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1. Investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment

Author

Kashi Raj Bhattarai, Robert J. Mobley, Kelly R. Barnett, Daniel C. Ferguson, Baranda S. Hansen, Jonathan D. Diedrich, Brennan P. Bergeron, Satoshi Yoshimura, Wenjian Yang, Kristine R. Crews, Christopher S. Manring, Elias Jabbour, Elisabeth Paietta, Mark R. Litzow, Steven M. Kornblau, Wendy Stock, Hiroto Inaba, Sima Jeha, Ching-Hon Pui, Cheng Cheng, Shondra M. Pruett-Miller, Mary V. Relling, Jun J. Yang, William E. Evans, and Daniel Savic

Subjects
Science
Abstract

Abstract Defining genetic factors impacting chemotherapy failure can help to better predict response and identify drug resistance mechanisms. However, there is limited understanding of the contribution of inherited noncoding genetic variation on inter-individual differences in chemotherapy response in childhood acute lymphoblastic leukemia (ALL). Here we map inherited noncoding variants associated with treatment outcome and/or chemotherapeutic drug resistance to ALL cis-regulatory elements and investigate their gene regulatory potential and target gene connectivity using massively parallel reporter assays and three-dimensional chromatin looping assays, respectively. We identify 54 variants with transcriptional effects and high-confidence gene connectivity. Additionally, functional interrogation of the top variant, rs1247117, reveals changes in chromatin accessibility, PU.1 binding affinity and gene expression, and deletion of the genomic interval containing rs1247117 sensitizes cells to vincristine. Together, these data demonstrate that noncoding regulatory variants associated with diverse pharmacological traits harbor significant effects on allele-specific transcriptional activity and impact sensitivity to antileukemic agents.

Published
2024
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2. Endotracheal tube forces exerted on the larynx and a novel support device to reduce it

Author

Andrew M. Vahabzadeh‐Hagh, Brennan P. Marsh‐Armstrong, Shiv H. Patel, Luke Lindenmuth, Zeyu Feng, Rufu Gong, Yun‐An Lin, Taylor Pierce, and Kenneth J. Loh

Subjects
airway stenosis—clinical, endotracheal tube, laryngeal injury, laryngeal trauma, laryngology, larynx, Otorhinolaryngology, RF1-547, Surgery, RD1-811
Abstract

Abstract Objective Endotracheal tubes (ETTs) are commonly associated with laryngeal injury that may be short lasting and temporary or more severe and life altering. Injury is believed to result from forces that these ETTs exert on the larynx. Here we quantify the forces of ETTs of various sizes on the laryngotracheal complex to gain a more quantitative understanding of these potential damaging forces. Here we also perform preclinical testing of a novel support device to offload these forces. Methods Endotracheal intubation was performed on a fresh human cadaver using various ETT sizes. A strain‐sensitive graphene nanosheet sensor and a commercially available force sensing resistor were secured behind the larynx, anterior to the prevertebral fascia. The forces exerted on the larynx were measured for each of the commonly used ETTs. A novel support device, ETT clip (Endo Clip), was attached to the ETTs and changes in these forces were observed. Results Forces exerted on the laryngotracheal complex by various ETTs were observed to increase with increasing tube size. This pressure can be significantly reduced with a novel ETT clip. Conclusion Here we demonstrate the first quantitative measurement of forces that ETTs exert on the larynx. We demonstrate a novel device that can easily clip onto an ETT reducing pressure on the laryngotracheal complex. This preclinical test paves the way for a human clinical trial. Level of evidence 5.

Published
2023
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3. Relative Effects of Various Factors on Ice Ball Formation and Ablation Zone Size During Ultrasound-Guided Percutaneous Cryoneurolysis: A Laboratory Investigation to Inform Clinical Practice and Future Research

Author

Engy T. Said, Brennan P. Marsh-Armstrong, Seth J. Fischer, Preetham J. Suresh, Matthew W. Swisher, Andrea M. Trescot, J. David Prologo, Baharin Abdullah, and Brian M. Ilfeld

Subjects
Analgesia, Postoperative pain, Chronic pain, Acute pain, Cryoneurolysis, Cryoablation, Anesthesiology, RD78.3-87.3
Abstract

Abstract Introduction Ultrasound-guided percutaneous cryoneurolysis provides analgesia using cold temperatures to reversibly ablate peripheral nerves. Cryoneurolysis probes pass a gas through a small internal annulus, rapidly lowering the pressure and temperature, forming an ice ball to envelope the target nerve. Analgesia is compromised if a nerve is inadequately frozen, and laboratory studies suggest that pain may be paradoxically induced with a magnitude and duration in proportion with the incomplete ablation. We therefore investigated the relative effects of various factors that may contribute to the size of the ice ball and the effective cryoneurolysis zone. Methods A cryoprobe was inserted into a piece of meat, a gas was passed through for 2 min, and the resulting ice ball width (cross-section) and length (axis parallel to the probe) were measured using ultrasound, with the temperature evaluated in nine concentric locations concurrently. Results The factor with the greatest influence on ice ball size was probe gauge: in all probe types, a change from 18 to 14 increased ice ball width, length, and volume by up to 70%, 113%, and 512% respectively, with minimum internal temperature decreasing as much as from −5 to −32 °C. In contrast, alternating the type of meat (chicken, beef, pork) and the shape of the probe tip (straight, coudé) affected ice ball dimensions to a negligible degree. The ice ball dimensions and the zone of adequate temperature drop were not always correlated, and, even within a visualized ice ball, the temperature was often inadequate to induce Wallerian degeneration. Conclusions Percutaneous probe design can significantly influence the effective cryoneurolysis zone; visualizing a nerve fully encompassed in an ice ball does not guarantee adequate treatment to induce the desired Wallerian degeneration because ice forms at temperatures between 0 and −20 °C, whereas only temperatures below −20 °C induce Wallerian degeneration. The correlation between temperatures in isolated pieces of meat and perfused human tissue remains unknown, and further research to evaluate these findings in situ appears highly warranted.

Published
2023
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4. Mathematical Modeling of Multi-Phenomena Anisotropic Systems: Ejection of Primary Aerosols during the Fast Pyrolysis of Biomass

Author

Mario A. Sánchez, Juan C. Maya, Farid Chejne, Brennan Pecha, and Adriana M. Quinchía-Figueroa

Subjects
pyrolysis, biomass, single particle model, aerosols, liquid intermediate, population balance, Mathematics, QA1-939
Abstract

This study introduces a novel particle model for biomass fast pyrolysis, incorporating an anisotropic cylindrical particle to address mass and energy transport coupled with aerosol ejection, which previous models have overlooked. The main contribution lies in developing a model that considers aerosol generation in anisotropic cylindrical particles for the first time, addressing bubbling dynamics and bursting within the liquid phase. The population balance equation describes bubble dynamics and aerosol formation, capturing phenomena like nucleation, growth, coalescence, and bursting. The model employs the method of moments with bubble volume as an internal variable, substantially reducing computational costs by eliminating dependence on this variable. Results highlight the significant impact of anisotropy and particle size on aerosol ejection: smaller, less elongated particles experience faster heating, quicker conversion, and the increased accumulation of the liquid intermediate phase. Specifically, 1 mm diameter particles yield higher concentrations of metaplast and bio-oil aerosols, exceeding 15%, compared to concentrations below 11% for 3 mm particles. This model provides insights into aerosol structure (volume, surface area), aiding in understanding aerosol reactivity at the reactor scale.

Published
2024
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5. Effectiveness of rescue Me CPR! smartphone app providing real-time guidance to untrained bystanders performing CPR

Author

Brennan P. Marsh-Armstrong, Eri Seng, Fan Ting-Wei, Stella Saka, and Mark Greenberg

Subjects
Cardiopulmonary resuscitation, Cardiopulmonary resuscitation guidance application, Medical simulation, Smartphone application, Chest compression fraction, Rescue breath, Science (General), Q1-390, Social sciences (General), H1-99
Abstract

Background: Out-of-hospital cardiac arrest (OHCA) is a persistent global health challenge, owing, in part, to low rates of population CPR training. Smartphone applications have the potential to widely disseminate CPR basic training to a populace, but other studies have found multiple limitations in previously developed CPR guidance applications (CPR-GA). This study aims to use medical simulation to assess the relative CPR performance of novices using the ‘Rescue Me CPR!’ (RMC) app, a custom CPR-GA designed by this research team, to novices using ‘PG-CPR!’ (PGC), the most downloaded CPR-GA available in the USA, and to CPR certified medical personnel. Methods: In a prospective randomized experimental trial of 60 individuals, subjects were either given the RMC app, the PGC app, or had active CPR certification. They were presented a cardio-pulmonary arrest scenario and were observed while performing CPR on a high-fidelity manikin. Data was collected through four cycles of CPR, during which time 24 pertinent performance metrics and CPR steps were timed and recorded. These metrics were assessed on their own and used to calculate average time to compressions, average chest compression fraction, and rate of high-quality CPR for each study group. Results: CPR certified subjects called 911 in 100 % of simulation cases, started compressions 34 ± 10 s after first seeing the simulated patient, had an average chest compression fraction of 0.52, and performed high-quality CPR in 25 % of aggregate compression cycles. PGC app users called 911 in 70 % of simulation cases, started compressions 86 ± 17 s after first seeing the simulated patient, had an average chest compression fraction that could not be assessed due to inconsistent pauses during CPR, and performed high-quality CPR in 2.5 % of aggregate compression cycles. RMC app users called 911 in 100 % of simulation cases, started compressions 55 ± 6 s after first seeing the simulated patient, had an average chest compression fraction of 0.48, and performed high-quality CPR in 50 % of aggregate compression cycles. Conclusion: The results of this study demonstrate that in all studied metrics, except time-to-first-compression, CPR provided by individuals using the RMC app is statistically equivalent or superior to CPR performed by a CPR certified individual and, in almost every metric, superior to CPR performed by users of the most downloaded android CPR guidance application, PG-CPR.

Published
2023
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6. How to Effectively Monitor Aging Patients with Chronic Hepatitis B: A Review

Author

Kang CK, Brennan PN, and Dillon JF

Subjects
chronic hepatitis b, aging, elderly, effective monitoring, Geriatrics, RC952-954.6
Abstract

Chan Keat Kang, Paul N Brennan, John F Dillon Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UKCorrespondence: John F Dillon, Email j.f.dillon@dundee.ac.ukAbstract: Hepatitis B virus (HBV) infection is a major global public health challenge associated with significant morbidity and mortality. Due to worldwide population aging, HBV infection in the elderly will become increasingly prevalent. Effective universal vaccination programs exist but these are largely targeted towards the younger population. Therefore, the elderly population remains at risk of higher disease burden. New diagnoses of HBV infection in the elderly are usually asymptomatic chronic infections which increases their risk of developing cirrhosis, hepatocellular carcinoma, and liver disease-related mortality, especially if left untreated. Physiological changes and the increasing prevalence of multimorbidity associated with aging also potentially worsen outcomes in elderly patients with chronic HBV infection. Therefore, this cohort of patients should be monitored closely and effectively. Current international clinical practice guidelines unfortunately do not provide hard treatment endpoints specific to elderly patients with chronic HBV infection. Management of these patients is complex and requires an individualized approach. Multiple factors such as physiological changes, comorbidities, compliance, treatment tolerability and efficacy, burden of treatment, and realistic treatment goals need to be considered. Shared decision-making between patient and clinician is essential to ensure that the final decision for or against treatment aligns with the patient’s values and preferences. This review article aims to summarize the monitoring and management of chronic HBV infection in the aging population.Keywords: chronic hepatitis B, aging, elderly, effective monitoring

Published
2022

7. Blood-based biomarkers of frailty in solid tumors: a systematic review

Author

Dilorom Sass, Brennan Parmelee Streck, Vivian A. Guedes, Diane Cooper, Jennifer L. Guida, and Terri S. Armstrong

Subjects
biomarkers, molecular biomarkers, solid tumors, frailty, deficit accumulation, cancer survivors, Public aspects of medicine, RA1-1270
Abstract

This review examines the current literature to identify biomarkers of frailty across patients with solid tumors. We conducted the systematic review using preferred reporting items for systematic reviews and meta-analysis guidelines (PRISMA). PubMed, Web of Science, and Embase databases were searched from their inception to December 08, 2021, for reports of biomarkers and frailty. Two reviewers independently screened titles, abstracts, and full-text articles. A quality assessment was conducted using NHLBI Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies, and Quality Assessment of Case-Control Studies. In total, 915 reports were screened, and 14 full-text articles were included in the review. Most studies included breast tumors, were cross-sectional in design, and measured biomarkers at baseline or pre-treatment. Frailty tools varied with Fried Frailty Phenotype and the geriatric assessment most frequently used. Increased inflammatory parameters (i.e., Interleukin-6, Neutrophil Lymphocyte Ratio, Glasgow Prognostic Score-2) were associated with frailty severity. Only six studies were rated as good quality using assessment ratings. Together, the small number of studies and heterogeneity in frailty assessment limited our ability to draw conclusions from the extant literature. Future research is needed to identify potential target biomarkers of frailty in cancer survivors that may aid in early detection and referral.

Published
2023
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8. CRP Monitoring in Early Hospitalization: Implications for Predicting Outcomes in Patients with COVID-19

Author

Byron Avihai, Erin P. Sundel, Eileen Lee, Patricia J. Greenberg, Brennan P. Cook, Nicole J. Altomare, Tomohiro M. Ko, Angelo I. Chaia, Payal D. Parikh, and Martin J. Blaser

Subjects
C-reactive protein, COVID-19 hyperinflammatory syndromes, COVID-19 risk factors, Medicine
Abstract

Elevated C-reactive protein (CRP) levels have been associated with poorer COVID-19 outcomes. While baseline CRP levels are higher in women, obese individuals, and older adults, the relationship between CRP, sex, body mass index (BMI), age, and COVID-19 outcomes remains unknown. To investigate, we performed a retrospective analysis on 824 adult patients with COVID-19 admitted during the first pandemic wave, of whom 183 (22.2%) died. The maximum CRP value over the first five hospitalization days better predicted hospitalization outcome than the CRP level at admission, as a maximum CRP > 10 mg/dL independently quadrupled the risk of death (p < 0.001). Males (p < 0.001) and patients with a higher BMI (p = 0.001) had higher maximum CRP values, yet CRP levels did not impact their hospitalization outcome. While CRP levels did not statistically mediate any relation between sex, age, or BMI with clinical outcomes, age impacted the association between BMI and the risk of death. For patients 60 or over, a BMI < 25 kg/m2 increased the risk of death (p = 0.017), whereas the reverse was true for patients p = 0.030). Further impact of age on the association between BMI, CRP, and the risk of death could not be assessed due to a lack of statistical power but should be further investigated.

