Mapping and engineering the interaction between adiponectin and T-cadherin
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Pascolutti, Roberta↗
SEARCH · Engineering Papers
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Search for magnetically-induced signatures in the arrival directions of ultra-high-energy cosmic rays measured at the Pierre Auger Observatory
We search for signals of magnetically-induced effects in the arrival directions of ultra-high-energy cosmic rays detected at the Pierre Auger Observatory. We apply two different methods. One is a search for sets of events that show a correlation between their arrival direction and the inverse of their energy, which would be expected if they come from the same point-like source, they have the same electric charge and their deflection is relatively small and coherent. We refer to these sets of events as “multiplets”. The second method, called “thrust”, is a principal axis analysis aimed to detect the elongated patterns in a region of interest. We study the sensitivity of both methods using a benchmark simulation and we apply them to data in two different searches. The first search is done assuming as source candidates a list of nearby active galactic nuclei and starburst galaxies. The second is an all-sky blind search. We report the results and we find no statistically significant features. We discuss the compatibility of these results with the indications on the mass composition inferred from data of the Pierre Auger Observatory.
79 ASTRONOMY AND ASTROPHYSICS↗
Probing the hadronic nature of the gamma-ray emission associated with Westerlund 2
ABSTRACT Star-forming regions have been proposed as potential Galactic cosmic ray accelerators for decades. Cosmic ray acceleration can be probed through observations of gamma-rays produced in inelastic proton–proton collisions at GeV and TeV energies. In this paper, we analyse more than 11 yr of Fermi–LAT data from the direction of Westerlund 2, one of the most massive and best-studied star-forming regions in our Galaxy. In particular, we investigate the characteristics of the bright pulsar PSR J1023–5746 that dominates the gamma-ray emission below a few GeV at the position of Westerlund 2 and the underlying extended source FGES J1023.3–5747. The analysis results in a clear identification of FGES J1023.3–5747 as the GeV counterpart of the TeV source HESS J1023-575, through its morphological and spectral properties. This identification provides new clues about the origin of the HESS J1023-575 gamma-ray emission, favouring a hadronic origin of the emission, powered by Westerlund 2, rather than a leptonic origin related to either the pulsar wind nebula associated with PSR J1023–5746 or the cluster itself. This result indirectly supports the hypothesis that star-forming regions can contribute to the cosmic ray sea observed in our Galaxy.
Mestre, Enrique↗
Thermal and kinematic properties of ejecta in SN1987A revealed by XRISM
We present an analysis of high-resolution spectra from the shock-heated plasmas in SN 1987A, based on an observation using the Resolve instrument onboard the X-Ray Imaging and Spectroscopy Mission (XRISM). The 1.7–10 keV Resolve spectra are accurately represented by a single-component, plane-parallel shock plasma model, with a temperature of $2.84_{-0.08}^{+0.09}$ keV and an ionization parameter of $2.64_{-0.45}^{+0.58}$ × $10^{11}\,\,{\rm s\,\, cm}^{-3}$. The Resolve spectra are also well reproduced by the 3D magneto-hydrodynamic simulation presented by Orlando et al. (2020, A&A, 636, A22) suggesting substantial contribution from the ejecta. The metal abundances obtained with Resolve align with the Large Magellanic Cloud value, indicating that the X-rays in 2024 originate from “non-metal-rich” shock-heated ejecta and the reverse shock has not reached the inner metal-rich region of ejecta. Doppler widths of the atomic lines from Si, S, and Fe correspond to velocities of 1500–1700 km s$^{-1}$, where the thermal broadening effects in this non-metal-rich plasma are negligible. Therefore, the line broadening seen in Resolve spectra is determined by the large bulk motion of ejecta. For reference, we determined a $90\%$ upper limit on non-thermal emission from a pulsar wind nebula at $4.3 \times 10^{-13}$ erg cm$^{-2}$ s$^{-1}$ in the 2–10 keV range, aligning with NuSTAR findings by Greco et al. (2022, ApJ, 931, 132). Additionally, we searched for the $^{44}$Sc K line feature and found a $1\sigma$ upper limit of $1.0 \times 10^{-6}$ photons cm$^{-2}$ s$^{-1}$, which translates to an initial $^{44}$Ti mass of approximately $2 \times 10^{-4}\, M_{\odot }$, consistent with previous X-ray to soft gamma-ray observations (Boggs et al. 2015, Science, 348, 670; Grebenev et al. 2012, Nature, 490, 373; Leising 2006, ApJ, 651, 1019).
