53 results on '"D, Mullins"'
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2. Locking Machine Learning Models into Hardware.
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Eleanor Clifford, Adhithya Saravanan, Harry Langford, Cheng Zhang, Yiren Zhao, Robert D. Mullins, Ilia Shumailov, and Jamie Hayes
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- 2024
- Full Text
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3. Beyond Slow Signs in High-fidelity Model Extraction.
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Hanna Foerster, Robert D. Mullins, Ilia Shumailov, and Jamie Hayes
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- 2024
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4. Unlocking the Global Synergies in Low-Rank Adapters.
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Zixi Zhang, Cheng Zhang, Xitong Gao, Robert D. Mullins, George A. Constantinides, and Yiren Zhao
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- 2024
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5. Architectural Neural Backdoors from First Principles.
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Harry Langford, Ilia Shumailov, Yiren Zhao, Robert D. Mullins, and Nicolas Papernot
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- 2024
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6. Optimised Grouped-Query Attention Mechanism for Transformers.
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Yuang Chen, Cheng Zhang, Xitong Gao, Robert D. Mullins, George A. Constantinides, and Yiren Zhao
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- 2024
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7. Dynamic Stashing Quantization for Efficient Transformer Training.
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Guo Yang, Daniel Lo, Robert D. Mullins, and Yiren Zhao
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- 2023
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8. Architectural Backdoors in Neural Networks.
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Mikel Bober-Irizar, Ilia Shumailov, Yiren Zhao, Robert D. Mullins, and Nicolas Papernot
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- 2023
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9. Revisiting Automated Prompting: Are We Actually Doing Better?
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Yulin Zhou, Yiren Zhao, Ilia Shumailov, Robert D. Mullins, and Yarin Gal
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- 2023
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10. Revisiting Structured Dropout.
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Yiren Zhao, Oluwatomisin Dada, Robert D. Mullins, and Xitong Gao
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- 2023
11. Trace-and-brace (TAB): bespoke software countermeasures against soft errors.
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Yousun Ko 0001, Alex Bradbury, Bernd Burgstaller, and Robert D. Mullins
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- 2022
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12. DAdaQuant: Doubly-adaptive quantization for communication-efficient Federated Learning.
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Robert Hönig, Yiren Zhao, and Robert D. Mullins
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- 2022
13. Sim-D: A SIMD Accelerator for Hard Real-Time Systems.
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Roy Spliet and Robert D. Mullins
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- 2022
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14. LLM4DV: Using Large Language Models for Hardware Test Stimuli Generation.
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Zixi Zhang, Greg Chadwick, Hugo McNally, Yiren Zhao, and Robert D. Mullins
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- 2023
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15. Human-Producible Adversarial Examples.
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David Khachaturov, Yue Gao 0011, Ilia Shumailov, Robert D. Mullins, Ross J. Anderson, and Kassem Fawaz
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- 2023
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16. Rapid Model Architecture Adaption for Meta-Learning.
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Yiren Zhao, Xitong Gao, Ilia Shumailov, Nicolò Fusi, and Robert D. Mullins
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- 2022
17. Model Architecture Adaption for Bayesian Neural Networks.
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Duo Wang, Yiren Zhao, Ilia Shumailov, and Robert D. Mullins
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- 2022
18. Augmentation Backdoors.
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Joseph Rance, Yiren Zhao, Ilia Shumailov, and Robert D. Mullins
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- 2022
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19. Wide Attention Is The Way Forward For Transformers.
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Jason Ross Brown, Yiren Zhao, Ilia Shumailov, and Robert D. Mullins
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- 2022
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20. DARTFormer: Finding The Best Type Of Attention.
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Jason Ross Brown, Yiren Zhao, Ilia Shumailov, and Robert D. Mullins
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- 2022
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21. Efficient Adversarial Training With Data Pruning.
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Maximilian Kaufmann, Yiren Zhao, Ilia Shumailov, Robert D. Mullins, and Nicolas Papernot
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- 2022
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22. Revisiting Embeddings for Graph Neural Networks.
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Skye Purchase, Aaron Zhao, and Robert D. Mullins
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- 2022
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23. Revisiting Structured Dropout.
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Yiren Zhao, Oluwatomisin Dada, Xitong Gao, and Robert D. Mullins
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- 2022
- Full Text
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24. Architectural Backdoors in Neural Networks.
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Mikel Bober-Irizar, Ilia Shumailov, Yiren Zhao, Robert D. Mullins, and Nicolas Papernot
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- 2022
- Full Text
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25. ImpNet: Imperceptible and blackbox-undetectable backdoors in compiled neural networks.
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Tim Clifford, Ilia Shumailov, Yiren Zhao, Ross J. Anderson, and Robert D. Mullins
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- 2022
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26. Muntjac - Open Source Multicore RV64 Linux-capable SoC.
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Xuan Guo, Daniel Bates, Robert D. Mullins, and Alex Bradbury
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- 2022
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27. Blockade of Kv7 channels reverses the inhibitory effects of exchange protein directly activated by cAMP activation on purinergic contractions of the murine detrusor
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Zhihui Fong, Anshika Lall, Nicolas D. Mullins, L. Fernando Santana, Mark A. Hollywood, Keith D. Thornbury, and Gerard P. Sergeant
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Pharmacology ,General Medicine ,Toxicology - Published
- 2023
28. O129 Patient satisfaction with long-term sacral neuromodulation for faecal incontinence: experience from a single tertiary centre
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S A Martin, A D O'Connor, D Selvakumar, W Baraza, G Faulkner, D Mullins, E S Kiff, K J Telford, and A Sharma
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Surgery - Abstract
Introduction Sacral neuromodulation is an established intervention for faecal incontinence (FI). This investigation aimed to determine the relationship between patient satisfaction and (1) device status (active/inactive) and (2) long-term functional outcomes. Methods Patients treated with sacral neuromodulation for at least 5 years reported bowel habits, FI severity, and impact on quality of life via bowel diaries, St. Marks incontinence score, and the Manchester Health Questionnaire at baseline and follow-up. On all measures, lower scores represent favourable outcomes. Satisfaction since treatment initiation and over the preceding 2 weeks was assessed using visual analogue scales (0%-100%). Individuals with inactive devices were awaiting battery revision surgery due to service delays encountered during the COVID-19 pandemic. Results In total, 74/110 eligible individuals completed follow-up measures (median: 130 months). Median overall satisfaction was high at 80% (IQR:60%-95%, n=70). Median two-week satisfaction was 75% (IQR:40%-90%, n=50) for individuals with active devices, and 20% (IQR:0%-45%, n=17) for those with inactive devices. Between-group differences were significant for two-week satisfaction (p Conclusion Standardised outcome measures reflect subjective satisfaction but cannot be used alone to assess positive outcomes as perceived by patients. Timely device revision is imperative for continued success of treatment.