Published
2023
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10. Shape evolution in even-mass $^{98-104}$Zr isotopes via lifetime measurements using the $\gamma\gamma$-coincidence technique

Author

Pasqualato, G., Ansari, S., Heines, J. S., Modamio, V., Görgen, A., Korten, W., Ljungvall, J., Clément, E., Dudouet, J., Lemasson, A., Rodríguez, T. R., Allmond, J. M., Arici, T., Beckmann, K. S., Bruce, A. M., Doherty, D., Esmaylzadeh, A., Gamba, E. R., Gerhard, L., Gerl, J., Georgiev, G., Ivanova, D. P., Jolie, J., Kim, Y. -H., Knafla, L., Korichi, A., Koseoglou, P., Labiche, M., Lalkovski, S., Lauritsen, T., Li, H. -J., Pedersen, L. G., Pietri, S., Ralet, D., Regis, J. M., Rudigier, M., Saha, S., Sahin, E., Siem, S., Singh, P., öderström, P. -A., Theisen, C., Tornyi, T., Vandebrouck, M., Witt, W., Zielińska, M., Barrientos, D., Bednarczyk, P., Benzoni, G., Boston, A. J., Boston, H. C., Bracco, A., Cederwall, B, Ciemala, M., de France, G., Domingo-Pardo, C., Eberth, J., Gadea, A., González, V., Gottardo, A., Harkness-Brennan, L. J., Hess, H., Judson, D. S., Jungclaus, A., Lenzi, S. M., Leoni, S., Menegazzo, R., Mengoni, D., Michelagnoli, C., Napoli, D. R., Nyberg, J., Podolyak, Zs., Pullia, A., Recchia, F., Reiter, P., Rezynkina, K., Salsac, M. D., Sanchis, E., Şenyiğit, M., Siciliano, M., Simpson, J., Sohler, D., Stezowski, O., Valiente-Dobón, J. J., and Verney, D.

Subjects
Nuclear Experiment
Abstract

The Zirconium (Z = 40) isotopic chain has attracted interest for more than four decades. The abrupt lowering of the energy of the first $2^+$ state and the increase in the transition strength B(E2; $2_1^\rightarrow 0_1^+$ going from $^{98}$Zr to $^{100}$Zr has been the first example of "quantum phase transition" in nuclear shapes, which has few equivalents in the nuclear chart. Although a multitude of experiments have been performed to measure nuclear properties related to nuclear shapes and collectivity in the region, none of the measured lifetimes were obtained using the Recoil Distance Doppler Shift method in the $\gamma\gamma$-coincidence mode where a gate on the direct feeding transition of the state of interest allows a strict control of systematical errors. This work reports the results of lifetime measurements for the first yrast excited states in $^{98-104}$Zr carried out to extract reduced transition probabilities. The new lifetime values in $\gamma\gamma$-coincidence and $\gamma$-single mode are compared with the results of former experiments. Recent predictions of the Interacting Boson Model with Configuration Mixing, the Symmetry Conserving Configuration Mixing model based on the Hartree-Fock-Bogoliubov approach and the Monte Carlo Shell Model are presented and compared with the experimental data.

Published
2024
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11. Missing data imputation using a truncated infinite factor model with application to metabolomics data

Author

Finucane, Kate, Brennan, Lorraine, and Gormley, Isobel Claire

Subjects
Statistics - Methodology
Abstract

In metabolomics, the study of small molecules in biological samples, data are often acquired through mass spectrometry. The resulting data contain highly correlated variables, typically with a larger number of variables than observations. Missing data are prevalent, and imputation is critical as data acquisition can be difficult and expensive, and many analysis methods necessitate complete data. In such data, missing at random (MAR) missingness occurs due to acquisition or processing error, while missing not at random (MNAR) missingness occurs when true values lie below the threshold for detection. Existing imputation methods generally assume one missingness type, or impute values outside the physical constraints of the data, which lack utility. A truncated factor analysis model with an infinite number of factors (tIFA) is proposed to facilitate imputation in metabolomics data, in a statistically and physically principled manner. Truncated distributional assumptions underpin tIFA, ensuring cognisance of the data's physical constraints when imputing. Further, tIFA allows for both MAR and MNAR missingness, and a Bayesian inferential approach provides uncertainty quantification for imputed values and missingness types. The infinite factor model parsimoniously models the high-dimensional, multicollinear data, with nonparametric shrinkage priors obviating the need for model selection tools to infer the number of latent factors. A simulation study is performed to assess the performance of tIFA and an application to a urinary metabolomics dataset results in a full dataset with practically useful imputed values, and associated uncertainty, ready for use in metabolomics analyses. Open-source R code accompanies tIFA, facilitating its widespread use.

Published
2024

12. Automated Rewards via LLM-Generated Progress Functions

Author

Sarukkai, Vishnu, Shacklett, Brennan, Majercik, Zander, Bhatia, Kush, Ré, Christopher, and Fatahalian, Kayvon

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Computation and Language
Abstract

Large Language Models (LLMs) have the potential to automate reward engineering by leveraging their broad domain knowledge across various tasks. However, they often need many iterations of trial-and-error to generate effective reward functions. This process is costly because evaluating every sampled reward function requires completing the full policy optimization process for each function. In this paper, we introduce an LLM-driven reward generation framework that is able to produce state-of-the-art policies on the challenging Bi-DexHands benchmark with 20x fewer reward function samples than the prior state-of-the-art work. Our key insight is that we reduce the problem of generating task-specific rewards to the problem of coarsely estimating task progress. Our two-step solution leverages the task domain knowledge and the code synthesis abilities of LLMs to author progress functions that estimate task progress from a given state. Then, we use this notion of progress to discretize states, and generate count-based intrinsic rewards using the low-dimensional state space. We show that the combination of LLM-generated progress functions and count-based intrinsic rewards is essential for our performance gains, while alternatives such as generic hash-based counts or using progress directly as a reward function fall short., Comment: 26 pages, 5 figures

Published
2024

13. Eruptive mass-loss less than a year before the explosion of superluminous supernovae: I. The cases of SN 2020xga and SN 2022xgc

Author

Gkini, A., Fransson, C., Lunnan, R., Schulze, S., Poidevin, F., Sarin, N., Könyves-Tóth, R., Sollerman, J., Omand, C. M. B., Brennan, S. J., Hinds, K. R., Anderson, J. P., Bronikowski, M., Chen, T. -W., Dekany, R., Fraser, M., Fremling, C., Galbany, L., Gal-Yam, A., Gangopadhyay, A., Geier, S., Gonzalez, E. P., Gromadzki, M., Groom, S. L., Gutiérrez, C. P., Hiramatsu, D., Howell, D. A., Hu, Y., Inserra, C., Kopsacheili, M., Lacroix, L., Masci, F. J., Matilainen, K., McCully, C., Moore, T., Müller-Bravo, T. E., Nicholl, M., Pellegrino, C., Pérez-Fournon, I., Perley, D. A., Pessi, P. J., Petrushevska, T., Pignata, G., Ragosta, F., Sahu, A., Singh, A., Srivastav, S., Wise, J. L., Yan, L., and Young, D. R.

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

We present photometric and spectroscopic observations of SN2020xga and SN2022xgc, two hydrogen-poor superluminous supernovae (SLSNe-I) at $z = 0.4296$ and $z = 0.3103$ respectively, that show an additional set of broad Mg II absorption lines, blueshifted by a few thousand km s$^{-1}$ with respect to the host galaxy absorption system. Previous work interpreted this as due to resonance line scattering of the SLSN continuum by rapidly expanding CSM expelled shortly before the explosion. The peak rest-frame $g$-band magnitude of SN2020xga is $-22.30 \pm 0.04$ mag and of SN2022xgc is $-21.97 \pm 0.05$ mag, placing them among the brightest SLSNe-I. We use high-quality spectra from ultraviolet to near-infrared wavelengths to model the Mg II line profiles and infer the properties of the CSM shells. We find that the CSM shell of SN2020xga resides at $\sim 1.3 \times 10^{16} \rm cm$ moving with a maximum velocity of $4275~\rm km~s^{-1}$, and the shell of SN2022xgc is located at $\sim 0.8 \times 10^{16} \rm cm$ reaching up to $4400~\rm km~s^{-1}$. These shells were expelled $\sim 11$ and $\sim 5$ months before explosion for SN2020xga and SN2022xgc respectively, possibly as a result of Luminous Blue Variable-like eruptions or pulsational pair instability (PPI) mass loss. We also analyze optical photometric data and model the light curves considering powering from the magnetar spin-down mechanism. The results support very energetic magnetars, approaching the mass-shedding limit, powering these SNe with ejecta masses of $\sim 7-9 \rm~M_\odot$. The ejecta masses inferred from the magnetar modeling are not consistent with the PPI scenario pointing towards stars $> 50~\rm M_\odot$ He-core, hence alternative scenarios such as fallback accretion are discussed., Comment: 25 pages text, 8 pages appendix, 21 figures. Submitted to A&A

Published
2024

14. Probing exotic cross-shell interactions at N=28 with single-neutron transfer on 47K

Author

Paxman, C. J., Matta, A., Catford, W. N., Lotay, G., Assié, M., Clément, E., Lemasson, A., Ramos, D., Orr, N. A., Galtarossa, F., Girard-Alcindor, V., Dudouet, J., Achouri, N. L., Ackermann, D., Barrientos, D., Beaumel, D., Bednarczyk, P., Benzoni, G., Bracco, A., Canete, L., Cederwall, B., Ciemala, M., Delahaye, P., Doherty, D. T., Domingo-Pardo, C., Fernández-Domínguez, B., Fernández, D., Flavigny, F., Fougères, C., de France, G., Franchoo, S., Gadea, A., Gibelin, J., González, V., Gottardo, A., Goyal, N., Hammache, F., Harkness-Brennan, L. J., Harrouz, D. S., Jacquot, B., Judson, D. S., Jungclaus, A., Kaşkaş, A., Korten, W., Labiche, M., Lalanne, L., Lenain, C., Leoni, S., Ljungvall, J., Lois-Fuentes, J., Lokotko, T., Lopez-Martens, A., Maj, A., Marqués, F. M., Martel, I., Menegazzo, R., Mengoni, D., Million, B., Nyberg, J., Pérez-Vidal, R. M., Plagnol, L., Podolyák, Zs., Pullia, A., Quintana, B., Regueira-Castro, D., Reiter, P., Rejmund, M., Rezynkina, K., Sanchis, E., Şenyiğit, M., de Séréville, N., Siciliano, M., Sohler, D., Stezowski, O., Thomas, J. -C., Utepov, A., Valiente-Dobón, J. J., Verney, D., and Zielińska, M.

Subjects
Nuclear Experiment
Abstract

We present the first measurement of the $^{47}$K($d,p\gamma$)$^{48}$K transfer reaction, performed in inverse kinematics using a reaccelerated beam of $^{47}$K. The level scheme of $^{48}$K has been greatly extended with nine new bound excited states identified and spectroscopic factors deduced. Detailed comparisons with SDPF-U and SDPF-MU shell-model calculations reveal a number of discrepancies with these results, and a preference for SDPF-MU is found. Intriguingly, an apparent systematic overestimation of spectroscopic factors and a poor reproduction of the energies for 1$^-$ states suggests that the mixing between the $\pi s^{\,\,\,1}_{1/2} d^{\,\,\,4}_{3/2}$ and $\pi s^{\,\,\,2}_{1/2} d^{\,\,\,3}_{3/2}$ proton configurations in $^{48}$K is not correctly described using current interactions, challenging our descriptions of light $N=28$ nuclei., Comment: 7 pages, 3 figures, 1 table

Published
2024

15. How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities

Author

Bunne, Charlotte, Roohani, Yusuf, Rosen, Yanay, Gupta, Ankit, Zhang, Xikun, Roed, Marcel, Alexandrov, Theo, AlQuraishi, Mohammed, Brennan, Patricia, Burkhardt, Daniel B., Califano, Andrea, Cool, Jonah, Dernburg, Abby F., Ewing, Kirsty, Fox, Emily B., Haury, Matthias, Herr, Amy E., Horvitz, Eric, Hsu, Patrick D., Jain, Viren, Johnson, Gregory R., Kalil, Thomas, Kelley, David R., Kelley, Shana O., Kreshuk, Anna, Mitchison, Tim, Otte, Stephani, Shendure, Jay, Sofroniew, Nicholas J., Theis, Fabian, Theodoris, Christina V., Upadhyayula, Srigokul, Valer, Marc, Wang, Bo, Xing, Eric, Yeung-Levy, Serena, Zitnik, Marinka, Karaletsos, Theofanis, Regev, Aviv, Lundberg, Emma, Leskovec, Jure, and Quake, Stephen R.

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Artificial Intelligence, Computer Science - Machine Learning, Quantitative Biology - Neurons and Cognition
Abstract

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of leveraging advances in AI to construct virtual cells, high-fidelity simulations of cells and cellular systems under different conditions that are directly learned from biological data across measurements and scales. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using virtual instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions has come into reach.

Published
2024

16. High-fidelity heralded quantum state preparation and measurement

Author

Sotirova, A. S., Leppard, J. D., Vazquez-Brennan, A., Decoppet, S. M., Pokorny, F., Malinowski, M., and Ballance, C. J.

Subjects
Quantum Physics, Physics - Atomic Physics
Abstract

We present a novel protocol for high-fidelity qubit state preparation and measurement (SPAM) that combines standard SPAM methods with a series of in-sequence measurements to detect and remove errors. The protocol can be applied in any quantum system with a long-lived (metastable) level and a means to detect population outside of this level without coupling to it. We demonstrate the use of the protocol for three different qubit encodings in a single trapped $^{137}\mathrm{Ba}^+$ ion. For all three, we achieve the lowest reported SPAM infidelities of $7(4) \times 10^{-6}$ (optical qubit), $5(4) \times 10^{-6}$ (metastable-level qubit), and $8(4) \times 10^{-6}$ (ground-level qubit).

