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24,041 results on '"Thompson, A. C."'

1. The Epistemic Value of Novel Predictive Success in Scientific and Criminal Investigations: A Bayesian Explanation

Author

Mortera, Julia and Thompson, William C.

Subjects
Statistics - Applications, 62
Abstract

Because there are similarities between the evaluation of alternative stories in criminal trials and the evaluation of scientific theories, scholars have looked to literature in epistemology and the philosophy of science for insights on the evaluation of evidence in criminal trials. The philosophical literature is divided, however, on a key point -- the epistemic value of novel predictive success. This article uses a Bayesian network analysis to explore, in the context of a criminal case, the circumstances in which "new evidence" discovered after a theory is propounded, can provide stronger (or weaker) support for the theory than "old evidence" that was accommodated by the theory. It argues that insights from analysis of the strength of "new" and "old" evidence in the criminal case can be applied more generally when assessing the relative merits of prediction and accommodation in scientific theory development, and are thus helpful in addressing the longstanding philosophic controversy over this issue.

Published
2025

2. On topological defects in Chern-Simons theory

Author

Arvanitakis, Alex S., Cole, Lewis T., Demulder, Saskia, and Thompson, Daniel C.

Subjects
High Energy Physics - Theory
Abstract

We construct a new class of topological surface defects in Chern-Simons theory with non-compact, non-Abelian gauge groups. These defects are characterized by isotropic subalgebras defined by solutions of the modified classical Yang-Baxter equation, and their fusion realizes a semi-group structure with non-invertible elements. From a Hamiltonian perspective, we calculate this fusion using the composition of Lagrangian correspondences within the Weinstein symplectic category. Applications include boundary terms and conditions in $AdS_3$ gravity and higher-spin theories., Comment: 5 pages

Published
2024

3. Gauging The Diamond: Integrable Coset Models from Twistor Space

Author

Cole, Lewis T., Cullinan, Ryan A., Hoare, Ben, Liniado, Joaquin, and Thompson, Daniel C.

Subjects
High Energy Physics - Theory
Abstract

Recent work has shown that certain integrable and conformal field theories in two dimensions can be given a higher-dimensional origin from holomorphic Chern-Simons in six dimensions. Along with anti-self-dual Yang-Mills and four-dimensional Chern-Simons, this gives rise to a diamond correspondence of theories. In this work we extend this framework to incorporate models realised through gaugings. As well as describing a higher-dimensional origin of coset CFTs, by choosing the details of the reduction from higher dimensions, we obtain rich classes of two-dimensional integrable models including homogeneous sine-Gordon models and generalisations that are new to the literature., Comment: 44 pages

Published
2024
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4. A Note on a Generalized Two Component Camassa-Holm System in Sobolev Spaces

Author

Thompson, Ryan C.

Subjects
Mathematics - Analysis of PDEs, 35Q53
Abstract

In this paper, we consider a generalized two component Camassa-Holm system. Based on local well-posedness results and lifespan estimates, we establish sharpness of continuity on the data-to-solution map by showing that it is not uniformly continuous from product Sobolev spaces $H^s \times H^{s}$ to $C([0,T]; H^s \times H^{s})$. The proof of nonuniform dependence is based upon approximate solutions.

