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At least 109 records · Page 6

Poxvirus infection triggers remodeling of host m⁶A epitranscriptome and benefits from the m⁶A regulatory responses

Understanding how host gene regulation responds to viral infection is essential for developing effective antiviral strategies. Emerging evidence suggests that host transcripts undergo dynamic chemical modifications to counteract viral invasion. Conversely, viruses that rely on nuclear transcription exploit host RNA methyltransferases to enhance mRNA export and translation. Orthopoxviruses, however, complete their entire replication cycle within compartmentalized cytoplasmic “factories” utilizing enzymes encoded by their large double-stranded viral DNA genomes. The dynamic interplay between host and poxviral epitranscriptome remains poorly characterized. Using a temporally resolved model of Vaccinia virus (VV) infection, we investigated host-virus interactions through transcriptome and N6-methyladenosine (m⁶A) epitranscriptome whole genome sequencing. We found that host m⁶A modifications respond rapidly to VV infection, preceding the delayed transcriptional changes that emerge at later stages. Early m⁶A signatures included key innate immunity factors as well as host genes involved in transcriptional regulation, post-transcriptional modification, and protein ubiquitination. Functional assays validated two host factors with early m⁶A modification changes that are essential for VV infection: a m⁶A reader, YTHDF1, and a component of the SCF E3 ubiquitin ligase complex, FBXO31. The m⁶A gain on YTHDF1 enhanced its protein expression and promoted efficient VV replication. In addition, we identified previously unrecognized roles of FBXO31 and the SCF E3 ligase complex in supporting VV infection. Temporal profiling of the m⁶A epitranscriptome reveals how VV exploits host post-transcriptional regulatory pathways, specifically m⁶A RNA modification and protein ubiquitination. These findings highlight critical host factors co-opted during poxvirus infection and identify potential targets for therapeutic intervention.

59 BASIC BIOLOGICAL SCIENCES

Damage Dynamics and Problems of Scale for Induced and Triggered Seismicity in Reservoirs

In this report, we present a high-level summary of the research we performed on this grant during the years 2017-2024. It is important to note that several of these years were the years of the COVID pandemic, and our research activities were severely impacted by these events, as were many other groups and investigators. However, we can report that we largely achieved the results we proposed. We also list below the papers published under funding from this grant over all those years.

04 OIL SHALES AND TAR SANDS

Intelligent Triggers for Rare Event Detection in Liquid Argon Detectors

Next-generation neutrino experiments like SBND and DUNE rely on Liquid Argon Time Projection Chambers (LArTPCs), which produce exceptionally detailed data at high volume. Capturing rare or unexpected events in real-time is a major challenge. Our project explores the use of machine learning, specifically autoencoder-based anomaly detection, to identify unusual activity directly from raw detector signals. Inspired by successes at the CMS experiment, we demonstrate that such methods can be adapted to LArTPCs and show promising results in both simulated studies and early steps toward real-time hardware deployment. This approach could open new avenues for detecting signals from physics beyond the Standard Model.

Chung, Seokju [Columbia U. (main)]

Photochemically Triggered Para-Hydrogen-Induced Polarization in a Diplatinum Trihydride Complex

Transition metal complexes containing platinum(II) are of substantial interest for their rich photophysics, biomedical applications, and catalytic function. Nuclear magnetic resonance (NMR) spectra of the spin-1/2 isotope, 195Pt, offer detailed insights into the molecular structures of closed-shell Pt(II) complexes, including solvent effects. However, the sensitivity of 195Pt NMR is mediocre, and its NMR spectra are typically complex. As a result, 1H NMR spectra are used as the primary characterization tool for Pt(II)-based molecules, relying on J-coupling to the 195Pt nucleus to provide structural information from the resulting satellite peaks. In efforts to significantly improve the information content from 1H NMR spectroscopy in a Pt(II)-containing molecule, we utilize [Pt2H2(μ-H)(μ-dppm)2]PF6, where dppm is bis(diphenylphosphino)methane, and leverage its established photoactivity with UV light and H2 for para-hydrogen-induced polarization (PHIP) to enhance the resultant NMR signals, revealing numerous 195Pt J-couplings. Moreover, we investigate direct solvent hyperpolarization effects, as well as the indirect effects of solvent on the various observed J-coupling constants in the Pt species, demonstrating correlations with both Lewis basicity and dielectric constant.

