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1. Evaluation of prostate cancer detection using micro-ultrasound versus MRI through co-registration to whole-mount pathology.

Author

Pensa, Jake, Brisbane, Wayne, Kinnaird, Adam, Kuppermann, David, Hughes, Griffith, Ushko, Derrick, Priester, Alan, Gonzalez, Samantha, Reiter, Robert, Chin, Arnold, Sisk, Anthony, Felker, Ely, Marks, Leonard, and Geoghegan, Rory

Subjects
Co-registration, Image reconstruction, MRI, Micro-ultrasound, Prostate cancer, Whole-mount pathology, Humans, Prostatic Neoplasms, Male, Magnetic Resonance Imaging, Ultrasonography, Aged, Retrospective Studies, Middle Aged, Prostate, Prostatectomy, Image Processing, Computer-Assisted
Abstract

Micro-ultrasound has recently been introduced as a low-cost alternative to multi-parametric MRI for imaging prostate cancer. Early clinical studies have demonstrated promising results; however, robust validation via comparison with whole-mount pathology has yet to be achieved. Due to micro-ultrasound probe design and tissue deformation during scanning, it is difficult to accurately correlate micro-ultrasound imaging planes with ground truth whole-mount pathology slides. In this study, we developed a multi-step methodology to co-register micro-ultrasound and MRI to whole-mount pathology. The three-step process had a registration error of 3.90 ± 0.11 mm and consists of: (1) micro-ultrasound image reconstruction, (2) 3D landmark registration of micro-ultrasound to MRI, and (3) 2D capsule registration of MRI to whole-mount pathology. This process was then used in a preliminary reader study to compare the diagnostic accuracy of micro-ultrasound and MRI in 15 patients who underwent radical prostatectomy for prostate cancer. Micro-ultrasound was found to have equivalent performance to retrospective MRI review for index lesion detection (91.7% vs. 80%), while demonstrating an increased detection of tumor extent (52.5% vs. 36.7%) with similar false positive regions-of-interest (38.3% vs. 40.8%). Prospective MRI review had reduced detection of index lesions (73.3%) and tumor extent (18.9%) but improved false positive regions-of-interest (22.7%) relative to micro-ultrasound and retrospective MRI. Further evaluation is needed with a larger sample size.

Published
2024

2. Generating Music with Structure Using Self-Similarity as Attention

Author

Hager, Sophia, Hablutzel, Kathleen, and Kinnaird, Katherine M.

Subjects
Computer Science - Sound, Computer Science - Machine Learning, Electrical Engineering and Systems Science - Audio and Speech Processing
Abstract

Despite the innovations in deep learning and generative AI, creating long term structure as well as the layers of repeated structure common in musical works remains an open challenge in music generation. We propose an attention layer that uses a novel approach applying user-supplied self-similarity matrices to previous time steps, and demonstrate it in our Similarity Incentivized Neural Generator (SING) system, a deep learning autonomous music generation system with two layers. The first is a vanilla Long Short Term Memory layer, and the second is the proposed attention layer. During generation, this attention mechanism imposes a suggested structure from a template piece on the generated music. We train SING on the MAESTRO dataset using a novel variable batching method, and compare its performance to the same model without the attention mechanism. The addition of our proposed attention mechanism significantly improves the network's ability to replicate specific structures, and it performs better on an unseen test set than a model without the attention mechanism.

Published
2024

3. Global arthropod beta-diversity is spatially and temporally structured by latitude.

Author

Seymour, Mathew, Roslin, Tomas, deWaard, Jeremy R, Perez, Kate HJ, D'Souza, Michelle L, Ratnasingham, Sujeevan, Ashfaq, Muhammad, Levesque-Beaudin, Valerie, Blagoev, Gergin A, Bukowski, Belén, Cale, Peter, Crosbie, Denise, Decaëns, Thibaud, deWaard, Stephanie L, Ekrem, Torbjørn, El-Ansary, Hosam O, Evouna Ondo, Fidèle, Fraser, David, Geiger, Matthias F, Hajibabaei, Mehrdad, Hallwachs, Winnie, Hanisch, Priscila E, Hausmann, Axel, Heath, Mark, Hogg, Ian D, Janzen, Daniel H, Kinnaird, Margaret, Kohn, Joshua R, Larrivée, Maxim, Lees, David C, León-Règagnon, Virginia, Liddell, Michael, Lijtmaer, Darío A, Lipinskaya, Tatsiana, Locke, Sean A, Manjunath, Ramya, Martins, Dino J, Martins, Marlúcia B, Mazumdar, Santosh, McKeown, Jaclyn TA, Anderson-Teixeria, Kristina, Miller, Scott E, Milton, Megan A, Miskie, Renee, Morinière, Jérôme, Mutanen, Marko, Naik, Suresh, Nichols, Becky, Noguera, Felipe A, Novotny, Vojtech, Penev, Lyubomir, Pentinsaari, Mikko, Quinn, Jenna, Ramsay, Leah, Rochefort, Regina, Schmidt, Stefan, Smith, M Alex, Sobel, Crystal N, Somervuo, Panu, Sones, Jayme E, Staude, Hermann S, St Jaques, Brianne, Stur, Elisabeth, Telfer, Angela C, Tubaro, Pablo L, Wardlaw, Tim J, Worcester, Robyn, Yang, Zhaofu, Young, Monica R, Zemlak, Tyler, Zakharov, Evgeny V, Zlotnick, Bradley, Ovaskainen, Otso, and Hebert, Paul DN

Subjects
Animals, Arthropods, Biodiversity, Geography, Spatio-Temporal Analysis, Biological Sciences, Ecology, Evolutionary Biology, Life Below Water, Biological sciences, Biomedical and clinical sciences
Abstract

Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.

Published
2024

4. Detailed Report on the Measurement of the Positive Muon Anomalous Magnetic Moment to 0.20 ppm

Author

Aguillard, D. P., Albahri, T., Allspach, D., Anisenkov, A., Badgley, K., Baeßler, S., Bailey, I., Bailey, L., Baranov, V. A., Barlas-Yucel, E., Barrett, T., Barzi, E., Bedeschi, F., Berz, M., Bhattacharya, M., Binney, H. P., Bloom, P., Bono, J., Bottalico, E., Bowcock, T., Braun, S., Bressler, M., Cantatore, G., Carey, R. M., Casey, B. C. K., Cauz, D., Chakraborty, R., Chapelain, A., Chappa, S., Charity, S., Chen, C., Cheng, M., Chislett, R., Chu, Z., Chupp, T. E., Claessens, C., Convery, M. E., Corrodi, S., Cotrozzi, L., Crnkovic, J. D., Dabagov, S., Debevec, P. T., Di Falco, S., Di Sciascio, G., Donati, S., Drendel, B., Driutti, A., Duginov, V. N., Eads, M., Edmonds, A., Esquivel, J., Farooq, M., Fatemi, R., Ferrari, C., Fertl, M., Fienberg, A. T., Fioretti, A., Flay, D., Foster, S. B., Friedsam, H., Froemming, N. S., Gabbanini, C., Gaines, I., Galati, M. D., Ganguly, S., Garcia, A., George, J., Gibbons, L. K., Gioiosa, A., Giovanetti, K. L., Girotti, P., Gohn, W., Goodenough, L., Gorringe, T., Grange, J., Grant, S., Gray, F., Haciomeroglu, S., Halewood-Leagas, T., Hampai, D., Han, F., Hempstead, J., Hertzog, D. W., Hesketh, G., Hess, E., Hibbert, A., Hodge, Z., Hong, K. W., Hong, R., Hu, T., Hu, Y., Iacovacci, M., Incagli, M., Kammel, P., Kargiantoulakis, M., Karuza, M., Kaspar, J., Kawall, D., Kelton, L., Keshavarzi, A., Kessler, D. S., Khaw, K. S., Khechadoorian, Z., Khomutov, N. V., Kiburg, B., Kiburg, M., Kim, O., Kinnaird, N., Kraegeloh, E., Krylov, V. A., Kuchinskiy, N. A., Labe, K. R., LaBounty, J., Lancaster, M., Lee, S., Li, B., Li, D., Li, L., Logashenko, I., Campos, A. Lorente, Lu, Z., Lucà, A., Lukicov, G., Lusiani, A., Lyon, A. L., MacCoy, B., Madrak, R., Makino, K., Mastroianni, S., Miller, J. P., Miozzi, S., Mitra, B., Morgan, J. P., Morse, W. M., Mott, J., Nath, A., Ng, J. K., Nguyen, H., Oksuzian, Y., Omarov, Z., Osofsky, R., Park, S., Pauletta, G., Piacentino, G. M., Pilato, R. N., Pitts, K. T., Plaster, B., Počanić, D., Pohlman, N., Polly, C. C., Price, J., Quinn, B., Qureshi, M. U. H., Ramachandran, S., Ramberg, E., Reimann, R., Roberts, B. L., Rubin, D. L., Sakurai, M., Santi, L., Schlesier, C., Schreckenberger, A., Semertzidis, Y. K., Shemyakin, D., Sorbara, M., Stapleton, J., Still, D., Stöckinger, D., Stoughton, C., Stratakis, D., Swanson, H. E., Sweetmore, G., Sweigart, D. A., Syphers, M. J., Tarazona, D. A., Teubner, T., Tewsley-Booth, A. E., Tishchenko, V., Tran, N. H., Turner, W., Valetov, E., Vasilkova, D., Venanzoni, G., Volnykh, V. P., Walton, T., Weisskopf, A., Welty-Rieger, L., Winter, P., Wu, Y., Yu, B., Yucel, M., Zeng, Y., and Zhang, C.