Published
2024

17. SN 2021foa: Deriving a continuity between SN IIn and SN Ibn

Author

Gangopadhyay, Anjasha, Dukiya, Naveen, Moriya, Takashi J, Tanaka, Masaomi, Maeda, Keiichi, Howell, D. Andrew, Singh, Mridweeka, Singh, Avinash, Sollerman, Jesper, Kawabata, Koji S, Brennan, Sean J, Pellegrino, Craig, Dastidar, Raya, Nakaoka, Tatsuya, Kawabata, Miho, Misra, Kuntal, Schulze, Steve, Chandra, Poonam, Taguchi, Kenta, Sahu, Devendra K, McCully, Curtis, Bostroem, K. Azalee, Gonzalez, Estefania Padilla, Newsome, Megan, Hiramatsu, Daichi, Takei, Yuki, Yamanaka, Masayuki, Tajitsu, Akito, and Isogai, Keisuke

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

We present the long-term photometric and spectroscopic analysis of a transitioning SN~IIn/Ibn from $-$10.8 d to 150.7 d post $V$-band maximum. SN~2021foa shows prominent He {\sc i} lines comparable in strength to the H$\alpha$ line around peak, placing SN~2021foa between the SN~IIn and SN~Ibn populations. The spectral comparison shows that it resembles the SN~IIn population at pre-maximum, becomes intermediate between SNe~IIn/Ibn and at post-maximum matches with SN~IIn 1996al. The photometric evolution shows a precursor at $-$50 d and a light curve shoulder around 17d. The peak luminosity and color evolution of SN 2021foa are consistent with most SNe~IIn and Ibn in our comparison sample. SN~2021foa shows the unique case of a SN~IIn where the narrow P-Cygni in H$\alpha$ appear at later stages. The H$\alpha$ profile consists of a narrow (500 -- 1200 km s$^{-1}$) component, intermediate width (3000 -- 8000 km s$^{-1}$) and broad component in absorption. Temporal evolution of the H$\alpha$ profile favours a disk-like CSM geometry. Hydrodynamical modelling of the lightcurve well reproduces a two-component CSM structure with different densities ($\rho$ $\propto$ r$^{-2}$ -- $\rho$ $\propto$ r$^{-5}$), mass-loss rates (10$^{-3}$ -- 10$^{-1}$ M$_{\odot}$ yr$^{-1}$) assuming a wind velocity of 1000 km s$^{-1}$ and having a CSM mass of 0.18 M$_{\odot}$. The overall evolution indicates that SN~2021foa most likely originated from a LBV star transitioning to a WR star with the mass-loss rate increasing in the period from 5 to 0.5 years before the explosion or it could be due to a binary interaction., Comment: Submitted to MNRAS; 20 pages, 16 figures, 4 tables

Published
2024

18. A cosmic formation site of silicon and sulphur revealed by a new type of supernova explosion

Author

Schulze, Steve, Gal-Yam, Avishay, Dessart, Luc, Miller, Adam A., Woosley, Stan E., Yang, Yi, Bulla, Mattia, Yaron, Ofer, Sollerman, Jesper, Filippenko, Alexei V., Hinds, K-Ryan, Perley, Daniel A., Tsuna, Daichi, Lunnan, Ragnhild, Sarin, Nikhil, Brennan, Sean J., Brink, Thomas G., Bruch, Rachel J., Chen, Ping, Das, Kaustav K., Dhawan, Suhail, Fransson, Claes, Fremling, Christoffer, Gangopadhyay, Anjasha, Irani, Ido, Jerkstrand, Anders, Knezevic, Nikola, Kushnir, Doron, Maeda, Keiichi, Maguire, Kate, Ofek, Eran, Omand, Conor M. B., Qin, Yu-Jing, Sharma, Yashvi, Sit, Tawny, Srinivasaragavan, Gokul P., Strothjohann, Nora L., Takei, Yuki, Waxman, Eli, Yan, Lin, Yao, Yuhan, Zheng, WeiKang, Zimmerman, Erez A., Bellm, Eric C., Coughlin, Michael W., Masci, Frank. J., Purdum, Josiah, Rigault, Mickael, Wold, Avery, and Kulkarni, Shrinivas R.

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

The cores of stars are the cosmic furnaces where light elements are fused into heavier nuclei. The fusion of hydrogen to helium initially powers all stars. The ashes of the fusion reactions are then predicted to serve as fuel in a series of stages, eventually transforming massive stars into a structure of concentric shells. These are composed of natal hydrogen on the outside, and consecutively heavier compositions inside, predicted to be dominated by helium, carbon/oxygen, oxygen/neon/magnesium, and oxygen/silicon/sulphur. Silicon and sulphur are fused into inert iron, leading to the collapse of the core and either a supernova explosion or the direct formation of a black hole. Stripped stars, where the outer hydrogen layer has been removed and the internal He-rich layer (in Wolf-Rayet WN stars) or even the C/O layer below it (in Wolf-Rayet WC/WO stars) are exposed, provide evidence for this shell structure, and the cosmic element production mechanism it reflects. The types of supernova explosions that arise from stripped stars embedded in shells of circumstellar material (most notably Type Ibn supernovae from stars with outer He layers, and Type Icn supernovae from stars with outer C/O layers) confirm this scenario. However, direct evidence for the most interior shells, which are responsible for the production of elements heavier than oxygen, is lacking. Here, we report the discovery of the first-of-its-kind supernova arising from a star peculiarly stripped all the way to the silicon and sulphur-rich internal layer. Whereas the concentric shell structure of massive stars is not under debate, it is the first time that such a thick, massive silicon and sulphur-rich shell, expelled by the progenitor shortly before the SN explosion, has been directly revealed., Comment: 48 pages, 12 figures and 10 tables. Submitted to a high-impact journal. The reduced spectra and photometry will be made available via the journal webpage and the WISeREP archive after the acceptance of the paper

Published
2024

19. Testing an Explanation for Summer Learning Loss: Differential Examinee Effort between Spring and Fall

Author

Megan Kuhfeld, James Soland, Brennan Register, and Andrew McEachin

Abstract

Summer learning loss is a perennial concern for educators and parents alike. However, researchers have recently questioned whether summer learning loss is just a statistical artifact driven by how achievement is measured across the school year. In this study, we empirically investigated a plausible critique of summer learning loss research, namely that students do not put forth their best effort on the fall test compared with the spring test. While we cannot conclude based on our findings that students do in fact lose ground during the summer, we did not find evidence that seasonal differences in test effort are a main driver of summer learning patterns estimated with MAP Growth assessments.

Published
2024
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20. Modular variable laser cooling for efficient entropy extraction

Author

de Neeve, Brennan, Nguyen, Thanh-Long, Ferk, Alexander, Behrle, Tanja, Lancellotti, Francesco, Simoni, Matteo, Welte, Stephan, and Home, Jonathan

Subjects
Quantum Physics
Abstract

We propose and experimentally demonstrate a method for laser cooling an oscillator based on sequences of spin-state-dependent displacements followed by spin repumping. For a thermal state with mean occupation $\bar{n}\gg 1$ the method attains a reduction to 0.632 of the initial thermal oscillator occupation for two repumps of the two-level spin state. This is within a factor of 2.53 of the optimum that might be expected due to the reduction of the oscillator entropy by $2 \ln(2)$. We show that the method, which is based on encoding the value of the modular-variable of the oscillator into the spin, has a simple semi-classical description in terms of a Bayesian update. We demonstrate the method experimentally using the internal and motional states of a single trapped ion.

Published
2024

21. Sample of hydrogen-rich superluminous supernovae from the Zwicky Transient Facility

Author

Pessi, P. J., Lunnan, R., Sollerman, J., Schulze, S., Gkini, A., Gangopadhyay, A., Yan, L., Gal-Yam, A., Perley, D. A., Chen, T. -W., Hinds, K. R., Brennan, S. J., Hu, Y., Singh, A., Andreoni, I., Cook, D. O., Fremling, C., Ho, A. Y. Q., Sharma, Y., van Velzen, S., Wold, A., Bellm, E. C., Bloom, J. S., Graham, M. J., Kasliwal, M. M., Kulkarni, S. R., Riddle, R., and Rusholme, B.

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

Hydrogen-rich superluminous supernovae (SLSNe II) are rare. The exact mechanism producing their extreme light curve peaks is not understood. Analysis of single events and small samples suggest that CSM interaction is the main responsible for their features. However, other mechanisms can not be discarded. Large sample analysis can provide clarification. We aim to characterize the light curves of a sample of 107 SLSNe II to provide valuable information that can be used to validate theoretical models. We analyze the gri light curves of SLSNe II obtained through ZTF. We study peak absolute magnitudes and characteristic timescales. When possible we compute g-r colors, pseudo-bolometric light curves, and estimate lower limits for their total radiated energy. We also study the luminosity distribution of our sample and estimate the percentage of them that would be observable by the LSST. Finally, we compare our sample to other H-rich SNe and to H-poor SLSNe I. SLSNe II are heterogeneous. Their median peak absolute magnitude is -20.3 mag in optical bands. Their rise can take from two weeks to over three months, and their decline from twenty days to over a year. We found no significant correlations between peak magnitude and timescales. SLSNe II tend to show fainter peaks, longer declines and redder colors than SLSNe I. We present the largest sample of SLSNe II light curves to date, comprising of 107 events. Their diversity could be explained by considering different CSM morphologies. Although, theoretical analysis is needed to explore alternative scenarios. Other luminous transients, such as Active Galactic Nuclei, Tidal Disruption Events or SNe Ia-CSM, can easily become contaminants. Thus, good multi-wavelength light curve coverage becomes paramount. LSST could miss 30 percent of the ZTF events in the its footprint in gri bands. Redder bands become important to construct complete samples., Comment: 35 pages. 27 figures. 9 tables

Published
2024

22. Learning to Move Like Professional Counter-Strike Players

Author

Durst, David, Xie, Feng, Sarukkai, Vishnu, Shacklett, Brennan, Frosio, Iuri, Tessler, Chen, Kim, Joohwan, Taylor, Carly, Bernstein, Gilbert, Choudhury, Sanjiban, Hanrahan, Pat, and Fatahalian, Kayvon

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Graphics
Abstract

In multiplayer, first-person shooter games like Counter-Strike: Global Offensive (CS:GO), coordinated movement is a critical component of high-level strategic play. However, the complexity of team coordination and the variety of conditions present in popular game maps make it impractical to author hand-crafted movement policies for every scenario. We show that it is possible to take a data-driven approach to creating human-like movement controllers for CS:GO. We curate a team movement dataset comprising 123 hours of professional game play traces, and use this dataset to train a transformer-based movement model that generates human-like team movement for all players in a "Retakes" round of the game. Importantly, the movement prediction model is efficient. Performing inference for all players takes less than 0.5 ms per game step (amortized cost) on a single CPU core, making it plausible for use in commercial games today. Human evaluators assess that our model behaves more like humans than both commercially-available bots and procedural movement controllers scripted by experts (16% to 59% higher by TrueSkill rating of "human-like"). Using experiments involving in-game bot vs. bot self-play, we demonstrate that our model performs simple forms of teamwork, makes fewer common movement mistakes, and yields movement distributions, player lifetimes, and kill locations similar to those observed in professional CS:GO match play., Comment: The project website is at https://davidbdurst.com/mlmove/

Published
2024

23. Adaptive User Journeys in Pharma E-Commerce with Reinforcement Learning: Insights from SwipeRx

Author

del Río, Ana Fernández, Leong, Michael Brennan, Saraiva, Paulo, Nazarov, Ivan, Rastogi, Aditya, Hassan, Moiz, Tang, Dexian, and Periáñez, África

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Statistics - Machine Learning
Abstract

This paper introduces a reinforcement learning (RL) platform that enhances end-to-end user journeys in healthcare digital tools through personalization. We explore a case study with SwipeRx, the most popular all-in-one app for pharmacists in Southeast Asia, demonstrating how the platform can be used to personalize and adapt user experiences. Our RL framework is tested through a series of experiments with product recommendations tailored to each pharmacy based on real-time information on their purchasing history and in-app engagement, showing a significant increase in basket size. By integrating adaptive interventions into existing mobile health solutions and enriching user journeys, our platform offers a scalable solution to improve pharmaceutical supply chain management, health worker capacity building, and clinical decision and patient care, ultimately contributing to better healthcare outcomes., Comment: Presented at the Third Workshop on End-to-End Customer Journey Optimization at KDD 2024 (KDD CJ Workshop '24), August 26, Barcelona, Spain

Published
2024

24. Adaptive Behavioral AI: Reinforcement Learning to Enhance Pharmacy Services

Author

del Río, Ana Fernández, Leong, Michael Brennan, Saraiva, Paulo, Nazarov, Ivan, Rastogi, Aditya, Hassan, Moiz, Tang, Dexian, and Periáñez, África

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Computers and Society, Physics - Data Analysis, Statistics and Probability
Abstract

Pharmacies are critical in healthcare systems, particularly in low- and middle-income countries. Procuring pharmacists with the right behavioral interventions or nudges can enhance their skills, public health awareness, and pharmacy inventory management, ensuring access to essential medicines that ultimately benefit their patients. We introduce a reinforcement learning operational system to deliver personalized behavioral interventions through mobile health applications. We illustrate its potential by discussing a series of initial experiments run with SwipeRx, an all-in-one app for pharmacists, including B2B e-commerce, in Indonesia. The proposed method has broader applications extending beyond pharmacy operations to optimize healthcare delivery., Comment: Presented at The First Workshop on AI Behavioral Science (AIBS'24) at KDD 2024, August 25, Barcelona, Spain