Brown, Emily E. [Department of Chemistry; North Ca

Loss of Mitochondrial Tusc2/Fus1 Triggers a Brain Pro-Inflammatory Microenvironment and Early Spatial Memory Impairment

Brain pathological changes impair cognition early in disease etiology. There is an urgent need to understand aging-linked mechanisms of early memory loss to develop therapeutic strategies and prevent the development of cognitive impairment. Tusc2 is a mitochondrial-resident protein regulating Ca 2+ fluxes to and from mitochondria impacting overall health. We previously reported that Tusc2 –/– female mice develop chronic inflammation and age prematurely, causing age- and sex-dependent spatial memory deficits at 5 months old. Therefore, we investigated Tusc2-dependent mechanisms of memory impairment in 4-month-old mice, comparing changes in resident and brain-infiltrating immune cells. Interestingly, Tusc2 –/– female mice demonstrated a pro-inflammatory increase in astrocytes, expression of IFN-γ in CD4 + T cells and Granzyme-B in CD8 + T cells. We also found fewer FOXP3 + T-regulatory cells and Ly49G + NK and Ly49G + NKT cells in female Tusc2 –/– brains, suggesting a dampened anti-inflammatory response. Moreover, Tusc2 –/– hippocampi exhibited Tusc2- and sex-specific protein changes associated with brain plasticity, including mTOR activation, and Calbindin and CamKII dysregulation affecting intracellular Ca2 + dynamics. Overall, the data suggest that dysregulation of Ca 2+ -dependent processes and a heightened pro-inflammatory brain microenvironment in Tusc2 –/– mice could underlie cognitive impairment. Thus, strategies to modulate the mitochondrial Tusc2- and Ca 2+ - signaling pathways in the brain should be explored to improve cognitive health.

59 BASIC BIOLOGICAL SCIENCES

The ATLAS experiment at the CERN Large Hadron Collider: a description of the detector configuration for Run 3

The ATLAS detector is installed in its experimental cavern at Point 1 of the CERN Large Hadron Collider. During Run 2 of the LHC, a luminosity of ℒ = 2 × 10 34 cm -2 s -1 was routinely achieved at the start of fills, twice the design luminosity. For Run 3, accelerator improvements, notably luminosity levelling, allow sustained running at an instantaneous luminosity of ℒ = 2 × 10 34 cm -2 s -1 , with an average of up to 60 interactions per bunch crossing. The ATLAS detector has been upgraded to recover Run 1 single-lepton trigger thresholds while operating comfortably under Run 3 sustained pileup conditions. A fourth pixel layer 3.3 cm from the beam axis was added before Run 2 to improve vertex reconstruction and b-tagging performance. New Liquid Argon Calorimeter digital trigger electronics, with corresponding upgrades to the Trigger and Data Acquisition system, take advantage of a factor of 10 finer granularity to improve triggering on electrons, photons, taus, and hadronic signatures through increased pileup rejection. The inner muon endcap wheels were replaced by New Small Wheels with Micromegas and small-strip Thin Gap Chamber detectors, providing both precision tracking and Level-1 Muon trigger functionality. Trigger coverage of the inner barrel muon layer near one endcap region was augmented with modules integrating new thin-gap resistive plate chambers and smaller-diameter drift-tube chambers. Tile Calorimeter scintillation counters were added to improve electron energy resolution and background rejection. Upgrades to Minimum Bias Trigger Scintillators and Forward Detectors improve luminosity monitoring and enable total proton-proton cross section, diffractive physics, and heavy ion measurements. These upgrades are all compatible with operation in the much harsher environment anticipated after the High-Luminosity upgrade of the LHC and are the first steps towards preparing ATLAS for the High-Luminosity upgrade of the LHC. This paper describes the Run 3 configuration of the ATLAS detector.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