Subjects
High Energy Physics - Experiment, High Energy Physics - Phenomenology, Nuclear Experiment
Abstract

We present details on a new measurement of the muon magnetic anomaly, $a_\mu = (g_\mu -2)/2$. The result is based on positive muon data taken at Fermilab's Muon Campus during the 2019 and 2020 accelerator runs. The measurement uses $3.1$ GeV$/c$ polarized muons stored in a $7.1$-m-radius storage ring with a $1.45$ T uniform magnetic field. The value of $ a_{\mu}$ is determined from the measured difference between the muon spin precession frequency and its cyclotron frequency. This difference is normalized to the strength of the magnetic field, measured using Nuclear Magnetic Resonance (NMR). The ratio is then corrected for small contributions from beam motion, beam dispersion, and transient magnetic fields. We measure $a_\mu = 116 592 057 (25) \times 10^{-11}$ (0.21 ppm). This is the world's most precise measurement of this quantity and represents a factor of $2.2$ improvement over our previous result based on the 2018 dataset. In combination, the two datasets yield $a_\mu(\text{FNAL}) = 116 592 055 (24) \times 10^{-11}$ (0.20 ppm). Combining this with the measurements from Brookhaven National Laboratory for both positive and negative muons, the new world average is $a_\mu$(exp) $ = 116 592 059 (22) \times 10^{-11}$ (0.19 ppm)., Comment: 48 pages, 29 figures; 4 pages of Supplement Material; version accepted for publication in Physical Review D

Published
2024

5. Questions (and Answers) for Incorporating Nontraditional Grading in Your Statistics Courses

Author

Brenna Curley, Jillian Downey, Katherine M. Kinnaird, Adam Loy, and Eric Reyes

Abstract

Nontraditional grading methods have recently become more common, and as with any large pedagogical shift, there are a number of questions to consider when applying a new grading scheme to a course. This article summarizes four types of nontraditional grading and shares experiences from the authors who have applied them to a variety of courses in statistics. This article is structured as a set of questions and answers, seeking to address many of the concerns and considerations that one may face as they transition a course's grading structure. Supplementary materials for this article are available online.

Published
2024
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6. Measurement of the Positive Muon Anomalous Magnetic Moment to 0.20 ppm

Author

Aguillard, D. P., Albahri, T., Allspach, D., Anisenkov, A., Badgley, K., Baeßler, S., Bailey, I., Bailey, L., Baranov, V. A., Barlas-Yucel, E., Barrett, T., Barzi, E., Bedeschi, F., Berz, M., Bhattacharya, M., Binney, H. P., Bloom, P., Bono, J., Bottalico, E., Bowcock, T., Braun, S., Bressler, M., Cantatore, G., Carey, R. M., Casey, B. C. K., Cauz, D., Chakraborty, R., Chapelain, A., Chappa, S., Charity, S., Chen, C., Cheng, M., Chislett, R., Chu, Z., Chupp, T. E., Claessens, C., Convery, M. E., Corrodi, S., Cotrozzi, L., Crnkovic, J. D., Dabagov, S., Debevec, P. T., Di Falco, S., Di Sciascio, G., Drendel, B., Driutti, A., Duginov, V. N., Eads, M., Edmonds, A., Esquivel, J., Farooq, M., Fatemi, R., Ferrari, C., Fertl, M., Fienberg, A. T., Fioretti, A., Flay, D., Foster, S. B., Friedsam, H., Froemming, N. S., Gabbanini, C., Gaines, I., Galati, M. D., Ganguly, S., Garcia, A., George, J., Gibbons, L. K., Gioiosa, A., Giovanetti, K. L., Girotti, P., Gohn, W., Goodenough, L., Gorringe, T., Grange, J., Grant, S., Gray, F., Haciomeroglu, S., Halewood-Leagas, T., Hampai, D., Han, F., Hempstead, J., Hertzog, D. W., Hesketh, G., Hess, E., Hibbert, A., Hodge, Z., Hong, K. W., Hong, R., Hu, T., Hu, Y., Iacovacci, M., Incagli, M., Kammel, P., Kargiantoulakis, M., Karuza, M., Kaspar, J., Kawall, D., Kelton, L., Keshavarzi, A., Kessler, D. S., Khaw, K. S., Khechadoorian, Z., Khomutov, N. V., Kiburg, B., Kiburg, M., Kim, O., Kinnaird, N., Kraegeloh, E., Krylov, V. A., Kuchinskiy, N. A., Labe, K. R., LaBounty, J., Lancaster, M., Lee, S., Li, B., Li, D., Li, L., Logashenko, I., Campos, A. Lorente, Lu, Z., Lucà, A., Lukicov, G., Lusiani, A., Lyon, A. L., MacCoy, B., Madrak, R., Makino, K., Mastroianni, S., Miller, J. P., Miozzi, S., Mitra, B., Morgan, J. P., Morse, W. M., Mott, J., Nath, A., Ng, J. K., Nguyen, H., Oksuzian, Y., Omarov, Z., Osofsky, R., Park, S., Pauletta, G., Piacentino, G. M., Pilato, R. N., Pitts, K. T., Plaster, B., Počanić, D., Pohlman, N., Polly, C. C., Price, J., Quinn, B., Qureshi, M. U. H., Ramachandran, S., Ramberg, E., Reimann, R., Roberts, B. L., Rubin, D. L., Santi, L., Schlesier, C., Schreckenberger, A., Semertzidis, Y. K., Shemyakin, D., Sorbara, M., Stapleton, J., Still, D., Stöckinger, D., Stoughton, C., Stratakis, D., Swanson, H. E., Sweetmore, G., Sweigart, D. A., Syphers, M. J., Tarazona, D. A., Teubner, T., Tewsley-Booth, A. E., Tishchenko, V., Tran, N. H., Turner, W., Valetov, E., Vasilkova, D., Venanzoni, G., Volnykh, V. P., Walton, T., Weisskopf, A., Welty-Rieger, L., Winter, P., Wu, Y., Yu, B., Yucel, M., Zeng, Y., and Zhang, C.

Subjects
High Energy Physics - Experiment
Abstract

We present a new measurement of the positive muon magnetic anomaly, $a_\mu \equiv (g_\mu - 2)/2$, from the Fermilab Muon $g\!-\!2$ Experiment using data collected in 2019 and 2020. We have analyzed more than 4 times the number of positrons from muon decay than in our previous result from 2018 data. The systematic error is reduced by more than a factor of 2 due to better running conditions, a more stable beam, and improved knowledge of the magnetic field weighted by the muon distribution, $\tilde{\omega}'^{}_p$, and of the anomalous precession frequency corrected for beam dynamics effects, $\omega_a$. From the ratio $\omega_a / \tilde{\omega}'^{}_p$, together with precisely determined external parameters, we determine $a_\mu = 116\,592\,057(25) \times 10^{-11}$ (0.21 ppm). Combining this result with our previous result from the 2018 data, we obtain $a_\mu\text{(FNAL)} = 116\,592\,055(24) \times 10^{-11}$ (0.20 ppm). The new experimental world average is $a_\mu (\text{Exp}) = 116\,592\,059(22)\times 10^{-11}$ (0.19 ppm), which represents a factor of 2 improvement in precision., Comment: 8 pages, 3 figures

Published
2023
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7. Questions (and Answers) for Incorporating Nontraditional Grading in Your Statistics Courses

Author

Brenna Curley, Jillian Downey, Katherine M. Kinnaird, Adam Loy, and Eric Reyes

Subjects
Assessment, Contract grading, Specifications grading, Standards-based grading, Statistics education, Ungrading, Probabilities. Mathematical statistics, QA273-280, Special aspects of education, LC8-6691
Abstract

Nontraditional grading methods have recently become more common, and as with any large pedagogical shift, there are a number of questions to consider when applying a new grading scheme to a course. This article summarizes four types of nontraditional grading and shares experiences from the authors who have applied them to a variety of courses in statistics. This article is structured as a set of questions and answers, seeking to address many of the concerns and considerations that one may face as they transition a course’s grading structure. Supplementary materials for this article are available online.

Published
2024
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8. Evaluation of prostate cancer detection using micro-ultrasound versus MRI through co-registration to whole-mount pathology

Author

Jake Pensa, Wayne Brisbane, Adam Kinnaird, David Kuppermann, Griffith Hughes, Derrick Ushko, Alan Priester, Samantha Gonzalez, Robert Reiter, Arnold Chin, Anthony Sisk, Ely Felker, Leonard Marks, and Rory Geoghegan

Subjects
Co-registration, Image reconstruction, Micro-ultrasound, MRI, Prostate cancer, Whole-mount pathology, Medicine, Science
Abstract

Abstract Micro-ultrasound has recently been introduced as a low-cost alternative to multi-parametric MRI for imaging prostate cancer. Early clinical studies have demonstrated promising results; however, robust validation via comparison with whole-mount pathology has yet to be achieved. Due to micro-ultrasound probe design and tissue deformation during scanning, it is difficult to accurately correlate micro-ultrasound imaging planes with ground truth whole-mount pathology slides. In this study, we developed a multi-step methodology to co-register micro-ultrasound and MRI to whole-mount pathology. The three-step process had a registration error of 3.90 ± 0.11 mm and consists of: (1) micro-ultrasound image reconstruction, (2) 3D landmark registration of micro-ultrasound to MRI, and (3) 2D capsule registration of MRI to whole-mount pathology. This process was then used in a preliminary reader study to compare the diagnostic accuracy of micro-ultrasound and MRI in 15 patients who underwent radical prostatectomy for prostate cancer. Micro-ultrasound was found to have equivalent performance to retrospective MRI review for index lesion detection (91.7% vs. 80%), while demonstrating an increased detection of tumor extent (52.5% vs. 36.7%) with similar false positive regions-of-interest (38.3% vs. 40.8%). Prospective MRI review had reduced detection of index lesions (73.3%) and tumor extent (18.9%) but improved false positive regions-of-interest (22.7%) relative to micro-ultrasound and retrospective MRI. Further evaluation is needed with a larger sample size.