Published
2024

25. Imagen 3

Author

Imagen-Team-Google, Baldridge, Jason, Bauer, Jakob, Bhutani, Mukul, Brichtova, Nicole, Bunner, Andrew, Chan, Kelvin, Chen, Yichang, Dieleman, Sander, Du, Yuqing, Eaton-Rosen, Zach, Fei, Hongliang, de Freitas, Nando, Gao, Yilin, Gladchenko, Evgeny, Colmenarejo, Sergio Gómez, Guo, Mandy, Haig, Alex, Hawkins, Will, Hu, Hexiang, Huang, Huilian, Igwe, Tobenna Peter, Kaplanis, Christos, Khodadadeh, Siavash, Kim, Yelin, Konyushkova, Ksenia, Langner, Karol, Lau, Eric, Luo, Shixin, Mokrá, Soňa, Nandwani, Henna, Onoe, Yasumasa, Oord, Aäron van den, Parekh, Zarana, Pont-Tuset, Jordi, Qi, Hang, Qian, Rui, Ramachandran, Deepak, Rane, Poorva, Rashwan, Abdullah, Razavi, Ali, Riachi, Robert, Srinivasan, Hansa, Srinivasan, Srivatsan, Strudel, Robin, Uria, Benigno, Wang, Oliver, Wang, Su, Waters, Austin, Wolff, Chris, Wright, Auriel, Xiao, Zhisheng, Xiong, Hao, Xu, Keyang, van Zee, Marc, Zhang, Junlin, Zhang, Katie, Zhou, Wenlei, Zolna, Konrad, Aboubakar, Ola, Akbulut, Canfer, Akerlund, Oscar, Albuquerque, Isabela, Anderson, Nina, Andreetto, Marco, Aroyo, Lora, Bariach, Ben, Barker, David, Ben, Sherry, Berman, Dana, Biles, Courtney, Blok, Irina, Botadra, Pankil, Brennan, Jenny, Brown, Karla, Buckley, John, Bunel, Rudy, Bursztein, Elie, Butterfield, Christina, Caine, Ben, Carpenter, Viral, Casagrande, Norman, Chang, Ming-Wei, Chang, Solomon, Chaudhuri, Shamik, Chen, Tony, Choi, John, Churbanau, Dmitry, Clement, Nathan, Cohen, Matan, Cole, Forrester, Dektiarev, Mikhail, Du, Vincent, Dutta, Praneet, Eccles, Tom, Elue, Ndidi, Feden, Ashley, Fruchter, Shlomi, Garcia, Frankie, Garg, Roopal, Ge, Weina, Ghazy, Ahmed, Gipson, Bryant, Goodman, Andrew, Górny, Dawid, Gowal, Sven, Gupta, Khyatti, Halpern, Yoni, Han, Yena, Hao, Susan, Hayes, Jamie, Hertz, Amir, Hirst, Ed, Hou, Tingbo, Howard, Heidi, Ibrahim, Mohamed, Ike-Njoku, Dirichi, Iljazi, Joana, Ionescu, Vlad, Isaac, William, Jana, Reena, Jennings, Gemma, Jenson, Donovon, Jia, Xuhui, Jones, Kerry, Ju, Xiaoen, Kajic, Ivana, Ayan, Burcu Karagol, Kelly, Jacob, Kothawade, Suraj, Kouridi, Christina, Ktena, Ira, Kumakaw, Jolanda, Kurniawan, Dana, Lagun, Dmitry, Lavitas, Lily, Lee, Jason, Li, Tao, Liang, Marco, Li-Calis, Maggie, Liu, Yuchi, Alberca, Javier Lopez, Lu, Peggy, Lum, Kristian, Ma, Yukun, Malik, Chase, Mellor, John, Mosseri, Inbar, Murray, Tom, Nematzadeh, Aida, Nicholas, Paul, Oliveira, João Gabriel, Ortiz-Jimenez, Guillermo, Paganini, Michela, Paine, Tom Le, Paiss, Roni, Parrish, Alicia, Peckham, Anne, Peswani, Vikas, Petrovski, Igor, Pfaff, Tobias, Pirozhenko, Alex, Poplin, Ryan, Prabhu, Utsav, Qi, Yuan, Rahtz, Matthew, Rashtchian, Cyrus, Rastogi, Charvi, Raul, Amit, Rebuffi, Sylvestre-Alvise, Ricco, Susanna, Riedel, Felix, Robinson, Dirk, Rohatgi, Pankaj, Rosgen, Bill, Rumbley, Sarah, Ryu, Moonkyung, Salgado, Anthony, Singla, Sahil, Schroff, Florian, Schumann, Candice, Shah, Tanmay, Shillingford, Brendan, Shivakumar, Kaushik, Shtatnov, Dennis, Singer, Zach, Sluzhaev, Evgeny, Sokolov, Valerii, Sottiaux, Thibault, Stimberg, Florian, Stone, Brad, Stutz, David, Su, Yu-Chuan, Tabellion, Eric, Tang, Shuai, Tao, David, Thomas, Kurt, Thornton, Gregory, Toor, Andeep, Udrescu, Cristian, Upadhyay, Aayush, Vasconcelos, Cristina, Vasiloff, Alex, Voynov, Andrey, Walker, Amanda, Wang, Luyu, Wang, Miaosen, Wang, Simon, Wang, Stanley, Wang, Qifei, Wang, Yuxiao, Weisz, Ágoston, Wiles, Olivia, Wu, Chenxia, Xu, Xingyu Federico, Xue, Andrew, Yang, Jianbo, Yu, Luo, Yurtoglu, Mete, Zand, Ali, Zhang, Han, Zhang, Jiageng, Zhao, Catherine, Zhaxybay, Adilet, Zhou, Miao, Zhu, Shengqi, Zhu, Zhenkai, Bloxwich, Dawn, Bordbar, Mahyar, Cobo, Luis C., Collins, Eli, Dai, Shengyang, Doshi, Tulsee, Dragan, Anca, Eck, Douglas, Hassabis, Demis, Hsiao, Sissie, Hume, Tom, Kavukcuoglu, Koray, King, Helen, Krawczyk, Jack, Li, Yeqing, Meier-Hellstern, Kathy, Orban, Andras, Pinsky, Yury, Subramanya, Amar, Vinyals, Oriol, Yu, Ting, and Zwols, Yori

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We introduce Imagen 3, a latent diffusion model that generates high quality images from text prompts. We describe our quality and responsibility evaluations. Imagen 3 is preferred over other state-of-the-art (SOTA) models at the time of evaluation. In addition, we discuss issues around safety and representation, as well as methods we used to minimize the potential harm of our models.

Published
2024

26. Prospects for using drones to test formation-flying CubeSat concepts, and other astronomical applications

Author

Monnier, John D., Jain, Prachet, Gutierrez, Mayra, Han, Chi, Hezi, Sara, Kalluri, Shashank, Kabaria, Hirsh, Kompas, Brennan, Harikumar, Vaishnavi, Skifstad, Julian, Peri, Janani, Hernandez, Emmanuel, Bhaskarapanthula, Ramya, and Cutler, James

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Drones provide a versatile platform for remote sensing and atmospheric studies. However, strict payload mass limits and intense vibrations have proven obstacles to adoption for astronomy. We present a concept for system-level testing of a long-baseline CubeSat space interferometer using drones, taking advantage of their cm-level xyz station-keeping, 6-dof freedom of movement, large operational environment, access to guide stars for end-to-end testing of optical train and control algorithms, and comparable mass and power requirements. We have purchased two different drone platforms (Aurelia X6 Pro, Freefly Alta X) and present characterization studies of vibrations, flight stability, gps positioning precision, and more. We also describe our progress in sub-system development, including inter-drone laser metrology, realtime gimbal control, and LED beacon tracking. Lastly, we explore whether custom-built drone-borne telescopes could be used for interferometry of bright objects over km-level baselines using vibration-isolation platforms and a small fast delay for fringe-tracking., Comment: submitted to SPIE 2024 (Yokohama)

Published
2024

27. Training LLMs to Recognize Hedges in Spontaneous Narratives

Author

Paige, Amie J., Soubki, Adil, Murzaku, John, Rambow, Owen, and Brennan, Susan E.

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, I.2.7
Abstract

Hedges allow speakers to mark utterances as provisional, whether to signal non-prototypicality or "fuzziness", to indicate a lack of commitment to an utterance, to attribute responsibility for a statement to someone else, to invite input from a partner, or to soften critical feedback in the service of face-management needs. Here we focus on hedges in an experimentally parameterized corpus of 63 Roadrunner cartoon narratives spontaneously produced from memory by 21 speakers for co-present addressees, transcribed to text (Galati and Brennan, 2010). We created a gold standard of hedges annotated by human coders (the Roadrunner-Hedge corpus) and compared three LLM-based approaches for hedge detection: fine-tuning BERT, and zero and few-shot prompting with GPT-4o and LLaMA-3. The best-performing approach was a fine-tuned BERT model, followed by few-shot GPT-4o. After an error analysis on the top performing approaches, we used an LLM-in-the-Loop approach to improve the gold standard coding, as well as to highlight cases in which hedges are ambiguous in linguistically interesting ways that will guide future research. This is the first step in our research program to train LLMs to interpret and generate collateral signals appropriately and meaningfully in conversation., Comment: Amie Paige, Adil Soubki, and John Murzaku contributed equally to this study

Published
2024

28. GPUDrive: Data-driven, multi-agent driving simulation at 1 million FPS

Author

Kazemkhani, Saman, Pandya, Aarav, Cornelisse, Daphne, Shacklett, Brennan, and Vinitsky, Eugene

Subjects
Computer Science - Artificial Intelligence, Computer Science - Hardware Architecture, Computer Science - Graphics, Computer Science - Performance
Abstract

Multi-agent learning algorithms have been successful at generating superhuman planning in various games but have had limited impact on the design of deployed multi-agent planners. A key bottleneck in applying these techniques to multi-agent planning is that they require billions of steps of experience. To enable the study of multi-agent planning at scale, we present GPUDrive, a GPU-accelerated, multi-agent simulator built on top of the Madrona Game Engine that can generate over a million simulation steps per second. Observation, reward, and dynamics functions are written directly in C++, allowing users to define complex, heterogeneous agent behaviors that are lowered to high-performance CUDA. We show that using GPUDrive we can effectively train reinforcement learning agents over many scenes in the Waymo Open Motion Dataset, yielding highly effective goal-reaching agents in minutes for individual scenes and enabling agents to navigate thousands of scenarios within hours. The code base with pre-trained agents is available at \url{https://github.com/Emerge-Lab/gpudrive}.

Published
2024

29. A study in scarlet -- II. Spectroscopic properties of a sample of Intermediate Luminosity Red Transients

Author

Valerin, G., Pastorello, A., Mason, E., Reguitti, A., Benetti, S., Cai, Y. -Z., Chen, T. -W., Eappachen, D., Elias-Rosa, N., Fraser, M., Gangopadhyay, A., Hsiao, E. Y., Howell, D. A., Inserra, C., Izzo, L., Jencson, J., Kankare, E., Kotak, R., Lundqvist, P., Mazzali, P. A., Misra, K., Pignata, G., Prentice, S. J., Sand, D. J., Smartt, S. J., Stritzinger, M. D., Tartaglia, L., Valenti, S., Anderson, J. P., Andrews, J. E., Amaro, R. C., Barbarino, C., Brennan, S., Bufano, F., Callis, E., Cappellaro, E., Dastidar, R., Della Valle, M., Fiore, A., Fulton, M. D., Galbany, L., Gromadzki, M., Heikkilä, T., Hiramatsu, D., Karamehmetoglu, E., Kuncarayakti, H., Leloudas, G., Limongi, M., Lundquist, M., McCully, C., Müller-Bravo, T. E., Nicholl, M., Ochner, P., Gonzalez, E. Padilla, Paraskeva, E., Pellegrino, C., Rau, A., Reichart, D. E., Reynolds, T. M., Roy, R., Salmaso, I., Shahbandeh, M., Singh, M., Sollerman, J., Turatto, M., Tomasella, L., Wyatt, S., and Young, D. R.

Subjects
Astrophysics - Solar and Stellar Astrophysics, Astrophysics - High Energy Astrophysical Phenomena
Abstract

We investigate the spectroscopic characteristics of Intermediate Luminosity Red Transients (ILRTs), a class of elusive objects with peak luminosity between that of classical novae and standard supernovae. We present the extensive optical and near-infrared (NIR) spectroscopic monitoring of four ILRTs, namely NGC 300 2008OT-1, AT 2019abn, AT 2019ahd and AT 2019udc. First we focus on the evolution of the most prominent spectral features observed in the low resolution spectra, then we discuss more in detail the high resolution spectrum collected for NGC 300 2008OT-1 with the Very Large Telescope equipped with UVES. Finally we analyse late time spectra of NGC 300 2008OT-1 and AT 2019ahd through comparisons with both synthetic and observed spectra. Balmer and Ca lines dominate the optical spectra, revealing the presence of slowly moving circumstellar medium (CSM) around the objects. The line luminosity of H$\alpha$, H$\beta$ and Ca II NIR triplet presents a double peaked evolution with time, possibly indicative of interaction between fast ejecta and the slow CSM. The high resolution spectrum of NGC 300 2008OT-1 reveals a complex circumstellar environment, with the transient being surrounded by a slow ($\sim$30 km s$^{-1}$) progenitor wind. At late epochs, optical spectra of NGC 300 2008OT-1 and AT 2019ahd show broad ($\sim$2500 km s$^{-1}$) emission features at $\sim$6170 A and $\sim$7000 A which are unprecedented for ILRTs. We find that these lines originate most likely from the blending of several narrow lines, possibly of iron-peak elements., Comment: 28 pages, 19 figures. Submitted to A&A

Published
2024

30. A study in scarlet -- I. Photometric properties of a sample of Intermediate Luminosity Red Transients

Author

Valerin, G., Pastorello, A., Reguitti, A., Benetti, S., Cai, Y. -Z., Chen, T. -W., Eappachen, D., Elias-Rosa, N., Fraser, M., Gangopadhyay, A., Hsiao, E. Y., Howell, D. A., Inserra, C., Izzo, L., Jencson, J., Kankare, E., Kotak, R., Mazzali, P. A., Misra, K., Pignata, G., Prentice, S. J., Sand, D. J., Smartt, S. J., Stritzinger, M. D., Tartaglia, L., Valenti, S., Anderson, J. P., Andrews, J. E., Amaro, R. C., Brennan, S., Bufano, F., Callis, E., Cappellaro, E., Dastidar, R., Della Valle, M., Fiore, A., Fulton, M. D., Galbany, L., Heikkilä, T., Hiramatsu, D., Karamehmetoglu, E., Kuncarayakti, H., Leloudas, G., Lundquist, M., McCully, C., Müller-Bravo, T. E., Nicholl, M., Ochner, P., Gonzalez, E. Padilla, Paraskeva, E., Pellegrino, C., Reichart, D. E., Reynolds, T. M., Roy, R., Salmaso, I., Singh, M., Turatto, M., Tomasella, L., Wyatt, S., and Young, D. R.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

We investigate the photometric characteristics of a sample of Intermediate Luminosity Red Transients (ILRTs), a class of elusive objects with peak luminosity between that of classical novae and standard supernovae. We present the multi-wavelength photometric follow-up of four ILRTs, namely NGC 300 2008OT-1, AT 2019abn, AT 2019ahd and AT 2019udc. Through the analysis and modelling of their spectral energy distribution and bolometric light curves we infer the physical parameters associated with these transients. All four objects display a single peaked light curve which ends in a linear decline in magnitudes at late phases. A flux excess with respect to a single black body emission is detected in the infrared domain for three objects in our sample, a few months after maximum. This feature, commonly found in ILRTs, is interpreted as a sign of dust formation. Mid infrared monitoring of NGC 300 2008OT-1 761 days after maximum allows us to infer the presence of $\sim$10$^{-3}$-10$^{-5}$ M$_{\odot}$ of dust, depending on the chemical composition and the grain size adopted. The late time decline of the bolometric light curves of the considered ILRTs is shallower than expected for $^{56}$Ni decay, hence requiring an additional powering mechanism. James Webb Space Telescope observations of AT 2019abn prove that the object has faded below its progenitor luminosity in the mid-infrared domain, five years after its peak. Together with the disappearance of NGC 300 2008OT-1 in Spitzer images seven years after its discovery, this supports the terminal explosion scenario for ILRTs. With a simple semi-analytical model we try to reproduce the observed bolometric light curves in the context of few M$_{\odot}$ of material ejected at few 10$^{3}$ km s$^{-1}$ and enshrouded in an optically thick circumstellar medium., Comment: 21 pages, 15 figures plus 20 additional pages of data in appendix. Submitted to A&A

Published
2024

31. Connecting Zeros in Pisano Periods to Prime Factors of $K$-Fibonacci Numbers

Author

Benfield, Brennan and Lippard, Oliver

Subjects
Mathematics - Number Theory, 11B39, 11B50
Abstract

The Fibonacci sequence is periodic modulo every positive integer $m>1$, and perhaps more surprisingly, each period has exactly 1, 2, or 4 zeros that are evenly spaced, which also holds true for more general $K$-Fibonacci sequences. This paper proves several conjectures connecting the zeros in the Pisano period to the prime factors of $K$-Fibonacci numbers. The congruence classes of indices for $K$-Fibonacci numbers that are multiples of the prime factors of $m$ completely determine the number of zeroes in the Pisano period modulo $m$.

