9,873 results on '"P Parikh"'
Search Results
252. Design and Synthesis of an Efficient Fluorescent Probe Based on Oxacalix[4]arene for the Selective Detection of Trinitrophenol (TNP) Explosives in Aqueous System
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Desai, Vishv, Modi, Krunal, Panjwani, Falak, Seth, Banabithi Koley, Vora, Manoj, Parikh, Jaymin, and Jain, Vinod Kumar
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- 2024
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253. The Humanistic and Economic Burden Associated with Major Depressive Disorder: A Retrospective Cross-Sectional Analysis
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Culpepper, Larry, Martin, Ashley, Nabulsi, Nadia, and Parikh, Mousam
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- 2024
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254. Rebound Intracranial Hypertension
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Parikh, Simy K.
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- 2024
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255. A diffusion tensor imaging comparison of white matter development in nonsyndromic craniosynostosis to neurotypical infants
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Moscarelli, Jake, Almeida, Mariana N., Lacadie, Cheryl, Hu, Kevin G., Ihnat, Jacqueline M. H., Parikh, Neil, Persing, John A., and Alperovich, Michael
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- 2024
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256. The Busboy Problem: Efficient Tableware Decluttering Using Consolidation and Multi-Object Grasps
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Srinivas, Kishore, Ganti, Shreya, Parikh, Rishi, Ahmad, Ayah, Agboh, Wisdom, Dogar, Mehmet, and Goldberg, Ken
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Computer Science - Robotics - Abstract
We present the "Busboy Problem": automating an efficient decluttering of cups, bowls, and silverware from a planar surface. As grasping and transporting individual items is highly inefficient, we propose policies to generate grasps for multiple items. We introduce the metric of Objects per Trip (OpT) carried by the robot to the collection bin to analyze the improvement seen as a result of our policies. In physical experiments with singulated items, we find that consolidation and multi-object grasps resulted in an 1.8x improvement in OpT, compared to methods without multi-object grasps. See https://sites.google.com/berkeley.edu/busboyproblem for code and supplemental materials.
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- 2023
257. A Double Machine Learning Approach to Combining Experimental and Observational Data
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Parikh, Harsh, Morucci, Marco, Orlandi, Vittorio, Roy, Sudeepa, Rudin, Cynthia, and Volfovsky, Alexander
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Statistics - Methodology ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Economics - Econometrics - Abstract
Experimental and observational studies often lack validity due to untestable assumptions. We propose a double machine learning approach to combine experimental and observational studies, allowing practitioners to test for assumption violations and estimate treatment effects consistently. Our framework tests for violations of external validity and ignorability under milder assumptions. When only one of these assumptions is violated, we provide semiparametrically efficient treatment effect estimators. However, our no-free-lunch theorem highlights the necessity of accurately identifying the violated assumption for consistent treatment effect estimation. Through comparative analyses, we show our framework's superiority over existing data fusion methods. The practical utility of our approach is further exemplified by three real-world case studies, underscoring its potential for widespread application in empirical research.
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- 2023
258. GPT-FinRE: In-context Learning for Financial Relation Extraction using Large Language Models
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Rajpoot, Pawan Kumar and Parikh, Ankur
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Computer Science - Computation and Language - Abstract
Relation extraction (RE) is a crucial task in natural language processing (NLP) that aims to identify and classify relationships between entities mentioned in text. In the financial domain, relation extraction plays a vital role in extracting valuable information from financial documents, such as news articles, earnings reports, and company filings. This paper describes our solution to relation extraction on one such dataset REFinD. The dataset was released along with shared task as a part of the Fourth Workshop on Knowledge Discovery from Unstructured Data in Financial Services, co-located with SIGIR 2023. In this paper, we employed OpenAI models under the framework of in-context learning (ICL). We utilized two retrieval strategies to find top K relevant in-context learning demonstrations / examples from training data for a given test example. The first retrieval mechanism, we employed, is a learning-free dense retriever and the other system is a learning-based retriever. We were able to achieve 3rd rank overall. Our best F1-score is 0.718., Comment: arXiv admin note: text overlap with arXiv:2305.02105 by other authors
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- 2023
259. Can Machines Garden? Systematically Comparing the AlphaGarden vs. Professional Horticulturalists
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Adebola, Simeon, Parikh, Rishi, Presten, Mark, Sharma, Satvik, Aeron, Shrey, Rao, Ananth, Mukherjee, Sandeep, Qu, Tomson, Wistrom, Christina, Solowjow, Eugen, and Goldberg, Ken
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Computer Science - Robotics - Abstract
The AlphaGarden is an automated testbed for indoor polyculture farming which combines a first-order plant simulator, a gantry robot, a seed planting algorithm, plant phenotyping and tracking algorithms, irrigation sensors and algorithms, and custom pruning tools and algorithms. In this paper, we systematically compare the performance of the AlphaGarden to professional horticulturalists on the staff of the UC Berkeley Oxford Tract Greenhouse. The humans and the machine tend side-by-side polyculture gardens with the same seed arrangement. We compare performance in terms of canopy coverage, plant diversity, and water consumption. Results from two 60-day cycles suggest that the automated AlphaGarden performs comparably to professional horticulturalists in terms of coverage and diversity, and reduces water consumption by as much as 44%. Code, videos, and datasets are available at https://sites.google.com/berkeley.edu/systematiccomparison., Comment: International Conference on Robotics and Automation(ICRA) 2023 Oral
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- 2023
260. Minimum information and guidelines for reporting a Multiplexed Assay of Variant Effect
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Claussnitzer, Melina, Parikh, Victoria N., Wagner, Alex H., Arbesfeld, Jeremy A., Bult, Carol J., Firth, Helen V., Muffley, Lara A., Ba, Alex N. Nguyen, Riehle, Kevin, Roth, Frederick P., Tabet, Daniel, Bolognesi, Benedetta, Glazer, Andrew M., and Rubin, Alan F.
