UC Santa Cruz Previously Published Works

Extractivism and the ecology of research infrastructure: digitizing precarious materialities in Iquitos, Peru

Smith, Amanda M

(2024)

Deep Generative Models for Fast Photon Shower Simulation in ATLAS

(2024)

Abstract: The need for large-scale production of highly accurate simulated event samples for the extensive physics programme of the ATLAS experiment at the Large Hadron Collider motivates the development of new simulation techniques. Building on the recent success of deep learning algorithms, variational autoencoders and generative adversarial networks are investigated for modelling the response of the central region of the ATLAS electromagnetic calorimeter to photons of various energies. The properties of synthesised showers are compared with showers from a full detector simulation using geant4. Both variational autoencoders and generative adversarial networks are capable of quickly simulating electromagnetic showers with correct total energies and stochasticity, though the modelling of some shower shape distributions requires more refinement. This feasibility study demonstrates the potential of using such algorithms for ATLAS fast calorimeter simulation in the future and shows a possible way to complement current simulation techniques.

Software Performance of the ATLAS Track Reconstruction for LHC Run 3

(2024)

Charged particle reconstruction in the presence of many simultaneous proton–proton (pp) collisions in the LHC is a challenging task for the ATLAS experiment’s reconstruction software due to the combinatorial complexity. This paper describes the major changes made to adapt the software to reconstruct high-activity collisions with an average of 50 or more simultaneous pp interactions per bunch crossing (pile-up) promptly using the available computing resources. The performance of the key components of the track reconstruction chain and its dependence on pile-up are evaluated, and the improvement achieved compared to the previous software version is quantified. For events with an average of 60pp collisions per bunch crossing, the updated track reconstruction is twice as fast as the previous version, without significant reduction in reconstruction efficiency and while reducing the rate of combinatorial fake tracks by more than a factor two.

Translational modulator ISRIB alleviates synaptic and behavioral phenotypes in Fragile X syndrome.

(2024)

Fragile X syndrome (FXS) is caused by the loss of fragile X messenger ribonucleoprotein (FMRP), a translational regulator that binds the transcripts of proteins involved in synaptic function and plasticity. Dysregulated protein synthesis is a central effect of FMRP loss, however, direct translational modulation has not been leveraged in the treatment of FXS. Thus, we examined the effect of the translational modulator integrated stress response inhibitor (ISRIB) in treating synaptic and behavioral symptoms of FXS. We show that FMRP loss dysregulates synaptic protein abundance, stabilizing dendritic spines through increased PSD-95 levels while preventing spine maturation through reduced glutamate receptor accumulation, thus leading to the formation of dense, immature dendritic spines, characteristic of FXS patients and Fmr1 knockout (KO) mice. ISRIB rescues these deficits and improves social recognition in Fmr1 KO mice. These findings highlight the therapeutic potential of targeting core translational mechanisms in FXS and neurodevelopmental disorders more broadly.

Cover page of Helicobacter pylori cheV1 mutants recover semisolid agar migration due to loss of a previously uncharacterized Type IV filament membrane alignment complex homolog.

Helicobacter pylori cheV1 mutants recover semisolid agar migration due to loss of a previously uncharacterized Type IV filament membrane alignment complex homolog.

(2024)