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- 2023
29. Detection of clonotypic DNA in the cerebrospinal fluid as a marker of central nervous system invasion in lymphoma
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Andrew R. Hsu, Pamela C Egan, Diana O. Treaba, Max Petersen, James N. Butera, Rabin Niroula, Adam J. Olszewski, Anna Chorzalska, Patrycja M. Dubielecka, John L. Reagan, Thomas A Ollila, Adam Zayac, John Vatkevich, Jordan Robison, Ilyas Sahin, Chelsea D. Mullins, Habibe Kurt, and Allison P. Jacob
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Central Nervous System ,Pathology ,medicine.medical_specialty ,Lymphoma, B-Cell ,Clinical Trials and Observations ,Central nervous system ,Aggressive lymphoma ,Flow cytometry ,law.invention ,chemistry.chemical_compound ,Cerebrospinal fluid ,law ,Cytology ,hemic and lymphatic diseases ,Medicine ,Humans ,Polymerase chain reaction ,medicine.diagnostic_test ,business.industry ,Lymphoma, Non-Hodgkin ,Hematology ,DNA ,medicine.disease ,Lymphoma ,medicine.anatomical_structure ,chemistry ,business ,Biomarkers - Abstract
Key Points The NGS-MRD assay detected clonotypic DNA in 100% of CSF samples from patients who had lymphoma with parenchymal CNS involvement.Clonotypic DNA in CSF was present in 36% of newly diagnosed aggressive lymphomas and was associated with a 29% risk of CNS recurrence., Visual Abstract, The diagnosis of parenchymal central nervous system (CNS) invasion and prediction of risk for future CNS recurrence are major challenges in the management of aggressive lymphomas, and accurate biomarkers are needed to supplement clinical risk predictors. For this purpose, we studied the results of a next-generation sequencing (NGS)–based assay that detects tumor-derived DNA for clonotypic immunoglobulin gene rearrangements in the cerebrospinal fluid (CSF) of patients with lymphomas. Used as a diagnostic tool, the NGS-minimal residual disease (NGS-MRD) assay detected clonotypic DNA in 100% of CSF samples from 13 patients with known CNS involvement. They included 7 patients with parenchymal brain disease only, whose CSF tested negative by standard cytology and flow cytometry, and 6 historical DNA aliquots collected from patients at a median of 39 months before accession, which had failed to show clonal rearrangements using standard polymerase chain reaction. For risk prognostication, we prospectively collected CSF from 22 patients with newly diagnosed B-cell lymphomas at high clinical risk of CNS recurrence, of whom 8 (36%) had detectable clonotypic DNA in the CSF. Despite intrathecal prophylaxis, a positive assay of CSF was associated with a 29% cumulative risk of CNS recurrence within 12 months of diagnosis, in contrast with a 0% risk among patients with negative CSF (P = .045). These observations suggest that detection of clonotypic DNA can aid in the diagnosis of suspected parenchymal brain recurrence in aggressive lymphoma. Furthermore, the NGS-MRD assay may enhance clinical risk assessment for CNS recurrence among patients with newly diagnosed lymphomas and help select those who may benefit most from novel approaches to CNS-directed prophylaxis.
- Published
- 2021
30. Sacral neuromodulation: time to seize the opportunity to collaborate on a ‘de-prioritised’ service?
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A. O’Connor, D. Mullins, A. Sharma, G. Faulkner, and K. Telford
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Gastroenterology ,Surgery - Published
- 2023
31. Synthesis and Evaluation of Prodrugs of α-Carboxy Nucleoside Phosphonates
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Alan Ford, Nicholas D. Mullins, Jan Balzarini, and Anita R. Maguire
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Anti-HIV Agents ,Organic Chemistry ,Organophosphonates ,Prodrugs ,Nucleosides ,Esters - Abstract
A range of lipophilic prodrugs of α-carboxy nucleoside phosphonates, potent inhibitors of HIV-1 reverse transcriptase without requiring prior phosphorylation, were synthesized to evaluate their in vivo potency against HIV in cell culture. A series of prodrug derivatives bearing a free carboxylic acid where the phosphonate was masked with bispivaloyloxymethyl, diisopropyloxycarbonyloxymethyl, bisamidate, aryloxyphosphoramidate, hexadecyloxypropyl, CycloSal, and acycloxybenzyl moieties were synthesized, adapting existing methodologies for phosphonate protection to accommodate the adjacent carboxylic acid moiety. The prodrugs were assayed for anti-HIV activity in CEM cell cultures─the bispivaloyloxymethyl free acid monophosphonate prodrug exhibited some activity (inhibitory concentration-50 (IC
- Published
- 2022
32. Replicated Adsorption Technique used to Resolve ALX148 Interference in the Immunohematology Reference Laboratory
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M Flaws, K Hartman, C Geurkink, D Mullins, K Ha, J G Zinni, and A Pahomi
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General Medicine - Abstract
Introduction/Objective Increased expression of CD47 by cancer cells inhibits macrophages' phagocytic activity through CD47-SIRPα interactions, allowing evasion of the innate immune system. Several drugs on the market have been developed to target this interaction, including monoclonal therapeutics and fusion proteins. ALX148 is a genetically engineered SIRPα fusion protein with an inactivated Fc portion. CD47 is expressed highly on red blood cells (RBC), resulting in strong interference in pre-transfusion compatibility testing of patients receiving ALX148. Consequently, trial patients are at increased risk of transfusion-related adverse events or delay of needed transfusion. Few resolutions of ALX148 interference to assess underlying alloantibody development have been reported. One such examiniation demonstrated x6 linear papain-treated RBC adsorptions removed ALX148 interference. This study aimed to replicate these findings. Methods/Case Report Three patients receiving combination ALX148 (dose 6.57-20mg/mL) and Azacitidine therapy with broad-reactive RBC antibody reactivity were selected. High volume alloadsorptions (8:1 RBC:plasma) were performed with papain-treated rr (ccdee) RBCs. Adsorptions were incubated at 37C for 10 minutes. Polyethylene glycol (PEG) was utilized in test tube indirect antiglobulin testing (IAT). Results (if a Case Study enter NA) Initial reactivity strength was 3-4+ at PEG-IAT and saline-IAT with a three-cell screening RBC reagent. Alloadsorbed plasma was non-reactive at IAT with a three-cell screening RBC reagent enhanced by PEG. Drug interference was removed following three times high volume papain-treated alloadsorption. Conclusion Cancer immunotherapies have transformed the standard of care in oncology. Despite the evident clinical success, the medical laboratory has been challenged with adapting to cancer drug therapies capable of causing interference in routine laboratory testing. Clinical trials of ALX148 are associated with interference in pre-transfusion compatibility testing. The use of extended phenotype matching for RBC transfusion can be utilized but incurs additional time and resources. These results suggest high volume linear papain RBC alloadsorptions may be incorporated into antibody resolution for patients receiving ALX148.