Published
2024

5. ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip

Author

Lee, John J. Y., Tao, Ran, You, Zhen, Haldipur, Parthiv, Erickson, Anders W., Farooq, Hamza, Hendriske, Liam D., Abeysundara, Namal, Richman, Cory M., Wang, Evan Y., Das Gupta, Neha, Hadley, Jennifer, Batts, Melissa, Mount, Christopher W., Wu, Xiaochong, Rasnitsyn, Alex, Bailey, Swneke, Cavalli, Florence M. G., Morrissy, Sorana, Garzia, Livia, Michealraj, Kulandaimanuvel Antony, Visvanathan, Abhi, Fong, Vernon, Palotta, Jonelle, Suarez, Raul, Livingston, Bryn G., Liu, Miao, Luu, Betty, Daniels, Craig, Loukides, James, Bendel, Anne, French, Pim J., Kros, Johan M., Korshunov, Andrey, Kool, Marcel, Chico Ponce de León, Fernando, Perezpeña-Diazconti, Mario, Lach, Boleslaw, Singh, Sheila K., Leary, Sarah E. S., Cho, Byung-Kyu, Kim, Seung-Ki, Wang, Kyu-Chang, Lee, Ji-Yeoun, Tominaga, Teiji, Weiss, William A., Phillips, Joanna J., Dai, Shizhong, Zadeh, Gelareh, Saad, Ali G., Bognár, László, Klekner, Almos, Pollack, Ian F., Hamilton, Ronald L., Ra, Young-shin, Grajkowska, Wieslawa A., Perek-Polnik, Marta, Thompson, Reid C., Kenney, Anna M., Cooper, Michael K., Mack, Stephen C., Jabado, Nada, Lupien, Mathieu, Gallo, Marco, Ramaswamy, Vijay, Suva, Mario L., Suzuki, Hiromichi, Millen, Kathleen J., Huang, L. Frank, Northcott, Paul A., and Taylor, Michael D.

Published
2025
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8. Quantum-corrected anti-de Sitter space-time

Author

Thompson, Jacob C. and Winstanley, Elizabeth

Subjects
High Energy Physics - Theory, General Relativity and Quantum Cosmology
Abstract

We study the back-reaction of a quantum scalar field on anti-de Sitter (AdS) space-time. The renormalized expectation value of the stress-energy tensor operator for a massless, conformally-coupled quantum scalar field on global AdS space-time in four space-time dimensions acts as a source term on the right-hand-side of the Einstein equations for the quantum-corrected metric. We solve the quantum-corrected Einstein equations numerically and find deviations from pure AdS which increase as the temperature of the quantum scalar field state increases. We interpret these quantum-corrected metrics as asymptotically-AdS solitons, and study the mass of these solitons as a function of the temperature of the quantum scalar field., Comment: 19 pages, 11 figures, minor changes, accepted for publication in Physical Review D

Published
2024

9. $^{171}$Yb$^+$ optical clock with $2.2\times 10^{-18}$ systematic uncertainty and absolute frequency measurements

Author

Tofful, Alexandra, Baynham, Charles F. A., Curtis, E. Anne, Parsons, Adam O., Robertson, Billy I., Schioppo, Marco, Tunesi, Jacob, Margolis, Helen S., Hendricks, Richard J., Whale, Josh, Thompson, Richard C., and Godun, Rachel M.

Subjects
Physics - Atomic Physics
Abstract

A full evaluation of the uncertainty budget for the ytterbium ion optical clock at the National Physical Laboratory (NPL) was performed on the electric octupole (E3) $^2\mathrm{S}_{1/2}\,\rightarrow\, ^2\mathrm{F}_{7/2}$ transition. The total systematic frequency shift was measured with a fractional standard systematic uncertainty of $2.2\times 10^{-18}$. Furthermore, the absolute frequency of the E3 transition of the $^{171}$Yb$^+$ ion was measured between 2019 and 2023 via a link to International Atomic Time (TAI) and against the local caesium fountain NPL-CsF2. The absolute frequencies were measured with fractional standard uncertainties between $3.7 \times 10^{-16}$ and $1.1 \times 10^{-15}$, and all were in agreement with the 2021 BIPM recommended frequency., Comment: 16 pages, 8 figures, submitted to Metrologia

Published
2024
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10. Clinical recognition of frontotemporal dementia with right anterior temporal predominance: A multicenter retrospective cohort study