Published
2024

32. OpenHands: An Open Platform for AI Software Developers as Generalist Agents

Author

Wang, Xingyao, Li, Boxuan, Song, Yufan, Xu, Frank F., Tang, Xiangru, Zhuge, Mingchen, Pan, Jiayi, Song, Yueqi, Li, Bowen, Singh, Jaskirat, Tran, Hoang H., Li, Fuqiang, Ma, Ren, Zheng, Mingzhang, Qian, Bill, Shao, Yanjun, Muennighoff, Niklas, Zhang, Yizhe, Hui, Binyuan, Lin, Junyang, Brennan, Robert, Peng, Hao, Ji, Heng, and Neubig, Graham

Subjects
Computer Science - Software Engineering, Computer Science - Artificial Intelligence, Computer Science - Computation and Language
Abstract

Software is one of the most powerful tools that we humans have at our disposal; it allows a skilled programmer to interact with the world in complex and profound ways. At the same time, thanks to improvements in large language models (LLMs), there has also been a rapid development in AI agents that interact with and affect change in their surrounding environments. In this paper, we introduce OpenHands (f.k.a. OpenDevin), a platform for the development of powerful and flexible AI agents that interact with the world in similar ways to those of a human developer: by writing code, interacting with a command line, and browsing the web. We describe how the platform allows for the implementation of new agents, safe interaction with sandboxed environments for code execution, coordination between multiple agents, and incorporation of evaluation benchmarks. Based on our currently incorporated benchmarks, we perform an evaluation of agents over 15 challenging tasks, including software engineering (e.g., SWE-BENCH) and web browsing (e.g., WEBARENA), among others. Released under the permissive MIT license, OpenHands is a community project spanning academia and industry with more than 2.1K contributions from over 188 contributors., Comment: Code: https://github.com/All-Hands-AI/OpenHands

Published
2024

33. Personalization of Dataset Retrieval Results using a Metadata-based Data Valuation Method

Author

Ebiele, Malick, Bendechache, Malika, Clinton, Eamonn, and Brennan, Rob

Subjects
Computer Science - Information Retrieval, Computer Science - Databases, H.1.1
Abstract

In this paper, we propose a novel data valuation method for a Dataset Retrieval (DR) use case in Ireland's National mapping agency. To the best of our knowledge, data valuation has not yet been applied to Dataset Retrieval. By leveraging metadata and a user's preferences, we estimate the personal value of each dataset to facilitate dataset retrieval and filtering. We then validated the data value-based ranking against the stakeholders' ranking of the datasets. The proposed data valuation method and use case demonstrated that data valuation is promising for dataset retrieval. For instance, the outperforming dataset retrieval based on our approach obtained 0.8207 in terms of NDCG@5 (the truncated Normalized Discounted Cumulative Gain at 5). This study is unique in its exploration of a data valuation-based approach to dataset retrieval and stands out because, unlike most existing methods, our approach is validated using the stakeholders ranking of the datasets., Comment: 5 pages, 1 figure

Published
2024

34. Promoting AI Competencies for Medical Students: A Scoping Review on Frameworks, Programs, and Tools

Author

Ma, Yingbo, Song, Yukyeong, Balch, Jeremy A., Ren, Yuanfang, Vellanki, Divya, Hu, Zhenhong, Brennan, Meghan, Kolla, Suraj, Guan, Ziyuan, Armfield, Brooke, Ozrazgat-Baslanti, Tezcan, Rashidi, Parisa, Loftus, Tyler J., Bihorac, Azra, and Shickel, Benjamin

Subjects
Computer Science - Computers and Society, Computer Science - Artificial Intelligence
Abstract

As more clinical workflows continue to be augmented by artificial intelligence (AI), AI literacy among physicians will become a critical requirement for ensuring safe and ethical AI-enabled patient care. Despite the evolving importance of AI in healthcare, the extent to which it has been adopted into traditional and often-overloaded medical curricula is currently unknown. In a scoping review of 1,699 articles published between January 2016 and June 2024, we identified 18 studies which propose guiding frameworks, and 11 studies documenting real-world instruction, centered around the integration of AI into medical education. We found that comprehensive guidelines will require greater clinical relevance and personalization to suit medical student interests and career trajectories. Current efforts highlight discrepancies in the teaching guidelines, emphasizing AI evaluation and ethics over technical topics such as data science and coding. Additionally, we identified several challenges associated with integrating AI training into the medical education program, including a lack of guidelines to define medical students AI literacy, a perceived lack of proven clinical value, and a scarcity of qualified instructors. With this knowledge, we propose an AI literacy framework to define competencies for medical students. To prioritize relevant and personalized AI education, we categorize literacy into four dimensions: Foundational, Practical, Experimental, and Ethical, with tailored learning objectives to the pre-clinical, clinical, and clinical research stages of medical education. This review provides a road map for developing practical and relevant education strategies for building an AI-competent healthcare workforce., Comment: 25 pages, 2 figures, 3 tables

Published
2024

35. A network aggregation model for the dynamics and treatment of neurodegenerative diseases at the brain scale

Author

Brennan, Georgia S. and Goriely, Alain

Subjects
Mathematics - Dynamical Systems, Physics - Biological Physics, Physics - Medical Physics
Abstract

Neurodegenerative diseases are associated with the assembly of specific proteins into oligomers and fibrillar aggregates. At the brain scale, these protein assemblies can diffuse through the brain and seed other regions, creating an autocatalytic protein progression. The growth and transport of these assemblies depend on various mechanisms that can be targeted therapeutically. Here, we use spatially-extended nucleation-aggregation-fragmentation models for the dynamics of prion-like neurodegenerative protein-spreading in the brain to study the effect of different drugs on whole-brain Alzheimer's disease progression.

Published
2024

36. On the nature of yrast states in neutron-rich polonium isotopes

Author

Lică, R., Andreyev, A. N., Naïdja, H., Blazhev, A., Van Duppen, P., Andel, B., Algora, A., Antalic, S., Benito, J., Benzoni, G., Berry, T., Borge, M. J. G., Costache, C., Cubiss, J. G., De Witte, H., Fraile, L. M., Fynbo, H. O. U., Greenlees, P. T., Harkness-Brennan, L. J., Huyse, M., Illana, A., Jolie, J., Judson, D. S., Konki, J., Lazarus, I., Madurga, M., Marginean, N., Marginean, R., Mihai, C., Mihai, R. E., Mosat, P., Murias, J. R., Nacher, E., Negret, A., Page, R. D., Perea, A., Pucknell, V., Rahkila, P., Rezynkina, K., Sánchez-Tembleque, V., Schomacker, K., Stryjczyk, M., Sürder, C., Tengblad, O., Vedia, V., and Warr, N.

Subjects
Nuclear Experiment, Nuclear Theory
Abstract

Polonium isotopes having two protons above the shell closure at $Z=82$ show a wide variety of low-lying high-spin isomeric states across the whole chain. The structure of neutron-deficient isotopes up to $^{210}$Po ($N=126$) is well established as they are easily produced through various methods. However, there is not much information available for the neutron-rich counterparts for which only selective techniques can be used for their production. We report on the first fast-timing measurements of yrast states up to the 8$^+$ level in $^{214,216,218}$Po isotopes produced in the $\beta^-$ decay of $^{214,216,218}$Bi at ISOLDE, CERN. In particular, our new half-life value of 607(14) ps for the 8$_1^+$ state in $^{214}$Po is nearly 20 times shorter than the one available in literature and comparable with the newly measured half-lives of 409(16) and 628(25) ps for the corresponding 8$_1^+$ states in $^{216,218}$Po, respectively. The measured $B(E2;8_1^+ \to 6_1^+)$ transition probability values follow an increasing trend relative to isotope mass, reaching a maximum for $^{216}$Po. The increase contradicts the previous claims of isomerism for the $8^+$ yrast states in neutron-rich $^{214}$Po and beyond. Together with the other measured yrast transitions, the $B(E2)$ values provide a crucial test of the different theoretical approaches describing the underlying configurations of the yrast band. The new experimental results are compared to shell-model calculations using the KHPE and H208 effective interactions and their pairing modified versions, showing an increase in configuration mixing when moving towards the heavier isotopes., Comment: 6 pages, 5 figures (main manuscript), 2 pages (supplemental material)

Published
2024

37. Utility of virtual qubits in trapped-ion quantum computers

Author

Shivam, Saumya, Pokorny, Fabian, Vazquez-Brennan, Andres, Sotirova, Ana S., Leppard, Jamie D., Decoppet, Sophie M., Ballance, C. J., and Sondhi, S. L.

Subjects
Quantum Physics, Physics - Atomic Physics
Abstract

We propose encoding multiple qubits inside ions in existing trapped-ion quantum computers to access more qubits and to simplify circuits implementing standard algorithms. By using such `virtual' qubits, some inter-ion gates can be replaced by intra-ion gates, reducing the use of vibrational modes of the ion chain, leading to less noise. We discuss specific examples such as the Bernstein-Vazirani algorithm and random circuit sampling, using a small number of virtual qubits. Additionally, virtual qubits enable using larger number of data qubits for an error correcting code, and we consider the repetition code as an example. We also lay out practical considerations to be made when choosing states to encode virtual qubits in $^{137}\mathrm{Ba}^+$ ions, and for preparing states and performing measurements., Comment: 18+14 pages, 8+4 figures