TRAILS Output Files

Overview This data repository contains ZIP files that store compressed versions of the output of running the WaterPaths utility planning and management tool in the DU Re-Evaluation mode (to download the tool, please see this GitHub repository). The tool was used to simulate the six-utility North Carolina Research Triangle problem. Details on the contents of each ZIP file can be seen below. Data details Temporal range: Weekly data for 2,344 weeks from 2015 to 2060 (45 years). Spatial range: Six water utilities in the North Carolina Research Triangle region (0: Chapel Hil/OWASA, 1: Durham, 2: Cary, 3: Raleigh, 4: Pittsboro, and 5: Chatham) File types: CSV and OUT Different solutions available The solution numbers correspond to the different pathway strategies (henceforth referred to as "solutions") discussed in paper's main and supporting text (abstract and link to the paper here). They are as follows: Sol92: The Durham-focused pathway strategy Sol132: The Raleigh-focused pathway strategy Sol140: The regionally-robust pathway strategy Objectives files These files can be accessed by unzipping solXX_objectives_pathways.zip that contains 1,000 Objectives_RDMXX_solsXX_to_XX.csv files. Each CSV file will consist of a row representing all the objective values for that specific solution, while every six columns represents the reliability, restriction frequency, infrastructure net present value ($ mil), peak financial cost, worst-case cost, and unit cost ($ per MG; in that order) for each of the six utilities. There will be 1,000 such files, denoting the performance of the six utilities across the 1,000 deeply uncertain states of the world (DU SOWs). Pathway files These files can be accessed by unzipping solXX_objectives_pathways.zip that contains 1,000 Pathways_sXX_RDMXX.out file. Each OUT corresponds to the set of infrastructure being triggered in a specific DU SOW, and each file will have the name file will consist of four tab-delimited columns that are described as follows: Realization: The realization in which an infrastructure options being triggered utility: The utility currently triggering infrastructure week: The week in which a specific infrastructure option is being triggered infra.: The infrastructure option being triggered If the OUT file contains only the header line, no infrastructure was triggered for that specific DU SOW. Policies files These files can be obtained by unzipping Policies.zip. Each of the 1,000 CSV files within the unzipped folder will contain weekly water use restriction policies for all 1,000 hydroclimatic realizations within a specific DU SOW. The column structure is as follows: 0rest_m: restriction multiplier for utility 0 (values between 0 and 1) 1rest_m: restriction multiplier for utility 1 (values between 0 and 1) 2rest_m: restriction multiplier for utility 2 (values between 0 and 1) 3rest_m: restriction multiplier for utility 3 (values between 0 and 1) 4rest_m: restriction multiplier for utility 4 (values between 0 and 1) 5rest_m: restriction multiplier for utility 5 (values between 0 and 1) 0transf: transfer volume for utility 0 (in MGD) 1transf: transfer volume for utility 1 (in MGD) 2transf: transfer volume for utility 2 (in MGD) 3transf: transfer volume for utility 3 (in MGD) 4transf: transfer volume for utility 4 (in MGD) 5transf: transfer volume for utility 5 (in MGD) Water Sources files These files can be obtained by unzipping WaterSources_subset.zip. Each of the 100 CSV files within the unzipped folder will contain weekly state variables at each water source for all 1,000 hydroclimatic realizations within a specific DU SOW. The column structure is as follows: Xvolume: available water volume from source X (in MGD) Xs_area: surface area of source X (in ACF) Xdemand: demand drawn from a water source from source X (in MGD) Xup_spill: upstream spillage from source X (in MGD) Xww_inflow: wastewater inflow from source X (in MGD) Xcatch_inflow: upstream catchment inflow to source X (in MGD) Xevap: evaporation multiplier for source X (values between 0 and 1) Xds_spill: downstream spillage from source X (in MGD) X_Y_alloc_cap: the allocated capacity from source X to utility Y (values between 0 and 1) X_Y_alloc_dem: the allocated demand from source X to utility Y (values between 0 and 1) Xtrmt_alloc_Y: the allocated treatment capacity from source X to utility Y (values between 0 and 1) Utilities files These files can be obtained by unzipping Utilities_subset.zip. Each of the 100 CSV files within the unzipped folder will contain weekly state variables at each utility for all 1,000 hydroclimatic realizations within a specific DU SOW. The column structure is as follows: Xst_vol: total available storage volume of utility X (in MG) Xcapacity: total storage capacity of utility X (in MG) Xnet_inf: : net inflow for all storage infrastructure for utility X (in MGD) Xst_rof: short term ROF for utility X (values between 0 and 1) Xst_stor_rof: short-term storage ROF for utility X (values between 0 and 1) Xst_trmt_rof: short-term treatment ROF for utility X (values between 0 and 1) Xlt_rof: long-term ROF for utility X (values between 0 and 1) Xlt_stor_rof: long-term storage ROF for utility X (values between 0 and 1) Xlt_trmt_rof: long-term treatment ROF for utility X (values between 0 and 1) Xrest_demand: restricted demand for utility X (in MGD) Xunrest_demand: unrestricted demand for utility X (in MGD) Xunfulf_demand: unfulfilled demand for utility X (in MGD) Xwastewater: wastewater return for utility X (in MGD) Xtreat_capacity: total treatment capacity for utility X (in MG) Xcont_fund: reserve (contingency) fund balance for utility X Xins_pout: insurance payout for utility X (% annual volumetric revenue) Xins_price: insurance price for utility X (% annual volumetric revenue) Xinfra_npv: infrastructure net present value for utility ($mil) Xst_vol: total available storage volume of utility X (in MG) Xdebt_serv: debt service for utility X (usually once per year if the infrastructure is triggered; % annual volumetric revenue) Xstor_vol: total stored volume (in MGD) Xobs_ann_dem: observed annual demand for utility X (in MGD) Xproj_dem: projected annual demand for utility X (in MGD) Xpv_debt_serv: present value of debt service payments for utility X (% annual volumetric revenue) Xgross_rev: gross revenue for utility X ($mil) Acknowledgment IM3 is a multi-institutional effort led by Pacific Northwest National Laboratory and supported by the U.S. Department of Energy's Office of Science as part of research in MultiSector Dynamics, Earth and Environmental Systems Modeling Program.