Author

Ulugut, Hulya, Bertoux, Maxime, Younes, Kyan, Montembeault, Maxime, Fumagalli, Giorgio G, Samanci, Bedia, Illán‐Gala, Ignacio, Kuchcinski, Gregory, Leroy, Melanie, Thompson, Jennifer C, Kobylecki, Christopher, Santillo, Alexander F, Englund, Elisabet, Waldö, Maria Landqvist, Riedl, Lina, Van den Stock, Jan, Vandenbulcke, Mathieu, Vandenberghe, Rik, Laforce, Robert, Ducharme, Simon, Pressman, Peter S, Caramelli, Paulo, de Souza, Leonardo Cruz, Takada, Leonel T, Gurvit, Hakan, Hansson, Oskar, Diehl‐Schmid, Janine, Galimberti, Daniela, Pasquier, Florence, Miller, Bruce L, Scheltens, Philip, Ossenkoppele, Rik, van der Flier, Wiesje M, Barkhof, Frederik, Fox, Nick C, Sturm, Virginia E, Miyagawa, Toji, Whitwell, Jennifer L, Boeve, Bradley, Rohrer, Jonathan D, Gorno‐Tempini, Maria Luisa, Josephs, Keith A, Snowden, Julie, Warren, Jason D, Rankin, Katherine P, Pijnenburg, Yolande AL, and Group, International rtvFTD Working

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Psychology, Neurosciences, Behavioral and Social Science, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Rare Diseases, Mental Health, Frontotemporal Dementia (FTD), Brain Disorders, Neurodegenerative, Dementia, Aging, Clinical Research, Acquired Cognitive Impairment, Alzheimer's Disease Related Dementias (ADRD), Basic Behavioral and Social Science, Neurological, Mental health, Good Health and Well Being, Humans, Male, Frontotemporal Dementia, Retrospective Studies, Female, Temporal Lobe, Aged, Middle Aged, Neuropsychological Tests, Atrophy, emotion recognition, frontotemporal dementia, frontotemporal lobar degeneration, right anterior temporal lobe, semantic dementia, social cognition, International rtvFTD Working Group, Clinical Sciences, Geriatrics, Clinical sciences, Biological psychology
Abstract

IntroductionAlthough frontotemporal dementia (FTD) with right anterior temporal lobe (RATL) predominance has been recognized, a uniform description of the syndrome is still missing. This multicenter study aims to establish a cohesive clinical phenotype.MethodsRetrospective clinical data from 18 centers across 12 countries yielded 360 FTD patients with predominant RATL atrophy through initial neuroimaging assessments.ResultsCommon symptoms included mental rigidity/preoccupations (78%), disinhibition/socially inappropriate behavior (74%), naming/word-finding difficulties (70%), memory deficits (67%), apathy (65%), loss of empathy (65%), and face-recognition deficits (60%). Real-life examples unveiled impairments regarding landmarks, smells, sounds, tastes, and bodily sensations (74%). Cognitive test scores indicated deficits in emotion, people, social interactions, and visual semantics however, lacked objective assessments for mental rigidity and preoccupations.DiscussionThis study cumulates the largest RATL cohort unveiling unique RATL symptoms subdued in prior diagnostic guidelines. Our novel approach, combining real-life examples with cognitive tests, offers clinicians a comprehensive toolkit for managing these patients.HighlightsThis project is the first international collaboration and largest reported cohort. Further efforts are warranted for precise nomenclature reflecting neural mechanisms. Our results will serve as a clinical guideline for early and accurate diagnoses.

Published
2024

11. Safety of Extended Pirtobrutinib Exposure in Relapsed and/or Refractory B-Cell Malignancies.

Author

Roeker, Lindsey E, Coombs, Catherine C, Shah, Nirav N, Jurczak, Wojciech, Woyach, Jennifer A, Cheah, Chan Y, Patel, Krish, Maddocks, Kami, Wang, Yucai, Zinzani, Pier Luigi, Munir, Talha, Koh, Youngil, Thompson, Meghan C, Muehlenbein, Catherine E, Wang, Chunxiao, Sizelove, Richard, Abhyankar, Sarang, Hasanabba, Safarulla, Tsai, Donald E, Eyre, Toby A, and Wang, Michael

