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At least 451 records · Page 25

Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Symbiotic associations between bacteria and leguminous plants lead to the formation of root nodules that fix nitrogen needed for sustainable agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet an integrated understanding of the extent of chromatin changes and transcriptional networks that functionally regulate gene expression associated with symbiosis remains poorly understood. In particular, analyses of early temporal events driving this symbiosis have only captured correlative relationships between regulators and targets at mRNA level. Here, we characterize changes in transcriptome and chromatin accessibility in the model legume Medicago truncatula, in response to rhizobial signals that trigger the formation of root nodules. We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with bacterial small molecules called lipo-chitooligosaccharides that trigger host symbiotic pathways of nodule development. Using a novel approach, dynamic regulatory module networks, we integrated ATAC-seq and RNA-seq time courses to predict cis-regulatory elements and transcription factors that most significantly contribute to transcriptomic changes associated with symbiosis. Regulators involved in auxin (IAA4-5, SHY2), ethylene (EIN3, ERF1), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. Our transcriptomic and chromatin accessibility datasets provide a valuable resource to understand the gene regulatory programs controlling the early stages of the dynamic process of symbiosis. The regulators identified provide potential targets for future experimental validation, and the engineering of nodulation in species is unable to establish that symbiosis naturally.

59 BASIC BIOLOGICAL SCIENCES↗

Improved Beam Loss Accounting with Fast Data Acquisition (DAQ) Chassis

Identifying the source of beam loss events in the CE-BAF accelerator can be a challenging task. However, with our new prototype system, this task becomes more effi-cient. The system, developed in the fall of 2022, utilizes a dispersive beam position monitor (BPM) and the exist-ing switched electrode electronics BPM hardware. Previ-ously a commercial off-the-shelf data acquisition (DAQ) system was employed to capture BPM wire signals at a sample rate of 20 kS/s. The fast shutdown signal triggered the system, which disables the beam at the injector. Analysis of beam position and energy variation before a beam loss event was used to determine if the beam loss event was associated with an energy transient. The proto-type system, implemented using National Instruments hardware and LabVIEW® software, relied on a software trigger. Manual post-processing was required to ascertain whether the fault was due to an un-tripped cavity with a gradient or phase transient. This work focuses on deploying a Fast DAQ Chassis to monitor BPM hardware in real time and during beam loss events. This system was originally developed and in-stalled in CEBAF to monitor the time-domain RF control signals in the legacy analog RF systems. This technology was leveraged to also monitor BPM signals. As the new system employs a hardware trigger, developing tools to automatically identify faults linked to energy transients unrelated to cavity faults will be straightforward. This paper will discuss the project's initial updates, underlin-ing the crucial role of each member of our team in this achievement

Tiskumara, J.↗

Real-time data reduction at 100 Tbps: Challenge and opportunity for AI-based data reduction for next-generation large-scale nuclear physics collider experiment

The modern large-scale nuclear physics (NP) experiments in high-energy particle colliders utilize streaming-readout electronics to digitize detector response at O(100) Tbps bandwidth. Prominent examples at Brookhaven National Lab (BNL) include the sPHENIX experiment at Relativistic Heavy Ion Collider (RHIC), which is under construction, and the experiments proposed for the Electron-Ion Collider (EIC), planned for the 2030s . One of the main challenges for these streaming readout systems is to manage the data rate with sufficient data reduction in real time so the end-data fit persistent storage for offline analysis, which is typically at O(1000) times smaller and O(100) Gbps. Such data reduction traditionally is achieved via real-time high level triggers, which select and save a small subset of collisions of interest. Although triggering is applicable to high energy collider experiments such as those at the Large Hardron Collider at CERN, it is insufficient for these nuclear physics experiments which study diverse collision topologies. And traditional triggering approach is inefficient to preserve the max information harvested from the operation of colliders that costs O(100)M per year to DOE. Meanwhile, in recent years, ML-based high-throughput data reduction has emerged as a promising approach to efficiently preserve max information for a given space of persistent storage, e.g. via AI data compression, feature extraction, and noise filtering.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Online Optimization of NSLS-II Dynamic Aperture and Injection Transient (Facility Improvement Project)