ISM: supernova remnants↗
Perspectives on improving photosynthesis to increase crop yield
Abstract Improving photosynthesis, the fundamental process by which plants convert light energy into chemical energy, is a key area of research with great potential for enhancing sustainable agricultural productivity and addressing global food security challenges. This perspective delves into the latest advancements and approaches aimed at optimizing photosynthetic efficiency. Our discussion encompasses the entire process, beginning with light harvesting and its regulation and progressing through the bottleneck of electron transfer. We then delve into the carbon reactions of photosynthesis, focusing on strategies targeting the enzymes of the Calvin–Benson–Bassham (CBB) cycle. Additionally, we explore methods to increase carbon dioxide (CO2) concentration near the Rubisco, the enzyme responsible for the first step of CBB cycle, drawing inspiration from various photosynthetic organisms, and conclude this section by examining ways to enhance CO2 delivery into leaves. Moving beyond individual processes, we discuss two approaches to identifying key targets for photosynthesis improvement: systems modeling and the study of natural variation. Finally, we revisit some of the strategies mentioned above to provide a holistic view of the improvements, analyzing their impact on nitrogen use efficiency and on canopy photosynthesis.
59 BASIC BIOLOGICAL SCIENCES↗
The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses
Chemical modifications of DNA and histone proteins impact the organization of chromatin within the nucleus. Changes in these modifications, catalysed by different chromatin-modifying enzymes, influence chromatin organization, which in turn is thought to impact the spatial and temporal regulation of gene expression. While combinations of different histone modifications, the histone code, have been studied in several model species, we know very little about histone modifications in the fungal genus Aspergillus, whose members are generally well studied due to their importance as models in cell and molecular biology as well as their medical and biotechnological relevance. Here, we used phylogenetic analyses in 94 Aspergilli as well as other fungi to uncover the occurrence and evolutionary trajectories of enzymes and protein complexes with roles in chromatin modifications or regulation. We found that these enzymes and complexes are highly conserved in Aspergilli, pointing towards a complex repertoire of chromatin modifications. Nevertheless, we also observed few recent gene duplications or losses, highlighting Aspergillus species to further study the roles of specific chromatin modifications. SET7 (KMT6) and other components of PRC2 (Polycomb Repressive Complex 2), which is responsible for methylation on histone H3 at lysine 27 in many eukaryotes including fungi, are absent in Aspergilli as well as in closely related Penicillium species, suggesting that these lost the capacity for this histone modification. We corroborated our computational predictions by performing untargeted MS analysis of histone post-translational modifications in Aspergillus nidulans. This systematic analysis will pave the way for future research into the complexity of the histone code and its functional implications on genome architecture and gene regulation in fungi.