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Patient Safety, Infectious Diseases, Cancer, Clinical Trials and Supportive Activities, Rare Diseases, Hematology, Clinical Research, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, B-cell malignancies, Bruton tyrosine kinase inhibitor, Long-term safety, Toxicity, Cardiorespiratory Medicine and Haematology, Immunology, Cardiovascular medicine and haematology
Abstract

IntroductionPirtobrutinib, a highly selective, noncovalent (reversible) Bruton tyrosine kinase inhibitor, has demonstrated promising efficacy in B-cell malignancies and is associated with low rates of discontinuation and dose reduction. Pirtobrutinib is administered until disease progression or toxicity, necessitating an understanding of the safety profile in patients with extended treatment.MethodsHere we report the safety of pirtobrutinib in patients with relapsed/refractory B-cell malignancies with extended (≥12 months) drug exposure from the BRUIN trial. Assessments included median time-to-first-occurrence of adverse events (AEs), dose reductions, and discontinuations due to treatment-emergent AEs (TEAEs) and select AEs of interest (AESIs).ResultsOf 773 patients enrolled, 326 (42%) received treatment for ≥12 months. In the extended exposure cohort, the median time-on-treatment was 19 months. The most common all-cause TEAEs were fatigue (32%) and diarrhea (31%). TEAEs leading to dose reduction occurred in 23 (7%) and discontinuations in 11 (3%) extended exposure patients. One patient had a fatal treatment-related AE (COVID-19 pneumonia). Infections (73.0%) were the most common AESI with a median time-to-first-occurrence of 7.4 months. Majority of TEAEs and AESIs occurred during the first year of therapy.ConclusionsPirtobrutinib therapy continues to demonstrate an excellent safety profile amenable to long-term administration without evidence of new or worsening toxicity signals.

Published
2024

12. Gastric vagotomy blocks opioid analgesia enhancement produced by placenta ingestion

Author

Tarapacki, J. A., Thompson, A. C., and Kristal, Dr. Mark B.

Subjects
Psychology: Physiological Psychology, Neuroscience: Behavioral Neuroscience, Neuroscience: Neurochemistry, Physiological Psychology, Behavioral Neuroscience, Neurochemistry
Abstract

Ingestion of amniotic fluid or placenta by rats has been shown to enhance opioid-mediated analgesia induced by morphine injection, footshock, vaginal/cervical stimulation, or late pregnancy. This enhancement by ingestion appears to be specific to the central actions of opioids. The present study was designed to examine the possibility that information traveling via the vagus nerve might be involved in mediating this effect. Rats that had undergone either selective gastric vagotomy or sham vagotomy were injected with either morphine sulfate or vehicle and fed either placenta or a meat control. Enhancement was observed in rats that had undergone sham vagotomy but not in those that had undergone gastric vagotomy. These results support an interpretation of vagal involvement in the enhancement of opioid-mediated analgesia by placenta.

Published
1992

13. Placental opioid-enhancing factor (POEF): Generalizability of effects

Author

Abbott, P., Thompson, A. C., Ferguson, E.J., Doerr, J. C., Tarapacki, J. A., Kostyniak, Dr. P.J., Syracuse, J.A., Cartonia, D.M., and Kristal, Dr. Mark B.

Subjects
Neuroscience: Behavioral Neuroscience, Behavioral Neuroscience
Abstract

A substance in amniotic fluid and placenta (POEF for Placental Opioid-Enhancing Factor) has been shown to enhance opiate- or opioid-mediated analgesia in rats. Recent studies have only touched on the generalizability of the phenomenon. The present studies further tested the generalizability of the POEF effect: they examined sex specificity of the mechanism, whether POEF activity exists in afterbirth material of species other than the rat; whether POEF activity exists in tissue other than afterbirth material; whether POEF activity could be demonstrated after injection rather than ingestion of afterbirth material; and whether POEF enhances all opioid-mediated phenomena. We found that (a) POEF is effective in male rats as well as in female rats; (b) POEF activity exists in human and dolphin afterbirth material; (c) ingestion of pregnant-rat liver does not produce enhancement of opioid-mediated analgesia; (d) POEF does not seem to be effective when amniotic fluid is injected either IPO or SC; and (e) POEF does not modify morphine-induced hyperthermia.

