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At least 685 records · Page 38

Machine learning method for enforcing variable independence in background estimation with LHC data: ABCDisCoTEC

A novel solution is presented for the problem of estimating the backgrounds of a signal search using observed data while simultaneously maximizing the sensitivity of the search to the signal. The 'ABCD method' provides a reliable framework for background estimation by partitioning events into one signal-enhanced region (A) and three background-enhanced control regions (B, C, and D) via two smoothly varying, statistically independent variables. In practice, even slight correlations between the two variables can significantly undermine the method's performance. Thus, choosing appropriate variables by hand can present a formidable challenge, especially when background and signal differ only subtly. To address this issue, the ABCD with distance correlation (ABCDisCo) method was developed to construct two learned variables via a neural network trained to provide strong signal-background discrimination with small values of the distance correlation (DisCo) measure between the two learned variables. However, relying solely on minimizing the DisCo can result in learned variables that may not have distributions of background events that are smoothly varying and localized at extreme values, as necessary for the validity of the background estimation. The ABCDisCo training enhanced with closure (ABCDisCoTEC) method is introduced to solve this issue by directly minimizing the nonclosure, expressed as a dedicated differentiable loss term. This extended method is applied to a data set of proton-proton collisions at a center-of-mass energy of 13 TeV recorded by the CMS detector at the CERN Large Hadron Collider. Additionally, given the complexity of the minimization problem with constraints on multiple loss terms, the modified differential method of multipliers is applied and shown to greatly improve the stability and robustness of the ABCDisCoTEC method, compared to grid search hyperparameter optimization procedures.

Hayrapetyan, Aram [Yerevan Phys. Inst.]↗

Structure of human POFUT1, its requirement in ligand-independent oncogenic Notch signaling, and functional effects of Dowling-Degos mutations

Protein O-fucosyltransferase-1 (POFUT1), which transfers fucose residues to acceptor sites on serine and threonine residues of epidermal growth factor-like repeats of recipient proteins, is essential for Notch signal transduction in mammals. Here, we examine the consequences of POFUT1 loss on the oncogenic signaling associated with certain leukemia-associated mutations of human Notch1, report the structures of human POFUT1 in free and GDP-fucose bound states, and assess the effects of Dowling-Degos mutations on human POFUT1 function. CRISPR-mediated knockout of POFUT1 in U2OS cells suppresses both normal Notch1 signaling, and the ligand-independent signaling associated with leukemogenic mutations of Notch1. Normal and oncogenic signaling are rescued by wild-type POFUT1 but rescue is impaired by an active-site R240A mutation. The overall structure of the human enzyme closely resembles that of the Caenorhabditis elegans protein, with an overall backbone RMSD of 0.93 Å, despite primary sequence identity of only 39% in the mature protein. GDP-fucose binding to the human enzyme induces limited backbone conformational movement, though the side chains of R43 and D244 reorient to make direct contact with the fucose moiety in the complex. The reported Dowling-Degos mutations of POFUT1, except for M262T, fail to rescue Notch1 signaling efficiently in the CRISPR-engineered POFUT1 -/- background. Together, these studies identify POFUT1 as a potential target for cancers driven by Notch1 mutations and provide a structural roadmap for its inhibition.

59 BASIC BIOLOGICAL SCIENCES↗

Lensing without borders – I. A blind comparison of the amplitude of galaxy–galaxy lensing between independent imaging surveys

