ScholarWorks

ScholarWorks is an open access repository for the capture of the intellectual work of Montana State University (MSU) in support of its teaching, research and service missions. MSU ScholarWorks is a central point of discovery for accessing, collecting, sharing, preserving, and distributing knowledge to the Montana State University community and the world.

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Scholarship & Research

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Lost in OCR Translation? Vision-Based Approaches to Robust Document Retrieval
(ACM, 2025-08)
Most, Alexander
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Winjum, Joseph
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Bhattarai, Manish
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Jones, Shawn
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Ranasinghe, Nishath Rajiv
Retrieval-Augmented Generation (RAG) has become a popular technique for enhancing the reliability and utility of Large Language Models (LLMs) by grounding responses in external documents. Traditional RAG systems rely on Optical Character Recognition (OCR) to first process scanned documents into text. However, even state-of-the-art OCRs can introduce errors, especially in degraded or complex documents. Recent vision-language approaches, such as ColPali, propose direct visual embedding of documents, eliminating the need for OCR. This study presents a systematic comparison between a vision-based RAG system (ColPali) and more traditional OCR-based pipelines utilizing Llama 3.2 (90B) and Nougat OCR across varying document qualities. Beyond conventional retrieval accuracy metrics, we introduce a semantic answer evaluation benchmark to assess end-to-end question-answering performance. Our findings indicate that while vision-based RAG performs well on documents it has been fine-tuned on, OCR-based RAG is better able to generalize to unseen documents of varying quality. We highlight the key trade-offs between computational efficiency and semantic accuracy, offering practical guidance for RAG practitioners in selecting between OCR-dependent and vision-based document retrieval systems in production environments.
Structural basis of antiphage defence by an ATPase-associated reverse transcriptase
(Springer Science and Business Media LLC, 2025-09)
George, Jerrin Thomas
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Burman, Nathaniel
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Wilkinson, Royce A.
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de Silva, Senuri
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McKelvey-Pham, Quynh
Reverse transcriptases (RTs) have well-established roles in the replication and spread of retroviruses and retrotransposons. However, recent evidence suggests that RTs have been conscripted by cells for diverse roles in antiviral defence. Here we determine structures of a type I-A retron, which explain how RNA, DNA, RT, HNH-nuclease and four molecules of a structure maintenance of chromosome (SMC)-family ATPase assemble into a 364 kDa complex that provides phage defence. We show that phage-encoded nucleases trigger degradation of the retron-associated DNA, leading to activation of the HNH nuclease. The HNH nuclease cleaves tRNASer, stalling protein synthesis and arresting viral replication. Taken together, these data reveal diverse and paradoxical roles for RTs in the perpetuation and elimination of genetic parasites.
Quasiperiodic Oscillation Signatures of Disk Restoration after Type-I X-Ray Bursts from 4U 1636−536
(American Astronomical Society, 2025-09)
Chattopadhyay, Suchismito
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Chauhan, Jaiverdhan
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Misra, Ranjeev
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Lohfink, Anne
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Starling, Rhaana
Type-I thermonuclear bursts (TNBs) from neutron star low-mass X-ray binaries (NS LMXBs) originate on the neutron star’s surface from the unstable burning of the accreted material. On the other hand, kHz quasiperiodic oscillations (QPOs) are thought to originate in the innermost regions of the inspiralling accretion disk. Type-I TNBs are expected to impact the inner accretion flow, and consequently the kHz QPOs, due to the intense radiation pressure. In this work, we systematically study the evolution of the upper and the lower kHz QPOs immediately before and after a type-I TNB on 4U 1636−536 using AstroSat observations in the 3–20 keV band. The analysis of the power density spectra shows the presence of kHz QPOs within 200 s before the onset of the type-I burst. However, we have not detected any prominent signature of the same within 100–200 s after the burst. The kHz QPOs then reemerge after ≈200 s. The fractional rms variation in the 3–20 keV band drops by ≈5%–6%, supporting the nonexistence of kHz QPOs in the 200 s postburst zone. The timescale of 200 s coincides with the viscous timescale, highlighting a scenario where the inner disk is temporarily disrupted by the intense radiation from the type-I TNB. The kHz QPO then reestablishes as the inner disk is restored.
Managing cover crop mixtures over a decade via species replacement and seeding rate adjustment
(Wiley, 2025-08)
Hosler, Sheryl C.
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Murrell, Ebony G.
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Arrington, Kathleen E.
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Baraibar, Bárbara
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Barbercheck, Mary E.
Cover crop mixtures provide ecosystem services, but species’ relative abundance in mixtures is challenging to manage. We report on an 11-year experiment where our main objective was to use species selection and seeding rate adjustments over time to increase the evenness of mixtures. Replacing rye with triticale and red clover with crimson clover while adjusting seeding rates resulted in mixtures that were more even and closer to the desired composition (greater legume biomass) than the original communities. For example, the first version of a six-species mixture produced biomass composed of 81% grass, 5% brassica, and 14% legume, but after adjustments, subsequent versions contained 25% grass, 10% brassica, and 65% legume biomass. Substituting a less aggressive grass for a dominant grass and a more aggressive legume for a weaker legume better balanced the mixture to meet farmers’ ecosystem service goals, as did reducing the proportion of grass seed in the mixtures.
Regional Thermal History Trends From the Idaho-Montana Fold-Thrust Belt Using Multiple Low-T Thermochronometers
(American Geophysical Union, 2025-05)
Kaempfer, J. M.
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Guenthner, W. R.
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Pearson, D. M.
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Orme, Devon A.
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Crawford, B.
Low-temperature thermochronometric data can reveal the long-term evolution of erosion, uplift, and thrusting in fold-thrust belts. We present results from central Idaho and southwestern Montana, where the close spatial overlap of the Sevier fold-thrust belt and Laramide style, basement-involved foreland uplifts signify a complex region with an unresolved, long-term tectono-thermal history. Inverse QTQt thermal history modeling of new zircon (U-Th)/He (ZHe, n = 106), and apatite (U-Th)/He dates (AHe, n = 43) collected from hanging walls of major thrusts systems along a central Idaho to southwestern Montana transect, and apatite fission track results from 6 basement samples, reveal regional thermal and spatial trends related to Sevier and Laramide orogenesis. Inverse modeling of foreland basement uplift samples suggest Phanerozoic exhumation initiated as early as ∼80 Ma and continued through the early Paleogene. Inverse modeling of interior Idaho fold-thrust belt ZHe samples documents Early Cretaceous cooling at ∼125 Ma in the Lost River Range (western transect), and a younger cooling episode in the Lemhi Arch region (mid-transect) at ∼90–80 Ma through the late Paleogene. This cooling in the Lemhi Arch temporally overlaps with cooling in southwestern Montana's basement-cored uplifts, which we interpret as roughly synchronous exhumation related to contractional tectonics and post-orogenic collapse. These data and models, integrated with independent timing constraints from foreland basin strata and previously published thermochronometric results, suggests that middle Cretaceous deformation of southwestern Montana's basement-cored uplifts was low magnitude and preceded tectonism along the classic Arizona-Wyoming Laramide “corridor.” In contrast, Late Cretaceous and Paleogene thrust-related exhumation was more significant and largely complete by the Eocene. The basement-involved deformation was contemporaneous with and younger than along-strike Sevier belt thrusting in central Idaho.