- Published
- 2022
33. Functional expression of Na
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Ruth M, Matthews, Eamonn, Bradley, Caoimhin S, Griffin, Xin Rui, Lim, Nicolas D, Mullins, Mark A, Hollywood, Fionnuala T, Lundy, Lorcan P, McGarvey, Gerard P, Sergeant, and Keith D, Thornbury
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Mice ,Veratridine ,Myocytes, Smooth Muscle ,Sodium ,Animals ,Bronchi ,Atropine Derivatives ,Tetrodotoxin - Abstract
Isolated smooth muscle cells (SMCs) from mouse bronchus were studied using the whole cell patch-clamp technique at ∼21°C. Stepping from -100 mV to -20 mV evoked inward currents of mean amplitude -275 pA. These inactivated (tau = 1.1 ms) and were abolished when external Na
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- 2022
34. Illuminating the Motions of Jupiter's Auroral Dawn Storms
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M. J. Rutala, J. T. Clarke, J. D. Mullins, and J. D. Nichols
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Geophysics ,Space and Planetary Science - Published
- 2022
35. Modulation of carbachol-induced Ca2+ oscillations in airway smooth muscle cells by PGE2
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Leanna M Morgan, S Lorraine Martin, Nicholas D Mullins, Mark A Hollywood, Keith D Thornbury, and Gerard P Sergeant
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Smooth muscle ,Physiology ,Airways ,IP3 ,Calcium ,Cell Biology ,PGE2 ,Molecular Biology ,Cholinergic - Abstract
PGE2 is a potent bronchodilator, but the mechanisms underlying this effect have not been fully elucidated. Acetylcholine-induced contractions of airway smooth muscle (ASM) are associated with the generation of re- petitive Ca2+ oscillations in airway smooth muscle cells (ASMC) and the force of contraction is positively correlated with the frequency of the underlying Ca2+ oscillations. The purpose of the present study was to examine if carbachol-evoked Ca2+ oscillations in isolated ASMC were inhibited by PGE2.Isolated murine ASMC loaded with fluo4-AM were imaged with a Nipkow spinning disk confocal microscope. Cells responded to application of CCh (1 μM) by generating an initial Ca2+ transient followed by a series of Ca2+ oscillations. This activity was abolished by PGE2 (300 nM) and the EP2R agonist (R)-butaprost (3 μM) and the inhibitory effects of PGE2 were reversed by application of the EP2R antagonist PF-04418948 (100 nM). Acti- vation of adenylate cyclase using forskolin (1 μM) mimicked the effects of PGE2. The PKA activator, 6-MB-cAMP (300 μM) reduced the frequency of CCh-induced Ca2+ oscillations by 33% and the PKA inhibitor Rp-8-CPT- cAMPs partially reversed the inhibitory effects of PGE2. The EPAC activator 007-AM (10 μM) reduced the fre- quency of the oscillations by 60% and joint application of 007-AM and 6-MB-cAMP reduced oscillation frequency by ~85%. CCh-induced Ca2+ oscillations were inhibited by 2-APB and tetracaine, but caffeine-evoked Ca2+ transients were resistant to PGE2. These data suggest that PGE2 inhibits CCh-induced Ca and a mechanism involving activation of PKA and EPAC.oscillations in murine ASMC via stimulation of EP2Rs
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- 2022
36. Modulation of carbachol-induced Ca
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Leanna M, Morgan, S Lorraine, Martin, Nicholas D, Mullins, Mark A, Hollywood, Keith D, Thornbury, and Gerard P, Sergeant
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Mice ,Colforsin ,Myocytes, Smooth Muscle ,Animals ,Calcium ,Carbachol ,Muscle, Smooth ,Dinoprostone ,Muscle Contraction - Abstract
PGE
- Published
- 2022
37. P158 HEALTHCARE RESOURCE UTILIZATION AND ECONOMIC BURDEN OF EOSINOPHILIC ESOPHAGITIS: A US-BASED RETROSPECTIVE MATCHED COHORT STUDY
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J. Jiang, L. Chen, M. Lu, T. Fan, D. Mullins, M. Boules, S. Chen, and B. Goodwin
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Pulmonary and Respiratory Medicine ,medicine.medical_specialty ,Matched cohort ,business.industry ,Immunology ,Emergency medicine ,Health care ,medicine ,Immunology and Allergy ,Eosinophilic esophagitis ,medicine.disease ,business ,Resource utilization - Published
- 2021
38. A Prospective Multicenter Study of Minimal Residual Disease Assessment Using a Next-Generation Immunosequencing Assay and CT Monitoring for Surveillance after Frontline Treatment in Diffuse Large B-Cell Lymphoma
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Clare Grieve, Tania Veliz Rodriguez, Shreya Vemuri, Andrew D. Zelenetz, Leana Laraque, Devin Copley, Jason R. Westin, Stephen J. Schuster, Chelsea D. Mullins, Ellen Napier, Venkatraman E. Seshan, Gita Masand, Allison P. Jacob, A. Joseph, Grzegorz S. Nowakowski, Anita A Kumar, and Izidore S. Lossos
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medicine.medical_specialty ,Multicenter study ,business.industry ,Immunology ,medicine ,Cell Biology ,Hematology ,Radiology ,medicine.disease ,business ,Biochemistry ,Minimal residual disease ,Diffuse large B-cell lymphoma - Abstract
Background: Diffuse large B-cell lymphoma (DLBCL) is frequently curable after frontline therapy, however, relapses can occur after achievement of a PET-negative complete remission (CR). Early detection of relapse may be associated with improved outcomes, particularly given the development of more active therapies for relapsed, refractory DLBCL. Controversy exists regarding the utility of post-therapy surveillance imaging which is associated with patient (pt) anxiety, radiation exposure, false-positive results, and cost, without clear overall survival benefit in retrospective studies (Thompson JCO 2014). A retrospective study found that serial minimal residual disease (MRD) monitoring during DLBCL surveillance could identify pts at risk of relapse before clinical evidence of disease (Roschewski Lancet Oncol 2015). In this multicenter prospective study, we assessed whether a next-generation immunosequencing (IS) MRD assay could be used for early detection of molecular relapse in