Published
2024

38. Using graph neural networks to reconstruct charged pion showers in the CMS High Granularity Calorimeter

Author

Aamir, M., Acar, B., Adamov, G., Adams, T., Adloff, C., Afanasiev, S., Agrawal, C., Ahmad, A., Ahmed, H. A., Akbar, S., Akchurin, N., Akgul, B., Akgun, B., Akpinar, R. O., Aktas, E., AlKadhim, A., Alexakhin, V., Alimena, J., Alison, J., Alpana, A., Alshehri, W., Dominguez, P. Alvarez, Alyari, M., Amendola, C., Amir, R. B., Andersen, S. B., Andreev, Y., Antoszczuk, P. D., Aras, U., Ardila, L., Aspell, P., Avila, M., Awad, I., Aydilek, O., Azimi, Z., Pretel, A. Aznar, Bach, O. A., Bainbridge, R., Bakshi, A., Bam, B., Banerjee, S., Barney, D., Bayraktar, O., Beaudette, F., Beaujean, F., Becheva, E., Behera, P. K., Belloni, A., Bergauer, T., Besancon, M., Bylund, O. Bessidskaia, Bhatt, L., Bhowmil, D., Blekman, F., Blinov, P., Bloch, P., Bodek, A., Boger, a., Bonnemaison, A., Bouyjou, F., Brennan, L., Brondolin, E., Brusamolino, A., Bubanja, I., Perraguin, A. Buchot, Bunin, P., Misura, A. Burazin, Butler-nalin, A., Cakir, A., Callier, S., Campbell, S., Canderan, K., Cankocak, K., Cappati, A., Caregari, S., Carron, S., Carty, C., Cauchois, A., Ceard, L., Cerci, S., Chang, P. J., Chatterjee, R. M., Chatterjee, S., Chattopadhyay, P., Chatzistavrou, T., Chaudhary, M. S., Chauhan, A., Chen, J. A., Chen, J., Chen, Y., Cheng, K., Cheung, H., Chhikara, J., Chiron, A., Chiusi, M., Chokheli, D., Chudasama, R., Clement, E., Mendez, S. Coco, Coko, D., Coskun, K., Couderc, F., Crossman, B., Cui, Z., Cuisset, T., Cummings, G., Curtis, E. M., D'Alfonso, M., D-hler-ball, J., Dadazhanova, O., Damgov, J., Das, I., DasGupta, S., Dauncey, P., Mendes, A. David Tinoco, Davies, G., Davignon, O., DeLa, P. deBarbaroC., DeSilva, M., DeWit, A., Debbins, P., Defranchis, M. M., Delagnes, E., Devouge, P., Dewangan, C., DiGuglielmo, G., Diehl, L., Dilsiz, K., Dincer, G. G., Dittmann, J., Dragicevic, M., Du, D., Dubinchik, B., Dugad, S., Dulucq, F., Dumanoglu, I., Duran, B., Dutta, S., Dutta, V., Dychkant, A., Dünser, M., Edberg, T., Ehle, I. T., Berni, A. El, Elias, F., Eno, S. C., Erdogan, E. N., Erkmen, B., Ershov, Y., Ertorer, E. Y., Extier, S., Eychenne, L., Fedar, Y. E., Fedi, G., De Almeida, J. P. Figueiredo De De Sá Sousa, Alves, B. A. Fontana Santos Santos, Frahm, E., Francis, K., Freeman, J., French, T., Gaede, F., Gandhi, P. K., Ganjour, S., Garcia-Bellido, A., Gastaldi, F., Gazi, L., Gecse, Z., Gerwig, H., Gevin, O., Ghosh, S., Gill, K., Gleyzer, S., Godinovic, N., Goek, M., Goettlicher, P., Goff, R., Golunov, A., Gonultas, B., Martínez, J. D. González, Gorbounov, N., Gouskos, L., Gray, A., Gray, L., Grieco, C., Groenroos, S., Groner, D., Gruber, A., Grummer, A., Grönroos, S., Guilloux, F., Guler, Y., Gungordu, A. D., Guo, J., Guo, K., Guler, E. Gurpinar, Gutti, H. K., Guvenli, A. A., Gülmez, E., Hacisahinoglu, B., Halkin, Y., Machado, G. Hamilton Ilha, Hare, H. S., Hatakeyama, K., Heering, A. H., Hegde, V., Heintz, U., Hinton, N., Hinzmann, A., Hirschauer, J., Hitlin, D., Hos, İ., Hou, B., Hou, X., Howard, A., Howe, C., Hsieh, H., Hsu, T., Hua, H., Hummer, F., Imran, M., Incandela, J., Iren, E., Isildak, B., Jackson, P. S., Jackson, W. J., Jain, S., Jana, P., Jaroslavceva, J., Jena, S., Jige, A., Jordano, P. P., Joshi, U., Kaadze, K., Kafizov, A., Kalipoliti, L., Tharayil, A. Kallil, Kaluzinska, O., Kamble, S., Kaminskiy, A., Kanemura, M., Kanso, H., Kao, Y., Kapic, A., Kapsiak, C., Karjavine, V., Karmakar, S., Karneyeu, A., Kaya, M., Topaksu, A. Kayis, Kaynak, B., Kazhykarim, Y., Khan, F. A., Khudiakov, A., Kieseler, J., Kim, R. S., Klijnsma, T., Kloiber, E. G., Klute, M., Kocak, Z., Kodali, K. R., Koetz, K., Kolberg, T., Kolcu, O. B., Komaragiri, J. R., Komm, M., Kopsalis, I., Krause, H. A., Krawczyk, M. A., Vinayakam, T. R. Krishnaswamy, Kristiansen, K., Kristic, A., Krohn, M., Kronheim, B., Krüger, K., Kudtarkar, C., Kulis, S., Kumar, M., Kumar, N., Kumar, S., Verma, R. Kumar, Kunori, S., Kunts, A., Kuo, C., Kurenkov, A., Kuryatkov, V., Kyre, S., Ladenson, J., Lamichhane, K., Landsberg, G., Langford, J., Laudrain, A., Laughlin, R., Lawhorn, J., Dortz, O. Le, Lee, S. W., Lektauers, A., Lelas, D., Leon, M., Levchuk, L., Li, A. J., Li, J., Li, Y., Liang, Z., Liao, H., Lin, K., Lin, W., Lin, Z., Lincoln, D., Linssen, L., Litomin, A., Liu, G., Liu, Y., Lobanov, A., Lohezic, V., Loiseau, T., Lu, C., Lu, R., Lu, S. Y., Lukens, P., Mackenzie, M., Magnan, A., Magniette, F., Mahjoub, A., Mahon, D., Majumder, G., Makarenko, V., Malakhov, A., Malgeri, L., Mallios, S., Mandloi, C., Mankel, A., Mannelli, M., Mans, J., Mantilla, C., Martinez, G., Massa, C., Masterson, P., Matthewman, M., Matveev, V., Mayekar, S., Mazlov, I., Mehta, A., Mestvirishvili, A., Miao, Y., Milella, G., Mirza, I. R., Mitra, P., Moccia, S., Mohanty, G. B., Monti, F., Moortgat, F., Murthy, S., Music, J., Musienko, Y., Nabili, S., Nayak, S., Nelson, J. W., Nema, A., Neutelings, I., Niedziela, J., Nikitenko, A., Noonan, D., Noy, M., Nurdan, K., Obraztsov, S., Ochando, C., Ogul, H., Olsson, J., Onel, Y., Ozkorucuklu, S., Paganis, E., Palit, P., Pan, R., Pandey, S., Pantaleo, F., Papageorgakis, C., Paramesvaran, S., Paranjpe, M. M., Parolia, S., Parsons, A. G., Parygin, P., Paulini, M., Paus, C., Peñaló, K., Pedro, K., Pekic, V., Peltola, T., Peng, B., Perego, A., Perini, D., Petrilli, A., Pham, H., Pierre-Emile, T., Podem, S. K., Popov, V., Portales, L., Potok, O., Pradeep, P. B., Pramanik, R., Prosper, H., Prvan, M., Qasim, S. R., Qu, H., Quast, T., Trivino, A. Quiroga, Rabour, L., Raicevic, N., Rajpoot, H., Rao, M. A., Rapacz, K., Redjeb, W., Reinecke, M., Revering, M., Roberts, A., Rohlf, J., Rosado, P., Rose, A., Rothman, S., Rout, P. K., Rovere, M., Rumerio, P., Rusack, R., Rygaard, L., Ryjov, V., Sadivnycha, S., Sahin, M. Ö., Sakarya, U., Salerno, R., Saradhy, R., Saraf, M., Sarbandi, K., Sarkisla, M. A., Satyshev, I., Saud, N., Sauvan, J., Schindler, G., Schmidt, A., Schmidt, I., Schmitt, M. H., Sculac, A., Sculac, T., Sedelnikov, A., Seez, C., Sefkow, F., Selivanova, D., Selvaggi, M., Sergeychik, V., Sert, H., Shahid, M., Sharma, P., Sharma, R., Sharma, S., Shelake, M., Shenai, A., Shih, C. W., Shinde, R., Shmygol, D., Shukla, R., Sicking, E., Silva, P., Simsek, C., Simsek, E., Sirasva, B. K., Sirois, Y., Song, S., Song, Y., Soudais, G., Sriram, S., StJacques, R. R., StahlLeiton, A. G., Steen, A., Stein, J., Strait, J., Strobbe, N., Su, X., Sukhov, E., Suleiman, A., Cerci, D. Sunar, Suryadevara, P., Swain, K., Syal, C., Tali, B., Tanay, K., Tang, W., Tanvir, A., Tao, J., Tarabini, A., Tatli, T., Taylor, R., Taysi, Z. C., Teafoe, G., Tee, C. Z., Terrill, W., Thienpont, D., Thomas, R., Titov, M., Todd, C., Todd, E., Toms, M., Tosun, A., Troska, J., Tsai, L., Tsamalaidze, Z., Tsionou, D., Tsipolitis, G., Tsirigoti, M., Tu, R., Polat, S. N. Tural, Undleeb, S., Usai, E., Uslan, E., Ustinov, V., Vernazza, E., Viahin, O., Viazlo, O., Vichoudis, P., Vijay, A., Virdee, T., Voirin, E., Vojinovic, M., Voytishin, N., Vámi, T. Á., Wade, A., Walter, D., Wang, C., Wang, F., Wang, J., Wang, K., Wang, X., Wang, Y., Wang, Z., Wanlin, E., Wayne, M., Wetzel, J., Whitbeck, A., Wickwire, R., Wilmot, D., Wilson, J., Wu, H., Xiao, M., Yang, J., Yazici, B., Ye, Y., Yetkin, T., Yi, R., Yohay, R., Yu, T., Yuan, C., Yuan, X., Yuksel, O., YushmanoV, I., Yusuff, I., Zabi, A., Zareckis, D., Zarubin, A., Zehetner, P., Zghiche, A., Zhang, C., Zhang, D., Zhang, H., Zhang, J., Zhang, Z., Zhao, X., Zhong, J., Zhou, Y., and Zorbilmez, Ç.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment, Physics - Data Analysis, Statistics and Probability
Abstract

A novel method to reconstruct the energy of hadronic showers in the CMS High Granularity Calorimeter (HGCAL) is presented. The HGCAL is a sampling calorimeter with very fine transverse and longitudinal granularity. The active media are silicon sensors and scintillator tiles readout by SiPMs and the absorbers are a combination of lead and Cu/CuW in the electromagnetic section, and steel in the hadronic section. The shower reconstruction method is based on graph neural networks and it makes use of a dynamic reduction network architecture. It is shown that the algorithm is able to capture and mitigate the main effects that normally hinder the reconstruction of hadronic showers using classical reconstruction methods, by compensating for fluctuations in the multiplicity, energy, and spatial distributions of the shower's constituents. The performance of the algorithm is evaluated using test beam data collected in 2018 prototype of the CMS HGCAL accompanied by a section of the CALICE AHCAL prototype. The capability of the method to mitigate the impact of energy leakage from the calorimeter is also demonstrated., Comment: Prepared for submission to JINST

Published
2024

39. Knowledge, Attitude and Practice Around Breast Cancer and Mammography Screening Among Jordanian Women

Author

Al-Mousa DS, Alakhras M, Hossain SZ, Al-Sa’di AG, Al Hasan M, Al-Hayek Y, and Brennan PC

Subjects
breast cancer, knowledge, breast cancer screening, population health, mammography, jordan., Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Dana S Al-Mousa,1 Maram Alakhras,1 Syeda Z Hossain,2 Amani G Al-Sa’di,3 Marwa Al Hasan,1 Yazan Al-Hayek,4,5 Patrick C Brennan2 1Department of Allied Medical Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan; 2Sydney School of Health Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia; 3Technical Coordination and Consumer Education Section of the Jordanian Food and Drug Administration, Irbid 22110, Jordan; 4Medical Radiation Science, School of Dentistry and Health Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia; 5Faculty of Applied Health Sciences, The Hashemite University, Zarqa 13133, JordanCorrespondence: Dana S Al-Mousa Department of Allied Medical SciencesFaculty of Applied Medical Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, JordanTel +9622720100 Ext 26947Fax +96227095070Email dsalmusa@just.edu.joBackground: Breast cancer is the most common occurring cancer in women worldwide. To guide current breast cancer screening program, the level of knowledge about breast cancer should be evaluated. This study aims to ascertain the level of breast cancer knowledge including risk factors, signs and symptoms, and early detection methods, especially mammography screening.Methods: The study was conducted among 1353 Jordanian women from the public using a self-administered questionnaire. Responses to the knowledge test were summed for an overall knowledge score. Comparisons between socio-demographics and knowledge, attitude and practice were also measured using a Chi-square test.Results: About 76% of participants were aware that breast cancer is the most common cancer among women in Jordan. About 53.7% of our participants were rated as having an intermediate level of knowledge regarding risk factors, and 44% were rated as having a good to an excellent level of knowledge about breast cancer signs and symptoms. The participants’ level of education was the main factor identified as influencing the participants’ knowledge of the risk factors, signs and symptoms, and knowledge of early detection methods of breast cancer. The study sample was rated as having an intermediate level of knowledge regarding mammography screening; however, their participation in this screening method was low.Conclusion: Although Jordanian women had an acceptable level of knowledge of breast cancer, the screening rates for mammography were low. These findings suggest that there is a need to provide extra awareness programs for Jordanian women to improve their breast cancer knowledge and practice.Keywords: breast cancer, knowledge, breast cancer screening, population health, mammography, Jordan