UNLABELLED: The bacterial chemotaxis system is a well-understood signaling pathway that promotes bacterial success. Chemotaxis systems comprise chemoreceptors and the CheA kinase, linked by CheW or CheV scaffold proteins. Scaffold proteins provide connections between chemoreceptors and CheA and also between chemoreceptors to create macromolecular arrays. Chemotaxis is required for host colonization by many microbes, including the stomach pathogen Helicobacter pylori. This bacterium builds chemoreceptor-CheA contacts with two distinct scaffold proteins, CheW and CheV1. H. pylori cheW or cheV1 deletion mutants both lose chemoreceptor array formation, but show differing semisolid agar chemotaxis assay behaviors: ∆cheW mutants exhibit total migration failure, whereas ∆cheV1::cat mutants display a 50% reduction. On investigating these varied responses, we found that both mutants initially struggle with migration. However, over time, ∆cheV1::cat mutants develop a stable, enhanced migration capability, termed migration-able (Mig+). Whole-genome sequencing analysis of four distinct ∆cheV1::cat Mig+ strains identified single-nucleotide polymorphisms (SNPs) in hpg27_252 (hp0273) that were predicted to truncate the encoded protein. Computational analysis of the hpg27_252-encoded protein revealed it encoded a hypothetical protein that was a remote homolog of the PilO Type IV filament membrane alignment complex protein. Although H. pylori lacks Type IV filaments, our analysis showed it retains an operon of genes for homologs of PilO, PilN, and PilM. Deleting hpg27_252 in the ∆cheV1::cat or wild type strain resulted in enhanced migration in semisolid agar. Our study thus reveals that while cheV1 mutants initially have significant migration defects, they can recover the migration ability through genetic suppressors, highlighting a complex regulatory mechanism in bacterial migration. IMPORTANCE: Chemotactic motility, present in over half of bacteria, depends on chemotaxis signaling systems comprising receptors, kinases, and scaffold proteins. In Helicobacter pylori, a stomach pathogen, chemotaxis is crucial for colonization, with CheV1 and CheW as key scaffold proteins. While both scaffolds are essential for building chemoreceptor complexes, their roles vary in other assays. Our research reexamines cheV1 mutants behavior in semisolid agar, a standard chemotaxis test. Initially, cheV1 mutants exhibited defects similar to those of cheW mutants, but they evolved genetic suppressors that enhanced migration. These suppressors involve mutations in a previously uncharacterized gene, unknown in motility behavior. Our findings highlight the significant chemotaxis defects in cheV1 mutants and identify new elements influencing bacterial motility.

Cover page of Label-free and amplification-free viral RNA quantification from primate biofluids using a trapping-assisted optofluidic nanopore platform.

Label-free and amplification-free viral RNA quantification from primate biofluids using a trapping-assisted optofluidic nanopore platform.

(2024)

Viral outbreaks can cause widespread disruption, creating the need for diagnostic tools that provide high performance and sample versatility at the point of use with moderate complexity. Current gold standards such as PCR and rapid antigen tests fall short in one or more of these aspects. Here, we report a label-free and amplification-free nanopore sensor platform that overcomes these challenges via direct detection and quantification of viral RNA in clinical samples from a variety of biological fluids. The assay uses an optofluidic chip that combines optical waveguides with a fluidic channel and integrates a solid-state nanopore for sensing of individual biomolecules upon translocation through the pore. High specificity and low limit of detection are ensured by capturing RNA targets on microbeads and collecting them by optical trapping at the nanopore location where targets are released and rapidly detected. We use this device for longitudinal studies of the viral load progression for Zika and Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections in marmoset and baboon animal models, respectively. The up to million-fold trapping-based target concentration enhancement enables amplification-free RNA quantification across the clinically relevant concentration range down to the assay limit of RT-qPCR as well as cases in which PCR failed. The assay operates across all relevant biofluids, including semen, urine, and whole blood for Zika and nasopharyngeal and throat swab, rectal swab, and bronchoalveolar lavage for SARS-CoV-2. The versatility, performance, simplicity, and potential for full microfluidic integration of the amplification-free nanopore assay points toward a unique approach to molecular diagnostics for nucleic acids, proteins, and other targets.

