patterns of medical codes within each EHR system and (ii) semantic embeddings of the textual strings of all medical codes obtained from the Self-Aligning Pretrained BERT (SAPBERT) algorithm. Due to the heterogeneity in the coding across healthcare systems, each EHR source provides partial coverage of the available codes. MIKGI synthesizes the incomplete knowledge graphs derived from these multi-source embeddings by minimizing a spherical loss function that combines the pairwise directional similarities of embeddings computed from all available sources. MIKGI outputs harmonized semantic embedding vectors for all EHR codes, which improves the quality of the embeddings and enables direct assessment of both similarity and relatedness between any pair of codes from multiple healthcare systems. Results: With EHR co-occurrence data from Veteran Affairs (VA) healthcare and Mass General Brigham (MGB), MIKGI algorithm produces high quality embeddings for a variety of downstream tasks including detecting known similar or related entity pairs and mapping VA local codes to the relevant EHR codes used at MGB. Based on the cosine similarity of the MIKGI trained embeddings, the AUC was 0.918 for detecting similar entity pairs and 0.809 for detecting related pairs. For cross-institutional medical code mapping, the top 1 and top 5 accuracy were 91.0% and 97.5% when mapping medication codes at VA to RxNorm medication codes at MGB; 59.1% and 75.8% when mapping VA local laboratory codes to LOINC hierarchy. When trained with 500 labels, the lab code mapping attained top 1 and 5 accuracy at 77.7% and 87.9%. MIKGI also attained best performance in selecting VA local lab codes for desired laboratory tests and COVID-19 related features for COVID EHR studies. Compared to existing methods, MIKGI attained the most robust performance with accuracy the highest or near the highest across all tasks. Conclusions: The proposed MIKGI algorithm can effectively integrate incomplete summary data from biomedical text and EHR data to generate harmonized embeddings for EHR codes for knowledge graph modeling and cross-institutional translation of EHR codes.
Zhou, Doudou↗
Normalization of ZZ instanton amplitudes in type 0B minimal superstring theory
Abstract We study ZZ instanton corrections in the (2,4k)$$ \mathcal{N} $$ N = 1 minimal superstring theory with the type 0B GSO projection, which becomes the type 0B$$ \mathcal{N} $$ N = 1 super-JT gravity in thek→ ∞ limit. Each member of the (2,4k) family of theories has two phases distinguished by the sign of the Liouville bulk cosmological constant. The worldsheet method for computing the one-loop normalization constant multiplying the instanton corrections gives an ill-defined answer in both phases. We fix these divergences using insights from string field theory and find finite, unambiguous results. Each member of the (2,4k) family of theories is dual to a double-scaled one-matrix integral, where the double-scaling limit can be obtained starting either from a unitary matrix integral with a leading one-cut saddle point, or from a hermitian matrix integral with a leading two-cut saddle point. The matrix integral exhibits a gap-closing transition, which is the same as the double-scaled Gross-Witten-Wadia transition whenk= 1. We also compute instanton corrections in the double-scaled matrix integral for allkand in both phases, and find perfect agreement with the string theory results.
Physics↗
CMB internal delensing with general optimal estimator for higher-order correlations
We present here a new method for delensing B modes of the cosmic microwave background (CMB) using a lensing potential reconstructed from the same realization of the CMB polarization (CMB internal delensing). The B -mode delensing is required to improve sensitivity to primary B modes generated by, e.g., the inflationary gravitational waves, axionlike particles, modified gravity, primordial magnetic fields, and topological defects such as cosmic strings. However, the CMB internal delensing suffers from substantial biases due to correlations between observed CMB maps to be delensed and that used for reconstructing a lensing potential. Since the bias depends on realizations, we construct a realization-dependent (RD) estimator for correcting these biases by deriving a general optimal estimator for higher-order correlations. The RD method is less sensitive to simulation uncertainties. Compared to the previous ℓ -splitting method, we find that the RD method corrects the biases without substantial degradation of the delensing efficiency.
79 ASTRONOMY AND ASTROPHYSICS↗
Equivalence of emergent de Sitter spaces from conformal field theory
Recently, two groups have made distinct proposals for a de Sitter space that is emergent from conformal field theory (CFT). The first proposal is that, for two-dimensional holographic CFTs, the kinematic space of geodesics on a space-like slice of the asymptotically anti-de Sitter bulk is two-dimensional de Sitter space (dS 2 ), with a metric that can be derived from the entanglement entropy of intervals in the CFT. In the second proposal, de Sitter dynamics emerges naturally from the first law of entanglement entropy for perturbations around the vacuum state of CFTs. We provide support for the equivalence of these two emergent spacetimes in the vacuum case and beyond. In particular, we study the kinematic spaces of nontrivial solutions of 3d gravity, including the BTZ black string, BTZ black hole, and conical singularities. We argue that the resulting spaces are generically globally hyperbolic spacetimes that support dynamics given boundary conditions at future infinity. For the BTZ black string, corresponding to a thermal state of the CFT, we show that both prescriptions lead to an emergent hyperbolic patch of dS 2 . As a result, we offer a general method for relating kinematic space and the auxiliary de Sitter space that is valid in the vacuum and thermal cases.
