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At least 397 records · Page 22

Status of genome function annotation in model organisms and crops

Abstract Since the entry into genome‐enabled biology several decades ago, much progress has been made in determining, describing, and disseminating the functions of genes and their products. Yet, this information is still difficult to access for many scientists and for most genomes. To provide easy access and a graphical summary of the status of genome function annotation for model organisms and bioenergy and food crop species, we created a web application ( https://genomeannotation.rheelab.org ) to visualize, search, and download genome annotation data for 28 species. The summary graphics and data tables will be updated semi‐annually, and snapshots will be archived to provide a historical record of the progress of genome function annotation efforts. Clear and simple visualization of up‐to‐date genome function annotation status, including the extent of what is unknown, will help address the grand challenge of elucidating the functions of all genes in organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Search for flavor-changing neutral current interactions of the top quark and the Higgs boson decaying to a bottom quark-antiquark pair at $ \sqrt{s} $ = 13 TeV

A search for flavor-changing neutral current interactions of the top quark (t) and the Higgs boson (H) is presented. The search is based on a data sample corresponding to an integrated luminosity of 137 fb-1 recorded by the CMS experiment at the LHC in proton-proton collisions at √s = 13 TeV. Events containing exactly one lepton (muon or electron) and at least three jets, among which at least two are identified as originating from the hadronization of a bottom quark, are analyzed. A set of deep neural networks is used for kinematic event reconstruction, while boosted decision trees distinguish the signal from the background events. No significant excess over the background predictions is observed, and upper limits on the signal production cross sections are extracted. These limits are interpreted in terms of top quark decay branching fractions (B) to the Higgs boson and an up (u) or a charm quark (c). Assuming one nonvanishing extra coupling at a time, the observed (expected) upper limits at 95% confidence level are B(t → Hu) < 0.079 (0.11)% and B(t → Hc) < 0.094 (0.086)%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for heavy Higgs bosons with flavour-violating couplings in multi-lepton plus b-jets final states in pp collisions at 13 TeV with the ATLAS detector

A search for new heavy scalars with flavour-violating decays in final states with multiple leptons and b-tagged jets is presented. The results are interpreted in terms of a general two-Higgs-doublet model involving an additional scalar with couplings to the top-quark and the three up-type quarks (ρ tt , ρ tc , and ρ tu ). The targeted signals lead to final states with either a same-sign top-quark pair, three top-quarks, or four top-quarks. The search is based on a data sample of proton-proton collisions at $\sqrt{s}$ = 13 TeV recorded with the ATLAS detector during Run 2 of the Large Hadron Collider, corresponding to an integrated luminosity of 139 fb –1 . Events are categorised depending on the multiplicity of light charged leptons (electrons or muons), total lepton charge, and a deep-neural-network output to enhance the purity of each of the signals. Masses of an additional scalar boson m H between 200 – 630 GeV with couplings ρ tt = 0.4, ρ tc = 0.2, and ρ tu = 0.2 are excluded at 95% confidence level. Additional interpretations are provided in models of R-parity violating supersymmetry, motivated by the recent flavour and (g – 2) μ anomalies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Insight into ideal shear strength of Ni-based dilute alloys using first-principles calculations and correlational analysis

Here the present work examines the effect of alloying elements (denoted X) on the ideal shear strength for 26 dilute Ni-based alloys, Ni11X, as determined by first-principles calculations of pure alias shear deformations. The variations in ideal shear strength are quantitatively explored with correlational analysis techniques, showing the importance of atomic properties such as size and electronegativity. The shear moduli of the alloys are affirmed to show a strong linear relationship with their ideal shear strengths, while the shear moduli of the individual alloying elements were not indicative of alloy shear strength. Through combination with available ideal shear strength data on Mg alloys, a potential application of the Ni alloy data is demonstrated in the search for a set of atomic features suitable for machine learning applications to mechanical properties. As another illustration, the calculated Ni ideal shear strengths play a key role in a predictive multiscale framework for deformation behavior of single crystal alloys at large strains, as shown by simulated stress–strain curves.