The Facility Improvement Project (FIP) “Methods of online optimization of NSLS-II storage ring concurrent with user operations” proposed and approved in 2018 is now complete. The first goal is the online optimization of nonlinear beam dynamics to increase the beam lifetime and injection efficiency. We have developed a model-independent optimization technique using advanced algorithms. Using this technique, we increased the NSLS-II dynamic aperture by 20% and reduced the amplitude-dependent tune shift by a factor of two. We applied sextupole optimization to the new high-chromaticity lattice, which has been developed to improve the beam stability and to increase the single-bunch beam intensity. We were able to double the injection efficiency and exceed 90%. The second goal of this project is to provide the top-off injection with minimized perturbations of the beamline user operations. To achieve the transparent injection, we optimize the matching of four storage ring injection kickers reducing the perturbation of the stored beam orbit. The first application of the online optimization resulted in a reduction of the amplitude of residual beam oscillation by a factor of six, from 1300 μm down to 200 μm. Further improvement was limited by the timing jitter of the trigger boards. Then, we replaced all trigger boards with a new design and reduced the timing jitter by a factor of five, from 5 ns down to 1 ns. This upgrade resulted in the injection transient reduction from 200 μm to 120 μm. To optimize the full set of kicker parameters, including the trigger timing, amplitude, and pulse width, we upgraded all kicker power supplies with the capability of tunable waveform width. As a result, we have reduced the injection transient to the limit of 60 μm.

43 PARTICLE ACCELERATORS↗

Investigating Electro-Nuclear Interactions in a New Dark Matter Search

Electro-nuclear (EN) interactions are interactions in which an incident electron collides with a nucleus, scattering the electron and creating byproduct particles. Such interactions are of interest to neutrino physicists, who use EN interactions to inform model building of neutrino-nucleus interactions. The Light Dark Matter Experiment (LDMX) is a small-scale, fixed-target, electron beam experiment which seeks to probe for dark matter and mediator particle production in the sub-GeV mass region. The 8GeV LDMX electron beam will serve as an opportunity to study electro-nuclear interactions in their final states in the multi-GeV region. LDMX’s missing energy trigger however, will not be sufficient to efficiently capture EN interactions. An additional trigger needs to be created. Using simulated background events, including EN interactions, for the LDMX experiment, a trigger on momentum was developed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Fermilab Italian Student Program (Final Report)

I participated to the 2019 Fermilab Italian Student Program under the supervision of Anadi Canepa and Lorenzo Uplegger. I worked with the Fermilab research group that is involved with the R&D of the CMS Outer Tracker. The Compact Muon Solenoid (CMS) is a a general-purpose detector located at the Large Hadron Collider (LHC), the world's most powerful particle accelerator. In the next years LHC will undergo the High-Luminosity LHC upgrade, which will bring its luminosity from 1 × 10 34 cm -2 s -1 to 1.5 × 10 34 cm -2 s -1 . This increase in luminosity will require an upgrade of CMS as well, in order to comply with the augmented rate of particles which will cross the detector. The CMS tracker is a detector, composed of various modules made of silicon pixel trackers and silicon strip trackers, whose aim is to reconstruct the trajectories of the particles produced by the collisions in LHC. The tracker is ideally divided in Inner Tracker and Outer Tracker. The HL-LHC upgrade put important challenges in the designing of the tracker. It will have to withstand the irradiation of a large fluence of particles, without suffering a too severe deterioration of its performance. In addition to this, in order to comply with the increased rate of events that CMS will need to detect, the tracker will be exploited for triggering at the fully hardware Level 1 Trigger, in contrast to the current tracker, whose data are only used for the software High-Level Trigger. This feature is managed by the "stub logic", which will be explained in chapter 2. During the months of August and September at Fermilab I carried out the data analysis of three test beam runs performed in the last two years on the 2S Outer Tracker Minimules. The 2S Minimoule consists of two silicon strip trackers placed one upon the other with the strips kept parallel.