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Quantitative Biology - Other Quantitative Biology - Abstract
Multiplexed Assays of Variant Effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniques across diverse disciplines has led to a heterogeneous mix of data formats and descriptions, which complicates the downstream use of the resulting datasets. To address these issues and promote reproducibility and reuse of MAVE data, we define a set of minimum information standards for MAVE data and metadata and outline a controlled vocabulary aligned with established biomedical ontologies for describing these experimental designs.
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- 2023
261. Empowering Business Transformation: The Positive Impact and Ethical Considerations of Generative AI in Software Product Management -- A Systematic Literature Review
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Parikh, Nishant A.
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Computer Science - Software Engineering ,Computer Science - Artificial Intelligence - Abstract
Generative Artificial Intelligence (GAI) has made outstanding strides in recent years, with a good-sized impact on software product management. Drawing on pertinent articles from 2016 to 2023, this systematic literature evaluation reveals generative AI's potential applications, benefits, and constraints in this area. The study shows that technology can assist in idea generation, market research, customer insights, product requirements engineering, and product development. It can help reduce development time and costs through automatic code generation, customer feedback analysis, and more. However, the technology's accuracy, reliability, and ethical consideration persist. Ultimately, generative AI's practical application can significantly improve software product management activities, leading to more efficient use of resources, better product outcomes, and improved end-user experiences., Comment: 24 pages, 4 figures
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- 2023
262. Valorization of bio-renewably available ethanol over alkali-exchanged ZSM-5: improved aromatic selectivity and catalyst life
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Badghaiya, Digvijay, Parikh, Jigisha K., and Parikh, Parimal A.
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- 2024
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263. SEAHORSE: A Multilingual, Multifaceted Dataset for Summarization Evaluation
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Clark, Elizabeth, Rijhwani, Shruti, Gehrmann, Sebastian, Maynez, Joshua, Aharoni, Roee, Nikolaev, Vitaly, Sellam, Thibault, Siddhant, Aditya, Das, Dipanjan, and Parikh, Ankur P.
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Computer Science - Computation and Language - Abstract
Reliable automatic evaluation of summarization systems is challenging due to the multifaceted and subjective nature of the task. This is especially the case for languages other than English, where human evaluations are scarce. In this work, we introduce SEAHORSE, a dataset for multilingual, multifaceted summarization evaluation. SEAHORSE consists of 96K summaries with human ratings along 6 dimensions of text quality: comprehensibility, repetition, grammar, attribution, main ideas, and conciseness, covering 6 languages, 9 systems and 4 datasets. As a result of its size and scope, SEAHORSE can serve both as a benchmark to evaluate learnt metrics, as well as a large-scale resource for training such metrics. We show that metrics trained with SEAHORSE achieve strong performance on the out-of-domain meta-evaluation benchmarks TRUE (Honovich et al., 2022) and mFACE (Aharoni et al., 2022). We make the SEAHORSE dataset and metrics publicly available for future research on multilingual and multifaceted summarization evaluation.
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- 2023
264. Controlling the Extraction of Memorized Data from Large Language Models via Prompt-Tuning
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Ozdayi, Mustafa Safa, Peris, Charith, FitzGerald, Jack, Dupuy, Christophe, Majmudar, Jimit, Khan, Haidar, Parikh, Rahil, and Gupta, Rahul
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
Large Language Models (LLMs) are known to memorize significant portions of their training data. Parts of this memorized content have been shown to be extractable by simply querying the model, which poses a privacy risk. We present a novel approach which uses prompt-tuning to control the extraction rates of memorized content in LLMs. We present two prompt training strategies to increase and decrease extraction rates, which correspond to an attack and a defense, respectively. We demonstrate the effectiveness of our techniques by using models from the GPT-Neo family on a public benchmark. For the 1.3B parameter GPT-Neo model, our attack yields a 9.3 percentage point increase in extraction rate compared to our baseline. Our defense can be tuned to achieve different privacy-utility trade-offs by a user-specified hyperparameter. We achieve an extraction rate reduction of up to 97.7% relative to our baseline, with a perplexity increase of 16.9%., Comment: 5 pages, 3 Figures, ACL 2023
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- 2023
265. Make-An-Animation: Large-Scale Text-conditional 3D Human Motion Generation
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Azadi, Samaneh, Shah, Akbar, Hayes, Thomas, Parikh, Devi, and Gupta, Sonal
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
Text-guided human motion generation has drawn significant interest because of its impactful applications spanning animation and robotics. Recently, application of diffusion models for motion generation has enabled improvements in the quality of generated motions. However, existing approaches are limited by their reliance on relatively small-scale motion capture data, leading to poor performance on more diverse, in-the-wild prompts. In this paper, we introduce Make-An-Animation, a text-conditioned human motion generation model which learns more diverse poses and prompts from large-scale image-text datasets, enabling significant improvement in performance over prior works. Make-An-Animation is trained in two stages. First, we train on a curated large-scale dataset of (text, static pseudo-pose) pairs extracted from image-text datasets. Second, we fine-tune on motion capture data, adding additional layers to model the temporal dimension. Unlike prior diffusion models for motion generation, Make-An-Animation uses a U-Net architecture similar to recent text-to-video generation models. Human evaluation of motion realism and alignment with input text shows that our model reaches state-of-the-art performance on text-to-motion generation., Comment: arXiv admin note: text overlap with arXiv:2304.07410
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- 2023
266. Exploring Zero and Few-shot Techniques for Intent Classification
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Parikh, Soham, Vohra, Quaizar, Tumbade, Prashil, and Tiwari, Mitul
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
Conversational NLU providers often need to scale to thousands of intent-classification models where new customers often face the cold-start problem. Scaling to so many customers puts a constraint on storage space as well. In this paper, we explore four different zero and few-shot intent classification approaches with this low-resource constraint: 1) domain adaptation, 2) data augmentation, 3) zero-shot intent classification using descriptions large language models (LLMs), and 4) parameter-efficient fine-tuning of instruction-finetuned language models. Our results show that all these approaches are effective to different degrees in low-resource settings. Parameter-efficient fine-tuning using T-few recipe (Liu et al., 2022) on Flan-T5 (Chang et al., 2022) yields the best performance even with just one sample per intent. We also show that the zero-shot method of prompting LLMs using intent descriptions, Comment: ACL 2023 Industry Track. 8 pages, 2 figures, 5 tables
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- 2023
267. Mitochondrial genetic variation and risk of chronic kidney disease and acute kidney injury in UK Biobank participants
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Jotwani, Vasantha, Yang, Stephanie Y., Thiessen-Philbrook, Heather, Parikh, Chirag R., Katz, Ronit, Tranah, Gregory J., Ix, Joachim H., Cummings, Steve, Waikar, Sushrut S., Shlipak, Michael G., Sarnak, Mark J., Parikh, Samir M., and Arking, Dan E.