59 BASIC BIOLOGICAL SCIENCES↗
Hidden diversity: Transcriptomic and photosynthetic variation among common ‘wild type’ Chlamydomonas strains
The unicellular green alga Chlamydomonas reinhardtii is a widely studied reference organism, particularly in photosynthesis research. It employs photoprotective mechanisms, such as state transitions (ST) and non-photochemical quenching (NPQ), to cope with rapid light changes. Most widely used strains share a recent common ancestor yet differ by up to ~50 000 nuclear variants—genetic diversity that is often overlooked. Even among ‘wild type’ strains, we document significant phenotypic differences, such as pigment accumulation, and nutrient utilization. To elucidate the basis for this variation, we compared transcriptomes and physiological traits of seven commonly used laboratory strains, including the reference strain and the CLiP mutant library parental strain. Despite identical growth conditions, ~40% of genes were differentially expressed between strains. Most of these differences are attributable to changes that have accrued during laboratory propagation, and adverse conditions may have driven transcriptomic drift. At the physiological level, we catalog the range of strain-dependent responses related to photosynthesis and high light (HL) acclimation. Specifically, (i) all strains develop NPQ upon HL exposure, but to various degrees, (ii) they show a substantial variation in ST capacity, and (iii) they regulate the composition of the photosynthetic apparatus differently. We find that NPQ levels do not correlate with LHCSR3 expression, suggesting an additional layer of NPQ regulation. STs are constantly activated and independent of growth light intensities. Overall, our findings highlight significant strain-to-strain differences in virtually all photosynthetic parameters, emphasizing the importance of careful strain selection in future research endeavors.
59 BASIC BIOLOGICAL SCIENCES↗
Helical allophycocyanin nanotubes absorb far-red light in a thermophilic cyanobacterium
To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using cryo–electron microscopy and time-resolved absorption spectroscopy, we reveal the structure-function relationship of this FRL-absorbing AP complex (FRL-AP) that is expressed during acclimation to low light and that likely associates with chlorophyll a–containing photosystem I. FRL-AP assembles as helical nanotubes rather than typical toroids due to alterations of the domain geometry within each subunit. Spectroscopic characterization suggests that FRL-AP nanotubes are somewhat inefficient antenna; however, the enhanced ability to harvest FRL when visible light is severely attenuated represents a beneficial trade-off. The results expand the known diversity of light-harvesting proteins in nature and exemplify how biological plasticity is achieved by balancing resource accessibility with efficiency.
59 BASIC BIOLOGICAL SCIENCES↗
Broad betacoronavirus neutralization by a stem helix–specific human antibody
Targeting a range of betacoranaviruses In the past 20 years, three highly pathogenic β-coronaviruses have crossed from animals to humans, including the most recent: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A spike protein that decorates these viruses has an S1 domain that binds host cell receptors and an S2 domain that fuses the viral and cell membranes to allow cell entry. The S1 domain is the target of many neutralizing antibodies but is more genetically variable than S2, and antibodies can exert selective pressure, leading to resistant variants. Pinto et al . identified five monoclonal antibodies that interact with a helix in the S2 domain. The most broadly neutralizing antibody inhibited all β-coronavirus subgenera and reduced viral burden in hamsters infected with SARS-CoV-2. —VV
59 BASIC BIOLOGICAL SCIENCES↗
The 22Ne($$\alpha $$,n)25Mg reaction - state of the art, astrophysics, and perspectives
Abstract One of the most important stellar neutron sources is the 22 Ne( $$\alpha ,n$$ α , n ) 25 Mg reaction, which gets activated both during the helium intershell burning in asymptotic giant branch stars and in core helium and shell carbon burning in massive stars. The 22 Ne( $$\alpha ,n$$ α , n ) 25 Mg reaction serves as the main neutron producer for the weak s -process and provides a short but strong neutron exposure during the helium flash phase of the main s -process, significantly affecting the abundances at the s -process branch points. The cross section needs to be known at very low energies, as close as possible to the neutron threshold at $$E_\alpha =$$ E α = 562 keV ( Q = −478 keV), but both direct and indirect measurements have turned out to be very challenging, leading to significant uncertainties. Here we discuss the current status of the reaction, including recent and upcoming measurements, and provide a discussion on the astrophysical implications as well as an outlook into the near future.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Hybrid Simulation Framework
HYBRID is a modeling toolset to assess the economic viability of Nuclear-Renewable Integrated Energy Systems (N-R IES). The frameworks enabling this toolset are INL’s RAVEN, its CashFlow plugin and the Modelica language. The toolset includes sample RAVEN workflows performing economic assessments. These workflows consist of: generation of stochastic time series and application of probabilistic analysis and optimization algorithms (RAVEN); a library of Modelica models representing the physical behavior of N-R IES; and the CashFlow plugin mapping physical performance to economic performance. The toolset allows assembling existing and new models such as nuclear reactors, renewable energy sources, energy storage, gas turbines, industrial processes, etc. into an N-R IES. The toolset workflows evaluate the dynamics of the N-R IES responding to stochastic conditions (electricity demand, price, etc.) and optimize the dispatch economics as well as N-R IES capacity planning.