DLBCL. Methods: Eligible pts with DLBCL or high-grade B-cell lymphoma (HGBCL) who received anthracycline-containing chemotherapy were enrolled across five cancer centers. In pts who achieved a PET-negative CR, serial peripheral blood samples were obtained every 3 months (mos) and CT scans every 6 mos for 2 years (yrs) post-treatment. The IS MRD assay (Adaptive Biotechnologies, Seattle, WA) that leverages multiplex PCR followed by NGS to identify and track rearrangements of IgH, V-J, D-J and IgK/L loci and translocations in Bcl1/2-IgH was used. MRD positive was defined as any detectable rearrangement and MRD undetectable as no evidence of rearrangement. Results: 500 pts were enrolled and 400 were evaluable (pre-treatment tumor pathology available, completed frontline treatment, and achieved PET-negative CR at end-of-treatment). Baseline characteristics were median age of 62 yrs (range 19-95), male sex 58%, advanced stage 61%, and poor-risk by R-IPI 42%. Histologies included DLBCL, NOS (88%), primary mediastinal B-cell lymphoma (6%), HGBCL (5%), T-cell rich B-cell lymphoma (3%), and other (1%). Pts received regimens including RCHOP x 6 cycles (37%), REPOCH x 6 cycles (20%), clinical trial (15%), combined modality therapy (RCHOP+RT) (9%), and other RCHOP variations (19%). Among the 400 evaluable pts, 44 relapses have occurred as of July 1, 2021. In 45% of pts (20/44), clinical relapse was detected using surveillance imaging alone (typically CT CAP with IV contrast) in an otherwise asymptomatic pt with a normal physical exam and laboratory evaluation . In 10% of pts (4/44), relapse was detected by patient-reported clinical symptoms alone. In 45% of pts (20/44), relapse was detected by imaging, clinical symptoms, and/or evaluation by an oncologist. With a median follow-up of 34 months, the 2-year PFS was 88.9% (85.8, 92.1). Advanced age, advanced stage, and poor-risk R-IPI were associated with inferior PFS. Of the 44 relapses, tumor-specific clonotypes were identified in 39 pts (4 failed quality control (QC), 1 failed calibration) and 38 pts had ≥1 sample available within 90 days of relapse. Of 356 patients in ongoing CR, tumor-specific clonotypes were identified in 279 patients (29 failed QC, 33 failed calibration, and 15 are pending sequencing). The patient-level prospective MRD results are shown in Figure 1. The overall sensitivity, specificity, positive predictive value, and negative predictive value of the IS MRD assay was 63% (24/38), 78% (218/279), 28% (24/85), and 94% (218/232), respectively. Plasma MRD detection had improved sensitivity and specificity compared with circulating cells. Among the 24 relapsed patients with a positive MRD result at or before relapse, the median anticipation of the test was 3 months (range 0 to 24 months). Conclusion: Overall outcomes are excellent for DLBCL and HGBCL pts who achieve PET-negative CR. In this multicenter prospective analysis with standardized follow up, a substantial proportion (45%) of clinical relapses are detected radiographically in asymptomatic pts, supporting the value of CT surveillance imaging in DLBCL, particularly for pts with advanced stage or high-risk disease. MRD assessment using the IS MRD assay had suboptimal sensitivity and specificity in the post-treatment surveillance setting in DLBCL. Further study of the clinical context and its correlation with test performance is ongoing. Figure 1 Figure 1. Disclosures Kumar: Kite Pharmaceuticals: Other: advisory board , Research Funding; Abbvie Pharmaceuticals: Research Funding; Celgene: Honoraria, Other: advisory board, Research Funding; Adaptive Biotechnologies, Celgene, Abbvie Pharmaceticals, Pharmacyclics, Seattle Genetics: Research Funding; Pharmacyclics: Research Funding; Astra Zeneca: Honoraria, Other: Advisory Board, Research Funding; Seattle Genetics: Research Funding. Westin: Novartis: Consultancy, Research Funding; Genentech: Consultancy, Research Funding; Curis: Research Funding; Morphosys: Research Funding; ADC Therapeutics: Consultancy, Research Funding; Iksuda Therapeutics: Consultancy; Umoja: Consultancy; MorphoSys: Consultancy, Research Funding; Kite, a Gilead Company: Consultancy, Research Funding; AstraZeneca: Consultancy, Research Funding; Bristol Myers Squibb: Consultancy, Research Funding; 47 Inc: Research Funding. Schuster: TG Theraputics: Research Funding; Incyte: Research Funding; Adaptive Biotechnologies: Research Funding; Pharmacyclics: Research Funding; Merck: Research Funding; Genentech/Roche: Consultancy, Research Funding; Tessa Theraputics: Consultancy; Loxo Oncology: Consultancy; Juno Theraputics: Consultancy, Research Funding; BeiGene: Consultancy; Alimera Sciences: Consultancy; Acerta Pharma/AstraZeneca: Consultancy; Novartis: Consultancy, Honoraria, Patents & Royalties, Research Funding; Abbvie: Consultancy, Research Funding; Nordic Nanovector: Consultancy; Celgene: Consultancy, Honoraria, Research Funding. Nowakowski: Celgene, NanoString Technologies, MorphoSys: Research Funding; Celgene, MorphoSys, Genentech, Selvita, Debiopharm Group, Kite/Gilead: Consultancy, Membership on an entity's Board of Directors or advisory committees. Lossos: Lymphoma Research Foundation: Membership on an entity's Board of Directors or advisory committees; Seattle Genetics: Consultancy; Janssen: Consultancy, Honoraria; NCI: Research Funding; University of Miami: Current Employment; NIH grants: Research Funding; Stanford University: Patents & Royalties; Verastem: Consultancy, Honoraria. Jacob: Adaptive Biotechnologies: Current Employment. Mullins: Adaptive Biotechnologies: Current Employment. Zelenetz: AstraZeneca: Honoraria; Amgen: Honoraria; Beigene: Honoraria, Other, Research Funding; Gilead: Honoraria, Research Funding; SecuraBio: Honoraria; Genentech/Roche: Honoraria, Research Funding; BMS/Celgene/JUNO: Honoraria, Other; Janssen: Honoraria; LFR: Other; MEI Pharma: Honoraria, Research Funding; Abbvie: Honoraria, Research Funding; Verastem: Honoraria; MethylGene: Research Funding; NCCN: Other; Pharmacyclics: Honoraria; Novartis: Honoraria; Gilead: Honoraria; MorphoSys: Honoraria.