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- 2024
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268. A fluorescent particle for PIV in gas phase flows
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Okada, Mizuki, Parikh, Agastya, Pinho, Jorge, Kähler, Christian, and Lavagnoli, Sergio
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- 2024
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269. Innovations in Date palm(Phoenix dactylifera L.) micropropagation: detailed review of in vitro culture methods and plant growth regulator applications
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Nimavat, Nayan and Parikh, Punita
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- 2024
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270. HLH and Recurrent EBV Lymphoma as the presenting manifestation of MAGT1 Deficiency: A Systematic Review of the Expanding Disease Spectrum
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Golloshi, Klevi, Mitchell, William, Kumar, Deepak, Malik, Sakshi, Parikh, Suhag, Aljudi, Ahmed A., Castellino, Sharon M., and Chandrakasan, Shanmuganathan
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- 2024
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271. WE-ROCK and the challenge of global accessibility: are we reaching children worldwide?
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Shirode, Parth and Parikh, Krish
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- 2025
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272. Brief Report: Single and Repeat Screening with the Modified Checklist for Autism in Toddlers-Revised in Young Children at Higher Likelihood for Autism Spectrum Disorder
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Parikh, Chandni and Ozonoff, Sally
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Psychology ,Prevention ,Intellectual and Developmental Disabilities (IDD) ,Autism ,Behavioral and Social Science ,Clinical Research ,Pediatric ,Mental Health ,Brain Disorders ,4.2 Evaluation of markers and technologies ,Autism screening ,Psychometrics ,Infant siblings ,Education ,Psychology and Cognitive Sciences ,Developmental & Child Psychology ,Health sciences - Abstract
PurposeTo compare the utility of single versus repeated autism screening in a sample at higher likelihood (HL) for ASD, following both screen positives and all screen negatives to diagnostic outcome.MethodsUsing a prospective infant sibling design, the current study followed 135 toddlers at HL for ASD and conducted diagnostic evaluations on the full sample at 18, 24, and 36 months. The psychometric properties of the M-CHAT-R using both concurrent and predictive diagnostic evaluations were compared in a group screened once (at 18 months only, n = 60) or twice (at both 18 and 24 months, n = 75). The study also examined consistency in reporting of ASD symptoms across the M-CHAT-R and a developmental concerns interview, comparing the HL group to a group with lower likelihood (LL) for ASD (n = 88).ResultsSensitivity and specificity of the M-CHAT-R were high (75 - 95%), consistent with previous research. Positive predictive value (43 - 76%) was higher in this HL group than in previous community samples. Repeat screening improved sensitivity with little cost to specificity. At both 18 and 24 months, HL parents were more consistent in their reporting on the M-CHAT-R and a concerns interview than LL parents.ConclusionThe M-CHAT-R has strong psychometric properties when used with groups at HL for ASD, suggesting that scores over the screening cutoff of 3 should lead to prompt diagnostic evaluation referrals in children with older siblings on the spectrum.
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- 2023
273. Impact of Age and Variant Time Period on Clinical Presentation and Outcomes of Hospitalized Coronavirus Disease 2019 Patients.
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Srivastava, Pratyaksh K, Klomhaus, Alexandra M, Tehrani, David M, Fonarow, Gregg C, Ziaeian, Boback, Desai, Pooja S, Rafique, Asim, de Lemos, James, Parikh, Rushi V, and Yang, Eric H
- Abstract
To evaluate the impact of age and COVID-19 variant time period on morbidity and mortality among those hospitalized with COVID-19.Patients from the American Heart Association's Get With The Guidelines COVID-19 cardiovascular disease registry (January 20, 2020-February 14, 2022) were divided into groups based on whether they presented during periods of wild type/alpha, delta, or omicron predominance. They were further subdivided by age (young: 18-40 years; older: more than 40 years), and characteristics and outcomes were compared.The cohort consisted of 45,421 hospitalized COVID-19 patients (wild type/alpha period: 41,426, delta period: 3349, and omicron period: 646). Among young patients (18-40 years), presentation during delta was associated with increased odds of severe COVID-19 (OR, 1.6; 95% CI, 1.3-2.1), major adverse cardiovascular events (MACE) (OR, 1.8; 95% CI, 1.3-2.5), and in-hospital mortality (OR, 2.2; 95% CI, 1.5-3.3) when compared with presentation during wild type/alpha. Among older patients (more than 40 years), presentation during delta was associated with increased odds of severe COVID-19 (OR, 1.2; 95% CI, 1.1-1.3), MACE (OR, 1.5; 95% CI, 1.4-1.7), and in-hospital mortality (OR, 1.4; 95% CI, 1.3-1.6) when compared with wild type/alpha. Among older patients (more than 40 years), presentation during omicron associated with decreased odds of severe COVID-19 (OR, 0.7; 95% CI, 0.5-0.9) and in-hospital mortality (OR, 0.6; 95% CI, 0.5-0.9) when compared with wild type/alpha.Among hospitalized adults with COVID-19, presentation during a time of delta predominance was associated with increased odds of severe COVID-19, MACE, and in-hospital mortality compared with presentation during wild type/alpha. Among older patients (aged more than 40 years), presentation during omicron was associated with decreased odds of severe COVID-19 and in-hospital mortality compared with wild type/alpha.