36 MATERIALS SCIENCE↗

Predicting U 3 O 8 powder processing conditions: An AI/ML approach analyzing deep learning embeddings of SEM micrographs

High-resolution SEM images of uranium-oxide powders encode micro- and nanoscale clues to their synthesis route and calcination temperature. We trained a ResNet-50 model on 11 commercial-scale U₃O₈ classes, ammonium diuranate (ADU) or uranyl peroxide (H₂O₂) precursors calcined at temperatures ranging from 400 to 750 °C and added a 256-D projection head before the classifier to analyze the learned representation. The best of eight seeds reached 92.4 % accuracy on reserved testing data, but our focus is the structure of the embedding space rather than the accuracy and labels. We quantify class relatedness in the original 256-D space using centroid similarity and distributional distances, and we use Uniform Manifold Approximation Projection (UMAP) for visualization. ‘Unknown’ images from different preparation methods, SEM operators, and from the literature localized near the expected classes under a nearest-centroid analysis without retraining, as well as clustered in similar UMAP space. In conclusion, this embedding-centered workflow complements black-box classification by providing quantitative, similarity-based comparisons of U₃O₈ morphologies and reduces storage space by up to 98 % for image data used in millisecond vector search comparisons.

36 MATERIALS SCIENCE↗

Search for the chiral magnetic effect in Au+Au collisions at $\sqrt{s_{NN}}$ = 27 GeV with the STAR forward event plane detectors

A decisive experimental test of the Chiral Magnetic Effect (CME) is considered one of the major scientific goals at the Relativistic Heavy-Ion Collider (RHIC) towards understanding the nontrivial topological fluctuations of the Quantum Chromodynamics vacuum. In heavy-ion collisions, the CME is expected to result in a charge separation phenomenon across the reaction plane, whose strength could be strongly energy dependent. The previous CME searches have been focused on top RHIC energy collisions. In this Letter, we present a low energy search for the CME in Au+Au collisions at $\sqrt{s_{NN}}$ = 27 GeV. We measure elliptic flow scaled charge-dependent correlators relative to the event planes that are defined at both mid-rapidity |η| < 1.0 and at forward rapidity 2.1 < |η| < 5.1. We compare the results based on the directed flow plane ( $Ψ$ 1 ) at forward rapidity and the elliptic flow plane ( $Ψ$ 2 ) at both central and forward rapidity. The CME scenario is expected to result in a larger correlation relative to $Ψ$ 1 than to $Ψ$ 2 , while a flow driven background scenario would lead to a consistent result for both event planes. In 10-50% centrality, results using three different event planes are found to be consistent within experimental uncertainties, suggesting a flow driven background scenario dominating the measurement. We obtain an upper limit on the deviation from a flow driven background scenario at the 95% confidence level. This work opens up a possible road map towards future CME search with the high statistics data from the RHIC Beam Energy Scan Phase-II.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for a new scalar decaying into new spin-1 bosons in four-lepton final states with the ATLAS detector

A search is conducted for a new scalar boson S, with a mass distinct from that of the Higgs boson, decaying promptly into four leptons ( ℓ = e , μ) via an intermediate state containing two on-shell, promptly decaying new spin-1 bosons Z d : S → Z d Z d → 4 ℓ , where the Z d boson has a mass between 15 and 300 GeV, and the S boson has a mass between either 30 and 115 GeV or 130 and 800 GeV. The search uses proton–proton collision data collected with the ATLAS detector at the Large Hadron Collider with an integrated luminosity of 139 fb−1 at a centre-of-mass energy of s = 13 TeV. No significant excess above the Standard Model background expectation is observed. Upper limits at 95% confidence level are set on the production cross-section times branching ratio, σ ( g g → S ) × B ( S → Z d Z d → 4 ℓ ) , as a function of the mass of both particles, m S and m Z d .

Aad, G↗

Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry

Top-down proteomics by mass spectrometry (MS) involves the mass measurement of an intact protein followed by subsequent activation of the protein to generate product ions. Electron-based fragmentation methods like electron capture dissociation and electron transfer dissociation are widely used for these types of analyses. Recently, electron ionization dissociation (EID), which utilizes higher energy electrons (>20 eV) has been suggested to be more efficient for top-down protein fragmentation compared to other electron-based dissociation methods. In this paper, we demonstrate that the use of EID enhances protein fragmentation and subsequent detection of protein fragments. Protein product ions can form by either single cleavage events, resulting in terminal fragments containing the C-terminus or N-terminus of the protein, or by multiple cleavage events to give rise to internal fragments that include neither the C-terminus nor the N-terminus of the protein. Conventionally, internal fragments have been disregarded, as reliable assignments of these fragments were limited. Here, we demonstrate that internal fragments generated by EID can account for ~20–40% of the mass spectral signals detected by top-down EID-MS experiments. By including internal fragments, the extent of the protein sequence that can be explained from a single tandem mass spectrum increases from ~50 to ~99% for 29 kDa carbonic anhydrase II and 8.6 kDa ubiquitin. When searching for internal fragments during data analysis, previously unassigned peaks can be readily and accurately assigned to confirm a given protein sequence and to enhance the utility of top-down protein sequencing experiments.