Cover page of Sea Ice Loss, Water Vapor Increases, and Their Interactions with Atmospheric Energy Transport in Driving Seasonal Polar Amplification

Sea Ice Loss, Water Vapor Increases, and Their Interactions with Atmospheric Energy Transport in Driving Seasonal Polar Amplification

(2024)

Abstract: The ice–albedo feedback associated with sea ice loss contributes to polar amplification, while the water vapor feedback contributes to tropical amplification of surface warming. However, these feedbacks are not independent of atmospheric energy transport, raising the possibility of complex interactions that may obscure the drivers of polar amplification, in particular its manifestation across the seasonal cycle. Here, we apply a radiative transfer hierarchy to an idealized aquaplanet global climate model coupled to a thermodynamic sea ice model. The climate responses and radiative feedbacks are decomposed into the contributions from sea ice loss, including both retreat and thinning, and the radiative effect of water vapor changes. We find that summer sea ice retreat causes winter polar amplification through ocean heat uptake and release, and the resulting decrease in dry energy transport weakens the magnitude of warming. Moreover, sea ice thinning is found to suppress summer warming and enhance winter warming, additionally contributing to winter amplification. The water vapor radiative effect produces seasonally symmetric polar warming via offsetting effects: enhanced moisture in the summer hemisphere induces the summer water vapor feedback and simultaneously strengthens the winter latent energy transport in the winter hemisphere by increasing the meridional moisture gradient. These results reveal the importance of changes in atmospheric energy transport induced by sea ice retreat and increased water vapor to seasonal polar amplification, elucidating the interactions among these physical processes.

Reading with Screen Magnification: Eye Movement Analysis Using Compensated Gaze Tracks

(2024)

Eye movements while reading with screen magnification (which requires manual scrolling to center the magnified portion of the screen within the viewport) pose interpretation challenges. Standard representations in terms of alternating fixations and saccades don’t apply to this case. This is because, during scrolling, eyes often track a moving text element, generating a movement akin to smooth pursuit. We propose a new representation that uses information from the mouse (which the reader uses to move the center of magnification) to undo the effect of magnification and scrolling. After this “compensation” operation, gaze tracks can again be described as alternating fixations and saccades. We present an analysis of gaze tracks obtained by applying this transformation on an existing dataset, recorded from low vision readers using two modalities of screen magnification. This analysis highlights similarities and differences in terms of dynamic properties of compensated gaze tracks vis-à-vis gaze during regular reading.

Towards Personalized Head-Tracking Pointing

(2024)

Head-based pointing is an effective interface for those with limited hand control, though it may involve a learning curve due to discrepancies between desired pointer movement and actual system response to head motion. We theorize that individuals have unique head movement patterns for similar tasks, necessitating tailored mappings from head to pointer motion. This was explored by analyzing video data of participants tracking a moving target on-screen using head movements. The study found that using a select set of facial landmarks outperforms other methods, like focusing on the nose-tip or rotation angles, in aligning head and pointer movements. Despite this, there is still notable bias inherent in the simple affine mapping model used. Significant variations were observed in participants' head movements when responding to similar target paths, with diagonal movements showing a higher error rate. These insights could be crucial in creating new, personalized head-tracking interfaces, enhancing ease and efficiency.

Study of High-Transverse-Momentum Higgs Boson Production in Association with a Vector Boson in the qqbb Final State with the ATLAS Detector

(2024)

This Letter presents the first study of Higgs boson production in association with a vector boson (V=W or Z) in the fully hadronic qqbb final state using data recorded by the ATLAS detector at the LHC in proton-proton collisions at sqrt[s]=13 TeV and corresponding to an integrated luminosity of 137 fb^{-1}. The vector bosons and Higgs bosons are each reconstructed as large-radius jets and tagged using jet substructure techniques. Dedicated tagging algorithms exploiting b-tagging properties are used to identify jets consistent with Higgs bosons decaying into bb[over ¯]. Dominant backgrounds from multijet production are determined directly from the data, and a likelihood fit to the jet mass distribution of Higgs boson candidates is used to extract the number of signal events. The VH production cross section is measured inclusively and differentially in several ranges of Higgs boson transverse momentum: 250-450, 450-650, and greater than 650 GeV. The inclusive signal yield relative to the standard model expectation is observed to be μ=1.4_{-0.9}^{+1.0} and the corresponding cross section is 3.1±1.3(stat)_{-1.4}^{+1.8}(syst) pb.