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- 2023
274. Racial/Ethnic Disparities in Outcomes After Percutaneous Coronary Intervention
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Wang, Daniel R, Li, Joshua, Parikh, Rushi V, Ziaeian, Boback, Aksoy, Olcay, Jackson, Nicholas J, and Hsu, Jeffrey J
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Clinical Research ,Heart Disease - Coronary Heart Disease ,Heart Disease ,Cardiovascular ,Good Health and Well Being ,Asian American/Pacific Islanders ,Hispanics ,health disparities ,race/ethnic disparities ,social determinants of health ,Cardiorespiratory Medicine and Haematology ,Cardiovascular System & Hematology ,Cardiovascular medicine and haematology - Abstract
Asian American/Pacific Islanders (AAPIs) and Hispanics are growing minority United States populations, but are poorly represented in the cardiovascular literature. This study examines guideline adherence and outcomes in AAPIs and Hispanics compared with non-Hispanic Whites (NHWs) in a quaternary care center after inpatient percutaneous coronary intervention (PCI). The primary end points were inpatient post-PCI bleed, heart failure, cardiogenic shock, and all-cause mortality, whereas the secondary end point was the prescription rate of post-PCI guideline-directed medical therapy including aspirin, statins, P2Y12 receptor blockers, and cardiopulmonary rehabilitation. Intergroup differences were assessed through analysis of variance or two-way chi-square tests, and the association of race with binary outcomes was examined through logistic regression with NHW as the reference group. Compared with NHW, AAPIs, and Hispanics had higher odds of diabetes mellitus, and AAPIs had higher odds of hypertension and being on dialysis. Hispanics had higher odds of post-PCI mortality versus NHW, both in acute coronary syndrome (odds ratio [OR] 2.04, p = 0.03) and elective PCI (OR 2.51, p = 0.04). AAPI also trended toward higher mortality than NHW in both categories. AAPIs were found to have higher odds of statin prescription (OR 1.91, p = 0.04). Hispanics had lower odds of ticagrelor prescription versus NHW (OR 0.65, p = 0.04), and AAPIs trended toward such. No differences were found for cardiopulmonary rehabilitation prescriptions in groups. This study suggests that despite quality improvement efforts, disparities remain in postprocedural outcomes in minority groups in comparison with NHW.
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- 2023
275. Oblique lessons from the W-mass measurement at CDF II
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Asadi, Pouya, Cesarotti, Cari, Fraser, Katherine, Homiller, Samuel, and Parikh, Aditya
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Nuclear and Plasma Physics ,Particle and High Energy Physics ,Physical Sciences - Abstract
The CDF Collaboration recently reported a new precise measurement of the W-boson mass MW with a central value significantly larger than the SM prediction. We explore the effects of including this new measurement on a fit of the Standard Model (SM) to electroweak precision data. We characterize the tension of this new measurement with the SM and explore potential beyond the SM phenomena within the electroweak sector in terms of the oblique parameters S, T and U. We show that the large MW value can be accommodated in the fit by a large, nonzero value of U, which is difficult to construct in explicit models. Assuming U=0, the electroweak fit strongly prefers large, positive values of T. Finally, we study how the preferred values of the oblique parameters may be generated in the context of models affecting the electroweak sector at tree and loop level. In particular, we demonstrate that the preferred values of T and S can be generated with a real SU(2)L triplet scalar, the humble swino, which can be heavy enough to evade current collider constraints, or by (multiple) species of singlet-doublet fermion pairs. We highlight challenges in constructing other simple models for explaining a large MW value and several directions for further study.
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- 2023
276. Changes over time in POLST use and content by race and ethnicity among California nursing home residents.
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Zingmond, David, Powell, David, Jennings, Lee, Liang, Li-Jung, Escarce, Jose, Parikh, Punam, and Wenger, Neil
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POLST ,end-of-life care ,long-term care ,nursing home ,race disparity ,Humans ,Advance Directives ,Ethnicity ,Advance Care Planning ,Nursing Homes ,Resuscitation Orders ,California - Abstract
BACKGROUND: Physician Orders for Life-Sustaining Treatment (POLST) are commonly used for nursing home (NH) residents. Treatment orders differ across race and ethnicity, presumably related to cultural and socioeconomic variation and levels of access to care and trust. Because national efforts focus on addressing the underpinnings of racial and ethnic differences in treatment (i.e., access to care and trust), we describe POLST use and content by race and ethnicity. METHODS: California requires NHs to document POLST completion and content in the Minimum Data Set. We describe POLST completion and content for all California NH residents from 2011 to 2016 (N = 1,120,376). Adjusting for resident characteristics, we compared changes in completion rate and differences by race and ethnicity in POLST content-orders for cardiopulmonary resuscitation (CPR), do not resuscitate (DNR), CPR with full treatment, DNR with selective treatment or comfort orders, and if unsigned. RESULTS: POLST completion increased across all racial and ethnic groups from 2011 to 2016; by 2016, NH residents had a POLST two-thirds or more of the time. In 2011, Black residents had a POLST with a CPR order 30.4% of the time, Hispanic residents 25.6%, and White residents 19.7%. By 2016, this grew to 42.5%, 38.2%, and 28.1%, respectively, with Black and Hispanic residents demonstrating larger increases than White residents (p
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- 2023
277. Evaluating Neighborhood-Level Differences in Hair Product Safety by Environmental Working Group Ratings among Retailers in Boston, Massachusetts
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Chan, Marissa, Parikh, Shivani, Shyr, Derek, Shamasunder, Bhavna, Adamkiewicz, Gary, and James-Todd, Tamarra
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Epidemiology ,Public Health ,Health Sciences ,Clinical Research ,Child ,Female ,Humans ,Boston ,Massachusetts ,Hair ,Ethnicity ,Commerce ,Endocrine Disruptors ,Environmental Sciences ,Medical and Health Sciences ,Toxicology ,Biomedical and clinical sciences ,Environmental sciences ,Health sciences - Abstract