ABSTRACT Lensing without borders is a cross-survey collaboration created to assess the consistency of galaxy–galaxy lensing signals (ΔΣ) across different data sets and to carry out end-to-end tests of systematic errors. We perform a blind comparison of the amplitude of ΔΣ using lens samples from BOSS and six independent lensing surveys. We find good agreement between empirically estimated and reported systematic errors which agree to better than 2.3σ in four lens bins and three radial ranges. For lenses with zL > 0.43 and considering statistical errors, we detect a 3–4σ correlation between lensing amplitude and survey depth. This correlation could arise from the increasing impact at higher redshift of unrecognized galaxy blends on shear calibration and imperfections in photometric redshift calibration. At zL > 0.54, amplitudes may additionally correlate with foreground stellar density. The amplitude of these trends is within survey-defined systematic error budgets that are designed to include known shear and redshift calibration uncertainty. Using a fully empirical and conservative method, we do not find evidence for large unknown systematics. Systematic errors greater than 15 per cent (25 per cent) ruled out in three lens bins at 68 per cent (95 per cent) confidence at z < 0.54. Differences with respect to predictions based on clustering are observed to be at the 20–30 per cent level. Our results therefore suggest that lensing systematics alone are unlikely to fully explain the ‘lensing is low’ effect at z < 0.54. This analysis demonstrates the power of cross-survey comparisons and provides a promising path for identifying and reducing systematics in future lensing analyses.

79 ASTRONOMY AND ASTROPHYSICS↗

X-ray emission of the radio-loud quasar SDSS J121426.52+140258.9: independent variations between optical/UV and X-ray emission

To understand the X-ray emission of active galactic nuclei (AGNs), we explored the optical-to-X-ray variation correlation of a radio-loud quasar (RLQ) SDSS J121426.52+140258.9 (hereafter J1214+1402) with multi-epoch observations by the Swift and XMM–Newton telescopes. With the historical multiband data, we found that the infrared-to-X-ray flux of RLQ J1214+1402 should not be dominated by the beamed-jet emission. The Swift optical/UV and X-ray light curves showed that J1214+1402 has two optical states, with low flux before 2014 April 8 and high flux after 2014 June 11, but has no significant X-ray variations during the time range between 2007 March 9 and 2014 August 4. This result was supported by the XMM–Newton observations in the time overlapping with Swift. Interestingly, the early XMM–Newton data prior to the Swift time present two unusual emission epochs when J1214+1402 has relatively low optical fluxes but has the brightest X-ray fluxes. The overall independence of optical-to-X-ray variation seems hard to describe by the disc–corona model. With the X-ray spectral fitting, we find that the soft X-ray excess in J1214+1402 appears only during the high optical state when the X-ray emission is at a low state. The soft X-ray excess in J1214+1402 is difficult to explain by an ionized accretion disc; instead, it may be related to the warm corona.

79 ASTRONOMY AND ASTROPHYSICS↗

VDES J2325-5229 a z = 2.7 gravitationally lensed quasar discovered using morphology-independent supervised machine learning

In this paper, we present the discovery and preliminary characterization of a gravitationally lensed quasar with a source redshift z s = 2.74 and image separation of 2.9 arcsec lensed by a foreground z l = 0.40 elliptical galaxy. Since optical observations of gravitationally lensed quasars show the lens system as a superposition of multiple point sources and a foreground lensing galaxy, we have developed a morphology-independent multi-wavelength approach to the photometric selection of lensed quasar candidates based on Gaussian Mixture Models (GMM) supervised machine learning. Using this technique and gi multicolour photometric observations from the Dark Energy Survey (DES), near-IR JK photometry from the VISTA Hemisphere Survey (VHS) and WISE mid-IR photometry, we have identified a candidate system with two catalogue components with i AB = 18.61 and i AB = 20.44 comprising an elliptical galaxy and two blue point sources. Spectroscopic follow-up with NTT and the use of an archival AAT spectrum show that the point sources can be identified as a lensed quasar with an emission line redshift of z = 2.739 ± 0.003 and a foreground early-type galaxy with z = 0.400 ± 0.002. We model the system as a single isothermal ellipsoid and find the Einstein radius θ E ~ 1.47 arcsec, enclosed mass M enc ~ 4 × 10 11 M ⊙ and a time delay of ~52 d. Finally, the relatively wide separation, month scale time delay duration and high redshift make this an ideal system for constraining the expansion rate beyond a redshift of 1.