Published
2024
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9. Induction of osteoblast apoptosis stimulates macrophage efferocytosis and paradoxical bone formation

Author

Lena Batoon, Amy Jean Koh, Susan Marie Millard, Jobanpreet Grewal, Fang Ming Choo, Rahasudha Kannan, Aysia Kinnaird, Megan Avey, Tatyana Teslya, Allison Robyn Pettit, Laurie K. McCauley, and Hernan Roca

Subjects
Biology (General), QH301-705.5, Physiology, QP1-981
Abstract

Abstract Apoptosis is crucial for tissue homeostasis and organ development. In bone, apoptosis is recognized to be a main fate of osteoblasts, yet the relevance of this process remains underexplored. Using our murine model with inducible Caspase 9, the enzyme that initiates intrinsic apoptosis, we triggered apoptosis in a proportion of mature osteocalcin (OCN+) osteoblasts and investigated the impact on postnatal bone development. Osteoblast apoptosis stimulated efferocytosis by osteal macrophages. A five-week stimulation of OCN+ osteoblast apoptosis in 3-week-old male and female mice significantly enhanced vertebral bone formation while increasing osteoblast precursors. A similar treatment regimen to stimulate osterix+ cell apoptosis had no impact on bone volume or density. The vertebral bone accrual following stimulation of OCN+ osteoblast apoptosis did not translate in improved mechanical strength due to disruption of the lacunocanalicular network. The observed bone phenotype was not influenced by changes in osteoclasts but was associated with stimulation of macrophage efferocytosis and vasculature formation. Phenotyping of efferocytic macrophages revealed a unique transcriptomic signature and expression of factors including VEGFA. To examine whether macrophages participated in the osteoblast precursor increase following osteoblast apoptosis, macrophage depletion models were employed. Depletion of macrophages via clodronate-liposomes and the CD169-diphtheria toxin receptor mouse model resulted in marked reduction in leptin receptor+ and osterix+ osteoblast precursors. Collectively, this work demonstrates the significance of osteoblast turnover via apoptosis and efferocytosis in postnatal bone formation. Importantly, it exposes the potential of targeting this mechanism to promote bone anabolism in the clinical setting.

Published
2024
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10. Inter-reader Agreement for Prostate Cancer Detection Using Micro-ultrasound: A Multi-institutional Study

Author

Steve R. Zhou, Moon Hyung Choi, Sulaiman Vesal, Adam Kinnaird, Wayne G. Brisbane, Giovanni Lughezzani, Davide Maffei, Vittorio Fasulo, Patrick Albers, Lichun Zhang, Zachary Kornberg, Richard E. Fan, Wei Shao, Mirabela Rusu, and Geoffrey A. Sonn

Subjects
Inter-reader agreement, Micro-ultrasound, Prostate cancer, Targeted biopsy, Diseases of the genitourinary system. Urology, RC870-923, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Background and objective: Micro-ultrasound (MUS) uses a high-frequency transducer with superior resolution to conventional ultrasound, which may differentiate prostate cancer from normal tissue and thereby allow targeted biopsy. Preliminary evidence has shown comparable sensitivity to magnetic resonance imaging (MRI), but consistency between users has yet to be described. Our objective was to assess agreement of MUS interpretation across multiple readers. Methods: After institutional review board approval, we prospectively collected MUS images for 57 patients referred for prostate biopsy after multiparametric MRI from 2022 to 2023. MUS images were interpreted by six urologists at four institutions with varying experience (range 2–6 yr). Readers were blinded to MRI results and clinical data. The primary outcome was reader agreement on the locations of suspicious lesions, measured in terms of Light’s κ and positive percent agreement (PPA). Reader sensitivity for identification of grade group (GG) ≥2 prostate cancer was a secondary outcome. Key findings and limitations: Analysis revealed a κ value of 0.30 (95% confidence interval [CI] 0.21–0.39). PPA was 33% (95% CI 25–42%). The mean patient-level sensitivity for GG ≥2 cancer was 0.66 ± 0.05 overall and 0.87 ± 0.09 when cases with anterior lesions were excluded. Readers were 12 times more likely to detect higher-grade cancers (GG ≥3), with higher levels of agreement for this subgroup (κ 0.41, PPA 45%). Key limitations include the inability to prospectively biopsy reader-delineated targets and the inability of readers to perform live transducer maneuvers. Conclusions and clinical implications: Inter-reader agreement on the location of suspicious lesions on MUS is lower than rates previously reported for MRI. MUS sensitivity for cancer in the anterior gland is lacking. Patient summary: The ability to find cancer on imaging scans can vary between doctors. We found that there was frequent disagreement on the location of prostate cancer when doctors were using a new high-resolution scan method called micro-ultrasound. This suggests that the performance of micro-ultrasound is not yet consistent enough to replace MRI (magnetic resonance imaging) for diagnosis of prostate cancer.

Published
2024
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13. On definitions of 'mathematician'

Author

Buckmire, Ron, Eaton, Carrie Diaz, Hibdon, Jr., Joseph E., Kinnaird, Katherine M., Lewis, Drew, Libertini, Jessica, Ortega, Omayra, Roca, Rachel, and Vindas-Meléndez, Andrés R.

Subjects
Mathematics - History and Overview, 00-02, 00A35, 00A69, 97-01, 97A40
Abstract

The definition of who is or what makes a ``mathematician" is an important and urgent issue to be addressed in the mathematics community. Too often, a narrower definition of who is considered a mathematician (and what is considered mathematics) is used to exclude people from the discipline -- both explicitly and implicitly. However, using a narrow definition of a mathematician allows us to examine and challenge systemic barriers that exist in certain spaces of the community. This paper explores and illuminates tensions between narrow and broad definitions and how they can be used to promote both inclusion and exclusion simultaneously. In this article, we present a framework of definitions based on identity, function, and qualification and exploring several different meanings of ``mathematician". By interrogating various definitions, we highlight their risks and opportunities, with an emphasis on implications for broadening and/or narrowing participation of underrepresented groups., Comment: 21 pages, 2 figures

Published
2023

14. Development of an effective predictive screening tool for prostate cancer using the ClarityDX machine learning platform

Author

M. Eric Hyndman, Robert J. Paproski, Adam Kinnaird, Adrian Fairey, Leonard Marks, Christian P. Pavlovich, Sean A. Fletcher, Roman Zachoval, Vanda Adamcova, Jiri Stejskal, Armen Aprikian, Christopher J. D. Wallis, Desmond Pink, Catalina Vasquez, Perrin H. Beatty, and John D. Lewis

Subjects
Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract The current prostate cancer (PCa) screen test, prostate-specific antigen (PSA), has a high sensitivity for PCa but low specificity for high-risk, clinically significant PCa (csPCa), resulting in overdiagnosis and overtreatment of non-csPCa. Early identification of csPCa while avoiding unnecessary biopsies in men with non-csPCa is challenging. We built an optimized machine learning platform (ClarityDX) and showed its utility in generating models predicting csPCa. Integrating the ClarityDX platform with blood-based biomarkers for clinically significant PCa and clinical biomarker data from a 3448-patient cohort, we developed a test to stratify patients’ risk of csPCa; called ClarityDX Prostate. When predicting high risk cancer in the validation cohort, ClarityDX Prostate showed 95% sensitivity, 35% specificity, 54% positive predictive value, and 91% negative predictive value, at a ≥ 25% threshold. Using ClarityDX Prostate at this threshold could avoid up to 35% of unnecessary prostate biopsies. ClarityDX Prostate showed higher accuracy for predicting the risk of csPCa than PSA alone and the tested model-based risk calculators. Using this test as a reflex test in men with elevated PSA levels may help patients and their healthcare providers decide if a prostate biopsy is necessary.

Published
2024
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15. Global arthropod beta-diversity is spatially and temporally structured by latitude

Author

Mathew Seymour, Tomas Roslin, Jeremy R. deWaard, Kate H. J. Perez, Michelle L. D’Souza, Sujeevan Ratnasingham, Muhammad Ashfaq, Valerie Levesque-Beaudin, Gergin A. Blagoev, Belén Bukowski, Peter Cale, Denise Crosbie, Thibaud Decaëns, Stephanie L. deWaard, Torbjørn Ekrem, Hosam O. El-Ansary, Fidèle Evouna Ondo, David Fraser, Matthias F. Geiger, Mehrdad Hajibabaei, Winnie Hallwachs, Priscila E. Hanisch, Axel Hausmann, Mark Heath, Ian D. Hogg, Daniel H. Janzen, Margaret Kinnaird, Joshua R. Kohn, Maxim Larrivée, David C. Lees, Virginia León-Règagnon, Michael Liddell, Darío A. Lijtmaer, Tatsiana Lipinskaya, Sean A. Locke, Ramya Manjunath, Dino J. Martins, Marlúcia B. Martins, Santosh Mazumdar, Jaclyn T. A. McKeown, Kristina Anderson-Teixeria, Scott E. Miller, Megan A. Milton, Renee Miskie, Jérôme Morinière, Marko Mutanen, Suresh Naik, Becky Nichols, Felipe A. Noguera, Vojtech Novotny, Lyubomir Penev, Mikko Pentinsaari, Jenna Quinn, Leah Ramsay, Regina Rochefort, Stefan Schmidt, M. Alex Smith, Crystal N. Sobel, Panu Somervuo, Jayme E. Sones, Hermann S. Staude, Brianne St. Jaques, Elisabeth Stur, Angela C. Telfer, Pablo L. Tubaro, Tim J. Wardlaw, Robyn Worcester, Zhaofu Yang, Monica R. Young, Tyler Zemlak, Evgeny V. Zakharov, Bradley Zlotnick, Otso Ovaskainen, and Paul D. N. Hebert

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.