Epiney, Aaron↗
Axom
Axom is an open-source library of "building block" software components that provide core infrastructure capabilities for HPC applications. Such capabilities include: input file parsing and verification for various file formats, format specification for material shape input to multi-material simulations and tools for placing those shapes on meshes, parallel distributed coordination of diagnostic messages, geometric primitives, spatial queries and spatial search acceleration data structures, in memory key-value data store for managing simulation data and parallel file I/O. Axom components are used widely across LLNL Advanced Simulation and Computing program applications. It is also part of the LLNL institutionally-supported RADIUSS project, which promotes and funds its adoption by projects across LLNL.
Zagaris, George↗
Analytic_Deflection_of_Asteroids_by_NEDs
This package evaluates an analytic formula for the change in velocity imparted to an asteroid by a 1 or 2 keV black body source given the radius of the asteroid, the standoff distance, the x-ray yield, the density of the asteroid, and the fit coefficients for the 1 or 2 keV black body source (provided in the module). Three variations of the formula are given; the "original" form, the "modified" form that accounts for the angle of incidence in calculating the melt depth, and a form based on an "impulse" model. Each formula is fit to simulations of spherical asteroids of uniform composition illuminated by black body x-rays.
Managan, RobertA↗
NED_Asteroid_Energy_Deposition
In the event of a potentially catastrophic asteroid impact, with sufficient warning time, deploying a nuclear device remains a powerful option for planetary defense if a kinetic impactor proves insufficient. Predicting the effectiveness of a potential nuclear deflection or disruption mission depends on accurate multiphysics simulations of the device's x-ray energy deposition into the asteroid and the resulting material ablation. These simulations span many orders of magnitude, require a variety of different complex physics packages, and are computationally expensive. Having an efficient and accurate way of modeling this system is necessary for exploring a mission's sensitivity to the asteroid's range of physical properties. To expedite future simulations, we present a completed x-ray energy deposition model developed using the radiation-hydrodynamics code Kull which can be used to initiate a nuclear mitigation mission hydrocode. The model spans a wide variety of possible mission initial conditions: four different asteroid-like materials (Silicon Dioxide, Forsterite, Iron, and Ice), two different source spectra (1 and 2 keV blackbodies), and then a broad range of radiation fluences (0.0001 to 1 kt per square meter), source durations (10 to 100 ns), and asteroid porosities (0 to 80 percent). Using blowoff momentum as the primary metric, the modelinitiated simulation results match the full radiation-hydrodynamics results to within 10 percent. Please reference the journal article: Burkey et al., X-Ray Energy Deposition Model for Simulating Asteroid Response to a Nuclear Planetary Defense Mitigation Mission, Planetary Science Journal, (2023) for more information.
Managan, RobertA↗
ExpM+NF MIMIC III experiments
This code allows reproduction of results in the paper "Are Normalizing Flows the Key to Unlocking the Exponential Mechanism? " https://arxiv.org/abs/2311.09200 The code here provides implementation of our experiments where we test if we can training models with ExpM+NF alongside and in comparison with DPSGD and non-private training.
Tombs, VandyJ↗
SCALE
SCALE v6.3.1 is a beta version built from existing SCALE code. This code provides modeling and simulation of nuclear reactor physics, criticality safety, radiation shielding, and associated spent fuel characterization for nuclear facilities and nuclear fuel transportation and storage package designs (please see attachment for more details).
Ade, Brian↗
Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells
Patients with estrogen receptor–positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs.
60 APPLIED LIFE SCIENCES↗