Published
1991

16. Spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle

Author

Caserta, Leonardo C., Frye, Elisha A., Butt, Salman L., Laverack, Melissa, Nooruzzaman, Mohammed, Covaleda, Lina M., Thompson, Alexis C., Koscielny, Melanie Prarat, Cronk, Brittany, Johnson, Ashley, Kleinhenz, Katie, Edwards, Erin E., Gomez, Gabriel, Hitchener, Gavin, Martins, Mathias, Kapczynski, Darrell R., Suarez, David L., Alexander Morris, Ellen Ruth, Hensley, Terry, Beeby, John S., Lejeune, Manigandan, Swinford, Amy K., Elvinger, François, Dimitrov, Kiril M., and Diel, Diego G.

Published
2024
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18. Increases in regional brain volume across two native South American male populations

Author

Chaudhari, Nikhil N., Imms, Phoebe E., Chowdhury, Nahian F., Gatz, Margaret, Trumble, Benjamin C., Mack, Wendy J., Law, E. Meng, Sutherland, M. Linda, Sutherland, James D., Rowan, Christopher J., Wann, L. Samuel, Allam, Adel H., Thompson, Randall C., Michalik, David E., Miyamoto, Michael, Lombardi, Guido, Cummings, Daniel K., Seabright, Edmond, Alami, Sarah, Garcia, Angela R., Rodriguez, Daniel E., Gutierrez, Raul Quispe, Copajira, Adrian J., Hooper, Paul L., Buetow, Kenneth H., Stieglitz, Jonathan, Gurven, Michael D., Thomas, Gregory S., Kaplan, Hillard S., Finch, Caleb E., and Irimia, Andrei

Published
2024
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20. Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography

Author

Smith, Nathan, Dasgupta, Medhanjali, Wych, David C, Dolamore, Cole, Sierra, Raymond G, Lisova, Stella, Marchany-Rivera, Darya, Cohen, Aina E, Boutet, Sébastien, Hunter, Mark S, Kupitz, Christopher, Poitevin, Frédéric, Moss, Frank R, Mittan-Moreau, David W, Brewster, Aaron S, Sauter, Nicholas K, Young, Iris D, Wolff, Alexander M, Tiwari, Virendra K, Kumar, Nivesh, Berkowitz, David B, Hadt, Ryan G, Thompson, Michael C, Follmer, Alec H, Wall, Michael E, and Wilson, Mark A

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Bioengineering, Crystallography, X-Ray, Proteins, Catalysis, Molecular Dynamics Simulation, Protein Conformation, Hydrolases
Abstract

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

Published
2024

21. Validation of a prognostic blood-based sphingolipid panel for men with localized prostate cancer followed on active surveillance

Author

Gregg, Justin R., Newcomb, Lisa, Wu, Ranran, Dennison, Jennifer, Davis, John W., Pettaway, Curtis, Pisters, Louis, Ward, John F., Chapin, Brian F., Chéry, Lisly, Urkmez, Ahmet, Fang, Andrew M., Higgason, Noel, Troncoso, Patricia, Daniel, Carrie R., Logothetis, Christopher, Thompson, Timothy C., Hahn, Andrew W., Liu, Menghan, Zheng, Yingye, Lin, Dan W., Hanash, Samir, Irajizad, Ehsan, and Fahrmann, Johannes

Published
2024
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26. Author Correction: Divergent landscapes of A-to-I editing in postmortem and living human brain