Published
2024
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16. Cryotherapy for partial gland ablation of prostate cancer: Oncologic and safety outcomes

Author

Aker, Mamdouh N, Brisbane, Wayne G, Kwan, Lorna, Gonzalez, Samantha, Priester, Alan M, Kinnaird, Adam, Delfin, Merdie K, Felker, Ely, Sisk, Anthony E, Kuppermann, David, and Marks, Leonard S

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Clinical Research, Prostate Cancer, Clinical Trials and Supportive Activities, Urologic Diseases, Cancer, Aging, Male, Humans, Prostate-Specific Antigen, Prospective Studies, Prostatic Neoplasms, Cryotherapy, Image-Guided Biopsy, Magnetic Resonance Imaging, Prostate cancer, cryotherapy, focal therapy, Biochemistry and Cell Biology, Oncology and carcinogenesis
Abstract

BackgroundPartial gland ablation (PGA) is a new option for treatment of prostate cancer (PCa). Cryotherapy, an early method of PGA, has had favorable evaluations, but few studies have employed a strict protocol using biopsy endpoints in men with clinically significant prostate cancer (csPCa).Methods143 men with unilateral csPCa were enrolled in a prospective, observational trial of outpatient PGA-cryotherapy. Treatment was a 2-cycle freeze of the affected prostate part. Participants were evaluated with MRI-guided biopsy (MRGB) at baseline and at 6 months and 18 months after treatment. Absence of csPCa upon MRGB was the primary endpoint; quality-of-life at baseline and at 6 months after treatment was assessed by EPIC-CP questionnaires in the domains of urinary and sexual function.ResultsOf the 143 participants, 136 (95%) completed MRGB at 6 months after treatment. In 103/136 (76%), the biopsy revealed no csPCa. Of the 103, 71 subsequently had an 18-month comprehensive biopsy; of the 71 with 18-month biopsies, 46 (65%) were found to have no csPCa. MRI lesions became undetectable in 96/130 (74%); declines in median serum PSA levels (6.9 to 2.5 ng/mL), PSA density (0.15 to 0.07), and prostate volume (42 to 34cc) were observed (all p

Published
2023

17. Thesis submitted in partial fulfilment for the degree of Doctorate in Clinical Psychology (DClinPsych)

Author

Kinnaird, Emma, Cooper, Myra, Anna, Crabtree, and Evans, Kathryn

Abstract

Systematic Literature Review. Objective: If a psychotherapeutic intervention has the capacity to produce positive change, the "deterioration effect" theory holds that it must also have the potential for negative effects. However, the definition, measurement, and reporting of unwanted events in psychotherapy is a topic of ongoing discussion. At present this area is under-explored in interventions for anorexia nervosa (AN), a severe mental illness associated with high medical and psychiatric risks. The aim of this paper was to undertake a systematic review of published randomised control trials (RCTs) evaluating psychotherapeutic interventions for AN, and to assess how unwanted events were defined, monitored and reported alongside the trial's key findings. Method: Using a systematic review methodology, this paper identified 23 RCTs through database searches meeting eligibility criteria. Results are presented using a narrative summary approach. Results: Unwanted event reporting varied widely, both regarding definitions of key unwanted events (such as non-compliance or symptom deterioration) and in the amount of detail captured in each paper. Discussion: The review identified two key issues: firstly, a lack of consistent definitions and unclear causality made it difficult to distinguish between unwanted events, and adverse events caused by the interventions. Secondly, it highlighted the difficulty of defining unwanted events where different studies have different populations and goals. Recommendations are made around how the area of defining, monitoring, and reporting unwanted events in RCTs for AN can be taken forward. Service Improvement Project. Autistic adults are at higher risk of experiencing mental health problems compared to their neurotypical peers and are more likely to report unmet healthcare needs and poor service experiences. Research suggests that this is closely related to a lack of understanding of autism by clinicians working in this area. Therefore, there is an increasing impetus in the National Health Service (NHS) for staff working in mental healthcare to receive autism training. However, there is a lack of understanding around autism in older adulthood, and whether older adult mental health teams could benefit from specialised training that reflects the specific needs of this population. This project used clinical audit and needs survey methodologies to explore whether an older adult mental health team might benefit from autism training, and to understand what clinicians might find helpful from a training intervention. Whilst the audit identified that the team did see patients on the autism spectrum, it was rare for the team to work with patients with a diagnosis of autism. Rather, clinicians were more likely to work with patients where autism is suspected but unconfirmed. Most clinicians reported having never received training in autism, and highlighted autism in older adults, and autism and mental health, as specific training priorities. A training programme based on these responses was developed, implemented, and evaluated using pre- and post-training surveys. The training was rated as useful by attendees and resulted in non-statistically significant increases in self-rated knowledge. The findings of this study suggest that clinicians working in older adult mental health can benefit from autism training. However, instead of generic autism training, clinicians may particularly benefit from training specialised to their older adult context. Further research is required to better understand the area of older adulthood and autism, and to evaluate how to effectively enhance the capability of staff working in this area. Theory Driven Research Project. Background: Whilst recovery from anorexia nervosa (AN) has traditionally been defined in relation to behavioural symptoms, the presence of cognitions, and weight, there is increasing research interest around understanding recovery from AN from the perspective of personal models of recovery, which emphasise factors such as personal growth and leading a meaningful life. Whilst previous research has suggested that clinical and personal recovery factors may exist in a complimentary relationship, with reduced clinical symptoms enabling growth in personal domains, to date this association has not been empirically explored. Understanding this relationship is particularly important in the context of proposals that there is a need to develop a universal definition of recovery from AN. Methods: The current study used a mixed methods approach to explore the relationship between personal and clinical models of recovery in AN. Eighty-one adults who self-defined as fully or partially recovered from AN were recruited into an online study and completed self-report measures of clinical and personal recovery. Participants were also asked questions about their views on the personal relevance of clinical criteria, and this data was analysed using thematic analysis. Results: The study found that there was good agreement between self-defined and clinically defined full recovery from AN. People who were clinically defined as fully recovered scored significantly higher on measures of personal recovery compared to those defined as not recovered, and there were strong positive associations between lower behavioural and cognitive symptoms, and personal recovery. However, there was a weaker relationship between personal recovery measures and BMI. Finally, qualitative data indicated that most participants felt that the clinical criteria were not a sufficient definition of recovery. Whilst participants suggested potential additional criteria, and raised ideas around how these might relate to traditional symptom-based approaches, the qualitative analysis also highlighted concerns around how far a universal recovery criteria-based approach can capture individual experience. Conclusions: Implications for the development of future universal clinical criteria for recovery from AN are discussed, including how a clinical approach can best be combined with personal understandings of recovery.

Published
2023

22. Symptoms as a Predictor of the Placebo-Controlled Efficacy of PCI in Stable Coronary Artery Disease

Author

Rajkumar, Christopher, Foley, Michael, Ahmed-Jushuf, Fiyyaz, Simader, Florentina, Ganesananthan, Sashiananthan, Wang, Danqi, Mohsin, Muhammad, Pathimagaraj, Rachel, Macierzanka, Krzysztof, Petraco, Ricardo, Khamis, Ramzi, Cole, Graham, Howard, James, Mayet, Jamil, Francis, Darrel, Kokhar, Arif, Gohar, Aisha, Lampadakis, Ioannis, Seligman, Henry, Kaura, Amit, Nijjer, Sukhjinder, Sen, Sayan, Ramrakha, Punit, Kaprielian, Raffi, Malik, Iqbal, Khan, Masood, Sethi, Amarjit, Foale, Rodney, Keeble, Thomas, Tang, Kare, Davies, John, Gamma, Reto, Clesham, Gerald, Dungu, Jason, Kabir, Alamgir, Nazri, Shah Mohd, O’Kane, Peter, Hinton, Jonathan, Din, Jehangir, Nowbar, Alexandra, Kotecha, Tushar, Haworth, Peter, Spratt, James, Williams, Rupert, Cosgrove, Claudia, Lim, Pitt, Routledge, Helen, Mughal, Lal, Trevelyan, Jasper, Sinha, Manas, Curzen, Nick, Wilkinson, James, Sirohi, Rohit, Calver, Alison, Rawlins, John, Jabbour, Richard, Ruparelia, Neil, Sehmi, Joban, Kinnaird, Tim, Abdul, Fairoz, Panoulas, Vasileios, Collier, David, Thornton, George, Sohaib, Afzal, Al-Lamee, Rasha K., Simader, Florentina A., Rajkumar, Christopher A., Foley, Michael J., Chotai, Shayna, Bual, Nina, Khokhar, Arif, Pathimagaraj, Rachel H., Davies, John R., Keeble, Tom R., O’Kane, Peter D., Spratt, James C., Nijjer, Sukhjinder S., Howard, James P., Harrell, Frank E., Jr., Francis, Darrel P., and Shun-Shin, Matthew J.

Published
2024
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25. Gleason Grade Group 4 prostate biopsy with no cancer seen on final pathology in the magnetic resonance imaging and Prostate Specific Membrane Antigen‐Positron Emission Tomography era

Author

Nikhile Mookerji, Rohan Mittal, Amaris Hui, Tyler Pfanner, Stacey Broomfield, Luke Dean, Benjamin Adam, Christopher Fung, Alexander Tamm, and Adam Kinnaird

Subjects
multiparametric MRI, prostate cancer, PSMA PET, vanishing cancer, Diseases of the genitourinary system. Urology, RC870-923
Abstract

Introduction The absence of prostate cancer on final surgical pathology after biopsy‐proven prostate cancer is a rare finding. Case presentation Case of pT0 prostate cancer following Gleason Grade Group 4 in 1 out of 12 cores from a transrectal ultrasound‐guided biopsy in a man who underwent both magnetic resonance imaging and 18F‐PSMA‐1007 Positron Emission Tomography prior to radical prostatectomy. Conclusion pT0 prostate cancer is rare. The use of novel imaging modalities may help in the workup of prostate cancer.

Published
2023
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26. The Straw Tracking Detector for the Fermilab Muon $g-2$ Experiment

Author

King, B. T., Albahri, T., Al-Kilani, S., Allspach, D., Beckner, D., Behnke, A., Bowcock, T. J. V., Boyden, D., Carey, R. M., Carroll, J., Casey, B. C. K., Charity, S., Chislett, R., Eads, M., Epps, A., Foster, S. B., Gastler, D., Grant, S., Halewood-Leagas, T., Hardin, K., Hazen, E., Hesketh, G., Hollywood, D. J., Jones, T., Kenziora, C., Keshavarzi, A., Kiburg, M., Kinnaird, N., Kintner, J., Lancaster, M., Lucà, A., Lukicov, G., Luo, G., Mapar, L., Maxfield, S. J., Mott, J., Motuk, E., Mourato, H., Pohlman, N., Price, J., Roberts, B. L., Sathyan, D., Shenk, M., Sim, D., Stuttard, T., Sweetmore, G., Thayer, G., Thomson, K., Turner, W., Vasilkova, D., Velho, J., Voirin, E., Walton, T., Warren, M., Welty-Reiger, L., Whitley, M., and Wormald, M.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

The Muon $g-2$ Experiment at Fermilab uses a gaseous straw tracking detector to make detailed measurements of the stored muon beam profile, which are essential for the experiment to achieve its uncertainty goals. Positrons from muon decays spiral inward and pass through the tracking detector before striking an electromagnetic calorimeter. The tracking detector is therefore located inside the vacuum chamber in a region where the magnetic field is large and non-uniform. As such, the tracking detector must have a low leak rate to maintain a high-quality vacuum, must be non-magnetic so as not to perturb the magnetic field and, to minimize energy loss, must have a low radiation length. The performance of the tracking detector has met or surpassed the design requirements, with adequate electronic noise levels, an average straw hit resolution of $(110 \pm 20) \,\mu$m, a detection efficiency of 97% or higher, and no performance degradation or signs of aging. The tracking detector's measurements result in an otherwise unachievable understanding of the muon's beam motion, particularly at early times in the experiment's measurement period when there are a significantly greater number of muons decaying. This is vital to the statistical power of the experiment, as well as facilitating the precise extraction of several systematic corrections and uncertainties. This paper describes the design, construction, testing, commissioning, and performance of the tracking detector., Comment: 37 pages, 27 figures

Published
2021
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27. Magnetic Resonance Imaging-Guided Biopsy in Active Surveillance of Prostate Cancer.