Published
2020

40. Gemini 1.5: Unlocking multimodal understanding across millions of tokens of context

Author

Gemini Team, Georgiev, Petko, Lei, Ving Ian, Burnell, Ryan, Bai, Libin, Gulati, Anmol, Tanzer, Garrett, Vincent, Damien, Pan, Zhufeng, Wang, Shibo, Mariooryad, Soroosh, Ding, Yifan, Geng, Xinyang, Alcober, Fred, Frostig, Roy, Omernick, Mark, Walker, Lexi, Paduraru, Cosmin, Sorokin, Christina, Tacchetti, Andrea, Gaffney, Colin, Daruki, Samira, Sercinoglu, Olcan, Gleicher, Zach, Love, Juliette, Voigtlaender, Paul, Jain, Rohan, Surita, Gabriela, Mohamed, Kareem, Blevins, Rory, Ahn, Junwhan, Zhu, Tao, Kawintiranon, Kornraphop, Firat, Orhan, Gu, Yiming, Zhang, Yujing, Rahtz, Matthew, Faruqui, Manaal, Clay, Natalie, Gilmer, Justin, Co-Reyes, JD, Penchev, Ivo, Zhu, Rui, Morioka, Nobuyuki, Hui, Kevin, Haridasan, Krishna, Campos, Victor, Mahdieh, Mahdis, Guo, Mandy, Hassan, Samer, Kilgour, Kevin, Vezer, Arpi, Cheng, Heng-Tze, de Liedekerke, Raoul, Goyal, Siddharth, Barham, Paul, Strouse, DJ, Noury, Seb, Adler, Jonas, Sundararajan, Mukund, Vikram, Sharad, Lepikhin, Dmitry, Paganini, Michela, Garcia, Xavier, Yang, Fan, Valter, Dasha, Trebacz, Maja, Vodrahalli, Kiran, Asawaroengchai, Chulayuth, Ring, Roman, Kalb, Norbert, Soares, Livio Baldini, Brahma, Siddhartha, Steiner, David, Yu, Tianhe, Mentzer, Fabian, He, Antoine, Gonzalez, Lucas, Xu, Bibo, Kaufman, Raphael Lopez, Shafey, Laurent El, Oh, Junhyuk, Hennigan, Tom, Driessche, George van den, Odoom, Seth, Lucic, Mario, Roelofs, Becca, Lall, Sid, Marathe, Amit, Chan, Betty, Ontanon, Santiago, He, Luheng, Teplyashin, Denis, Lai, Jonathan, Crone, Phil, Damoc, Bogdan, Ho, Lewis, Riedel, Sebastian, Lenc, Karel, Yeh, Chih-Kuan, Chowdhery, Aakanksha, Xu, Yang, Kazemi, Mehran, Amid, Ehsan, Petrushkina, Anastasia, Swersky, Kevin, Khodaei, Ali, Chen, Gowoon, Larkin, Chris, Pinto, Mario, Yan, Geng, Badia, Adria Puigdomenech, Patil, Piyush, Hansen, Steven, Orr, Dave, Arnold, Sebastien M. R., Grimstad, Jordan, Dai, Andrew, Douglas, Sholto, Sinha, Rishika, Yadav, Vikas, Chen, Xi, Gribovskaya, Elena, Austin, Jacob, Zhao, Jeffrey, Patel, Kaushal, Komarek, Paul, Austin, Sophia, Borgeaud, Sebastian, Friso, Linda, Goyal, Abhimanyu, Caine, Ben, Cao, Kris, Chung, Da-Woon, Lamm, Matthew, Barth-Maron, Gabe, Kagohara, Thais, Olszewska, Kate, Chen, Mia, Shivakumar, Kaushik, Agarwal, Rishabh, Godhia, Harshal, Rajwar, Ravi, Snaider, Javier, Dotiwalla, Xerxes, Liu, Yuan, Barua, Aditya, Ungureanu, Victor, Zhang, Yuan, Batsaikhan, Bat-Orgil, Wirth, Mateo, Qin, James, Danihelka, Ivo, Doshi, Tulsee, Chadwick, Martin, Chen, Jilin, Jain, Sanil, Le, Quoc, Kar, Arjun, Gurumurthy, Madhu, Li, Cheng, Sang, Ruoxin, Liu, Fangyu, Lamprou, Lampros, Munoz, Rich, Lintz, Nathan, Mehta, Harsh, Howard, Heidi, Reynolds, Malcolm, Aroyo, Lora, Wang, Quan, Blanco, Lorenzo, Cassirer, Albin, Griffith, Jordan, Das, Dipanjan, Lee, Stephan, Sygnowski, Jakub, Fisher, Zach, Besley, James, Powell, Richard, Ahmed, 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Henryk, Viola, Fabio, Quitry, Felix de Chaumont, Lan, Charline Le, Hudson, Tom, Wang, Qingze, Fischer, Felix, Zheng, Ivy, White, Elspeth, Dragan, Anca, Alayrac, Jean-baptiste, Ni, Eric, Pritzel, Alexander, Iwanicki, Adam, Isard, Michael, Bulanova, Anna, Zilka, Lukas, Dyer, Ethan, Sachan, Devendra, Srinivasan, Srivatsan, Muckenhirn, Hannah, Cai, Honglong, Mandhane, Amol, Tariq, Mukarram, Rae, Jack W., Wang, Gary, Ayoub, Kareem, FitzGerald, Nicholas, Zhao, Yao, Han, Woohyun, Alberti, Chris, Garrette, Dan, Krishnakumar, Kashyap, Gimenez, Mai, Levskaya, Anselm, Sohn, Daniel, Matak, Josip, Iturrate, Inaki, Chang, Michael B., Xiang, Jackie, Cao, Yuan, Ranka, Nishant, Brown, Geoff, Hutter, Adrian, Mirrokni, Vahab, Chen, Nanxin, Yao, Kaisheng, Egyed, Zoltan, Galilee, Francois, Liechty, Tyler, Kallakuri, Praveen, Palmer, Evan, Ghemawat, Sanjay, Liu, Jasmine, Tao, David, Thornton, Chloe, Green, Tim, Jasarevic, Mimi, Lin, Sharon, Cotruta, Victor, Tan, Yi-Xuan, Fiedel, Noah, Yu, Hongkun, Chi, Ed, Neitz, Alexander, Heitkaemper, Jens, Sinha, Anu, Zhou, Denny, Sun, Yi, Kaed, Charbel, Hulse, Brice, Mishra, Swaroop, Georgaki, Maria, Kudugunta, Sneha, Farabet, Clement, Shafran, Izhak, Vlasic, Daniel, Tsitsulin, Anton, Ananthanarayanan, Rajagopal, Carin, Alen, Su, Guolong, Sun, Pei, V, Shashank, Carvajal, Gabriel, Broder, Josef, Comsa, Iulia, Repina, Alena, Wong, William, Chen, Warren Weilun, Hawkins, Peter, Filonov, Egor, Loher, Lucia, Hirnschall, Christoph, Wang, Weiyi, Ye, Jingchen, Burns, Andrea, Cate, Hardie, Wright, Diana Gage, Piccinini, Federico, Zhang, Lei, Lin, Chu-Cheng, Gog, Ionel, Kulizhskaya, Yana, Sreevatsa, Ashwin, Song, Shuang, Cobo, Luis C., Iyer, Anand, Tekur, Chetan, Garrido, Guillermo, Xiao, Zhuyun, Kemp, Rupert, Zheng, Huaixiu Steven, Li, Hui, Agarwal, Ananth, Ngani, Christel, Goshvadi, Kati, Santamaria-Fernandez, Rebeca, Fica, Wojciech, Chen, Xinyun, Gorgolewski, Chris, Sun, Sean, Garg, Roopal, Ye, Xinyu, Eslami, S. M. Ali, Hua, Nan, Simon, Jon, Joshi, Pratik, Kim, Yelin, Tenney, Ian, Potluri, Sahitya, Thiet, Lam Nguyen, Yuan, Quan, Luisier, Florian, Chronopoulou, Alexandra, Scellato, Salvatore, Srinivasan, Praveen, Chen, Minmin, Koverkathu, Vinod, Dalibard, Valentin, Xu, Yaming, Saeta, Brennan, Anderson, Keith, Sellam, Thibault, Fernando, Nick, Huot, Fantine, Jung, Junehyuk, Varadarajan, Mani, Quinn, Michael, Raul, Amit, Le, Maigo, Habalov, Ruslan, Clark, Jon, Jalan, Komal, Bullard, Kalesha, Singhal, Achintya, Luong, Thang, Wang, Boyu, Rajayogam, Sujeevan, Eisenschlos, Julian, Jia, Johnson, Finchelstein, Daniel, Yakubovich, Alex, Balle, Daniel, Fink, Michael, Agarwal, Sameer, Li, Jing, Dvijotham, Dj, Pal, Shalini, Kang, Kai, Konzelmann, Jaclyn, Beattie, Jennifer, Dousse, Olivier, Wu, Diane, Crocker, Remi, Elkind, Chen, Jonnalagadda, Siddhartha Reddy, Lee, Jong, Holtmann-Rice, Dan, Kallarackal, Krystal, Liu, Rosanne, Vnukov, Denis, Vats, Neera, Invernizzi, Luca, Jafari, Mohsen, Zhou, Huanjie, Taylor, Lilly, Prendki, Jennifer, Wu, Marcus, Eccles, Tom, Liu, Tianqi, Kopparapu, Kavya, Beaufays, Francoise, Angermueller, Christof, Marzoca, Andreea, Sarcar, Shourya, Dib, Hilal, Stanway, Jeff, Perbet, Frank, Trdin, Nejc, Sterneck, Rachel, Khorlin, Andrey, Li, Dinghua, Wu, Xihui, Goenka, Sonam, Madras, David, Goldshtein, Sasha, Gierke, Willi, Zhou, Tong, Liu, Yaxin, Liang, Yannie, White, Anais, Li, Yunjie, Singh, Shreya, Bahargam, Sanaz, Epstein, Mark, Basu, Sujoy, Lao, Li, Ozturel, Adnan, Crous, Carl, Zhai, Alex, Lu, Han, Tung, Zora, Gaur, Neeraj, Walton, Alanna, Dixon, Lucas, Zhang, Ming, Globerson, Amir, Uy, Grant, Bolt, Andrew, Wiles, Olivia, Nasr, Milad, Shumailov, Ilia, Selvi, Marco, Piccinno, Francesco, Aguilar, Ricardo, McCarthy, Sara, Khalman, Misha, Shukla, Mrinal, Galic, Vlado, Carpenter, John, Villela, Kevin, Zhang, Haibin, Richardson, Harry, Martens, James, Bosnjak, Matko, Belle, Shreyas Rammohan, Seibert, Jeff, Alnahlawi, Mahmoud, McWilliams, Brian, Singh, Sankalp, Louis, Annie, Ding, Wen, Popovici, Dan, Simicich, Lenin, Knight, Laura, Mehta, Pulkit, Gupta, Nishesh, Shi, Chongyang, Fatehi, Saaber, Mitrovic, Jovana, Grills, Alex, Pagadora, Joseph, Petrova, Dessie, Eisenbud, Danielle, Zhang, Zhishuai, Yates, Damion, Mittal, Bhavishya, Tripuraneni, Nilesh, Assael, Yannis, Brovelli, Thomas, Jain, Prateek, Velimirovic, Mihajlo, Akbulut, Canfer, Mu, Jiaqi, Macherey, Wolfgang, Kumar, Ravin, Xu, Jun, Qureshi, Haroon, Comanici, Gheorghe, Wiesner, Jeremy, Gong, Zhitao, Ruddock, Anton, Bauer, Matthias, Felt, Nick, GP, Anirudh, Arnab, Anurag, Zelle, Dustin, Rothfuss, Jonas, Rosgen, Bill, Shenoy, Ashish, Seybold, Bryan, Li, Xinjian, Mudigonda, Jayaram, Erdogan, Goker, Xia, Jiawei, Simsa, Jiri, Michi, Andrea, Yao, Yi, Yew, Christopher, Kan, Steven, Caswell, Isaac, Radebaugh, Carey, Elisseeff, Andre, Valenzuela, Pedro, McKinney, Kay, Paterson, Kim, Cui, Albert, Latorre-Chimoto, Eri, Kim, Solomon, Zeng, William, Durden, Ken, Ponnapalli, Priya, Sosea, Tiberiu, 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Pongetti, Francesco, de Cesare, Dario, Hwang, Dongseong, Yu, Lily, Pullman, Jennifer, Narayanan, Srini, Levin, Kyle, Gopal, Siddharth, Li, Megan, Aharoni, Asaf, Trinh, Trieu, Lo, Jessica, Casagrande, Norman, Vij, Roopali, Matthey, Loic, Ramadhana, Bramandia, Matthews, Austin, Carey, CJ, Johnson, Matthew, Goranova, Kremena, Shah, Rohin, Ashraf, Shereen, Dasgupta, Kingshuk, Larsen, Rasmus, Wang, Yicheng, Vuyyuru, Manish Reddy, Jiang, Chong, Ijazi, Joana, Osawa, Kazuki, Smith, Celine, Boppana, Ramya Sree, Bilal, Taylan, Koizumi, Yuma, Xu, Ying, Altun, Yasemin, Shabat, Nir, Bariach, Ben, Korchemniy, Alex, Choo, Kiam, Ronneberger, Olaf, Iwuanyanwu, Chimezie, Zhao, Shubin, Soergel, David, Hsieh, Cho-Jui, Cai, Irene, Iqbal, Shariq, Sundermeyer, Martin, Chen, Zhe, Bursztein, Elie, Malaviya, Chaitanya, Biadsy, Fadi, Shroff, Prakash, Dhillon, Inderjit, Latkar, Tejasi, Dyer, Chris, Forbes, Hannah, Nicosia, Massimo, Nikolaev, Vitaly, Greene, Somer, Georgiev, Marin, Wang, Pidong, Martin, Nina, Sedghi, Hanie, Zhang, John, Banzal, Praseem, Fritz, Doug, Rao, Vikram, Wang, Xuezhi, Zhang, Jiageng, Patraucean, Viorica, Du, Dayou, Mordatch, Igor, Jurin, Ivan, Liu, Lewis, Dubey, Ayush, Mohan, Abhi, Nowakowski, Janek, Ion, Vlad-Doru, Wei, Nan, Tojo, Reiko, Raad, Maria Abi, Hudson, Drew A., Keshava, Vaishakh, Agrawal, Shubham, Ramirez, Kevin, Wu, Zhichun, Nguyen, Hoang, Liu, Ji, Sewak, Madhavi, Petrini, Bryce, Choi, DongHyun, Philips, Ivan, Wang, Ziyue, Bica, Ioana, Garg, Ankush, Wilkiewicz, Jarek, Agrawal, Priyanka, Guo, Danhao, Xue, Emily, Shaik, Naseer, Leach, Andrew, Khan, Sadh MNM, Wiesinger, Julia, Jerome, Sammy, Chakladar, Abhishek, Wang, Alek Wenjiao, Ornduff, Tina, Abu, Folake, Ghaffarkhah, Alireza, Wainwright, Marcus, Cortes, Mario, Liu, Frederick, Maynez, Joshua, Terzis, Andreas, Samangouei, Pouya, Mansour, Riham, Kępa, Tomasz, Aubet, François-Xavier, Algymr, Anton, Banica, Dan, Weisz, Agoston, Orban, Andras, Senges, Alexandre, Andrejczuk, Ewa, Geller, Mark, Santo, Niccolo Dal, Anklin, Valentin, Merey, Majd Al, Baeuml, Martin, Strohman, Trevor, Bai, Junwen, Petrov, Slav, Wu, Yonghui, Hassabis, Demis, Kavukcuoglu, Koray, Dean, Jeffrey, and Vinyals, Oriol

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

In this report, we introduce the Gemini 1.5 family of models, representing the next generation of highly compute-efficient multimodal models capable of recalling and reasoning over fine-grained information from millions of tokens of context, including multiple long documents and hours of video and audio. The family includes two new models: (1) an updated Gemini 1.5 Pro, which exceeds the February version on the great majority of capabilities and benchmarks; (2) Gemini 1.5 Flash, a more lightweight variant designed for efficiency with minimal regression in quality. Gemini 1.5 models achieve near-perfect recall on long-context retrieval tasks across modalities, improve the state-of-the-art in long-document QA, long-video QA and long-context ASR, and match or surpass Gemini 1.0 Ultra's state-of-the-art performance across a broad set of benchmarks. Studying the limits of Gemini 1.5's long-context ability, we find continued improvement in next-token prediction and near-perfect retrieval (>99%) up to at least 10M tokens, a generational leap over existing models such as Claude 3.0 (200k) and GPT-4 Turbo (128k). Finally, we highlight real-world use cases, such as Gemini 1.5 collaborating with professionals on completing their tasks achieving 26 to 75% time savings across 10 different job categories, as well as surprising new capabilities of large language models at the frontier; when given a grammar manual for Kalamang, a language with fewer than 200 speakers worldwide, the model learns to translate English to Kalamang at a similar level to a person who learned from the same content.

Published
2024

41. Cohort study: Apparent redundancy of fibrosis assessment in young persons with HCV; development of realistic approaches to break the paradigm

Author

Brennan Paul Noel, Cartlidge Peter, Robinson Emma, Amarthingalam Asthika, and Dillon John Francis

Subjects
Hepatitis C Virus (HCV), Fibrosis assessment, Transient elastography, Non-invasive fibrosis markers, Specialties of internal medicine, RC581-951
Abstract

Introduction and Objectives: Hepatitis C Virus (HCV) is a blood-borne, hepatotropic RNA virus causing both acute and chronic infection. Chronic HCV infection predisposes individuals to liver fibrosis, cirrhosis and hepatocellular carcinoma. Staging of fibrosis prior to treatment to determine either treatment choice or required follow up, is standard practice. However, this often acts as a barrier to treatment initiation. We sought to validate the hypothesis that those individuals; mono-infected with HCV, ≤35 years of age; with no additional hepatic insult were unlikely to have significant fibrosis. Methods: We performed a retrospective analysis of a Hepatitis C Virus database; with collation of relevant basic demographics including age, sex and baseline Transient Elastography measurements pre-treatment. Additionally, we compared the reliability of biochemical fibrosis scores with corresponding transient elastography scores. Results: Our results support the hypothesis that those individuals with chronic HCV ≤35 years old, with no additional risk for fibrogenesis did not have significant liver fibrosis within our cohort. Conclusion: Patients ≤35 years old likely do not necessitate fibrosis assessment prior to Direct Acting Antiviral (DAA) treatment in the absence of other significant risk factors for fibrosis. Given the emerging evidence that DAA treatment results in a significant decrease in all-cause mortality and hepatocellular carcinoma development, treatment of those with chronic HCV represents a global priority.