43 PARTICLE ACCELERATORS↗

Exploring the Energy Frontier through Precision Tests and Fast Tracking with the CMS Detector (Final Technical Report)

This Early Career Award supported a research program using the CMS experiment at the CERN LHC to probe physics beyond the Standard Model in the top quark and Higgs boson sectors, alongside detector and trigger developments for the High-Luminosity LHC (HL-LHC) upgrade. The program (i) searched for charged lepton flavor violation (LFV) in the top quark sector with the full CMS Run-2 data set, placing the world’s strongest limits to date on the $t → eµq\ (q = u/c)$ branching fraction; (ii) developed preliminary analysis methods toward a boosted $t\bar{t}H(b\bar{b})$ measurement of the top quark Yukawa coupling and its CP properties; (iii) made leading contributions to the hardware-based Level-1 (L1) track finding system for the upgraded CMS detector for HL-LHC; and (iv) developed novel L1 trigger algorithms, notably a displaced vertex trigger enabling new searches for exotic long-lived particles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Low-latency Jet Tagging for HL-LHC Using Transformer Architectures

Transformers are the state-of-the-art model architectures and widely used in application areas of machine learning. However the performance of such architectures is less well explored in the ultra-low latency domains where deployment on FPGAs or ASICs is required. Such domains include the trigger and data acquisition systems of the LHC experiments. We present a transformer-based algorithm for jet tagging built with the HGQ2 framework, which is able to produce a model with heterogeneous bitwidths for fast inference on FPGAs, as required in the trigger systems at the LHC experiments. The bitwidths are acquired during training by minimizing the total bit operations as an additional parameter. By allowing a bitwidth of zero, the model is pruned in-situ during training. Using this quantization-aware approach, our algorithm achieves state-of-the-art performance while also retaining permutation invariance which is a key property for particle physics applications. Due to the strength of transformers in representation learning, our work also serves as a stepping stone for the development of a larger foundation model for trigger applications.

Laatu, Lauri [Imperial Coll., London]↗

Adenosine A2A Receptor Up-Regulation Pre-Dates Deficits of Synaptic Plasticity and of Memory in Mice Exposed to Aβ1–42 to Model Early Alzheimer’s Disease

The intracerebroventricular (icv) injection of amyloid peptides (Aβ) models Alzheimer’s disease (AD) in mice, as typified by the onset within 15 days of deficits of memory and of hippocampal long-term potentiation (LTP) that are prevented by the blockade of adenosine A2A receptors (A2AR). Since A2AR overfunction is sufficient to trigger memory deficits, we tested if A2AR were upregulated in hippocampal synapses before the onset of memory deficits to support the hypothesis that A2AR overfunction could be a trigger of AD. Six to eight days after Aβ-icv injection, mice displayed no alterations of hippocampal dependent memory; however, they presented an increased excitability of hippocampal synapses, a slight increase in LTP magnitude in Schaffer fiber-CA1 pyramid synapses and an increased density of A2AR in hippocampal synapses. A2AR blockade with SCH58261 (50 nM) normalized excitability and LTP in hippocampal slices from mice sacrificed 7–8 days after Aβ-icv injection. Fifteen days after Aβ-icv injection, mice displayed evident deficits of hippocampal-dependent memory deterioration, with reduced hippocampal CA1 LTP but no hyperexcitability and a sustained increase in synaptic A2AR, which blockade restored LTP magnitude. This shows that the upregulation of synaptic A2AR precedes the onset of deterioration of memory and of hippocampal synaptic plasticity, supporting the hypothesis that the overfunction of synaptic A2AR could be a trigger of memory deterioration in AD.

Lopes, Cátia R.↗

Two-Stage Wildlife Event Classification for Edge Deployment

Camera-based wildlife monitoring is often overwhelmed by non-target triggers and slowed by manual review or cloud-dependent inference, which can prevent timely intervention for high stakes human–wildlife conflicts. Our key contribution is a deployable, fully offline edge vision sensor that achieves near-real-time, highly accurate wildlife event classification by combining detector-based empty-image suppression with a lightweight classifier trained with a staged transfer-learning curriculum. Specifically, Stage 1 uses a pretrained You Only Look Once (YOLO)-family detector for permissive animal localization and empty-trigger suppression, and Stage 2 uses a lightweight EfficientNet-based binary classifier to confirm puma on detector crops and gate downstream actions. Our design is robust to low-quality nighttime monochrome imagery (motion blur, low contrast, illumination artifacts, and partial-body captures) and operates using commercially available components in connectivity-limited settings. In field deployments running since May 2025, end-to-end latency from camera trigger to action command is approximately 4 s. Ablation studies using a dataset of labeled wildlife images (pumas, not pumas) show that the two-stage approach substantially reduces false alarms in identifying pumas relative to a full-image classifier while maintaining high recall. On the held-out test set (N = 1434 events), the proposed two-stage cascade achieves precision 0.983, recall 0.975, F1 0.979, accuracy 0.986, and balanced accuracy 0.983, with only 8 false positives and 12 false negatives. The system can be easily adapted for other species, as demonstrated by rapid retraining of the second stage to classify ringtails. Downstream responses (e.g., notifications and optional audio/light outputs) provide flexible actuation capabilities that can be configured to support intervention.