BackgroundPersonal care products are a notable source of exposure to endocrine-disrupting chemicals (EDCs). Racial/ethnic differences in the use of hair products containing EDCs are reported, with women and children of color more commonly using hair products that are hormonally active and contain EDCs than other racial/ethnic groups. There is limited research examining the neighborhood-level social and economic factors that may contribute to these reported disparities.ObjectivesWe aimed to examine the safety of hair products across sociodemographically diverse neighborhoods in Boston, Massachusetts.MethodsEight neighborhoods were identified based on indicators of race/ethnicity and socioeconomic status (SES). We randomly selected 50 stores and collected data on the hair products for sale and their corresponding Environmental Working Group (EWG) Skin Deep hazard score. The association between neighborhood and EWG hazard category (low, moderate, high) was examined using a multinomial logistic regression.ResultsA total of 14,019 hair products were identified in the eight neighborhoods. When considering products with EWG hazard scores, Roxbury, a lower income community of color, and Mission Hill, a lower income community, were reported to have a higher percentage of high-hazard hair products in comparison with Beacon Hill [12.2% (163/1,332), 11.4% (65/571) vs. 7.9% (30/382), respectively]. Differences between the safety of hair products were observed, with Roxbury and Mission Hill reporting more than a 2-fold higher risk ratio (RR) of finding hair products with high vs. low EWG scores in comparison with that of Beacon Hill [RR for Roxbury: 2.3, 95% confidence interval (CI): 1.1, 4.6; RR for Mission Hill: 2.3, 95% CI: 1.0, 5.4]. Other neighborhoods were also observed to have an increased RR in comparison with Beacon Hill, however, with 95% CIs that extended beyond the null.DiscussionRetail stores in neighborhoods with a higher percentage of residents of color and lower SES were found to be more likely to sell products with high hazard scores than stores in a higher SES and predominately non-Hispanic White neighborhood. https://doi.org/10.1289/EHP10653.
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- 2023
278. Cardiovascular events more than 6 months after pregnancy in patients with congenital heart disease.
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Schultz, Hayley, Sobhani, Nasim, Blissett, Sarah, Yogeswaran, Vidhushei, Hong, Jessica, Harris, Ian, Parikh, Nisha, Gonzalez, Juan, and Agarwal, Anushree
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Arrhythmias ,Cardiac ,Heart Defects ,Congenital ,Pregnancy ,Pregnancy ,Humans ,Female ,Heart Defects ,Congenital ,Heart Failure ,Endocarditis ,Patients ,Peripartum Period - Abstract
OBJECTIVES: Patients with congenital heart disease (CHD) are increasingly pursuing pregnancy, highlighting the need for data on late cardiovascular events (more than 6 months after delivery). We aimed to determine the incidence of late cardiovascular events in postpartum patients with CHD and evaluate the accuracy of the existing risk scores in predicting these events. STUDY DESIGN: We identified patients with CHD who delivered between 2008 and 2020 at a tertiary centre and had follow-up data for greater than 6 months post partum. Late cardiovascular events were defined as heart failure, arrhythmia, thromboembolic events, endocarditis, urgent cardiovascular interventions or death. Survival analysis and Cox proportional model were used to estimate the incidence of late cardiovascular events and determine the hazard ratio of factors associated with these events. RESULTS: Of 117 patients, 19% had 36 late cardiovascular events over a median follow-up of 3.8 years. Annual incidence of any late cardiovascular event was 5.7%. Hazards of late cardiovascular events were significantly higher among those with higher Cardiac Disease in Pregnancy Study (CARPREG) II and Zwangerschap bij Aangeboren HARtAfwijking-Pregnancy in Women With Congenital Heart Disease (ZAHARA) risk scores and among patients with prepregnancy New York Heart Association class≥II. C-statistic to predict the late cardiovascular events was highest for ZAHARA (0.7823), followed by CARPREG II (0.6902) and prepregnancy New York Heart Association class≥ II (0.6677). CONCLUSIONS: Currently available risk tools designed for prognostication during the peripartum period can also be used to determine risks of late maternal cardiovascular events among those with CHD. These findings provide important new information for counselling and risk modification.
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- 2023
279. Prostate cancer and bone: clinical presentation and molecular mechanisms.
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Wells, Kristina V, Krackeler, Margaret L, Jathal, Maitreyee K, Parikh, Mamta, Ghosh, Paramita M, Leach, J Kent, and Genetos, Damian C
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Prostate Cancer ,Aging ,Cancer ,Urologic Diseases ,Musculoskeletal ,Male ,Humans ,Prostatic Neoplasms ,Bone Neoplasms ,Androgen Antagonists ,Bone and Bones ,Treatment Outcome ,Tumor Microenvironment ,androgen receptor ,bone ,hypoxia ,metastasis ,prostate cancer ,tissue engineering ,Biological Sciences ,Medical and Health Sciences ,Oncology & Carcinogenesis - Abstract
Prostate cancer (PCa) is an increasingly prevalent health problem in the developed world. Effective treatment options exist for localized PCa, but metastatic PCa has fewer treatment options and shorter patient survival. PCa and bone health are strongly entwined, as PCa commonly metastasizes to the skeleton. Since androgen receptor signaling drives PCa growth, androgen-deprivation therapy whose sequelae reduce bone strength constitutes the foundation of advanced PCa treatment. The homeostatic process of bone remodeling - produced by concerted actions of bone-building osteoblasts, bone-resorbing osteoclasts, and regulatory osteocytes - may also be subverted by PCa to promote metastatic growth. Mechanisms driving skeletal development and homeostasis, such as regional hypoxia or matrix-embedded growth factors, may be subjugated by bone metastatic PCa. In this way, the biology that sustains bone is integrated into adaptive mechanisms for the growth and survival of PCa in bone. Skeletally metastatic PCa is difficult to investigate due to the entwined nature of bone biology and cancer biology. Herein, we survey PCa from origin, presentation, and clinical treatment to bone composition and structure and molecular mediators of PCa metastasis to bone. Our intent is to quickly yet effectively reduce barriers to team science across multiple disciplines that focuses on PCa and metastatic bone disease. We also introduce concepts of tissue engineering as a novel perspective to model, capture, and study complex cancer-microenvironment interactions.