Author

Rodriguez de los Santos, Miguel, Kopell, Brian H., Buxbaum Grice, Ariela, Ganesh, Gauri, Yang, Andy, Amini, Pardis, Liharska, Lora E., Vornholt, Eric, Fullard, John F., Dong, Pengfei, Park, Eric, Zipkowitz, Sarah, Kaji, Deepak A., Thompson, Ryan C., Liu, Donjing, Park, You Jeong, Cheng, Esther, Ziafat, Kimia, Moya, Emily, Fennessy, Brian, Wilkins, Lillian, Silk, Hannah, Linares, Lisa M., Sullivan, Brendan, Cohen, Vanessa, Kota, Prashant, Feng, Claudia, Johnson, Jessica S., Rieder, Marysia-Kolbe, Scarpa, Joseph, Nadkarni, Girish N., Wang, Minghui, Zhang, Bin, Sklar, Pamela, Beckmann, Noam D., Schadt, Eric E., Roussos, Panos, Charney, Alexander W., and Breen, Michael S.

Published
2024
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27. Epigenetic signals associated with delirium replicated across four independent cohorts

Author

Nishizawa, Yoshitaka, Thompson, Kaitlyn C., Yamanashi, Takehiko, Wahba, Nadia E., Saito, Taku, Marra, Pedro S., Nagao, Takaaki, Nishiguchi, Tsuyoshi, Shibata, Kazuki, Yamanishi, Kyosuke, Hughes, Christopher G., Pandharipande, Pratik, Cho, Hyunkeun, Howard, III, Matthew A., Kawasaki, Hiroto, Toda, Hiroyuki, Kanazawa, Tetsufumi, Iwata, Masaaki, and Shinozaki, Gen

Published
2024
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29. Divergent landscapes of A-to-I editing in postmortem and living human brain

Author

Rodriguez de los Santos, Miguel, Kopell, Brian H., Buxbaum Grice, Ariela, Ganesh, Gauri, Yang, Andy, Amini, Pardis, Liharska, Lora E., Vornholt, Eric, Fullard, John F., Dong, Pengfei, Park, Eric, Zipkowitz, Sarah, Kaji, Deepak A., Thompson, Ryan C., Liu, Donjing, Park, You Jeong, Cheng, Esther, Ziafat, Kimia, Moya, Emily, Fennessy, Brian, Wilkins, Lillian, Silk, Hannah, Linares, Lisa M., Sullivan, Brendan, Cohen, Vanessa, Kota, Prashant, Feng, Claudia, Johnson, Jessica S., Rieder, Marysia-Kolbe, Scarpa, Joseph, Nadkarni, Girish N., Wang, Minghui, Zhang, Bin, Sklar, Pamela, Beckmann, Noam D., Schadt, Eric E., Roussos, Panos, Charney, Alexander W., and Breen, Michael S.

Published
2024
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30. Integrable Deformations from Twistor Space

Author

Cole, Lewis T., Cullinan, Ryan A., Hoare, Ben, Liniado, Joaquin, and Thompson, Daniel C.

Subjects
High Energy Physics - Theory, 81T13, 81R25
Abstract

Integrable field theories in two dimensions are known to originate as defect theories of 4d Chern-Simons and as symmetry reductions of the 4d anti-self-dual Yang-Mills equations. Based on ideas of Costello, it has been proposed in work of Bittleston and Skinner that these two approaches can be unified starting from holomorphic Chern-Simons in 6 dimensions. We provide the first complete description of this diamond of integrable theories for a family of deformed sigma models, going beyond the Dirichlet boundary conditions that have been considered thus far. Starting from 6d holomorphic Chern-Simons theory on twistor space with a particular meromorphic 3-form $\Omega$, we construct the defect theory to find a novel 4d integrable field theory, whose equations of motion can be recast as the 4d anti-self-dual Yang-Mills equations. Symmetry reducing, we find a multi-parameter 2d integrable model, which specialises to the $\lambda$-deformation at a certain point in parameter space. The same model is recovered by first symmetry reducing, to give 4d Chern-Simons with generalised boundary conditions, and then constructing the defect theory., Comment: 38 pages, 1 figure

Published
2023
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31. Commentary on Guyll et al. (2023): Misuse of Statistical Method Results in Highly Biased Interpretation of Forensic Evidence

Author

Rosenblum, Michael, Chin, Elizabeth T., Ogburn, Elizabeth L., Nishimura, Akihiko, Westreich, Daniel, Datta, Abhirup, Vanderplas, Susan, Cuellar, Maria, and Thompson, William C.