59 BASIC BIOLOGICAL SCIENCES↗

Autonomous reinforcement learning agent for stretchable kirigami design of 2D materials

Abstract Mechanical behavior of 2D materials such as MoS 2 can be tuned by the ancient art of kirigami. Experiments and atomistic simulations show that 2D materials can be stretched more than 50% by strategic insertion of cuts. However, designing kirigami structures with desired mechanical properties is highly sensitive to the pattern and location of kirigami cuts. We use reinforcement learning (RL) to generate a wide range of highly stretchable MoS 2 kirigami structures. The RL agent is trained by a small fraction (1.45%) of molecular dynamics simulation data, randomly sampled from a search space of over 4 million candidates for MoS 2 kirigami structures with 6 cuts. After training, the RL agent not only proposes 6-cut kirigami structures that have stretchability above 45%, but also gains mechanistic insight to propose highly stretchable (above 40%) kirigami structures consisting of 8 and 10 cuts from a search space of billion candidates as zero-shot predictions.

36 MATERIALS SCIENCE↗

SENSEI: Direct-Detection Results on sub-GeV Dark Matter from a New Skipper CCD

In this work, we present the first direct-detection search for sub-GeV dark matter using a new ~2-gram high-resistivity Skipper CCD from a dedicated fabrication batch that was optimized for dark matter searches. Using 24 days of data acquired in the MINOS cavern at the Fermi National Accelerator Laboratory, we measure the lowest rates in silicon detectors of events containing one, two, three, or four electrons, and achieve world-leading sensitivity for a large range of sub-GeV dark matter masses. Data taken with different thicknesses of the detector shield suggest a correlation between the rate of high-energy tracks and the rate of single-electron events previously classified as “dark current.” We detail key characteristics of the new Skipper CCDs, which augur well for the planned construction of the ~100-gram SENSEI experiment at SNOLAB.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Search for type-III seesaw heavy leptons in dilepton final states in pp collisions at $\sqrt{s} = 13\,{\text {TeV}}$ with the ATLAS detector

A search for the pair production of heavy leptons as predicted by the type-III seesaw mechanism is presented. The search uses proton–proton collision data at a centre-of-mass energy of 13 TeV, corresponding to 139 fb –1 of integrated luminosity recorded by the ATLAS detector during Run 2 of the Large Hadron Collider. The analysis focuses on the final state with two light leptons (electrons or muons) of different flavour and charge combinations, with at least two jets and large missing transverse momentum. No significant excess over the Standard Model expectation is observed. The results are translated into exclusion limits on heavy-lepton masses, and the observed lower limit on the mass of the type-III seesaw heavy leptons is 790 GeV at 95% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for heavy resonances decaying into a pair of Z bosons in the $\ell ^+\ell ^-\ell '^+\ell '^-$ and $\ell ^+\ell ^-\nu {{\bar{\nu }}}$ final states using 139 $\mathrm {fb}^{-1}$ of proton–proton collisions at $\sqrt{s} = 13$ TeV with the ATLAS detector

A search for heavy resonances decaying into a pair of Z bosons leading to $\ell ^+\ell ^-\ell '^+\ell '^-$ and $\ell ^+\ell ^-\nu {{\bar{\nu }}}$ final states, where ℓ stands for either an electron or a muon, is presented. The search uses proton–proton collision data at a centre-of-mass energy of 13 TeV collected from 2015 to 2018 that corresponds to the integrated luminosity of 139 fb -1 recorded by the ATLAS detector during Run 2 of the Large Hadron Collider. Different mass ranges spanning 200 GeV to 2000 GeV for the hypothetical resonances are considered, depending on the final state and model. In the absence of a significant observed excess, the results are interpreted as upper limits on the production cross section of a spin-0 or spin-2 resonance. The upper limits for the spin-0 resonance are translated to exclusion contours in the context of Type-I and Type-II two-Higgs-doublet models, and the limits for the spin-2 resonance are used to constrain the Randall–Sundrum model with an extra dimension giving rise to spin-2 graviton excitations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for low-mass dilepton resonances in Higgs boson decays to four-lepton final states in proton–proton collisions at $\sqrt{s}=13\,\text {TeV} $