58 GEOSCIENCES↗

GRB 191016A: A Long Gamma-Ray Burst Detected by TESS

The Transiting Exoplanet Survey Satellite (TESS) exoplanet-hunting mission detected the rising and decaying optical afterglow of GRB 191016A, a long gamma-ray burst (GRB) detected by Swift-BAT but without prompt XRT or UVOT follow-up due to proximity to the Moon. The afterglow has a late peak at least 1000 s after the BAT trigger, with a brightest-detected TESS data point at 2589.7 s post-trigger. The burst was not detected by Fermi-LAT, but was detected by Fermi-GBM without triggering, possibly due to the gradual nature of the rising light curve. Using ground-based photometry, we estimate a photometric redshift of z phot = 3.29 ± 0.40. Combined with the high-energy emission and optical peak time derived from TESS, estimates of the bulk Lorentz factor Γ BL range from 90 to 133. The burst is relatively bright, with a peak optical magnitude in ground-based follow-up of R = 15.1 mag. Using published distributions of GRB afterglows and considering the TESS sensitivity and sampling, we estimate that TESS is likely to detect ~1 GRB afterglow per year above its magnitude limit.

79 ASTRONOMY AND ASTROPHYSICS↗

Data-Driven Adaptive Damping Controller for Wind Power Plants with Doubly-Fed Induction Generators: Preprint

This paper presents an adaptive damping controller for wind power plants in which the turbines are equipped with doubly-fed induction generators. The controller is designed to respond to an input control signal that is triggered according to the system operating conditions. A processing unit continuously estimates the electromechanical modes of oscillation based on real-time streaming data acquired from a phasor measurement unit that is strategically positioned on the grid. The decision to trigger (or not trigger) the control signal is automatic, based on the relative damping of the dominant mode. The modes are estimated using the dynamic mode decomposition algorithm with time-delay embedding. Numerical simulations performed on the two-area system demonstrate that the proposed controller enhances the rotor angle stability for both small-signal and large disturbances, and is adaptive to changing grid conditions.

61 RADIATION PROTECTION AND DOSIMETRY↗

Mechanisms of Low-Level Jet Formation in the U.S. Mid-Atlantic Offshore

Low level jets (LLJs) in the atmosphere exhibit a local windspeed maximum inthe boundary layer and are commonly observed both over land and in coastal environments. Because LLJs present strong positive shear beneath the maximum (or "jet nose") and negative shear above the nose, they pose a challenge to future offshore wind technology through their impacts on turbine performance and wakes. Summertime LLJs in the Great Plains have been attributed to frictional decoupling triggering an inertial oscillation, whilecoastal LLJs in California or the North Sea have additional driving mechanisms such as baroclinic forcing. By comparison, LLJs in the coastal US Mid-Atlantic have received less attention, with conflicting evidence about the mechanism that triggers these high shear events. Motivated by future wind energy development in the region, this work elucidates the atmospheric mechanisms of LLJ formation in the US Mid-Atlantic. Using observational data from two floating LiDAR buoys deployed bythe New York State Energy Research and Development Authority in the NY Bight, we identify four sustained LLJ events whose windspeeds and directions are well predicted by a WRF simulation (Weather Research and Forecasting Model). From analysis of the WRF data, we find that the four case studies provide evidence of concurrent inertial oscillation, reduced vertical mixing, and baroclinicity. In addition, we use simple atmospheric dynamics and a single-column-model to compare the relative contribution of each of these mechanisms to triggering the LLJ. By improving understanding and predictability of coastal mid-Atlantic LLJs, this work reduces uncertaintiesof wind energy deployment in the region, aiding the US's transition toward renewable energy.

atmospheric boundary layers↗

Latency hiding for caches

A technique for accessing a memory having a high latency portion and a low latency portion is provided. The technique includes detecting a promotion trigger to promote data from the high latency portion to the low latency portion, in response to the promotion trigger, copying cache lines associated with the promotion trigger from the high latency portion to the low latency portion, and in response to a read request, providing data from either or both of the high latency portion or the low latency portion, based on a state associated with data in the high latency portion and the low latency portion.