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- 2023
280. Immune Status and SARS-CoV-2 Viral Dynamics
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Li, Yijia, Moser, Carlee, Aga, Evgenia, Currier, Judith S, Wohl, David A, Daar, Eric S, Ritz, Justin, Greninger, Alexander L, Sieg, Scott, Parikh, Urvi M, Coombs, Robert W, Hughes, Michael D, Eron, Joseph J, Smith, Davey M, Chew, Kara W, Li, Jonathan Z, Hosey, Lara, Roa, Jhoanna, Patel, Nilam, Degli-Angeli, Emily, Goecker, Erin, Daza, Glenda, Harb, Socorro, Dragavon, Joan, Aldrovandi, Grace, Murtaugh, William, Cooper, Marlene, Gutzman, Howard, Knowles, Kevin, Bowman, Rachel, Erhardt, Bill, Warring, Lorraine, Hessinger, Diane, and Adams, Stacey
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Biomedical and Clinical Sciences ,Immunology ,Clinical Research ,Infectious Diseases ,Coronaviruses ,Emerging Infectious Diseases ,Clinical Trials and Supportive Activities ,Infection ,Good Health and Well Being ,Humans ,COVID-19 ,Immunocompromised Host ,Immunosuppression Therapy ,Kinetics ,SARS-CoV-2 ,RNA ,immunocompromise ,ACTIV-2/A5401 Study Team ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Immunocompromised individuals are disproportionately affected by severe coronavirus disease 2019, but immune compromise is heterogenous, and viral dynamics may vary by the degree of immunosuppression. In this study, we categorized ACTIV-2/A5401 participants based on the extent of immunocompromise into none, mild, moderate, and severe immunocompromise. Moderate/severe immunocompromise was associated with higher nasal viral load at enrollment (adjusted difference in means: 0.47 95% confidence interval, .12-.83 log10 copies/mL) and showed a trend toward higher cumulative nasal RNA levels and plasma viremia compared to nonimmunocompromised individuals. Immunosuppression leads to greater viral shedding and altered severe acute respiratory syndrome coronavirus 2 viral decay kinetics. Clinical Trials Registration. NCT04518410.
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- 2023
281. Surfactant-Mediated Structural Modulations to Planar, Amphiphilic Multilamellar Stacks.
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Speer, Daniel, Salvador-Castell, Marta, Huang, Yuqi, Liu, Gang-Yu, Sinha, Sunil, and Parikh, Atul
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Lipid Bilayers ,Phosphatidylcholines ,Surface-Active Agents ,Phospholipids ,Pulmonary Surfactants ,Lipoproteins - Abstract
The hydrophobic effect, a ubiquitous process in biology, is a primary thermodynamic driver of amphiphilic self-assembly. It leads to the formation of unique morphologies including two highly important classes of lamellar and micellar mesophases. The interactions between these two types of structures and their involved components have garnered significant interest because of their importance in key biochemical technologies related to the isolation, purification, and reconstitution of membrane proteins. This work investigates the structural organization of mixtures of the lamellar-forming phospholipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and two zwitterionic micelle-forming surfactants, being n-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (Zwittergent 3-12 or DDAPS) and 1-oleoyl-2-hydroxy-sn-glycero-3-phosphocholine (O-Lyso-PC), when assembled by water vapor hydration with X-ray diffraction measurements, brightfield optical microscopy, wide-field fluorescence microscopy, and atomic force microscopy. The results reveal that multilamellar mesophases of these mixtures can be assembled across a wide range of POPC to surfactant (POPC:surfactant) concentration ratios, including ratios far surpassing the classical detergent-saturation limit of POPC bilayers without significant morphological disruptions to the lamellar motif. The mixed mesophases generally decreased in lamellar spacing (D) and headgroup-to-headgroup distance (Dhh) with a higher concentration of the doped surfactant, but trends in water layer thickness (Dw) between each bilayer in the stack are highly variable. Further structural characteristics including mesophase topography, bilayer thickness, and lamellar rupture force were revealed by atomic force microscopy (AFM), exhibiting homogeneous multilamellar stacks with no significant physical differences with changes in the surfactant concentration within the mesophases. Taken together, the outcomes present the assembly of unanticipated and highly unique mixed mesophases with varied structural trends from the involved surfactant and lipidic components. Modulations in their structural properties can be attributed to the surfactants chemical specificity in relation to POPC, such as the headgroup hydration and the hydrophobic chain tail mismatch. Taken together, our results illustrate how specific chemical complexities of surfactant-lipid interactions can alter the morphologies of mixed mesophases and thereby alter the kinetic pathways by which surfactants dissolve lipid mesophases in bulk aqueous solutions.
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- 2023
282. Associations of Biomarkers of Kidney Tubule Health, Injury, and Inflammation with Left Ventricular Hypertrophy in Children with CKD.