Subjects
Statistics - Applications
Abstract

Since the National Academy of Sciences released their report outlining paths for improving reliability, standards, and policies in the forensic sciences NAS (2009), there has been heightened interest in evaluating and improving the scientific validity within forensic science disciplines. Guyll et al. (2023) seek to evaluate the validity of forensic cartridge-case comparisons. However, they make a serious statistical error that leads to highly inflated claims about the probability that a cartridge case from a crime scene was fired from a reference gun, typically a gun found in the possession of a defendant. It is urgent to address this error since these claims, which are generally biased against defendants, are being presented by the prosecution in an ongoing homicide case where the defendant faces the possibility of a lengthy prison sentence (DC Superior Court, 2023).

Published
2023

32. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

Author

Díaz, Roberto Efraín, Ecker, Andrew K, Correy, Galen J, Asthana, Pooja, Young, Iris D, Faust, Bryan, Thompson, Michael C, Seiple, Ian B, Van Dyken, Steven, Locksley, Richard M, and Fraser, James S

Subjects
Biochemistry and Cell Biology, Biological Sciences, Underpinning research, 1.1 Normal biological development and functioning, Chitinases, Animals, Hydrogen-Ion Concentration, Mice, Molecular Dynamics Simulation, Chitin, Protein Conformation, Crystallography, X-Ray, Protein Binding, Ligands, Kinetics, Acetylglucosamine, Models, Molecular, enzyme, chitin, lung, E. coli, Human, Mouse, biochemistry, chemical biology, human, molecular biophysics, mouse, structural biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high-resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.

Published
2024

33. Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus Infection in Domestic Dairy Cattle and Cats, United States, 2024

Author

Burrough, Eric R., Magstadt, Drew R., Petersen, Barbara, Timmermans, Simon J., Gauger, Phillip C., Zhang, Jianqiang, Siepker, Chris, Mainenti, Marta, Li, Ganwu, Thompson, Alexis C., Gorden, Patrick J., Plummer, Paul J., and Main, Rodger

Subjects
Distribution, Genetic aspects, Health aspects, Company distribution practices, Dairy cattle -- Health aspects, Avian influenza -- Genetic aspects -- Distribution, Domestic cats -- Health aspects, Cats -- Health aspects
Abstract

Highly pathogenic avian influenza (HPAI) viruses pose a threat to wild birds and poultry globally, and HPAI H5N1 viruses are of even greater concern because of their frequent spillover into [...]

Published
2024
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38. Nuclear quantum effect on the elasticity of ice VII under pressure: A path-integral molecular dynamics study

Author

Tsuchiya, Jun, Shiga, Motoyuki, Tsuneyuki, Shinji, and Thompson, Elizabeth C.

Subjects
Condensed Matter - Materials Science, Physics - Chemical Physics
Abstract

We investigate the effect of nuclear quantum effects (NQEs) of hydrogen atoms on the elasticity of ice VII at high pressure and ambient temperature conditions using ab initio path-integral molecular dynamics (PIMD) calculations. We find that the NQEs of hydrogen contributes to the transition of ice VII from a static disordered structure to a dynamically disordered structure at pressures exceeding 40 GPa. This transition is marked by a discontinuous increase of the elastic constants. Comparison of ab initio molecular dynamics and PIMD calculations reveal that NQEs increase the elastic constants of ice by about 20% at 70 GPa and 300 K.