A search for low-mass dilepton resonances in Higgs boson decays is conducted in the four-lepton final state. The decay is assumed to proceed via a pair of beyond the standard model particles, or one such particle and a ${\mathrm{Z}}$ boson. The search uses proton–proton collision data collected with the CMS detector at the CERN LHC, corresponding to an integrated luminosity of 137$\,\text {fb}^{-1}$, at a center-of-mass energy $\sqrt{s} = 13\,\text {TeV} $. No significant deviation from the standard model expectation is observed. Upper limits at 95% confidence level are set on model-independent Higgs boson decay branching fractions. Additionally, limits on dark photon and axion-like particle production, based on two specific models, are reported.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for type-III seesaw heavy leptons in leptonic final states in $pp$ collisions at $\sqrt{s} = 13~\text {TeV}$ with the ATLAS detector

A search for the pair production of heavy leptons as predicted by the type-III seesaw mechanism is presented. The search uses proton–proton collision data at a centre-of-mass energy of 13 TeV, corresponding to 139 fb –1 of integrated luminosity recorded by the ATLAS detector during Run 2 of the Large Hadron Collider. The analysis focuses on final states with three or four electrons or muons from the possible decays of new heavy leptons via intermediate electroweak bosons. No significant deviations above the Standard Model expectation are observed; upper and lower limits on the heavy lepton production cross-section and masses are derived respectively. These results are then combined for the first time with the ones already published by ATLAS using the channel with two leptons in the final state. The observed lower limit on the mass of the type-III seesaw heavy leptons combining two, three and four lepton channels together is 910 GeV at the 95% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for heavy resonances decaying into two Higgs bosons in the $\text {b}{\bar{\text {b}}} \tau ^{+} \tau ^{-}$ final state in proton–proton collisions at $\sqrt{s} = 13\,\text {Te}\hspace{-.08em}\text {V}$

A search is presented for massive narrow-width resonances in the mass range of 1–4.5 TeV , decaying into pairs of Higgs bosons (HH). The search uses proton–proton collision data at a center-of-mass energy of 13 TeV collected with the CMS detector at the CERN LHC during 2016–2018, corresponding to an integrated luminosity of 138 fb -1 . The analysis targets final states where one Higgs boson decays into a pair of bottom quarks and the other into a pair of tau leptons, ${\text {X}} \rightarrow {\text {HH}} \rightarrow \text {b}{\bar{\text {b}}}\,\tau ^{+}\tau ^{-}$. It uses a single large radius jet to reconstruct the ${\text {H}} \rightarrow \text {b}{\bar{\text {b}}}$ decay, while the ${\text {H}} \rightarrow \tau ^{+}\tau ^{-}$ decay products can either be contained within a single large radius jet or appear as two isolated tau leptons. The observed data are consistent with standard model background expectations. Upper limits at 95% confidence level are set on the production cross section for resonant HH production for masses between 1 and 4.5 TeV. This analysis sets the most sensitive limits to date on ${\text {X}} \rightarrow {\text {HH}} \rightarrow \text {b}\bar{\hbox {b}}\, \tau ^{+}\tau ^{-}$ decays in the mass range of 1.4–4.5 TeV.

Hayrapetyan, A. [Yerevan Physics Institute]↗

Chemical Asset Tracker (CAT)

The Chemical Asset Tracker, CAT, is a web-based (browser) application for tracking chemical inventories. The application records information about stored chemicals from user input (via the keyboard, barcode readers, or mobile device) and stores that information into a database. A tiered user login controls access to functions in the application. A user interface is provided that allows users to search the database and update data in the database. SAND2019-7525 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Bolles, Jason↗

Chemical Webscraper [SWR-24-105]

Chemical Webscraper uses the chrome web browser to search for and collect cost data for chemicals from specified distribution websites.

Cordell, Jacob↗

Dataset for First Full Dalitz Plot Measurement in Neutron β-Decay using the Nab Spectrometer and Implications for New Physics

The Nab apparatus at the Fundamental Neutron Physics Beamline at the Spallation Neutron Source was designed to measure key observations in neutron beta decay, test the Standard Model's description of the weak interaction, and search for new physics. This data was collected using the Nab apparatus and are presented in the article "First Full Dalitz Plot Measurement in Neutron β-Decay using the Nab Spectrometer and Implications for New Physics." This data publication includes CSV (comma-separated values) files which are used to generate Figures 3 - 11 in the linked journal article.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