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Jiang, Kuan, Greenberg, Jason, Abraham, Alison, Xu, Yunwen, Schelling, Jeffrey, Feldman, Harold, Schrauben, Sarah, Waikar, Sushrut, Shlipak, Michael, Coca, Steven, Vasan, Ramachandran, Gutierrez, Orlando, Ix, Joachim, Warady, Bradley, Kimmel, Paul, Bonventre, Joseph, Parikh, Chirag, Mitsnefes, Mark, Denburg, Michelle, Furth, Susan, and Wettersten, Nicholas
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Humans ,Child ,Hypertrophy ,Left Ventricular ,Inflammation ,Renal Insufficiency ,Chronic ,Kidney Tubules ,Biomarkers - Abstract
KEY POINTS: Higher plasma and urine kidney injury molecule-1, urine monocyte chemoattractant protein-1, and lower urine alpha-1-microglobulin were associated with left ventricular hypertrophy, even after adjustment for confounders. Biomarkers of tubular injury, dysfunction, and inflammation may indicate the severity of kidney pathology and are associated with left ventricular hypertrophy. BACKGROUND: Left ventricular hypertrophy (LVH) is common in children with CKD and is associated with an increased risk of cardiovascular disease and mortality. We have shown that several plasma and urine biomarkers are associated with increased risk of CKD progression. As CKD is associated with LVH, we sought to investigate the association between the biomarkers and LVH. METHODS: In the CKD in Children Cohort Study, children aged 6 months to 16 years with an eGFR of 30–90 ml/min per 1.73 m2 were enrolled at 54 centers in the United States and Canada. We measured plasma biomarkers kidney injury molecule-1 (KIM-1), tumor necrosis factor receptor-1, tumor necrosis factor receptor-2, soluble urokinase-type plasminogen activator receptor and urine KIM-1, monocyte chemoattractant protein-1 (MCP-1), YKL-40, alpha-1-microglobulin (alpha-1m), and epidermal growth factor in stored plasma and urine collected 5 months after enrollment. Echocardiograms were performed 1 year after enrollment. We assessed the cross-sectional association between the log2 biomarker levels and LVH (left ventricular mass index greater than or equal to the 95th percentile) using a Poisson regression model, adjusted for age, sex, race, body mass index, hypertension, glomerular diagnosis, urine protein-to-creatinine ratio, and eGFR at study entry. RESULTS: Among the 504 children, LVH prevalence was 12% (n=59) 1 year after enrollment. In a multivariable-adjusted model, higher plasma and urine KIM-1 and urine MCP-1 concentrations were associated with a higher prevalence of LVH (plasma KIM-1 prevalence ratio [PR] per log2: 1.27, 95% confidence interval [CI], 1.02 to 1.58; urine KIM-1 PR: 1.21, 95% CI, 1.11 to 1.48; and urine MCP-1 PR: 1.18, 95% CI, 1.04 to 1.34). After multivariable adjustment for covariates, lower urine alpha-1m was also associated with a higher prevalence of LVH (PR: 0.90, 95% CI, 0.82 to 0.99). CONCLUSIONS: Higher plasma and urine KIM-1, urine MCP-1, and lower urine alpha-1m were each associated with LVH prevalence in children with CKD. These biomarkers may better inform risk and help elucidate the pathophysiology of LVH in pediatric CKD.
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- 2023
283. A Phase I Study of Combination Olaparib and Radium-223 in Men with Metastatic Castration-Resistant Prostate Cancer (mCRPC) with Bone Metastases (COMRADE).
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Pan, Elizabeth, Xie, Wanling, Ajmera, Archana, Araneta, Arlene, Jamieson, Christina, Folefac, Edmund, Hussain, Arif, Kyriakopoulos, Christos, Olson, Adam, Parikh, Rahul, Saraiya, Biren, Ivy, S, Van Allen, Eliezer, Lindeman, Neal, Kochupurakkal, Bose, Shapiro, Geoffrey, McKay, Rana, and Parikh, Mamta
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Male ,Humans ,Prostatic Neoplasms ,Castration-Resistant ,Antineoplastic Agents ,Fatigue - Abstract
Given that radium-223 is a radiopharmaceutical that induces DNA damage, and olaparib is a PARP inhibitor that interferes with DNA repair mechanisms, we hypothesized their synergy in metastatic castration-resistant prostate cancer (mCRPC). We sought to demonstrate the safety and efficacy of olaparib + radium-223. We conducted a multicenter phase I 3+3 dose escalation study of olaparib with fixed dose radium-223 in patients with mCRPC with bone metastases. The primary objective was to establish the RP2D of olaparib, with secondary objectives of safety, PSA response, alkaline phosphatase response, radiographic progression-free survival (rPFS), overall survival, and efficacy by homologous recombination repair (HRR) gene status. Twelve patients were enrolled; all patients received a prior androgen receptor signaling inhibitor (ARSI; 100%) and 3 patients (25%) prior docetaxel. Dose-limiting toxicities (DLT) included cytopenias, fatigue, and nausea. No DLTs were seen in the observation period however delayed toxicities guided the RP2D. The RP2D of olaparib was 200 mg orally twice daily with radium-223. The most common treatment-related adverse events were fatigue (92%) and anemia (58%). The rPFS at 6 months was 58% (95% confidence interval, 27%-80%). Nine patients were evaluable for HRR gene status; 1 had a BRCA2 alteration (rPFS 11.8 months) and 1 had a CDK12 alteration (rPFS 3.1 months). Olaparib can be safely combined with radium-223 at the RP2D 200 mg orally twice daily with fixed dose radium-223. Early clinical benefit was observed and will be investigated in a phase II study.
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- 2023
284. Text-Conditional Contextualized Avatars For Zero-Shot Personalization
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Azadi, Samaneh, Hayes, Thomas, Shah, Akbar, Pang, Guan, Parikh, Devi, and Gupta, Sonal
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
Recent large-scale text-to-image generation models have made significant improvements in the quality, realism, and diversity of the synthesized images and enable users to control the created content through language. However, the personalization aspect of these generative models is still challenging and under-explored. In this work, we propose a pipeline that enables personalization of image generation with avatars capturing a user's identity in a delightful way. Our pipeline is zero-shot, avatar texture and style agnostic, and does not require training on the avatar at all - it is scalable to millions of users who can generate a scene with their avatar. To render the avatar in a pose faithful to the given text prompt, we propose a novel text-to-3D pose diffusion model trained on a curated large-scale dataset of in-the-wild human poses improving the performance of the SOTA text-to-motion models significantly. We show, for the first time, how to leverage large-scale image datasets to learn human 3D pose parameters and overcome the limitations of motion capture datasets.
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- 2023
285. Extrapolative Controlled Sequence Generation via Iterative Refinement
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Padmakumar, Vishakh, Pang, Richard Yuanzhe, He, He, and Parikh, Ankur P.