Published
2022
Full Text
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42. Widening Participation in Scotland 1997-2021: A Semi-Systematic Literature Review and Avenues for Further Research

Author

Michelle O'Toole, Susan Dunnett, Mary Brennan, Thomas Calvard, and Liudmila Fakeyeva

Abstract

This article sets out and critically analyses the state of current knowledge on Widening Participation at higher education institutions in Scotland and sets forth avenues for further research. Through a semi-systematic review of the literature, six discrete but overlapping themes relating to Widening Participation are identified, namely, (1) factors affecting the decision to apply to university, (2) the transition from high school or further education into university, (3) contextualised admissions, (4) completion and level of attainment, (5) economic, social and cultural capital and (6) equality, diversity and inclusion. The study finds that while clear progress has been made by higher education institutions towards achieving quantitative government targets for student recruitment from underrepresented groups, there is an absence of studies and knowledge about the qualitative lived experiences of students as they transition through university, how students negotiate a sense of fit with institutional systems, and what targeted supports they may require to succeed. Avenues for further research which addresses these gaps in the knowledge base are put forward, namely, (1) broaden the academic base and interdisciplinarity of Widening Participation research, (2) reform and extend measures of success beyond admissions and attainment, (3) evolve institutional level support for transition into higher education, (4) develop more nuanced understandings of contextualised admissions and (5) investigate and gain deeper understandings of how the lived experiences of Widening Participation students shape and inform their journey through, experience of and attainment at university.

Published
2024
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43. Prenatal Cannabis Use and Offspring Autism-Related Behaviors: Examining Maternal Stress as a Moderator in a Black American Cohort

Author

C. Nutor, A. Dunlop, O. Sadler, and P. A. Brennan

Abstract

Prenatal cannabis use and maternal stress have been proposed as risk factors for autism spectrum disorder (ASD). Black mothers and mothers of lower socioeconomic status (SES) may be especially likely to experience high levels of stress. This study examined the impact of prenatal cannabis use and maternal stress (i.e., prenatal distress, racial discrimination, and lower SES) on child ASD-related behaviors in a sample of 172 Black mother-child pairs. We found that prenatal stress was significantly associated with ASD-related behaviors. Prenatal cannabis use did not predict ASD-related behaviors and did not interact with maternal stress to predict ASD-related behaviors. These findings replicate previous work on prenatal stress-ASD associations and add to the limited literature on prenatal cannabis-ASD associations in Black samples.

Published
2024
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44. A National Cohort Study of Spiritual and Religious Practices of Older People with Intellectual Disability

Author

Fiona Timmins, Darren McCausland, Damien Brennan, Fintan Sheerin, Retha Luus, Philip McCallion, and Mary McCarron

Abstract

Background: Spirituality and spiritual support for older people with intellectual disability are deemed important, however little is known about their specific needs. This paper reports for the first time on the religious and spiritual practices of older adults with intellectual disability. Methods: A national longitudinal study examined the prevalence of spiritual practices among older people with intellectual disability in the Republic of Ireland. Results: Older people with intellectual disability seek and receive solace from religious and spiritual practices, especially if they are lonely, in poor health, distressed or bereaved. There is likely a social benefit to spiritual and religious aspects of life that would be beneficial to explore further. Conclusions: Globally more research is required and efforts should be made to ensure greater opportunities for inclusion in societal spiritual and religious activities and to more clearly determine the spiritual needs of this population.

Published
2024
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45. Unpacking Power: The Role of Critical Reflection in Preschool Internship

Author

Charlene Montaño Nolan, Carolyn Brennan, and Tasha Tropp Laman

Abstract

This study examined the potential role of critical reflection as a tool to support pre-service early childhood teacher interns in understanding and questioning pedagogical choices witnessed in their preschool internships while developing their own socially responsible teaching capacity. This study contributes to the field of critical reflection in teacher education by emphasizing an analysis of power, using Patricia Hill Collins' matrices of power to understand the complexities of systemic injustices and identify potential solutions. The authors conducted an analysis of students' critical reflections, which were completed weekly during their quarter-long preschool internship. The authors found that a critical analytic lens, using power, created intentional space to pause and expand interpretations of unequal and inequitable dynamics within the students' preschool internship experiences, and had the potential to impact their subsequent pedagogical decisions. These findings hold the possibility for teacher preparation programs to bolster students' reflective praxis and seed justice-oriented possibilities in early childhood education.

Published
2024
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46. Gasification of coal, Chenopodium Album biomass, and co-gasification of a coal-biomass mixture by thermogravimetric-gas analysis

Author

Marco Antonio Ardila-Barragán, Ph. D. (c), Carlos Francisco Valdés-Rentería, Ph. D., Brennan Pecha, Ph. D., Alfonso López-Díaz, Ph. D., Eduardo Gil-Lancheros, M.Sc., Marley Cecilia Vanegas-Chamorro, Ph. D., Jesús Emilio Camporredondo-Saucedo, Ph. D., and Luis Fernando Lozano-Gómez, M.Sc.

Subjects
agglomerated mixtures, chenopodium album, coal-biomass, co-gasification, synergy, syngas, Engineering (General). Civil engineering (General), TA1-2040
Abstract

Gasification studies were performed on sub-bituminous coal of the province Centro in Boyacá state of Colombia, vegetable biomass Chenopodium album (cenizo) and co-gasification of coal-biomass mixtures agglomerated with paraffin in a thermogravimetric analyzer. Biomass synergistically promoted thermochemical transformation of the coal was observed. Experimental results were compared to equilibrium composition simulations. Ash fusibility tests of the coal-biomass mixture were carried out, which allowed to clarify its behavior, such as dry or fluid ash according to own chemical composition, during the gasification process. The experimental tests allowed determining the differences in thermal decomposition, between coal, cenizo and coal-biomass blend, which are attributable to the physicochemical properties of each one solid fuel. During the tests, gas chromatography analyses were performed to establish the compositions of the syngas. The syngas obtained from biomass had the highest concentration of CO and the lowest H2; the coal and the coal-biomass mixture were slightly minor respectively. Concentrations of CH4, CO2 and C2H4 were similar between coal and biomass. This result is consistent with the higher calorific value of the coal syngas. The production of syngas from the coal-biomass mixture had the lowest contents of H2 and CO due to synergistic phenomena that occur with the fuel mixture. The co-gasification of the mixture gave the highest syngas production, carbon conversion, and thermal efficiency. These results indicate the viability of co-gasification of coal-Chenopodium album agglomerated mixtures. In gasification of non-agglomerated mixtures of coal-cenizo, the biomass can be burned directly without producing syngas.

Published
2019
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47. Impaired ATP hydrolysis in blood plasma contributes to age-related neutrophil dysfunction.

Author

Ledderose, Carola, Valsami, Eleftheria-Angeliki, Elevado, Mark, Liu, Qing, Giva, Brennan, Curatolo, Julian, Delfin, Joshua, Abutabikh, Reem, and Junger, Wolfgang

Subjects
ATP hydrolysis, Aging, Mice, Neutrophil dysfunction, Purinergic signaling
Abstract

BACKGROUND: The function of polymorphonuclear neutrophils (PMNs) decreases with age, which results in infectious and inflammatory complications in older individuals. The underlying causes are not fully understood. ATP release and autocrine stimulation of purinergic receptors help PMNs combat microbial invaders. Excessive extracellular ATP interferes with these mechanisms and promotes inflammatory PMN responses. Here, we studied whether dysregulated purinergic signaling in PMNs contributes to their dysfunction in older individuals. RESULTS: Bacterial infection of C57BL/6 mice resulted in exaggerated PMN activation that was significantly greater in old mice (64 weeks) than in young animals (10 weeks). In contrast to young animals, old mice were unable to prevent the systemic spread of bacteria, resulting in lethal sepsis and significantly greater mortality in old mice than in their younger counterparts. We found that the ATP levels in the plasma of mice increased with age and that, along with the extracellular accumulation of ATP, the PMNs of old mice became increasingly primed. Stimulation of the formyl peptide receptors of those primed PMNs triggered inflammatory responses that were significantly more pronounced in old mice than in young animals. However, bacterial phagocytosis and killing by PMNs of old mice were significantly lower than that of young mice. These age-dependent PMN dysfunctions correlated with a decrease in the enzymatic activity of plasma ATPases that convert extracellular ATP to adenosine. ATPases depend on divalent metal ions, including Ca2+, Mg2+, and Zn2+, and we found that depletion of these ions blocked the hydrolysis of ATP and the formation of adenosine in human blood, resulting in ATP accumulation and dysregulation of PMN functions equivalent to those observed in response to aging. CONCLUSIONS: Our findings suggest that impaired hydrolysis of plasma ATP dysregulates PMN function in older individuals. We conclude that strategies aimed at restoring plasma ATPase activity may offer novel therapeutic opportunities to reduce immune dysfunction, inflammation, and infectious complications in older patients.

Published
2024

48. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi.

Author

Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Aguilar-Trigueros, Carlos, Andrew, Nigel, Babiy, Ulyana, Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana, Bonebrake, Timothy, Brennan, Georgina, Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin, Chapurlat, Elodie, Creer, Simon, DAcqui, Luigi, de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel, Jacobsen, Ida, Fisher, Brian, Flores de Jesus, Miguel, Gilbert, Gregory, Griffith, Gareth, Gritsuk, Anna, Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars, Hegbe, Apollon, Hill, Sarah, Hogg, Ian, Hultman, Jenni, Hyde, Kevin, Hynson, Nicole, Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhouse, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R, Nonti, Puani, Nordén, Jenni, Nordén, Björn, Norros, Veera, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala, Raundrup, Katrine, Rebriev, Yury, Rikkinen, Jouko, Rogers, Hanna, Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana, Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, van der Bank, F, and Vandenbrink, Bryan

Subjects
Air Microbiology, Biodiversity, DNA, Fungal, Fungi, Mycorrhizae, Phylogeny, Seasons, Spatio-Temporal Analysis, Spores, Fungal, Temperature, Tropical Climate, Geographic Mapping
Abstract

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5.

Published
2024

49. Liver disease and transplantation in telomere biology disorders: An international multicenter cohort.

Author

Wang, YunZu, Kaj-Carbaidwala, Batul, Lane, Adam, Agarwal, Suneet, Beier, Fabian, Bertuch, Alison, Borovsky, Kristin, Brennan, Steven, Calado, Rodrigo, Catto, Luiz, Dufour, Carlo, Ebens, Christen, Fioredda, Francesca, Giri, Neelam, Gloude, Nicholas, Goldman, Frederick, Hertel, Paula, Himes, Ryan, Keel, Sioban, Koura, Divya, Kratz, Christian, Kulkarni, Sakil, Liou, Iris, Nakano, Taizo, Nastasio, Silvia, Niewisch, Marena, Penrice, Daniel, Sasa, Ghadir, Savage, Sharon, Simonetto, Douglas, Ziegler, David, Miethke, Alexander, and Myers, Kasiani

Subjects
Humans, Liver Transplantation, Female, Male, Retrospective Studies, Adult, Middle Aged, Telomere, Adolescent, Liver Diseases, Young Adult, Child, Treatment Outcome, Child, Preschool
Abstract

BACKGROUND: Patients with telomere biology disorders (TBD) develop hepatic disease, including hepatitis, cirrhosis, and hepatopulmonary syndrome. No specific treatment exists for TBD-related liver disease, and the role of liver transplantation (LT) remains controversial. Our study objectives were to describe the clinical characteristics, management, and outcomes in patients with TBD-related liver disease, and their LT outcomes. METHODS: Data from 83 patients with TBD-associated liver disease were obtained from 17 participating centers in the Clinical Care Consortium of Telomere-Associated Ailments and by self-report for our retrospective, multicenter, international cohort study. RESULTS: Group A (Advanced) included 40 patients with advanced liver disease. Of these, 20 underwent LT (Group AT). Group M (Mild) included 43 patients not warranting LT evaluation, none of whom were felt to be medically unfit for liver transplantation. Supplemental oxygen requirement, pulmonary arteriovenous malformation, hepatopulmonary syndrome, and higher bilirubin and international normalized ratio values were associated with Group A. Other demographics, clinical manifestations, and laboratory findings were similar between groups. Six group A patients were declined for LT; 3 died on the waitlist. Median follow-up post-LT was 2.9 years (range 0.6-13.2 y). One-year survival post-LT was 73%. Median survival post-LT has not been reached. Group AT patients had improved survival by age compared to all nontransplant patients (log-rank test p = 0.02). Of 14 patients with pretransplant hypoxemia, 8 (57%) had improved oxygenation after transplant. CONCLUSIONS: LT recipients with TBD do not exhibit excessive posttransplant mortality, and LT improved respiratory status in 57%. A TBD diagnosis should not exclude LT consideration.

Published
2024

50. Development and validation of a biomarker index for HCC treatment response.

Author

Liang, Jeff, Li, Po-Yi, Norman, Joshua, Lauzon, Marie, Yeo, Yee, Trivedi, Hirsh, Ayoub, Walid, Kuo, Alexander, Friedman, Marc, Sankar, Kamya, Gong, Jun, Osipov, Arsen, Hendifar, Andrew, Todo, Tsuyoshi, Kim, Irene, Voidonikolas, Georgios, Brennan, Todd, Wisel, Steven, Steggarda, Justin, Kosari, Kambiz, Saouaf, Rola, Nissen, Nicholas, Yao, Francis, Mehta, Neil, and Yang, Ju

Subjects
Humans, Liver Neoplasms, Carcinoma, Hepatocellular, Female, Male, Middle Aged, Biomarkers, Tumor, Liver Transplantation, alpha-Fetoproteins, Aged, Treatment Outcome, Sensitivity and Specificity, Retrospective Studies
Abstract

BACKGROUND: Serum AFP-L3%, AFP, and DCP are useful biomarkers for HCC detection, but their utility in assessing treatment response remains unknown. We aim to evaluate the accuracy of a biomarker model in the detection of posttreatment viable tumors. METHODS: For model derivation, recipients with HCC undergoing liver transplant from 2018 to 2022 who had biomarkers collected within 3 months before transplant were included. We developed a generalized linear model for detecting posttreatment viable tumors with the 3 biomarkers as covariates, which we termed the LAD Score. An independent cohort of 117 patients with HCC was used for external validation. RESULTS: Among 205 recipients of transplant, 70.2% had evidence of viable tumor on explant. The median LAD score was higher among patients with viable versus nonviable tumors (1.06 vs. 0.465, p < 0.001). The LAD score had a sensitivity of 55.6% and a specificity of 85.1% at the cutoff of 0.927, which was more accurate than imaging for detecting posttreatment viable tumors (AUROC 0.736 vs. 0.643, respectively; p = 0.045). The superior performance of the LAD score over imaging is primarily driven by its greater accuracy in detecting tumors

Published
2024

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