- Published
- 2021
39. Two Individuals with Rare Blocked Antigen Phenomenon and Coinciding Warm Autoantibody Mimicking Alloanti-Jk3 Resolved with JK Analysis
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B Vission, J G Zinni, Glenn Ramsey, M Stef, Phillip J. DeChristopher, and D Mullins
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Antigen ,Immunology ,Autoantibody ,General Medicine ,Biology - Abstract
Introduction/Objective Kidd antigens can bind complement (C3) as well as Kidd specific warm autoantibodies (WAAb). An 838G>A single nucleotide variant (SNV) defines JK*01 and JK*02 which codes the antithetical Jka and Jk b, respectively. Both alleles translate the high prevalence (>99%) Jk3 (JK3). The 130G>A is associated with weak Jka and weak Jkb expression. In vivo binding of non-agglutinating globulins can cause false-negative phenotypes by means of the blocked antigen phenomenon (BAP). Methods/Case Report Transfusions were requested for a 74-year-old Caucasian (CA) female with Evan’s Syndrome, and an 85-year-old African American (AA) female with metastatic uterine cancer. Both had a history of nonspecific WAAb. Direct antiglobulin testing (DAT) detected moderate in vivo sensitization of IgG and C3. They phenotyped Jk(a- b-) with untreated and EDTA glycine-acid (EGA) treated IgG DAT-negative cells. Their serum contained anti-Jk3 reactivity, while a panreactive WAAb in the eluate reacted with Jk3- donor and EGA treated DAT-negative autologous cells. Weak anti-Jka and anti-Jkb reactivity remained in the alloadsorbed serum of the antithetical adsorbing cells. Genetic testing of the CA revealed JK*01W.01(130A)/02 alleles, while cDNA confirmed the alleles would be transcribed into mRNA. Sequencing of the AA detected 130G/A, and 838G/A as well as other silent mutations predicting either a Jk(a+wb+) or Jk(a+b+w) phenotype. The CA received one compatible JK:-3 transfusion, and both individuals benefited from multiple least incompatible transfusions of Jk a+ and/or Jk b+ donors with expected hemoglobin increases (1 g/dL per transfusion). The CA serologically phenotyped Jk(a-b+) 132 days later following prolonged immunosuppressive therapy while a normocytic normochromic anemia and the WAAb persisted. No follow up evaluations of the AA are available. Results (if a Case Study enter NA) NA Conclusion Unexpected BAP can confound immunohematology testing and lead WAAbs mimicking alloanti-Jk3 to be mischaracterized as allogeneic. By predicting phenotypes, genetic analysis can aid serological techniques in antibody characterization and help circumvent complications searching for rare JK:-3 donors.
- Published
- 2021
40. Patient Satisfaction With Long-term Sacral Neuromodulation for Fecal Incontinence: Experience From a Single Tertiary Center.
- Author
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Martin SA, O'Connor AD, Selvakumar D, Baraza W, Faulkner G, Mullins D, Kiff ES, Telford KJ, and Sharma A
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- Humans, Female, Middle Aged, Male, Aged, Treatment Outcome, Surveys and Questionnaires, Lumbosacral Plexus, Tertiary Care Centers, Prospective Studies, Fecal Incontinence therapy, Fecal Incontinence psychology, Patient Satisfaction statistics & numerical data, Quality of Life, Electric Stimulation Therapy methods, Electric Stimulation Therapy instrumentation
- Abstract
Background: Sacral neuromodulation is an effective treatment for fecal incontinence in the long term. Efficacy is typically assessed using bowel diary, symptom severity, and quality-of-life questionnaires, and "success" is defined as more than 50% improvement in these measures. However, patient satisfaction may be a more meaningful and individualized measure of treatment efficacy., Objective: To assess patient-reported satisfaction with long-term sacral neuromodulation and compare it to the frequently applied efficacy measures., Design: An observational study of a prospectively maintained database., Setting: A single tertiary pelvic floor referral unit., Patients: Data from 70 patients (68 women, median age 69 [60-74] years) were available. The median time since implantation was 11 (9-14) years. Nineteen patients reported inactive neuromodulation devices., Main Outcome Measures: Bowel diaries, the Manchester Health Questionnaire, and the St. Mark's Incontinence Score were recorded at baseline, after percutaneous nerve evaluation, and at the last follow-up. Patient-reported satisfaction, using a 0% to 100% visual analog scale, with treatment since implantation (overall) and in the 2 weeks preceding completion of the last outcome measures (current) were also assessed., Results: Satisfaction was significantly higher in those with active sacral neuromodulation devices (75% vs 20%, p < 0.001) at follow-up. No significant relationships exist between symptom improvement using conventional measures and patient-reported satisfaction. Current satisfaction was not associated with changes in bowel diary data after percutaneous nerve evaluation. Despite improvements in the St. Mark's Incontinence Score and Manchester Health Questionnaire below the 50% improvement threshold used to define "success," patients reported high (80%) satisfaction., Limitations: Retrospective design with gaps in the available data., Conclusions: High patient satisfaction with sacral neuromodulation can be achieved; however, the response to percutaneous nerve evaluation may not predict treatment satisfaction in the long term. The change in questionnaire results, which measure the use of compensatory behaviors and quality-of-life impact, may better correspond to treatment satisfaction., Satisfaccin a Largo Plazo En Los Pacientes Con La Neuromodulacin Sacra Para La Incontinencia Fecal Experiencia De Un Nico Centro Terciario: ANTECEDENTES:La neuromodulación sacra es un tratamiento eficaz para la incontinencia fecal a largo plazo. La eficacia suele evaluarse mediante cuestionarios sobre la frecuencia diaria intestinal, la gravedad de los síntomas o la calidad de vida, y el "éxito" se define como una mejoría >50% en estas medidas. Sin embargo, la satisfacción del paciente puede ser una medida más significativa e individualizada de la eficacia del tratamiento.OBJETIVO:Evaluar la satisfacción a largo plazo de los pacientes con la neuromodulación sacra y compararla con las medidas de eficacia aplicadas con frecuencia.DISEÑO:Estudio observacional de una base de datos mantenida prospectivamente.LUGAR:Unidad terciaria única de referencia de suelo pélvico.PACIENTES:Se dispuso de datos de 70 pacientes (68 mujeres, mediana de edad 69 [60-74]). La mediana de tiempo transcurrido desde la implantación fue de 11 (9-14) años. Diecinueve pacientes informaron de dispositivos de neuromodulación inactivos.PRINCIPALES MEDIDAS DE VALORACIÓN:Diarios intestinales, el Cuestionario de Salud de Manchester y la Puntuación de Incontinencia de St Marks registrados al inicio, tras la evaluación percutánea del nervio y en el último seguimiento. Los pacientes informaron de su satisfacción, utilizando una escala analógica visual de 0%-100%, con el tratamiento desde la implantación (global) y en las dos semanas anteriores a la realización de las últimas medidas de resultado (actual).RESULTADOS:La satisfacción fue significativamente mayor en los pacientes con dispositivos de neuromodulación sacra activos (75% frente a 20%, p < 0,001) durante el seguimiento. No existen relaciones significativas entre la mejoría de los síntomas mediante medidas convencionales y la satisfacción comunicada por el paciente. La satisfacción actual no se asoció con los cambios en los datos de la frecuencia diaria intestinal tras la evaluación percutánea de los nervios. A pesar de que las mejoras en la puntuación de incontinencia de St Mark y el Cuestionario de Salud de Manchester se situaron por debajo del umbral de mejora del 50% utilizado para definir el "éxito", los pacientes declararon un alto grado de satisfacción (80%).LIMITACIONES:Retrospectivo con lagunas en los datos disponibles.CONCLUSIONES:Puede lograrse una alta satisfacción de los pacientes con la neuromodulación sacra; sin embargo, la respuesta a la evaluación percutánea del nervio puede no predecir la satisfacción con el tratamiento a largo plazo. El cambio en los resultados del cuestionario, que mide el uso de conductas compensatorias y el impacto en la calidad de vida, puede corresponder mejor a la satisfacción con el tratamiento. (Traducción-Dr. Ingrid Melo )., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Society of Colon and Rectal Surgeons.)