79 ASTRONOMY AND ASTROPHYSICS↗

Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species

C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort revealed that the set of parallel duplicated and retained genes is enriched for genes that are preferentially expressed in bundle sheath cells, the cell type in which photosynthesis was activated during C4 evolution. Moreover, functional analysis of the cohort of parallel duplicated genes identified SWEET-13 as a potential key transporter in the evolution of C4 photosynthesis in grasses, and provides new insight into the mechanism of phloem loading in these C4 species.

59 BASIC BIOLOGICAL SCIENCES↗

A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR

Abstract Bromodomain and extraterminal (BET) proteins are extensively studied in multiple pathologies, including cancer. BET proteins modulate transcription of various genes, including those synonymous with cancer, such as MYC. Thus, BET inhibitors are a major area of drug development efforts. (+)-JQ1 (JQ1) is the prototype inhibitor and is a common tool to probe BET functions. While showing therapeutic promise, JQ1 is not clinically usable, partly due to metabolic instability. Here, we show that JQ1 and the BET-inactive (−)-JQ1 are agonists of pregnane X receptor (PXR), a nuclear receptor that transcriptionally regulates genes encoding drug-metabolizing enzymes such as CYP3A4, which was previously shown to oxidize JQ1. A PXR-JQ1 co-crystal structure identified JQ1′s tert-butyl moiety as a PXR anchor and explains binding by (−)-JQ1. Analogs differing at the tert-butyl lost PXR binding, validating our structural findings. Evaluation in liver cell models revealed both PXR-dependent and PXR-independent modulation of CYP3A4 expression by BET inhibitors. We have characterized a non-BET JQ1 target, a mechanism of physiological JQ1 instability, a biological function of (−)-JQ1, and BET-dependent transcriptional regulation of drug metabolism genes.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure of a cap-independent translation enhancer RNA

In eukaryotic messenger RNAs, the 5' cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although many plant viruses lack the 5' cap structure, some contain cap-independent translation elements (CITEs) in their 3' untranslated region. The PTE (Panicum mosaic virus translation element) class of CITEs contains a G-rich asymmetric bulge and a C-rich helical junction that were proposed to interact via formation of a pseudoknot. SHAPE analysis of PTE homologs reveals a highly reactive guanosine residue within the G-rich region proposed to mediate eukaryotic initiation factor 4E (eIF4E) recognition. Here we have obtained the crystal structure of the PTE from Pea enation mosaic virus 2 (PEMV 2 ) RNA in complex with our structural chaperone, Fab BL3–6. The structure reveals that the G-rich and C-rich regions interact through a complex network of interactions distinct from those expected for a pseudoknot. The motif, which contains a short parallel duplex, provides a structural mechanism for how the guanosine is extruded from the core stack to enable eIF4E recognition. Homologous PTE elements harbor a G-rich bulge and a three-way junction and exhibit covariation at crucial positions, suggesting that the PEMV 2 tertiary architecture is conserved among these homologs.

59 BASIC BIOLOGICAL SCIENCES↗

Modular 5'-UTR hexamers for context-independent tuning of protein expression in eukaryotes

Functional characterization of regulatory DNA elements in broad genetic contexts is a prerequisite for forward engineering of biological systems. Translation initiation site (TIS) sequences are attractive to use for regulating gene activity and metabolic pathway fluxes because the genetic changes are minimal. However, limited knowledge is available on tuning gene outputs by varying TISs in different genetic and environmental contexts. Here, we created TIS hexamer libraries in baker’s yeast Saccharomyces cerevisiae directly 5' end of a reporter gene in various promoter contexts and measured gene activity distributions for each library. Next, selected TIS sequences, resulted in almost 10-fold changes in reporter outputs, were experimentally characterized in various environmental and genetic contexts in both yeast and mammalian cells. From our analyses, we observed strong linear correlations (R 2 = 0.75–0.98) between all pairwise combinations of TIS order and gene activity. Finally, our analysis enabled the identification of a TIS with almost 50% stronger output than a commonly used TIS for protein expression in mammalian cells, and selected TISs were also used to tune gene activities in yeast at a metabolic branch point in order to prototype fitness and carotenoid production landscapes. Taken together, the characterized TISs support reliable context-independent forward engineering of translation initiation in eukaryotes.