74 ATOMIC AND MOLECULAR PHYSICS↗
Simulating self-powered neutron detector responses to infer burnup-induced power distribution perturbations in next-generation light water reactors
Understanding how 3D power distribution will be monitored throughout reactor core volumetric space in next-generation nuclear power reactors is crucial to the design, deployment, and licensing of these reactors. Although numerous techniques exist for 3D power distribution monitoring based on the response of both in situ and ex situ sensors currently implemented or proposed for use in the US reactor fleet, crucial details about these techniques are often unclear. The publicly available documentation does not include information such as how well these techniques are characterized and optimized in their implementations and the levels of uncertainty in the inferred 3D power distribution. The work described herein investigated a recently developed 3D power distribution inferencing method as applied to two next-generation reactor simulations: (1) the NuScale small modular reactor design and (2) the Westinghouse AP1000 design, both of which contain in-core strings of vanadium self-powered neutron detectors (SPNDs). This investigation considered a range of SPND string sensor densities, as well as a range of 3D power distribution axial segment sizes. In this work, SPND response simulation is informed by neutron flux calculations in representative homogenized cores. For the different sensor densities and power distribution axial segment sizes in these simulations, the average solution error, solver iterations, and run time were tracked to parameterize the sensor-core configuration.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Two-dimensional shape recognition using sparse distributed memory
Researchers propose a method for recognizing two-dimensional shapes (hand-drawn characters, for example) with an associative memory. The method consists of two stages: first, the image is preprocessed to extract tangents to the contour of the shape; second, the set of tangents is converted to a long bit string for recognition with sparse distributed memory (SDM). SDM provides a simple, massively parallel architecture for an associative memory. Long bit vectors (256 to 1000 bits, for example) serve as both data and addresses to the memory, and patterns are grouped or classified according to similarity in Hamming distance. At the moment, tangents are extracted in a simple manner by progressively blurring the image and then using a Canny-type edge detector (Canny, 1986) to find edges at each stage of blurring. This results in a grid of tangents. While the technique used for obtaining the tangents is at present rather ad hoc, researchers plan to adopt an existing framework for extracting edge orientation information over a variety of resolutions, such as suggested by Watson (1987, 1983), Marr and Hildreth (1980), or Canny (1986).
Kanerva, Pentti↗
Physics-Based Method for Generating Fully Synthetic IV Curve Training Datasets for Machine Learning Classification of PV Failures
Classification machine learning models require high-quality labeled datasets for training. Among the most useful datasets for photovoltaic array fault detection and diagnosis are module or string current-voltage (IV) curves. Unfortunately, such datasets are rarely collected due to the cost of high fidelity monitoring, and the data that is available is generally not ideal, often consisting of unbalanced classes, noisy data due to environmental conditions, and few samples. In this paper, we propose an alternate approach that utilizes physics-based simulations of string-level IV curves as a fully synthetic training corpus that is independent of the test dataset. In our example, the training corpus consists of baseline (no fault), partial soiling, and cell crack system modes. The training corpus is used to train a 1D convolutional neural network (CNN) for failure classification. The approach is validated by comparing the model’s ability to classify failures detected on a real, measured IV curve testing corpus obtained from laboratory and field experiments. Results obtained using a fully synthetic training dataset achieve identical accuracy to those obtained with use of a measured training dataset. When evaluating the measured data’s test split, a 100% accuracy was found both when using simulations or measured data as the training corpus. When evaluating all of the measured data, a 96% accuracy was found when using a fully synthetic training dataset. The use of physics-based modeling results as a training corpus for failure detection and classification has many advantages for implementation as each PV system is configured differently, and it would be nearly impossible to train using labeled measured data.
Hopwood, Michael W. (ORCID:0000000161901767)↗
One-loop holography with strings in AdS 4 × $\mathbb{CP}$ 3
We compute the one-loop effective action of string configurations embedded in AdS 4 × CP 3 which are dual to 1/6-BPS latitude Wilson Loops in the ABJM theory. To avoid ambiguities in the string path integral we subtract the 1/2-BPS case. The one-loop determinants are computed by Fourier-decomposing the two dimensional operators and then using the Gel’fand-Yaglom method. We comment on various aspects related to the regularization procedure, showing the cancellation of a hierarchy of divergences. After taking into account an IR anomaly from a change in topology, we find a precise agreement with the field theory result known from supersymmetric localization.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Accelerated pattern matching method on a quantum computing system
A method of determining a pattern in a sequence of bits using a quantum computing system includes setting a first register of a quantum processor in a superposition of a plurality of string index states, encoding a bit string in a second register of the quantum processor, encoding a bit pattern in a third register of the quantum processor, circularly shifting qubits of the second register conditioned on the first register, amplifying an amplitude of a state combined with the first register in which the circularly shifted qubits of the second register matches qubits of the third register, measuring an amplitude of the first register and determining a string index state of the plurality of string index states associated with the amplified state, and outputting, by use of a classical computer, a string index associated with the first register in the measured state.
NIROULA, Pradeep↗
BRST symmetry and the convolutional double copy
Motivated by the results of Anastasiou et al., we consider the convolutional double copy for BRST and anti-BRST covariant formulations of gravitational and gauge theories in more detail. We give a general BRST and anti-BRST invariant formulation of linearised $\mathcal{N}$ = 0 supergravity using superspace methods and show how this may be obtained from the square of linearised Yang-Mills theories. We demonstrate this relation for the Schwarzschild black hole and the ten-dimensional black string solution as two concrete examples.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