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- 2024
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41. Optimizing Camera Exposure Time for Automotive Applications.
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Lin H, Mullins D, Molloy D, Ward E, Collins F, Denny P, Glavin M, Deegan B, and Jones E
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Camera-based object detection is integral to advanced driver assistance systems (ADAS) and autonomous vehicle research, and RGB cameras remain indispensable for their spatial resolution and color information. This study investigates exposure time optimization for such cameras, considering image quality in dynamic ADAS scenarios. Exposure time, the period during which the camera sensor is exposed to light, directly influences the amount of information captured. In dynamic scenarios, such as those encountered in typical driving scenarios, optimizing exposure time becomes challenging due to the inherent trade-off between Signal-to-Noise Ratio (SNR) and motion blur, i.e., extending exposure time to maximize information capture increases SNR, but also increases the risk of motion blur and overexposure, particularly in low-light conditions where objects may not be fully illuminated. The study introduces a comprehensive methodology for exposure time optimization under various lighting conditions, examining its impact on image quality and computer vision performance. Traditional image quality metrics show a poor correlation with computer vision performance, highlighting the need for newer metrics that demonstrate improved correlation. The research presented in this paper offers guidance into the enhancement of single-exposure camera-based systems for automotive applications. By addressing the balance between exposure time, image quality, and computer vision performance, the findings provide a road map for optimizing camera settings for ADAS and autonomous driving technologies, contributing to safety and performance advancements in the automotive landscape.
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- 2024
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42. A Study on Data Selection for Object Detection in Various Lighting Conditions for Autonomous Vehicles.
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Lin H, Parsi A, Mullins D, Horgan J, Ward E, Eising C, Denny P, Deegan B, Glavin M, and Jones E
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In recent years, significant advances have been made in the development of Advanced Driver Assistance Systems (ADAS) and other technology for autonomous vehicles. Automated object detection is a crucial component of autonomous driving; however, there are still known issues that affect its performance. For automotive applications, object detection algorithms are required to perform at a high standard in all lighting conditions; however, a major problem for object detection is poor performance in low-light conditions due to objects being less visible. This study considers the impact of training data composition on object detection performance in low-light conditions. In particular, this study evaluates the effect of different combinations of images of outdoor scenes, from different times of day, on the performance of deep neural networks, and considers the different challenges encountered during the training of a neural network. Through experiments with a widely used public database, as well as a number of commonly used object detection architectures, we show that more robust performance can be obtained with an appropriate balance of classes and illumination levels in the training data. The results also highlight the potential of adding images obtained in dusk and dawn conditions for improving object detection performance in day and night.
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- 2024
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43. Tumor-targeted therapy with BRAF-inhibitor recruits activated dendritic cells to promote tumor immunity in melanoma.
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Hornsteiner F, Vierthaler J, Strandt H, Resag A, Fu Z, Ausserhofer M, Tripp CH, Dieckmann S, Kanduth M, Farrand K, Bregar S, Nemati N, Hermann-Kleiter N, Seretis A, Morla S, Mullins D, Finotello F, Trajanoski Z, Wollmann G, Ronchese F, Schmitz M, Hermans IF, and Stoitzner P
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- Humans, Animals, Mice, CD8-Positive T-Lymphocytes, Proto-Oncogene Proteins B-raf genetics, Dendritic Cells, Antigens, Neoplasm, Tumor Microenvironment, Melanoma metabolism
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Background: Tumor-targeted therapy causes impressive tumor regression, but the emergence of resistance limits long-term survival benefits in patients. Little information is available on the role of the myeloid cell network, especially dendritic cells (DC) during tumor-targeted therapy., Methods: Here, we investigated therapy-mediated immunological alterations in the tumor microenvironment (TME) and tumor-draining lymph nodes (LN) in the D4M.3A preclinical melanoma mouse model (harboring the V-Raf murine sarcoma viral oncogene homolog B (BRAF)
V600E mutation) by using high-dimensional multicolor flow cytometry in combination with multiplex immunohistochemistry. This was complemented with RNA sequencing and cytokine quantification to characterize the immune status of the tumors. The importance of T cells during tumor-targeted therapy was investigated by depleting CD4+ or CD8+ T cells in tumor-bearing mice. Tumor antigen-specific T-cell responses were characterized by performing in vivo T-cell proliferation assays and the contribution of conventional type 1 DC (cDC1) to T-cell immunity during tumor-targeted therapy was assessed using Batf3-/- mice lacking cDC1., Results: Our findings reveal that BRAF-inhibitor therapy increased tumor immunogenicity, reflected by an upregulation of genes associated with immune activation. The T cell-inflamed TME contained higher numbers of activated cDC1 and cDC2 but also inflammatory CCR2-expressing monocytes. At the same time, tumor-targeted therapy enhanced the frequency of migratory, activated DC subsets in tumor-draining LN. Even more, we identified a cDC2 population expressing the Fc gamma receptor I (FcγRI)/CD64 in tumors and LN that displayed high levels of CD40 and CCR7 indicating involvement in T cell-mediated tumor immunity. The importance of cDC2 is underlined by just a partial loss of therapy response in a cDC1-deficient mouse model. Both CD4+ and CD8+ T cells were essential for therapy response as their respective depletion impaired therapy success. On resistance development, the tumors reverted to an immunologically inert state with a loss of DC and inflammatory monocytes together with the accumulation of regulatory T cells. Moreover, tumor antigen-specific CD8+ T cells were compromised in proliferation and interferon-γ-production., Conclusion: Our results give novel insights into the remodeling of the myeloid landscape by tumor-targeted therapy. We demonstrate that the transient immunogenic tumor milieu contains more activated DC. This knowledge has important implications for the development of future combinatorial therapies., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY. Published by BMJ.)- Published
- 2024
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44. The Long-term Outcomes of Sacral Neuromodulation for Fecal Incontinence: A Single-Center Experience.