Biochemistry & Molecular Biology↗

H-lignin can be deposited independently of CINNAMYL ALCOHOL DEHYDROGENASE C and D in Arabidopsis

Abstract Lignin contributes substantially to the recalcitrance of biomass toward saccharification. To circumvent this problem, researchers have genetically altered lignin, although, in a number of cases, these efforts have resulted in an undesirable yield penalty. Recent findings have shown that by knocking out two subunits (MED5A and MED5B) of the transcriptional regulatory complex Mediator, the stunted growth phenotype of mutants in p-coumaroyl shikimate 3′-hydroxylase, reduced epidermal fluorescence 8-1 (ref8-1), can be alleviated. Furthermore, these plants synthesize a lignin polymer almost entirely derived from p-coumaryl alcohol. Plants deficient in cinnamyl alcohol dehydrogenase (CAD) are notable in that they primarily incorporate coniferaldehyde and sinapaldehyde into their lignin. We tested the hypothesis that by stacking mutations in the genes encoding for the CAD paralogs C and D on an Arabidopsis (Arabidopsis thaliana) med5a/5b ref8-1 genetic background, the biosynthesis of p-coumaryl alcohol would be blocked, making p-coumaraldehyde available for polymerization into a novel kind of lignin. The med5a/5b ref8-1 cadc cadd plants are viable, but lignin analysis demonstrated that they continue to synthesize p-hydroxyphenyl lignin despite being mutated for the CADs typically considered to be required for monolignol biosynthesis. In addition, enzyme activity tests showed that even in the absence of CADC and CADD, there is high CAD activity in stems. We tested the potential involvement of other CADs in p-coumaraldehyde biosynthesis in the quintuple mutant by mutating them using the CRISPR/Cas9 system. Lignin analysis demonstrated that the resulting hextuple mutant plants continue to deposit p-coumaryl alcohol-derived lignin, demonstrating a route for the synthesis of p-hydroxyphenyl lignin in Arabidopsis independent of four CAD isoforms.

59 BASIC BIOLOGICAL SCIENCES↗

Arabidopsis ACYL CARRIER PROTEIN4 and RHOMBOID LIKE10 act independently in chloroplast phosphatidate synthesis

Abstract ACYL CARRIER PROTEIN4 (ACP4) is the most abundant ACP isoform in Arabidopsis (Arabidopsis thaliana) leaves and acts as a scaffold for de novo fatty acid biosynthesis and as a substrate for acyl-ACP-utilizing enzymes. Recently, ACP4 was found to interact with a protein-designated plastid RHOMBOID LIKE10 (RBL10) that affects chloroplast monogalactosyldiacylglycerol (MGDG) biosynthesis, but the cellular function of this interaction remains to be explored. Here, we generated and characterized acp4 rbl10 double mutants to explore whether ACP4 and RBL10 directly interact in influencing chloroplast lipid metabolism. Alterations in the content and molecular species of chloroplast lipids such as MGDG and phosphatidylglycerol were observed in the acp4 and rbl10 mutants, which are likely associated with the changes in the size and profiles of diacylglycerol (DAG), phosphatidic acid (PA), and acyl-ACP precursor pools. ACP4 contributed to the size and profile of the acyl-ACP pool and interacted with acyl-ACP-utilizing enzymes, as expected for its role in fatty acid biosynthesis and chloroplast lipid assembly. RBL10 appeared to be involved in the conversion of PA to DAG precursors for MGDG biosynthesis as evidenced by the increased 34:x PA and decreased 34:x DAG in the rbl10 mutant and the slow turnover of radiolabeled PA in isolated chloroplasts fed with [14C] acetate. Interestingly, the impaired PA turnover in rbl10 was partially reversed in the acp4 rbl10 double mutant. Collectively, this study shows that ACP4 and RBL10 affect chloroplast lipid biosynthesis by modulating substrate precursor pools and appear to act independently.