Author

Kinnaird, Adam, Yerram, Nitin, OConnor, Luke, Brisbane, Wayne, Sharma, Vidit, Chuang, Ryan, Jayadevan, Rajiv, Ahdoot, Michael, Daneshvar, Michael, Priester, Alan, Delfin, Merdie, Tran, Elizabeth, Barsa, Danielle, Sisk, Anthony, Reiter, Robert, Felker, Ely, Raman, Steve, Kwan, Lorna, Choyke, Peter, Merino, Maria, Wood, Bradford, Turkbey, Baris, Pinto, Peter, and Marks, Leonard

Subjects
image-guided biopsy, magnetic resonance imaging, observation, prostatic neoplasms, Aged, Follow-Up Studies, Humans, Image-Guided Biopsy, Magnetic Resonance Imaging, Male, Middle Aged, Neoplasm Grading, Prospective Studies, Prostatectomy, Prostatic Neoplasms, Risk Factors, Watchful Waiting
Abstract

PURPOSE: The underlying premise of prostate cancer active surveillance (AS) is that cancers likely to metastasize will be recognized and eliminated before cancer-related disease can ensue. Our study was designed to determine the prostate cancer upgrading rate when biopsy guided by magnetic resonance imaging (MRGBx) is used before entry and during AS. MATERIALS AND METHODS: The cohort included 519 men with low- or intermediate-risk prostate cancer who enrolled in prospective studies (NCT00949819 and NCT00102544) between February 2008 and February 2020. Subjects were preliminarily diagnosed with Gleason Grade Group (GG) 1 cancer; AS began when subsequent MRGBx confirmed GG1 or GG2. Participants underwent confirmatory MRGBx (targeted and systematic) followed by surveillance MRGBx approximately every 12 to 24 months. The primary outcome was tumor upgrading to ≥GG3. RESULTS: Upgrading to ≥GG3 was found in 92 men after a median followup of 4.8 years (IQR 3.1-6.5) after confirmatory MRGBx. Upgrade-free probability after 5 years was 0.85 (95% CI 0.81-0.88). Cancer detected in a magnetic resonance imaging lesion at confirmatory MRGBx increased risk of subsequent upgrading during AS (HR 2.8; 95% CI 1.3-6.0), as did presence of GG2 (HR 2.9; 95% CI 1.1-8.2) In men who upgraded ≥GG3 during AS, upgrading was detected by targeted cores only in 27%, systematic cores only in 25% and both in 47%. In 63 men undergoing prostatectomy, upgrading from MRGBx was found in only 5 (8%). CONCLUSIONS: When AS begins and follows with MRGBx (targeted and systematic), upgrading rate (≥GG3) is greater when tumor is initially present within a magnetic resonance imaging lesion or when pathology is GG2 than when these features are absent.

Published
2022

29. Clinical Characterization of Patients Diagnosed with Prostate Cancer and Undergoing Conservative Management: A PIONEER Analysis Based on Big Data

Author

Gandaglia, Giorgio, Pellegrino, Francesco, Golozar, Asieh, De Meulder, Bertrand, Abbott, Thomas, Achtman, Ariel, Imran Omar, Muhammad, Alshammari, Thamir, Areia, Carlos, Asiimwe, Alex, Beyer, Katharina, Bjartell, Anders, Campi, Riccardo, Cornford, Philip, Falconer, Thomas, Feng, Qi, Gong, Mengchun, Herrera, Ronald, Hughes, Nigel, Hulsen, Tim, Kinnaird, Adam, Lai, Lana Y.H., Maresca, Gianluca, Mottet, Nicolas, Oja, Marek, Prinsen, Peter, Reich, Christian, Remmers, Sebastiaan, Roobol, Monique J., Sakalis, Vasileios, Seager, Sarah, Smith, Emma J., Snijder, Robert, Steinbeisser, Carl, Thurin, Nicolas H., Hijazy, Ayman, van Bochove, Kees, Van den Bergh, Roderick C.N., Van Hemelrijck, Mieke, Willemse, Peter-Paul, Williams, Andrew E., Zounemat Kermani, Nazanin, Evans-Axelsson, Susan, Briganti, Alberto, and N'Dow, James

Published
2024
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32. A prostate cancer risk calculator (PCRC-MRI): Use of clinical and magnetic resonance imaging data to predict biopsy outcome in North American men

Author

Kinnaird, Adam, Brisbane, Wayne, Kwan, Lorna, Priester, Alan, Chuang, Ryan, Barsa, Danielle E, Delfin, Merdie, Sisk, Anthony, Margolis, Daniel, Felker, Ely, Hu, Jim, and Marks, Leonard S

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Prostate Cancer, Cancer, Prevention, Clinical Research, Biomedical Imaging, Urologic Diseases, Aging, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, 4.2 Evaluation of markers and technologies, Urology & Nephrology, Clinical sciences, Oncology and carcinogenesis
Abstract

IntroductionA functional tool to optimize patient selection for magnetic resonance imaging (MRI)-guided prostate biopsy (MRGB) is an unmet clinical need. We sought to develop a prostate cancer risk calculator (PCRC-MRI) that combines MRI and clinical characteristics to aid decision-making for MRGB in North American men.MethodsTwo prospective registries containing 2354 consecutive men undergoing MRGB (September 2009 to April 2019) were analyzed. Patients were randomized into five groups, with one group randomly assigned to be the validation cohort against the other four groups as the discovery cohort. The primary outcome was detection of clinically significant prostate cancer (csPCa) defined as Gleason grade group ≥2. Variables included age, ethnicity, digital rectal exam (DRE), prior biopsy, prostate-specific antigen (PSA), prostate volume, PSA density, and MRI score. Odds ratios (OR) were calculated from multivariate logistic regression comparing two models: one with clinical variables only (clinical) against a second combining clinical variables with MRI data (clinical+MRI).ResultscsPCa was present in 942 (40%) of the 2354 men available for study. The positive and negative predictive values for csPCa in the clinical+MRI model were 57% and 89%, respectively. The area under the curve of the clinical+MRI model was superior to the clinical model in discovery (0.843 vs. 0.707, p

Published
2022

33. Measurement of the anomalous precession frequency of the muon in the Fermilab Muon g-2 experiment

Author

Albahri, T., Anastasi, A., Anisenkov, A., Badgley, K., Baeßler, S., Bailey, I., Baranov, V. A., Barlas-Yucel, E., Barrett, T., Basti, A., Bedeschi, F., Berz, M., Bhattacharya, M., Binney, H. P., Bloom, P., Bono, J., Bottalico, E., Bowcock, T., Cantatore, G., Carey, R. M., Casey, B. C. K., Cauz, D., Chakraborty, R., Chang, S. P., Chapelain, A., Charity, S., Chislett, R., Choi, J., Chu, Z., Chupp, T. E., Corrodi, S., Cotrozzi, L., Crnkovic, J. D., Dabagov, S., Debevec, P. T., Di Falco, S., Di Meo, P., Di Sciascio, G., Di Stefano, R., Driutti, A., Duginov, V. N., Eads, M., Esquivel, J., Farooq, M., Fatemi, R., Ferrari, C., Fertl, M., Fienberg, A. T., Fioretti, A., Flay, D., Frlež, E., Froemming, N. S., Fry, J., Gabbanini, C., Galati, M. D., Ganguly, S., Garcia, A., George, J., Gibbons, L. K., Gioiosa, A., Giovanetti, K. L., Girotti, P., Gohn, W., Gorringe, T., Grange, J., Grant, S., Gray, F., Haciomeroglu, S., Halewood-Leagas, T., Hampai, D., Han, F., Hempstead, J., Herrod, A. T., Hertzog, D. W., Hesketh, G., Hibbert, A., Hodge, Z., Holzbauer, J. L., Hong, K. W., Hong, R., Iacovacci, M., Incagli, M., Kammel, P., Kargiantoulakis, M., Karuza, M., Kaspar, J., Kawall, D., Kelton, L., Keshavarzi, A., Kessler, D., Khaw, K. S., Khechadoorian, Z., Khomutov, N. V., Kiburg, B., Kiburg, M., Kim, O., Kim, Y. I., King, B., Kinnaird, N., Kraegeloh, E., Kuchibhotla, A., Kuchinskiy, N. A., Labe, K. R., LaBounty, J., Lancaster, M., Lee, M. J., Lee, S., Leo, S., Li, B., Li, D., Li, L., Logashenko, I., Campos, A. Lorente, Lucà, A., Lukicov, G., Lusiani, A., Lyon, A. L., MacCoy, B., Madrak, R., Makino, K., Marignetti, F., Mastroianni, S., Miller, J. P., Miozzi, S., Morse, W. M., Mott, J., Nath, A., Nguyen, H., Osofsky, R., Park, S., Pauletta, G., Piacentino, G. M., Pilato, R. N., Pitts, K. T., Plaster, B., Počanić, D., Pohlman, N., Polly, C. C., Price, J., Quinn, B., Raha, N., Ramachandran, S., Ramberg, E., Ritchie, J. L., Roberts, B. L., Rubin, D. L., Santi, L., Schlesier, C., Schreckenberger, A., Semertzidis, Y. K., Shemyakin, D., Smith, M. W., Sorbara, M., Stöckinger, D., Stapleton, J., Stoughton, C., Stratakis, D., Stuttard, T., Swanson, H. E., Sweetmore, G., Sweigart, D. A., Syphers, M. J., Tarazona, D. A., Teubner, T., Tewsley-Booth, A. E., Thomson, K., Tishchenko, V., Tran, N. H., Turner, W., Valetov, E., Vasilkova, D., Venanzoni, G., Walton, T., Weisskopf, A., Welty-Rieger, L., Winter, P., Wolski, A., and Wu, W.