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Martin S, O'Connor AD, Selvakumar D, Baraza W, Faulkner G, Mullins D, Kiff ES, Telford KJ, and Sharma A
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- Humans, Female, Retrospective Studies, Follow-Up Studies, Sacrum, Fecal Incontinence therapy, Electric Stimulation Therapy
- Abstract
Background: Sacral neuromodulation is an effective treatment for fecal incontinence., Objective: To assess the long-term outcomes of sacral neuromodulation and establish the outcomes of patients with inactive devices., Design: This is an observational study of patients treated for >5 years. A positive outcome was defined as a more than 50% reduction in fecal incontinence episodes or improvement in a symptom severity score. Data were reviewed from a prospectively managed database., Settings: This study was conducted at a single tertiary referral center., Patients: Data from 74 patients (72 women) were available at long-term follow-up., Main Outcome Measures: Bowel diary, St. Mark's incontinence score, and Manchester Health Questionnaire data were prospectively recorded at baseline, after percutaneous nerve evaluation, and at last follow-up., Results: Patients were analyzed in cohorts based on time since sacral neuromodulation implantation: group 1: 5 to 10 years (n = 20), group 2: >10 years (n = 35), and group 3: inactive sacral neuromodulation devices (n = 19). Median St. Mark's incontinence score and Manchester Health Questionnaire improved from baseline to last follow-up in group 1 ( p ≤ 0.05) and group 2 ( p ≤ 0.05), but in group 3, results returned to baseline levels at the last follow-up. Similarly, weekly fecal incontinence episodes improved in both active device groups at the last follow-up. However, in group 3, incontinence episodes were no different from baseline ( p = 0.722). Despite active devices, fecal urgency episodes increased at the last follow-up after >10 years since percutaneous nerve evaluation ( p ≤ 0.05). Complete continence was reported by 44% of patients, and at least a 50% improvement was seen in 77% of patients with active devices., Limitations: This study is retrospective with some gaps in the available data at the last follow-up., Conclusions: Sacral neuromodulation is an effective treatment for fecal incontinence in the long term, but all outcomes are adversely affected by device inactivity. Therefore, ongoing stimulation is required for continued benefit. See Video Abstract., Resultados a Largo Plazo De La Neuromodulacin Sacra Para La Incontinencia Fecal Experiencia De Un Solo Centro: ANTECEDENTES:La neuromodulación sacra es un tratamiento eficaz para la incontinencia fecal.OBJETIVO:Este estudio tuvo como objetivo evaluar los resultados a largo plazo de la neuromodulación sacra y establecer los resultados de los pacientes con dispositivos inactivos.DISEÑO:Este es un estudio observacional de pacientes tratados durante más de 5 años. Un resultado positivo se definió como una reducción >50 % en los episodios de incontinencia fecal o una mejoría en la puntuación de gravedad de los síntomas. Los datos se revisaron a partir de una base de datos administrada prospectivamente.ENTERNO CLINICO:Este estudio se realizó en un solo centro de referencia terciario.PACIENTES:Los datos de 74 pacientes (72 mujeres) estaban disponibles en el seguimiento a largo plazo.PRINCIPALES MEDIDAS DE RESULTADO:Diario intestinal, puntuación de incontinencia de St. Mark y datos del Cuestionario de salud de Manchester se registraron prospectivamente al inicio, después de la evaluación de nervio periférico y en el último seguimiento.RESULTADOS:Los pacientes se analizaron en cohortes según el tiempo transcurrido desde la implantación de la neuromodulación sacra: Grupo 1: 5-10 años (n = 20), Grupo 2: >10 años (n = 35) y Grupo 3: dispositivos SNM inactivos (n = 19). La mediana de la puntuación de incontinencia de St. Mark y Questionnaire Cuestionario de salud de Manchester mejoraron desde el inicio hasta el último seguimiento en el Grupo 1 (p = < 0,05) y el Grupo 2 (p = < 0,05), pero en el Grupo 3 los resultados volvieron a los niveles iniciales en el último seguimiento. arriba. De manera similar, los episodios semanales de incontinencia fecal mejoraron en ambos grupos de dispositivos activos en el último seguimiento. Sin embargo, en el Grupo 3 los episodios de incontinencia no fueron diferentes de los basales (p = 0,722). A pesar de los dispositivos activos, los episodios de urgencia fecal aumentaron en el último seguimiento después de más de 10 años desde la evaluación del nervio periférico (p = < 0,05). Continencia completa se reportó en el 44 % de los pacientes, y al menos una mejora del 50 % en el 77 % con dispositivos activos.LIMITACIONES:Este estudio es retrospectivo con algunas vacíos en los datos disponibles en el último seguimiento.CONCLUSIONES:La neuromodulación sacra es un tratamiento eficaz para la incontinencia fecal a largo plazo, pero todos los resultados se ven afectados negativamente por la inactividad del dispositivo. Por lo tanto, se requiere estimulación continua para un beneficio continuo. (Traducción- Dr. Francisco M. Abarca-Rendon )., (Copyright © The ASCRS 2023.)
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- 2024
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45. Impact of ISP Tuning on Object Detection.
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Molloy D, Deegan B, Mullins D, Ward E, Horgan J, Eising C, Denny P, Jones E, and Glavin M
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In advanced driver assistance systems (ADAS) or autonomous vehicle research, acquiring semantic information about the surrounding environment generally relies heavily on camera-based object detection. Image signal processors (ISPs) in cameras are generally tuned for human perception. In most cases, ISP parameters are selected subjectively and the resulting image differs depending on the individual who tuned it. While the installation of cameras on cars started as a means of providing a view of the vehicle's environment to the driver, cameras are increasingly becoming part of safety-critical object detection systems for ADAS. Deep learning-based object detection has become prominent, but the effect of varying the ISP parameters has an unknown performance impact. In this study, we analyze the performance of 14 popular object detection models in the context of changes in the ISP parameters. We consider eight ISP blocks: demosaicing, gamma, denoising, edge enhancement, local tone mapping, saturation, contrast, and hue angle. We investigate two raw datasets, PASCALRAW and a custom raw dataset collected from an advanced driver assistance system (ADAS) perspective. We found that varying from a default ISP degrades the object detection performance and that the models differ in sensitivity to varying ISP parameters. Finally, we propose a novel methodology that increases object detection model robustness via ISP variation data augmentation.
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- 2023
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46. Sacral neuromodulation: time to seize the opportunity to collaborate on a 'de-prioritised' service?
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O'Connor A, Mullins D, Sharma A, Faulkner G, and Telford K
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- Humans, Sacrum, Sacrococcygeal Region, Lumbosacral Plexus, Electric Stimulation Therapy, Botulinum Toxins, Type A
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- 2023
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47. Pedestrian Crossing Intention Forecasting at Unsignalized Intersections Using Naturalistic Trajectories.
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Moreno E, Denny P, Ward E, Horgan J, Eising C, Jones E, Glavin M, Parsi A, Mullins D, and Deegan B
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Interacting with other roads users is a challenge for an autonomous vehicle, particularly in urban areas. Existing vehicle systems behave in a reactive manner, warning the driver or applying the brakes when the pedestrian is already in front of the vehicle. The ability to anticipate a pedestrian's crossing intention ahead of time will result in safer roads and smoother vehicle maneuvers. The problem of crossing intent forecasting at intersections is formulated in this paper as a classification task. A model that predicts pedestrian crossing behaviour at different locations around an urban intersection is proposed. The model not only provides a classification label (e.g., crossing, not-crossing), but a quantitative confidence level (i.e., probability). The training and evaluation are carried out using naturalistic trajectories provided by a publicly available dataset recorded from a drone. Results show that the model is able to predict crossing intention within a 3-s time window.