Published
2023
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42. Shifting decision thresholds can undermine the probative value and legal utility of forensic pattern-matching evidence

Author

Thompson, William C

Subjects
Psychology, Law and Legal Studies, Applied and Developmental Psychology, Bayes Theorem, Forensic Medicine, Bias, Dermatoglyphics, forensic science, decision threshold, signal detection theory, Bayesian network, error rates
Abstract

Forensic pattern analysis requires examiners to compare the patterns of items such as fingerprints or tool marks to assess whether they have a common source. This article uses signal detection theory to model examiners' reported conclusions (e.g., identification, inconclusive, or exclusion), focusing on the connection between the examiner's decision threshold and the probative value of the forensic evidence. It uses a Bayesian network model to explore how shifts in decision thresholds may affect rates and ratios of true and false convictions in a hypothetical legal system. It demonstrates that small shifts in decision thresholds, which may arise from contextual bias, can dramatically affect the value of forensic pattern-matching evidence and its utility in the legal system.

Published
2023

47. Asymptotics in an Asymptotic CFT

Author

Schepers, Lucas and Thompson, Daniel C.

Subjects
High Energy Physics - Theory, Mathematical Physics, Nonlinear Sciences - Exactly Solvable and Integrable Systems
Abstract

In this work we illustrate the resurgent structure of the $\lambda$-deformation; a two-dimensional integrable quantum field theory that has an RG flow with an $SU(N)_k$ Wess-Zumino-Witten conformal fixed point in the UV. To do so we use modern matched asymptotic techniques applied to the thermodynamic Bethe ansatz formulation to compute the free energy to 38 perturbative orders in an expansion of large applied chemical potential. We find numerical evidence for factorial asymptotic behaviour with both alternating and non-alternating character which we match to an analytic expression. A curiosity of the system is that it exhibits the Cheshire Cat phenomenon with the leading non-alternating factorial growth vanishing when $k$ divides $N$. The ambiguities associated to Borel resummation of this series are suggestive of non-perturbative contributions. This is verified with an analytic study of the TBA system demonstrating a cancellation between perturbative and non-perturbative ambiguities., Comment: 26 Pages, 7 figures

Published
2023
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49. Unifying Approaches to Chiral Bosons

Author

Arvanitakis, Alex S., Cole, Lewis T., Hulik, Ondrej, Sevrin, Alexander, and Thompson, Daniel C.

Subjects
High Energy Physics - Theory
Abstract

Chiral bosons, or self-dual p-form fields, are ubiquitous in string theoretic contexts but are challenging to treat. Lagrangian constructions invariably introduce a complexity be it auxiliary fields or sacrificing Lorentz invariance. In this note we show how to pass between such different approaches to chiral bosons starting from a Chern Simons point of view to recover formulations of Pasti, Sorokin and Tonin and of Mkrtchyan. This leads to a novel generalisation of the latter to include non-Abelian chiral bosons in 2-dimensions, and generalisations to include twisted self-duality which are relevant in T-duality symmetric approaches to string theory. Our approach also shows how global affine symmetries of two- and higher-dimensional chiral bosons emerge from broken Chern-Simons gauge transformations on the boundary., Comment: 23 pages. Minor updates, matches published version

Published
2022
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50. Classical Solutions of the Fornberg-Whitham Equation

Author

Burkhalter, Georgia, Thompson, Ryan C., and Waldrep, Madison

Subjects
Mathematics - Analysis of PDEs, 35Q53
Abstract

In this paper, we prove well-posedness in $C^1(\mathbb{R})$ (a.k.a. classical solutions) of the Fornberg-Whitham equation. To achieve this objective, we study its weak formulation under a Lagrangian framework. Applying the fundamental theorem of ordinary differential equations to the generated semi-linear system, we then construct a unique solution to the equation that is continuously dependent on the initial data. These results improve upon others in Sobolev and Besov spaces.

Published
2022

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