Subjects
High Energy Physics - Experiment, Nuclear Experiment
Abstract

The Muon g-2 Experiment at Fermi National Accelerator Laboratory (FNAL) has measured the muon anomalous precession frequency $\omega_a$ to an uncertainty of 434 parts per billion (ppb), statistical, and 56 ppb, systematic, with data collected in four storage ring configurations during its first physics run in 2018. When combined with a precision measurement of the magnetic field of the experiment's muon storage ring, the precession frequency measurement determines a muon magnetic anomaly of $a_{\mu}({\rm FNAL}) = 116\,592\,040(54) \times 10^{-11}$ (0.46 ppm). This article describes the multiple techniques employed in the reconstruction, analysis and fitting of the data to measure the precession frequency. It also presents the averaging of the results from the eleven separate determinations of \omega_a, and the systematic uncertainties on the result., Comment: 29 pages, 19 figures. Published in Physical Review D

Published
2021
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34. Magnetic Field Measurement and Analysis for the Muon g-2 Experiment at Fermilab

Author

Albahri, T., Anastasi, A., Badgley, K., Baeßler, S., Bailey, I., Baranov, V. A., Barlas-Yucel, E., Barrett, T., Bedeschi, F., Berz, M., Bhattacharya, M., Binney, H. P., Bloom, P., Bono, J., Bottalico, E., Bowcock, T., Cantatore, G., Carey, R. M., Casey, B. C. K., Cauz, D., Chakraborty, R., Chang, S. P., Chapelain, A., Charity, S., Chislett, R., Choi, J., Chu, Z., Chupp, T. E., Conway, A., Corrodi, S., Cotrozzi, L., Crnkovic, J. D., Dabagov, S., Debevec, P. T., Di Falco, S., Di Meo, P., Di Sciascio, G., Di Stefano, R., Driutti, A., Duginov, V. N., Eads, M., Esquivel, J., Farooq, M., Fatemi, R., Ferrari, C., Fertl, M., Fienberg, A. T., Fioretti, A., Flay, D., Froemming, N. S., Gabbanini, C., Galati, M. D., Ganguly, S., Garcia, A., George, J., Gibbons, L. K., Gioiosa, A., Giovanetti, K. L., Girotti, P., Gohn, W., Gorringe, T., Grange, J., Grant, S., Gray, F., Haciomeroglu, S., Halewood-Leagas, T., Hampai, D., Han, F., Hempstead, J., Herrod, A. T., Hertzog, D. W., Hesketh, G., Hibbert, A., Hodge, Z., Holzbauer, J. L., Hong, K. W., Hong, R., Iacovacci, M., Incagli, M., Kammel, P., Kargiantoulakis, M., Karuza, M., Kaspar, J., Kawall, D., Kelton, L., Keshavarzi, A., Kessler, D., Khaw, K. S., Khechadoorian, Z., Khomutov, N. V., Kiburg, B., Kiburg, M., Kim, O., Kim, Y. I., King, B., Kinnaird, N., Kraegeloh, E., Kuchinskiy, N. A., Labe, K. R., LaBounty, J., Lancaster, M., Lee, M. J., Lee, S., Li, B., Li, D., Li, L., Logashenko, I., Campos, A. Lorente, Lucà, A., Lukicov, G., Lusiani, A., Lyon, A. L., MacCoy, B., Madrak, R., Makino, K., Marignetti, F., Mastroianni, S., Miller, J. P., Miozzi, S., Morse, W. M., Mott, J., Nath, A., Nguyen, H., Osofsky, R., Park, S., Pauletta, G., Piacentino, G. M., Pilato, R. N., Pitts, K. T., Plaster, B., Počanić, D., Pohlman, N., Polly, C. C., Price, J., Quinn, B., Raha, N., Ramachandran, S., Ramberg, E., Ritchie, J. L., Roberts, B. L., Rubin, D. L., Santi, L., Schlesier, C., Schreckenberger, A., Semertzidis, Y. K., Shemyakin, D., Smith, M. W., Sorbara, M., Stöckinger, D., Stapleton, J., Stoughton, C., Stratakis, D., Stuttard, T., Swanson, H. E., Sweetmore, G., Sweigart, D. A., Syphers, M. J., Tarazona, D. A., Teubner, T., Tewsley-Booth, A. E., Thomson, K., Tishchenko, V., Tran, N. H., Turner, W., Valetov, E., Vasilkova, D., Venanzoni, G., Walton, T., Weisskopf, A., Welty-Rieger, L., Winter, P., Wolski, A., and Wu, W.

Subjects
High Energy Physics - Experiment, Nuclear Experiment
Abstract

The Fermi National Accelerator Laboratory has measured the anomalous precession frequency $a^{}_\mu = (g^{}_\mu-2)/2$ of the muon to a combined precision of 0.46 parts per million with data collected during its first physics run in 2018. This paper documents the measurement of the magnetic field in the muon storage ring. The magnetic field is monitored by nuclear magnetic resonance systems and calibrated in terms of the equivalent proton spin precession frequency in a spherical water sample at 34.7$^\circ$C. The measured field is weighted by the muon distribution resulting in $\tilde{\omega}'^{}_p$, the denominator in the ratio $\omega^{}_a$/$\tilde{\omega}'^{}_p$ that together with known fundamental constants yields $a^{}_\mu$. The reported uncertainty on $\tilde{\omega}'^{}_p$ for the Run-1 data set is 114 ppb consisting of uncertainty contributions from frequency extraction, calibration, mapping, tracking, and averaging of 56 ppb, and contributions from fast transient fields of 99 ppb., Comment: Added one citation and corrected missing normalization in Eqs (35) and (36)

Published
2021
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35. Measurement of the Positive Muon Anomalous Magnetic Moment to 0.46 ppm

Author

Abi, B., Albahri, T., Al-Kilani, S., Allspach, D., Alonzi, L. P., Anastasi, A., Anisenkov, A., Azfar, F., Badgley, K., Baeßler, S., Bailey, I., Baranov, V. A., Barlas-Yucel, E., Barrett, T., Barzi, E., Basti, A., Bedeschi, F., Behnke, A., Berz, M., Bhattacharya, M., Binney, H. P., Bjorkquist, R., Bloom, P., Bono, J., Bottalico, E., Bowcock, T., Boyden, D., Cantatore, G., Carey, R. M., Carroll, J., Casey, B. C. K., Cauz, D., Ceravolo, S., Chakraborty, R., Chang, S. P., Chapelain, A., Chappa, S., Charity, S., Chislett, R., Choi, J., Chu, Z., Chupp, T. E., Convery, M. E., Conway, A., Corradi, G., Corrodi, S., Cotrozzi, L., Crnkovic, J. D., Dabagov, S., De Lurgio, P. M., Debevec, P. T., Di Falco, S., Di Meo, P., Di Sciascio, G., Di Stefano, R., Drendel, B., Driutti, A., Duginov, V. N., Eads, M., Eggert, N., Epps, A., Esquivel, J., Farooq, M., Fatemi, R., Ferrari, C., Fertl, M., Fiedler, A., Fienberg, A. T., Fioretti, A., Flay, D., Foster, S. B., Friedsam, H., Frlež, E., Froemming, N. S., Fry, J., Fu, C., Gabbanini, C., Galati, M. D., Ganguly, S., Garcia, A., Gastler, D. E., George, J., Gibbons, L. K., Gioiosa, A., Giovanetti, K. L., Girotti, P., Gohn, W., Gorringe, T., Grange, J., Grant, S., Gray, F., Haciomeroglu, S., Hahn, D., Halewood-Leagas, T., Hampai, D., Han, F., Hazen, E., Hempstead, J., Henry, S., Herrod, A. T., Hertzog, D. W., Hesketh, G., Hibbert, A., Hodge, Z., Holzbauer, J. L., Hong, K. W., Hong, R., Iacovacci, M., Incagli, M., Johnstone, C., Johnstone, J. A., Kammel, P., Kargiantoulakis, M., Karuza, M., Kaspar, J., Kawall, D., Kelton, L., Keshavarzi, A., Kessler, D., Khaw, K. S., Khechadoorian, Z., Khomutov, N. V., Kiburg, B., Kiburg, M., Kim, O., Kim, S. C., Kim, Y. I., King, B., Kinnaird, N., Korostelev, M., Kourbanis, I., Kraegeloh, E., Krylov, V. A., Kuchibhotla, A., Kuchinskiy, N. A., Labe, K. R., LaBounty, J., Lancaster, M., Lee, M. J., Lee, S., Leo, S., Li, B., Li, D., Li, L., Logashenko, I., Campos, A. Lorente, Lucà, A., Lukicov, G., Luo, G., Lusiani, A., Lyon, A. L., MacCoy, B., Madrak, R., Makino, K., Marignetti, F., Mastroianni, S., Maxfield, S., McEvoy, M., Merritt, W., Mikhailichenko, A. A., Miller, J. P., Miozzi, S., Morgan, J. P., Morse, W. M., Mott, J., Motuk, E., Nath, A., Newton, D., Nguyen, H., Oberling, M., Osofsky, R., Ostiguy, J. -F., Park, S., Pauletta, G., Piacentino, G. M., Pilato, R. N., Pitts, K. T., Plaster, B., Počanić, D., Pohlman, N., Polly, C. C., Popovic, M., Price, J., Quinn, B., Raha, N., Ramachandran, S., Ramberg, E., Rider, N. T., Ritchie, J. L., Roberts, B. L., Rubin, D. L., Santi, L., Sathyan, D., Schellman, H., Schlesier, C., Schreckenberger, A., Semertzidis, Y. K., Shatunov, Y. M., Shemyakin, D., Shenk, M., Sim, D., Smith, M. W., Smith, A., Soha, A. K., Sorbara, M., Stöckinger, D., Stapleton, J., Still, D., Stoughton, C., Stratakis, D., Strohman, C., Stuttard, T., Swanson, H. E., Sweetmore, G., Sweigart, D. A., Syphers, M. J., Tarazona, D. A., Teubner, T., Tewsley-Booth, A. E., Thomson, K., Tishchenko, V., Tran, N. H., Turner, W., Valetov, E., Vasilkova, D., Venanzoni, G., Volnykh, V. P., Walton, T., Warren, M., Weisskopf, A., Welty-Rieger, L., Whitley, M., Winter, P., Wolski, A., Wormald, M., Wu, W., and Yoshikawa, C.