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- 2023
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48. ACR Appropriateness Criteria® Imaging After Breast Surgery.
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Mehta TS, Lourenco AP, Niell BL, Bennett DL, Brown A, Chetlen A, Freer P, Ivansco LK, Jochelson MS, Klein KA, Malak SF, McCrary M, Mullins D, Neal CH, Newell MS, Ulaner GA, and Moy L
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- Female, Humans, Early Detection of Cancer, Societies, Medical, Evidence-Based Medicine, Mammography, Breast Neoplasms diagnostic imaging, Breast Neoplasms surgery, Breast Neoplasms pathology
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Given that 20% to 40% of women who have percutaneous breast biopsy subsequently undergo breast surgery, knowledge of imaging women with a history of benign (including high-risk) disease or breast cancer is important. For women who had surgery for nonmalignant pathology, the surveillance recommendations are determined by their overall risk. Higher-than-average risk women with a history of benign surgery may require screening mammography starting at an earlier age before 40 and may benefit from screening MRI. For women with breast cancer who have undergone initial excision and have positive margins, imaging with diagnostic mammography or MRI can sometimes guide additional surgical planning. Women who have completed breast conservation therapy for cancer should get annual mammography and may benefit from the addition of MRI or ultrasound to their surveillance regimen. The ACR Appropriateness Criteria are evidence-based guidelines for specific clinical conditions that are reviewed annually by a multidisciplinary expert panel. The guideline development and revision process support the systematic analysis of the medical literature from peer reviewed journals. Established methodology principles such as Grading of Recommendations Assessment, Development, and Evaluation or GRADE are adapted to evaluate the evidence. The RAND/UCLA Appropriateness Method User Manual provides the methodology to determine the appropriateness of imaging and treatment procedures for specific clinical scenarios. In those instances in which peer reviewed literature is lacking or equivocal, experts may be the primary evidentiary source available to formulate a recommendation., (Copyright © 2022 American College of Radiology. Published by Elsevier Inc. All rights reserved.)
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- 2022
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49. HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery.
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Hayes M, Nguyen A, Islam R, Butler C, Tran E, Mullins D, and Hicks C
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- Humans, Chromosome Aberrations, Chromatin, Oncogenes, Chromosomes, Neoplasms genetics
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Motivation: Double minute (DM) chromosomes are acentric extrachromosomal DNA artifacts that are frequently observed in the cells of numerous cancers. They are highly amplified and contain oncogenes and drug-resistance genes, making their presence a challenge for effective cancer treatment. Algorithmic discovery of DM can potentially improve bench-derived therapies for cancer treatment. A hindrance to this task is that DMs evolve, yielding circular chromatin that shares segments from progenitor DMs. This creates DMs with overlapping amplicon coordinates. Existing DM discovery algorithms use whole genome shotgun sequencing (WGS) in isolation, which can potentially incorrectly classify DMs that share overlapping coordinates., Results: In this study, we describe an algorithm called 'HolistIC' that can predict DMs in tumor genomes by integrating WGS and Hi-C sequencing data. The consolidation of these sources of information resolves ambiguity in DM amplicon prediction that exists in DM prediction with WGS data used in isolation. We implemented and tested our algorithm on the tandem Hi-C and WGS datasets of three cancer datasets and a simulated dataset. Results on the cancer datasets demonstrated HolistIC's ability to predict DMs from Hi-C and WGS data in tandem. The results on the simulated data showed the HolistIC can accurately distinguish DMs that have overlapping amplicon coordinates, an advance over methods that predict extrachromosomal amplification using WGS data in isolation., Availability and Implementation: Our software, named 'HolistIC', is available at http://www.github.com/mhayes20/HolistIC., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
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- 2022
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50. Altered stress responses in adults born by Caesarean section.
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Dinan TG, Kennedy PJ, Morais LH, Murphy A, Long-Smith CM, Moloney GM, Bastiaanssen TFS, Allen AP, Collery A, Mullins D, Cusack AM, Berding K, O'Toole PW, Clarke G, Stanton C, and Cryan JF
- Abstract
Birth by Caesarean-section (C-section), which increases the risk for metabolic and immune disorders, disrupts the normal initial microbial colonisation of the gut, in addition to preventing early priming of the stress and immune-systems.. Animal studies have shown there are enduring psychological processes in C-section born mice. However, the long-term impact of microbiota-gut-brain axis disruptions due to birth by C-section on psychological processes in humans is unknown. Forty age matched healthy young male university students born vaginally and 36 C-section delivered male students were recruited. Participants underwent an acute stressor, the Trier social stress test (TSST), during a term-time study visit. A subset of participants also completed a study visit during the university exam period, representing a naturalistic stressor. Participants completed a battery of cognitive tests and self-report measures assessing mood, anxiety, and perceived stress. Saliva, blood, and stool samples were collected for analysis of cortisol, peripheral immune profile, and the gut microbiota. Young adults born by C-section exhibit increased psychological vulnerability to acute stress and a prolonged period of exam-related stress. They did not exhibit an altered salivary cortisol awakening response to the TSST, but their measures of positive affect were significantly lower than controls throughout the procedure. Both C-section and vaginally-delivered participants performed equally well on cognitive assessments. Most of the initial effects of delivery mode on the gut microbiome did not persist into adulthood as the gut microbiota profile showed modest changes in composition in adult vaginally-delivered and C-sectioned delivered subjects. From an immune perspective, concentrations of IL-1β and 1L-10 were higher in C-section participants. These data confirm that there is a potential enduring effect of delivery mode on the psychological responses to acute stress during early adulthood. The mental health implications of these observations require further study regarding policies on C-section use., Competing Interests: APC Microbiome Ireland has conducted studies in collaboration with several companies, including GSK, Pfizer, Cremo, Wyeth, Mead Johnson, Nutricia, 4D Pharma, and DuPont. T. G. Dinan has been an invited speaker at meetings organized by Servier, Lundbeck, Janssen, and AstraZeneca and has received research funding from Mead Johnson, Cremo, Nutricia, and 4D Pharma. J. F. Cryan has been an invited speaker at meetings organized by Mead Johnson, Yakult, and Alkermes, and has received research funding from Mead Johnson, Cremo, Nutricia, and IFF. GC has received honoraria from Janssen, Probi and Apsen as an invited speaker, is in receipt of research funding from Pharmavite and Fonterra and is a paid consultant for Yakult and Zentiva., (© 2021 Published by Elsevier Inc.)
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- 2021
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