59 BASIC BIOLOGICAL SCIENCES↗

Model-independent measurement of 𝐷 0 −$\overline{D}$ 0 mixing parameters in 𝐷 0 → 𝐾$^{0}_{𝑆}$⁢𝜋 + ⁢𝜋 − decays at Belle and Belle II

We perform a model-independent measurement of the 𝐷 0 −$\overline{D}$ 0 mixing parameters using samples of 𝑒 + ⁢𝑒 − -collision data collected by the Belle and Belle II experiments that have integrated luminosities of 951 fb −1 and 408 fb −1 , respectively. Approximately 2.05 × 10 6 neutral 𝐷 mesons are reconstructed in the 𝐷 0 → 𝐾$^{0}_{S}$⁢𝜋 + ⁢𝜋 − channel, with the neutral 𝐷 flavor tagged by the charge of the pion in the 𝐷* + → 𝐷 0⁢ 𝜋 + decay. Assuming charge-parity symmetry, the mixing parameters are measured to be 𝑥 = (4.0 ±1.7 ±0.4) × 10 −3 and 𝑦 = (2.9 ±1.4 ±0.3) × 10 −3 , where the first uncertainties are statistical and the second systematic. The results are consistent with previous determinations.

Charmed mesons↗

Dark Energy Survey: DESI-independent angular BAO measurement

In this work, we present a measurement of the angular baryon acoustic oscillation (BAO) scale from the completed Dark Energy Survey (DES) dataset excluding the area of overlap with the Dark Energy Spectroscopic Instrument (DESI). We follow the same methodology and validation process as in the DES Y6 BAO analysis. We interpret the impact of this measurement in the context of the statistical preference for 𝑤 0 ⁢𝑤 𝑎 cold dark matter (CDM) over Λ⁢CDM when combined with DES Y5 Type Ia supernovae (SN), Planck CMB, and DESI BAO. Based on our previous work, using the full Y6 DES BAO sample, in combination with SN, CMB and DESI data release 1 (DR1) BAO, added 0.3⁢𝜎 in this preference (from 3.7⁢𝜎 to 4.0⁢𝜎), but this ignored possible correlations between datasets. Using our new DESI-independent DES BAO likelihood instead, we find a smaller increase in the statistical preference for 𝑤 0 ⁢𝑤 𝑎 ⁢CDM, from 3.7⁢𝜎 to 3.8⁢𝜎 when using DESI DR1 BAO, and from 4.0⁢𝜎 to 4.1⁢𝜎 when updating to the more recent DESI data release 2 (DR2) BAO. These significances reduce to 3.1⁢𝜎 when using the new calibrated DES SN-Dovekie. Alongside this work, we publicly release baofit_wtheta, the BAO fitting code for the angular correlation function used in the DES Y6 BAO analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

Energy Independence of the Collins Asymmetry in 𝑝 ↑⁢ 𝑝 Collisions

The STAR experiment reports new, high-precision measurements of the transverse single-spin asymmetries for 𝜋 ± within jets, namely the Collins asymmetries, from transversely polarized 𝑝 ↑⁢ 𝑝 collisions at $\sqrt{s}$ = 510 GeV. The energy-scaled distribution of jet transverse momentum, 𝑥 T = 2⁢𝑝 T, jet /$\sqrt{s}$, shows a remarkable consistency for Collins asymmetries of 𝜋 ± in jets between $\sqrt{s}$ = 200 GeV and 510 GeV. This indicates that the Collins asymmetries are nearly energy independent, with, at most, a very weak scale dependence in 𝑝 ↑ ⁢𝑝 collisions. These results extend to high-momentum scales (𝑄 2 ≤ 3400 GeV 2 ) and enable unique tests of evolution and universality in the transverse-momentum-dependent formalism, thus providing important constraints for the Collins fragmentation functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Impossibility of obtaining time-independent, three-dimensional, spherically symmetric densities of confined systems of relativistically moving constituents