Subjects
High Energy Physics - Experiment, Nuclear Experiment
Abstract

We present the first results of the Fermilab Muon g-2 Experiment for the positive muon magnetic anomaly $a_\mu \equiv (g_\mu-2)/2$. The anomaly is determined from the precision measurements of two angular frequencies. Intensity variation of high-energy positrons from muon decays directly encodes the difference frequency $\omega_a$ between the spin-precession and cyclotron frequencies for polarized muons in a magnetic storage ring. The storage ring magnetic field is measured using nuclear magnetic resonance probes calibrated in terms of the equivalent proton spin precession frequency ${\tilde{\omega}'^{}_p}$ in a spherical water sample at 34.7$^{\circ}$C. The ratio $\omega_a / {\tilde{\omega}'^{}_p}$, together with known fundamental constants, determines $a_\mu({\rm FNAL}) = 116\,592\,040(54)\times 10^{-11}$ (0.46\,ppm). The result is 3.3 standard deviations greater than the standard model prediction and is in excellent agreement with the previous Brookhaven National Laboratory (BNL) E821 measurement. After combination with previous measurements of both $\mu^+$ and $\mu^-$, the new experimental average of $a_\mu({\rm Exp}) = 116\,592\,061(41)\times 10^{-11}$ (0.35\,ppm) increases the tension between experiment and theory to 4.2 standard deviations, Comment: 10 pages; 4 figures

Published
2021
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36. Beam dynamics corrections to the Run-1 measurement of the muon anomalous magnetic moment at Fermilab

Author

Albahri, T., Anastasi, A., Badgley, K., Baeßler, S., Bailey, I., Baranov, V. A., Barlas-Yucel, E., Barrett, T., Bedeschi, F., Berz, M., Bhattacharya, M., Binney, H. P., Bloom, P., Bono, J., Bottalico, E., Bowcock, T., Cantatore, G., Carey, R. M., Casey, B. C. K., Cauz, D., Chakraborty, R., Chang, S. P., Chapelain, A., Charity, S., Chislett, R., Choi, J., Chu, Z., Chupp, T. E., Corrodi, S., Cotrozzi, L., Crnkovic, J. D., Dabagov, S., Debevec, P. T., Di Falco, S., Di Meo, P., Di Sciascio, G., Di Stefano, R., Driutti, A., Duginov, V. N., Eads, M., Esquivel, J., Farooq, M., Fatemi, R., Ferrari, C., Fertl, M., Fiedler, A., Fienberg, A. T., Fioretti, A., Flay, D., Frlež, E., Froemming, N. S., Fry, J., Gabbanini, C., Galati, M. D., Ganguly, S., Garcia, A., George, J., Gibbons, L. K., Gioiosa, A., Giovanetti, K. L., Girotti, P., Gohn, W., Gorringe, T., Grange, J., Grant, S., Gray, F., Haciomeroglu, S., Halewood-Leagas, T., Hampai, D., Han, F., Hempstead, J., Herrod, A. T., Hertzog, D. W., Hesketh, G., Hibbert, A., Hodge, Z., Holzbauer, J. L., Hong, K. W., Hong, R., Iacovacci, M., Incagli, M., Kammel, P., Kargiantoulakis, M., Karuza, M., Kaspar, J., Kawall, D., Kelton, L., Keshavarzi, A., Kessler, D., Khaw, K. S., Khechadoorian, Z., Khomutov, N. V., Kiburg, B., Kiburg, M., Kim, O., Kim, Y. I., King, B., Kinnaird, N., Korostelev, M., Kraegeloh, E., Kuchinskiy, N. A., Labe, K. R., LaBounty, J., Lancaster, M., Lee, M. J., Lee, S., Li, B., Li, D., Li, L., Logashenko, I., Campos, A. Lorente, Lucà, A., Lukicov, G., Lusiani, A., Lyon, A. L., MacCoy, B., Madrak, R., Makino, K., Marignetti, F., Mastroianni, S., Miller, J. P., Miozzi, S., Morse, W. M., Mott, J., Nath, A., Newton, D., Nguyen, H., Osofsky, R., Park, S., Pauletta, G., Piacentino, G. M., Pilato, R. N., Pitts, K. T., Plaster, B., Počanić, D., Pohlman, N., Polly, C. C., Price, J., Quinn, B., Raha, N., Ramachandran, S., Ramberg, E., Ritchie, J. L., Roberts, B. L., Rubin, D. L., Santi, L., Sathyan, D., Schlesier, C., Schreckenberger, A., Semertzidis, Y. K., Smith, M. W., Sorbara, M., Stöckinger, D., Stapleton, J., Stoughton, C., Stratakis, D., Stuttard, T., Swanson, H. E., Sweetmore, G., Sweigart, D. A., Syphers, M. J., Tarazona, D. A., Teubner, T., Tewsley-Booth, A. E., Thomson, K., Tishchenko, V., Tran, N. H., Turner, W., Valetov, E., Vasilkova, D., Venanzoni, G., Walton, T., Weisskopf, A., Welty-Rieger, L., Winter, P., Wolski, A., and Wu, W.

Subjects
Physics - Accelerator Physics, High Energy Physics - Experiment
Abstract

This paper presents the beam dynamics systematic corrections and their uncertainties for the Run-1 data set of the Fermilab Muon g-2 Experiment. Two corrections to the measured muon precession frequency $\omega_a^m$ are associated with well-known effects owing to the use of electrostatic quadrupole (ESQ) vertical focusing in the storage ring. An average vertically oriented motional magnetic field is felt by relativistic muons passing transversely through the radial electric field components created by the ESQ system. The correction depends on the stored momentum distribution and the tunes of the ring, which has relatively weak vertical focusing. Vertical betatron motions imply that the muons do not orbit the ring in a plane exactly orthogonal to the vertical magnetic field direction. A correction is necessary to account for an average pitch angle associated with their trajectories. A third small correction is necessary because muons that escape the ring during the storage time are slightly biased in initial spin phase compared to the parent distribution. Finally, because two high-voltage resistors in the ESQ network had longer than designed RC time constants, the vertical and horizontal centroids and envelopes of the stored muon beam drifted slightly, but coherently, during each storage ring fill. This led to the discovery of an important phase-acceptance relationship that requires a correction. The sum of the corrections to $\omega_a^m$ is 0.50 $\pm$ 0.09 ppm; the uncertainty is small compared to the 0.43 ppm statistical precision of $\omega_a^m$., Comment: 35 pages, 29 figures. Accepted by Phys. Rev. Accel. Beams

Published
2021
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37. Clinical analysis of EV‐Fingerprint to predict grade group 3 and above prostate cancer and avoid prostate biopsy

Author

Adrian Fairey, Robert J. Paproski, Desmond Pink, Deborah L. Sosnowski, Catalina Vasquez, Bryan Donnelly, Eric Hyndman, Armen Aprikian, Adam Kinnaird, Perrin H. Beatty, and John D. Lewis

Subjects
biomarkers, clinical cancer research, prostate cancer, screening, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background There is an unmet clinical need for minimally invasive diagnostic tests to improve the detection of grade group (GG) ≥3 prostate cancer relative to prostate antigen‐specific risk calculators. We determined the accuracy of the blood‐based extracellular vesicle (EV) biomarker assay (EV Fingerprint test) at the point of a prostate biopsy decision to predict GG ≥3 from GG ≤2 and avoid unnecessary biopsies. Methods This study analyzed 415 men referred to urology clinics and scheduled for a prostate biopsy, were recruited to the APCaRI 01 prospective cohort study. The EV machine learning analysis platform was used to generate predictive EV models from microflow data. Logistic regression was then used to analyze the combined EV models and patient clinical data and generate the patients' risk score for GG ≥3 prostate cancer. Results The EV‐Fingerprint test was evaluated using the area under the curve (AUC) in discrimination of GG ≥3 from GG ≤2 and benign disease on initial biopsy. EV‐Fingerprint identified GG ≥3 cancer patients with high accuracy (0.81 AUC) at 95% sensitivity and 97% negative predictive value. Using a 7.85% probability cutoff, 95% of men with GG ≥3 would have been recommended a biopsy while avoiding 144 unnecessary biopsies (35%) and missing four GG ≥3 cancers (5%). Conversely, a 5% cutoff would have avoided 31 unnecessary biopsies (7%), missing no GG ≥3 cancers (0%). Conclusions EV‐Fingerprint accurately predicted GG ≥3 prostate cancer and would have significantly reduced unnecessary prostate biopsies.

Published
2023
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39. Optimizing Spatial Biopsy Sampling for the Detection of Prostate Cancer

Author

Raman, Alex G, Sarma, Karthik V, Raman, Steven S, Priester, Alan M, Mirak, Sohrab Afshari, Riskin-Jones, Hannah H, Dhinagar, Nikhil, Speier, William, Felker, Ely, Sisk, Anthony E, Lu, David, Kinnaird, Adam, Reiter, Robert E, Marks, Leonard S, and Arnold, Corey W

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Urologic Diseases, Prostate Cancer, Prevention, Biomedical Imaging, Clinical Research, Cancer, Aged, Biopsy, Large-Core Needle, Datasets as Topic, Feasibility Studies, Humans, Image-Guided Biopsy, Magnetic Resonance Imaging, Interventional, Male, Middle Aged, Multimodal Imaging, Multiparametric Magnetic Resonance Imaging, Neoplasm Grading, Prostate, Prostatectomy, Prostatic Neoplasms, Retrospective Studies, Spatial Analysis, Ultrasonography, Interventional, prostatic neoplasms, image-guided biopsy, biopsy, adverse effects, ultrasonography, interventional, magnetic resonance imaging
Abstract