Artificial Intelligence

Using pile-up collisions as an abundant source of low-energy hadronic physics processes in ATLAS and an extraction of the jet energy resolution

During the 2015–2018 data-taking period, the Large Hadron Collider delivered proton-proton bunch crossings at a centre-of-mass energy of 13 TeV to the ATLAS experiment at a rate of roughly 30 MHz, where each bunch crossing contained an average of 34 independent inelastic proton-proton collisions. The ATLAS trigger system selected roughly 1 kHz of these bunch crossings to be recorded to disk. Offline algorithms then identify one of the recorded collisions as the collision of interest for subsequent data analysis, and the remaining collisions are referred to as pile-up. Pile-up collisions represent a trigger-unbiased dataset, which is evaluated to have an integrated luminosity of 1.33 pb -1 in 2015–2018. This is small compared with the normal trigger-based ATLAS dataset, but when combined with vertex-by-vertex jet reconstruction it provides up to 50 times more dijet events than the conventional single-jet-trigger-based approach, and does so without adding any additional cost or requirements on the trigger system, readout, or storage. The pile-up dataset is validated through comparisons with a special trigger-unbiased dataset recorded by ATLAS, and its utility is demonstrated by means of a measurement of the jet energy resolution in dijet events, where the statistical uncertainty is significantly reduced for jet transverse momenta below 65 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Characterization of ELM pacing via vertical jogs on DIII-D

Edge localized mode (ELM) pacing via vertical plasma oscillations or jogging has been successfully demonstrated on DIII-D. Rapid vertical movement of the plasma toward the X-point has been shown to effectively trigger ELMs. By vertically oscillating the plasma at a rate of 10 Hz, the ELM frequency increased from ~5 Hz, the natural ELM frequency in similar DIII-D discharges, to 20 Hz. Downward jogs have been observed to trigger multiple ELMs in one cycle. ELMs triggered at higher than natural frequencies lead to smaller decreases in stored energy, from 8% to as little as below 1%. As a consequence, the peak heat flux to the divertor has been observed to be reduced by a factor of ~2. In addition, a reduction in the carbon impurity concentration has been observed. During downward jogs in the lower single null (LSN) configuration, the X-point movement is slower and smaller than the top of the plasma. As a result, a reduction in the plasma cross-section and hence volume has been observed. To understand the mechanism of ELM triggering by jogging, a toy model of the edge toroidal current has been built and tested with DIII-D experiment data. The experimental data and model suggest that when the plasma moves down toward the X-point, a net positive toroidal current is locally induced in the edge region. ELITE stability analysis suggests that this current pushes the plasma state across the peeling side of the peeling–ballooning stability boundary into the unstable region triggering ELMs.