The quantum-mechanical definition of probability, the uncertainty principle, and Poincaré invariance provide strong basic restrictions on the ability to define spatial densities associated with form factors describing the properties of confined systems of relativistically moving constituents. Despite this, many papers ignore one or more of these restrictions. Here I show how to obtain time-independent , two-dimensional densities that are consistent with the stated restrictions. This is done using the light-front, infinite momentum frame formalism. Two-dimensional density interpretations of the axial-vector form factor and all three gravitational form factors is obtained. The resulting mass radius is smaller than the charge radius. Additionally, an expression of a two-dimensional mass density related to the trace of the energy momentum tensor is obtained. I also show that all known methods for finding three-dimensional densities—using the Breit frame, Abel transformations, Wigner distributions, and spherically symmetric wave packets with vanishing spatial extent—violate the basic restrictions in different ways. Furthermore, the use of the latter leads to densities that vanish almost everywhere in space as time increases from an initial value.

form factors↗

Model-independent tuning for maximizing free electron laser pulse energy

The output power of a free electron laser (FEL) has extremely high variance even when all FEL parameter set points are held constant because of the stochastic nature of the self-amplified spontaneous emission (SASE) FEL process, drift of thousands of coupled parameters, such as thermal drifts, and uncertainty and time variation of the electron distribution coming off of the photo cathode and entering the accelerator. In this work, we demonstrate the application of automatic, model-independent feedback for the maximization of average pulse energy of the light produced by free electron lasers. We present experimental results from both the European x-ray free electron laser at DESY and from the Linac Coherent Light Source at SLAC. We demonstrate application of the technique on rf systems for automatically adjusting the longitudinal phase space of the beam, for adjusting the phase shifter gaps between the undulators, and for adjusting steering magnets between undulator sections to maximize the FEL output power. We show that we can tune up to 105 components simultaneously based only on noisy average bunch energy measurements.

47 OTHER INSTRUMENTATION↗

Evidence of a Shockley-Read-Hall Defect State Independent of Band-Edge Energy in InAs / In ( As , Sb ) Type-II Superlattices

A set of seven InAs/InAsSb type-II superlattices (T2SLs) were designed to have speci c bandgap energies between 290 meV (4.3 m) and 135 meV (9.2 m) in order to study the e ects of the T2SL bandgap energy on the minority carrier lifetime. A temperature dependent optical pump-probe technique is used to measure the carrier lifetimes, and the e ect of a mid-gap defect level on the carrier recombination dynamics is reported. The Shockley-Read-Hall (SRH) defect state is found to be at energy of approximately -250 12 meV relative to the valence band edge of bulk GaSb for the entire set of T2SL structures, even though the T2SL valence band edge shifts by 155 meV on the same scale. These results indicate that the SRH defect state in InAs/InAsSb T2SLs is singular and is nearly independent of the exact position of the T2SL bandgap or band edge energies. They also suggest the possibility of engineering the T2SL structure such that the SRH state is removed completely from the bandgap, a result that should signi cantly increase the minority carrier lifetime.

36 MATERIALS SCIENCE↗

Starting-point-independent quantum Monte Carlo calculations of iron oxide

Quantum Monte Carlo (QMC) methods are useful for studies of strongly correlated materials because they are many body in nature and use the physical Hamiltonian. Typical calculations assume as a starting point a wave function constructed from single-particle orbitals obtained from one-body methods, e.g., density functional theory. However, mean-field-derived wave functions can sometimes lead to systematic QMC biases if the mean-field result poorly describes the true ground state. In this study, we examine the accuracy and flexibility of QMC trial wave functions using variational and fixed-node diffusion QMC estimates of the total spin density and lattice distortion of antiferromagnetic iron oxide (FeO) in the ground state B1 crystal structure. We found that for relatively simple wave functions the predicted lattice distortion was controlled by the choice of single-particle orbitals used to construct the wave function, rather than by subsequent wave function optimization techniques within QMC. By optimizing the orbitals with QMC, we then demonstrate starting-point independence of the trial wave function with respect to the method by which the orbitals were constructed by demonstrating convergence of the energy, spin density, and predicted lattice distortion for two qualitatively different sets of orbitals. The results suggest that orbital optimization is a promising method for accurate many-body calculations of strongly correlated condensed phases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