PurposeThe appropriate number of systematic biopsy cores to retrieve during magnetic resonance imaging (MRI)-targeted prostate biopsy is not well defined. We aimed to demonstrate a biopsy sampling approach that reduces required core count while maintaining diagnostic performance.Materials and methodsWe collected data from a cohort of 971 men who underwent MRI-ultrasound fusion targeted biopsy for suspected prostate cancer. A regional targeted biopsy (RTB) was evaluated retrospectively; only cores within 2 cm of the margin of a radiologist-defined region of interest were considered part of the RTB. We compared detection rates for clinically significant prostate cancer (csPCa) and cancer upgrading rate on final whole mount pathology after prostatectomy between RTB, combined, MRI-targeted, and systematic biopsy.ResultsA total of 16,459 total cores from 971 men were included in the study data sets, of which 1,535 (9%) contained csPCa. The csPCa detection rates for systematic, MRI-targeted, combined, and RTB were 27.0% (262/971), 38.3% (372/971), 44.8% (435/971), and 44.0% (427/971), respectively. Combined biopsy detected significantly more csPCa than systematic and MRI-targeted biopsy (p

Published
2021

40. Antithrombotic Strategy in Secondary Prevention for High-Risk Patients with Previous Acute Coronary Syndrome: Overlap between the PEGASUS Eligibility and the COMPASS Eligibility in a Large Multicenter Registry

Author

Millesimo, Michele, Elia, Edoardo, Marengo, Giorgio, De Filippo, Ovidio, Raposeiras-Roubin, Sergio, Wańha, Wojciech, Abu-Assi, Emad, Kinnaird, Tim, Ariza-Solé, Albert, Liebetrau, Christoph, Manzano-Fernández, Sergio, Iannaccone, Mario, Henriques, Jose Paulo Simao, Templin, Christian, Wilton, Stephen B., Velicki, Lazar, Xanthopoulou, Ioanna, Correia, Luis, Cerrato, Enrico, Rognoni, Andrea, Nuñez-Gil, Iván, Song, Xiantao, Kawaji, Tetsuma, Quadri, Giorgio, Huczek, Zenon, Paz, Rafael Cobas, Juanatey, José Ramón González, Nie, Shao-Ping, Kawashiri, Masa-aki, Dominguez-Rodriguez, Alberto, Conrotto, Federico, D’Ascenzo, Fabrizio, and De Ferrari, Gaetano Maria

Published
2023
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41. Cryotherapy for partial gland ablation of prostate cancer: Oncologic and safety outcomes

Author

Mamdouh N. Aker, Wayne G. Brisbane, Lorna Kwan, Samantha Gonzalez, Alan M. Priester, Adam Kinnaird, Merdie K. Delfin, Ely Felker, Anthony E. Sisk, David Kuppermann, and Leonard S. Marks

Subjects
Prostate cancer, cryotherapy, focal therapy, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Partial gland ablation (PGA) is a new option for treatment of prostate cancer (PCa). Cryotherapy, an early method of PGA, has had favorable evaluations, but few studies have employed a strict protocol using biopsy endpoints in men with clinically significant prostate cancer (csPCa). Methods 143 men with unilateral csPCa were enrolled in a prospective, observational trial of outpatient PGA‐cryotherapy. Treatment was a 2‐cycle freeze of the affected prostate part. Participants were evaluated with MRI‐guided biopsy (MRGB) at baseline and at 6 months and 18 months after treatment. Absence of csPCa upon MRGB was the primary endpoint; quality‐of‐life at baseline and at 6 months after treatment was assessed by EPIC‐CP questionnaires in the domains of urinary and sexual function. Results Of the 143 participants, 136 (95%) completed MRGB at 6 months after treatment. In 103/136 (76%), the biopsy revealed no csPCa. Of the 103, 71 subsequently had an 18‐month comprehensive biopsy; of the 71 with 18‐month biopsies, 46 (65%) were found to have no csPCa. MRI lesions became undetectable in 96/130 (74%); declines in median serum PSA levels (6.9 to 2.5 ng/mL), PSA density (0.15 to 0.07), and prostate volume (42 to 34cc) were observed (all p

Published
2023
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42. Integrating data science ethics into an undergraduate major: A case study

Author

Baumer, Benjamin S., Garcia, Randi L., Kim, Albert Y., Kinnaird, Katherine M., and Ott, Miles Q.

Subjects
Statistics - Other Statistics, Computer Science - Other Computer Science, 00A05, K.7.4, K.3.2
Abstract

We present a programmatic approach to incorporating ethics into an undergraduate major in statistical and data sciences. We discuss departmental-level initiatives designed to meet the National Academy of Sciences recommendation for integrating ethics into the curriculum from top-to-bottom as our majors progress from our introductory courses to our senior capstone course, as well as from side-to-side through co-curricular programming. We also provide six examples of data science ethics modules used in five different courses at our liberal arts college, each focusing on a different ethical consideration. The modules are designed to be portable such that they can be flexibly incorporated into existing courses at different levels of instruction with minimal disruption to syllabi. We connect our efforts to a growing body of literature on the teaching of data science ethics, present assessments of our effectiveness, and conclude with next steps and final thoughts.

Published
2020

43. Assessing the potential of syn-rift sediments for geochronological dating and its implications for the development of Makanjira-Shire basin in south Malawi Rift

Author

Zuze Dulanya, Aayush Srivastava, Tim C. Kinnaird, Blackwell Manda, Dalitso Kafumbata, Edister Jamu, Alick Bwanali, and Winford Masanjala

Subjects
Malape, Likwenu, Tectonics, Geography. Anthropology. Recreation, Archaeology, CC1-960
Abstract

The Upper Shire River basin, located within the zone of progressive interaction and linkage between the southern Malawi Rift and Shire Rift Zone, East Africa, presents an early-stage rift setting where rapid denudation processes take place and have profound influence on the geomorphological evolution of the region. The basin is key to the understanding of mechanisms involved in propagation and growthin young rifts. Although the tectonics in the region are well studied, lack of age constraints due to well-dated strata poses challenges in the understanding of the timing and mechanisms of rift evolution in this section of the south Malawi Rift.We used syn-rift sediments deposited from the rift shoulders to test the applicability of OSL and radiocarbon dating techniques in a poorly dated data-constrained region of the Malawi Rift.Our results suggest that proper sampling strategy is paramount in using the OSL technique for dating in areas of high dosage such as the one under consideration. However, the technique offers potential for use in these areas. Furthermore, we conclude from these findings that the evolution of the Upper Shire basin was triggered by tectonic movements along the Makongwa scrap that were responsible for redirecting the Likwenu River into the in the Zomba Graben through the Upper Shire at least during the Upper Pleistocene.

Published
2023
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47. Integrating Data Science Ethics into an Undergraduate Major: A Case Study

Author

Baumer, Benjamin S., Garcia, Randi L., Kim, Albert Y., Kinnaird, Katherine M., and Ott, Miles Q.

Abstract

We present a programmatic approach to incorporating ethics into an undergraduate major in statistical and data sciences. We discuss departmental-level initiatives designed to meet the National Academy of Sciences recommendation for integrating ethics into the curriculum from top-to-bottom as our majors progress from our introductory courses to our senior capstone course, as well as from side-to-side through co-curricular programming. We also provide six examples of data science ethics modules used in five different courses at our liberal arts college, each focusing on a different ethical consideration. The modules are designed to be portable such that they can be flexibly incorporated into existing courses at different levels of instruction with minimal disruption to syllabi. We connect our efforts to a growing body of literature on the teaching of data science ethics, present assessments of our effectiveness, and conclude with next steps and final thoughts.

Published
2022
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48. Modelling the impact of historic landscape change on soil erosion and degradation

Author

Filippo Brandolini, Tim C. Kinnaird, Aayush Srivastava, and Sam Turner

Subjects
Medicine, Science
Abstract

Abstract International policies and guidelines often highlight the divide between ‘nature’ and ‘heritage’ in landscape management, and the weakness of monodisciplinary approaches. This study argues that historic agricultural practices have played a key role in shaping today’s landscapes, creating a heritage which affords opportunities for more sustainable landscape management. The paper develops a new interdisciplinary approach with particular reference to soil loss and degradation over the long term. It presents innovative methods for assessing and modelling how pre-industrial agricultural features can mitigate soil erosion risk in response to current environmental conditions. Landscape archaeology data presented through Historic Landscape Characterisation are integrated in a GIS-RUSLE model to illustrate the impact of varying historic land-uses on soil erosion. The resulting analyses could be used to inform strategies for sustainable land resource planning.

Published
2023
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49. How Waun Mawn stone circle was designed and built, and when the Bluestones arrived at Stonehenge: a response to Darvill

Author

Pearson, Mike Parker, Pollard, Josh, Richards, Colin, Welham, Kate, Kinnaird, Timothy, Srivastava, Aayush, Casswell, Chris, Shaw, Dave, Simmons, Ellen, Stanford, Adam, Bevins, Richard, Ixer, Rob, Ruggles, Clive, Rylatt, Jim, and Edinborough, Kevan

Subjects
Stonehenge Site, England -- History, Historic sites -- Design and construction -- Location, Cromlechs -- Design and construction -- Location, Anthropology/archeology/folklore
Abstract

In response to Timothy Darvill's article, 'Mythical rings?' (this issue), which argues for an alternative interpretation of Waun Mawn circle and its relationship with Stonehenge, Parker Pearson and colleagues report new evidence from the Welsh site and elaborate on aspects of their original argument. The discovery of a hearth at the centre of the circle, as well as further features around its circumference, reinforces the authors' original interpretation. The authors explore the evidence for the construction sequence, which was abandoned before the completion of the monument. Contesting Darvill's argument that the Aubrey Holes at Stonehenge originally held posts, the authors reassert their interpretation of this circle of cut features as Bluestone settings. Keywords: UK, Waun Mawn, Stonehenge, stone circles, Introduction In responding to our Antiquity article, The original Stonehenge?' (Parker Pearson et al. 2021b), Timothy Darvill (2022) questions both the interpretation of Waun Mawn as an unfinished stone circle [...]

Published
2022
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50. An integrated geoarchaeological approach to the investigation of multi-period prehistoric settlements – the case of Neolithic Drenovac

Author

De Smedt, Philippe, primary, French, Charles, additional, Kinnaird, Timothy, additional, Rajkovača, Tonko, additional, Milekić, Aleksandar, additional, Chatzimpaloglou, Petros, additional, Verhegge, Jeroen, additional, Hermans, Thomas, additional, Veirana, Gaston M., additional, Obradović, Djurdja, additional, Popović, Vesna, additional, and Perić, Slaviša, additional

Published
2023
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