97 MATHEMATICS AND COMPUTING↗

Investigating Electro-Nuclear Interactions in a New Dark Matter Search

Electro-nuclear (EN) interactions are interactions in which an incident electron collides with a nucleus, scattering the electron and creating byproduct particles. Such interactions are of interest to neutrino physicists, who use EN interactions to inform model building of neutrino-nucleus interactions. The Light Dark Matter Experiment (LDMX) is a small-scale, fixed-target, electron beam experiment which seeks to probe for dark matter and mediator particle production in the sub-GeV mass region. The 8GeV LDMX electron beam will serve as an opportunity to study electro-nuclear interactions in final states in the multi-GeV region. LDMX s missing energy trigger for dark matter interactions however, will not be sufficient to efficiently capture EN interactions. An additional trigger is needed. Using simulated events, that included background and EN interactions, a trigger on momentum was developed.

Croteau, Beatrice↗

Proactive and Reactive Thermal Comfort Behaviors

The expansion of renewable electricity generation, growing demands due to electrification, greater prevalence of working from home, and increasing frequency and severity of extreme weather events, will place new demands on the electric supply and distribution grid. Broader adoption of demand response programs (DRPs) for the residential sector may help meet these challenges; however, experience shows that occupant overrides in DRPs compromises their effectiveness. There is a lack of formal understanding of how discomfort, routines, and other motivations affect DRP overrides and other related human building interactions (HBI). This paper reports preliminary findings from a study of 20 households in Colorado and Massachusetts, US over three months. Participants responded to ecological momentary assessments (EMA) triggered by thermostat interactions and at random times throughout the day. EMAs included Likert-scale questions of thermal preference, preference intensity, and changes to 7 different activity types that could affect thermal comfort, and an opened ended question about motivations of such actions. Twelve tags were developed to categorize motivation responses and analyzed statistically to identify associations between motivations, preferences, and HBI actions. Reactions to changes in the thermal environment were the most frequently observed motivation (118 of 220 responses). On the other hand, almost half (47%) responses were at least partially motivated by non-thermal factors, suggesting limited utility for occupant behavior models founded solely on thermal comfort. Changes in activity level and clothing were less likely to be reported when EMAs were triggered by thermostat interactions, while fan interactions were more likely. Windows, shades, and portable heater interactions had no significant dependence on how the EMA was triggered. These results suggest that better understanding of motivations for HBI may improve effectiveness of demand response programs.

Pathak, Maharshi↗

Lowering the Energy Threshold of the CUORE Experiment: Benefits in the Surface Alpha Events Reconstruction

CUORE is a tonne-scale cryogenic experiment located at the Laboratori Nazionali del Gran Sasso that exploits bolometric technique to search for neutrinoless double beta decay of 130 Te. Thanks to its very low background and large mass, CUORE is also a powerful tool to study a broad class of phenomena, such as solar axions and WIMP scattering. The ability to conduct such sensitive searches crucially depends on the energy threshold, which has to be kept as low as possible. Here, we show how the trigger algorithm affects the sensitivity to low-energy phenomena and the interpretation of the energy spectrum. In particular, we focus on the impact that the trigger algorithm has on the identification of the coincidence events among different crystals and, consequently, on the reconstruction of the background.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The GlueX beamline and detector

The GlueX experiment at Jefferson Lab has been designed to study photoproduction reactions with a 9-GeV linearly polarized photon beam. The energy and arrival time of beam photons are tagged using a scintillator hodoscope and a scintillating fiber array. The photon flux is determined using a pair spectrometer, while the linear polarization of the photon beam is determined using a polarimeter based on triplet photoproduction. Charged-particle tracks from interactions in the central target are analyzed in a solenoidal field using a central straw-tube drift chamber and six packages of planar chambers with cathode strips and drift wires. Electromagnetic showers are reconstructed in a cylindrical scintillating fiber calorimeter inside the magnet and a lead-glass array downstream. Charged particle identification is achieved by measuring energy loss in the wire chambers and using the flight time of particles between the target and detectors outside the magnet. The signals from all detectors are recorded with flash ADCs and/or pipeline TDCs into memories allowing trigger decisions with a latency of 3.3 $μs$. The detector operates routinely at trigger rates of 40 kHz and data rates of 600 megabytes per second. Here, we describe the photon beam, the GlueX detector components, electronics, data-acquisition and monitoring systems, and the performance of the experiment during the first three years of operation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