ELM pacing

Medium-induced modification of azimuthal correlations of electrons from heavy-flavor hadron decays with charged particles in Pb–Pb collisions at $\mathbf {\sqrt{s_{\textrm{NN}}} = 5.02}$ TeV

The azimuthal-correlation distributions between electrons from the decays of heavy-flavor hadrons and associated charged particles in Pb–Pb collisions at $\sqrt{s_{\textrm{NN}}} = 5.02$ TeV are reported for the 0–10% and 30–50% centrality classes. This measurement provides access to the jet-like correlation observables in the heavy-flavor sector in Pb–Pb collisions. The analysis is performed for trigger electrons from heavy-flavor hadron decays with transverse momentum $4< p_\textrm{T}^\textrm{e} < 16~\textrm{GeV}/c$, considering associated particles within the transverse-momentum range $1< p_\textrm{T}^\textrm{assoc} < 7$ GeV/c, and a pseudorapidity difference of $|\Delta \eta |<1$ between the trigger electron and associated particles. The per-trigger nuclear modification factor ( I AA ) is calculated to compare the near- and away-side peak yields to those in pp collisions at $\sqrt{s} = 5.02$ TeV. In 0–10% central collisions, the indicates a hint of enhancement of associated-particle yields with $p_\textrm{T}<3$ GeV/c on the near side, and a suppression of yields with $p_\textrm{T}>4$ GeV/c on the away side. The I AA for electron triggers from heavy-flavor hadron decays is compared with that for light-flavor and strange-particle triggers to investigate the dependence on different fragmentation processes and parton-medium dynamics, and is found to be the same within uncertainties.

Abualrob, I. J. [University of Houston] (ORCID:000

Investigating strangeness enhancement with multiplicity in pp collisions using angular correlations

A study of strange hadron production associated with hard scattering processes and with the underlying event is conducted to investigate the origin of the enhanced production of strange hadrons in small collision systems characterised by large charged-particle multiplicities. For this purpose, the production of the single-strange meson ${\textrm{K}}_{\textrm{S}}^0$ and the double-strange baryon Ξ ± is measured, in each event, in the azimuthal direction of the highest-p T particle (“trigger” particle), related to hard scattering processes, and in the direction transverse to it in azimuth, associated with the underlying event, in pp collisions at $\sqrt{s}$ = 5.02 TeV and $\sqrt{s}$ = 13 TeV using the ALICE detector at the LHC. The per-trigger yields of ${\textrm{K}}_{\textrm{S}}^0$ and Ξ ± are dominated by the transverse-to-leading production (i.e., in the direction transverse to the trigger particle), whose contribution relative to the toward-leading production is observed to increase with the event charged-particle multiplicity. The transverse-to-leading and the toward-leading Ξ ± /${\textrm{K}}_{\textrm{S}}^0$ yield ratios increase with the multiplicity of charged particles, suggesting that strangeness enhancement with multiplicity is associated with both hard scattering processes and the underlying event. The relative production of Ξ ± with respect to ${\textrm{K}}_{\textrm{S}}^0$ is higher in transverse-to-leading processes over the whole multiplicity interval covered by the measurement. The ${\textrm{K}}_{\textrm{S}}^0$ and Ξ ± per-trigger yields and yield ratios are compared with predictions of three different phenomenological models, namely Pythia8.2 with the Monash tune, Pythia8.2 with ropes and EPOS LHC. The comparison shows that none of them can quantitatively describe either the transverse-to-leading or the toward-leading yields of ${\textrm{K}}_{\textrm{S}}^0$ and Ξ ± .

hadron-hadron scattering

Generating Buoyancy-Driven Convection in Membrane Distillation

Membrane distillation (MD) is a thermally-driven desalination process that can treat hypersaline brines. Considerable MD literature has focused on mitigating temperature and concentration polarization. This literature largely neglects that temperature and concentration polarization increase the feed density near the membrane. With gravity properly oriented, this increase in density could trigger buoyancy-driven convection and increase permeate production. Convection could also be strengthened by heating the feed channel wall opposite the membrane. To investigate that possibility, we perform a series of experiments using a plate-and-frame direct contact MD system with an active membrane area of 300 cm2 and a feed channel wall heated using a resistive heater. The experiments measure the average transmembrane permeate flux for two gravitational orientations, feed Reynolds numbers between 128 and 1128, and wall heat fluxes up to 12 kW/m2. The results confirm that with gravity properly oriented, wall-heating can trigger buoyancy-driven convection for a wide range of feed Reynolds numbers, and increase permeate production between roughly 20 and 130 %. We estimate, however, that at high Reynolds numbers (Re > 800), more than 70 % of the wall heat is carried out of the MD system by the feed flow, without contributing to permeate production. This suggests the need for longer membranes and heat recovery steps in any future practical implementation.

buoyancy-driven convection