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Computer Science - Machine Learning ,Computer Science - Computation and Language ,Quantitative Biology - Quantitative Methods - Abstract
We study the problem of extrapolative controlled generation, i.e., generating sequences with attribute values beyond the range seen in training. This task is of significant importance in automated design, especially drug discovery, where the goal is to design novel proteins that are \textit{better} (e.g., more stable) than existing sequences. Thus, by definition, the target sequences and their attribute values are out of the training distribution, posing challenges to existing methods that aim to directly generate the target sequence. Instead, in this work, we propose Iterative Controlled Extrapolation (ICE) which iteratively makes local edits to a sequence to enable extrapolation. We train the model on synthetically generated sequence pairs that demonstrate small improvement in the attribute value. Results on one natural language task (sentiment analysis) and two protein engineering tasks (ACE2 stability and AAV fitness) show that ICE considerably outperforms state-of-the-art approaches despite its simplicity. Our code and models are available at: https://github.com/vishakhpk/iter-extrapolation., Comment: ICML 2023 - Camera Ready Version
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- 2023
286. Cascading GEMM: High Precision from Low Precision
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Parikh, Devangi N., van de Geijn, Robert A., and Henry, Greg M.
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Computer Science - Mathematical Software ,G.4 - Abstract
This paper lays out insights and opportunities for implementing higher-precision matrix-matrix multiplication (GEMM) from (in terms of) lower-precision high-performance GEMM. The driving case study approximates double-double precision (FP64x2) GEMM in terms of double precision (FP64) GEMM, leveraging how the BLAS-like Library Instantiation Software (BLIS) framework refactors the Goto Algorithm. With this, it is shown how approximate FP64x2 GEMM accuracy can be cast in terms of ten ``cascading'' FP64 GEMMs. Promising results from preliminary performance and accuracy experiments are reported. The demonstrated techniques open up new research directions for more general cascading of higher-precision computation in terms of lower-precision computation for GEMM-like functionality., Comment: 26 pages, 9 figures
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- 2023
287. Detailed shapes of the line-of-sight velocity distributions in massive early-type galaxies from non-parametric spectral models
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Mehrgan, Kianusch, Thomas, Jens, Saglia, Roberto, Parikh, Taniya, and Bender, Ralf
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Astrophysics - Astrophysics of Galaxies - Abstract
We present the first systematic study of the detailed shapes of the line-of-sight velocity distributions (LOSVDs) in nine massive early-type galaxies (ETGs) using the novel non-parametric modelling code WINGFIT. High-signal spectral observations with MUSE at the VLT allow us to measure between 40 and 400 individual LOSVDs in each galaxy at a signal-to-noise level better than 100 per spectral bin and to trace the LOSVDs all the way out to the highest stellar velocities. We extensively discuss potential LOSVD distortions due to template mismatch and strategies to avoid them. Our analysis uncovers a plethora of complex, large scale kinematic structures for the shapes of the LOSVDs. Most notably, in the centers of all ETGs in our sample, we detect faint, broad LOSVD ``wings'' extending the line-of-sight velocities, v_los, well beyond 3 sigma to v_los = +- 1000 - 1500 km/s on both sides of the peak of the LOSVDs. These wings likely originate from PSF effects and contain velocity information about the very central unresolved regions of the galaxies. In several galaxies, we detect wings of similar shape also towards the outer parts of the MUSE field-of-view. We propose that these wings originate from faint halos of loosely bound stars around the ETGs, similar to the cluster-bound stellar envelopes found around many brightest cluster galaxies., Comment: Accepted for publication in the Astrophysical Journal
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- 2023
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288. Variable Importance Matching for Causal Inference
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Lanners, Quinn, Parikh, Harsh, Volfovsky, Alexander, Rudin, Cynthia, and Page, David
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Statistics - Methodology ,Computer Science - Machine Learning ,Economics - Econometrics - Abstract
Our goal is to produce methods for observational causal inference that are auditable, easy to troubleshoot, accurate for treatment effect estimation, and scalable to high-dimensional data. We describe a general framework called Model-to-Match that achieves these goals by (i) learning a distance metric via outcome modeling, (ii) creating matched groups using the distance metric, and (iii) using the matched groups to estimate treatment effects. Model-to-Match uses variable importance measurements to construct a distance metric, making it a flexible framework that can be adapted to various applications. Concentrating on the scalability of the problem in the number of potential confounders, we operationalize the Model-to-Match framework with LASSO. We derive performance guarantees for settings where LASSO outcome modeling consistently identifies all confounders (importantly without requiring the linear model to be correctly specified). We also provide experimental results demonstrating the method's auditability, accuracy, and scalability as well as extensions to more general nonparametric outcome modeling.
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- 2023
289. A Novel Collaborative Self-Supervised Learning Method for Radiomic Data
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Li, Zhiyuan, Li, Hailong, Ralescu, Anca L., Dillman, Jonathan R., Parikh, Nehal A., and He, Lili
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Artificial Intelligence ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
The computer-aided disease diagnosis from radiomic data is important in many medical applications. However, developing such a technique relies on annotating radiological images, which is a time-consuming, labor-intensive, and expensive process. In this work, we present the first novel collaborative self-supervised learning method to solve the challenge of insufficient labeled radiomic data, whose characteristics are different from text and image data. To achieve this, we present two collaborative pretext tasks that explore the latent pathological or biological relationships between regions of interest and the similarity and dissimilarity information between subjects. Our method collaboratively learns the robust latent feature representations from radiomic data in a self-supervised manner to reduce human annotation efforts, which benefits the disease diagnosis. We compared our proposed method with other state-of-the-art self-supervised learning methods on a simulation study and two independent datasets. Extensive experimental results demonstrated that our method outperforms other self-supervised learning methods on both classification and regression tasks. With further refinement, our method shows the potential advantage in automatic disease diagnosis with large-scale unlabeled data available., Comment: 14 pages, 7 figures
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- 2023
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290. Hairy cell leukemia variant and WHO classification correspondence Re: 5th edition WHO classification haematolymphoid tumors: lymphoid neoplasms
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Grever, Michael, Andritsos, Leslie, Anghelina, Mirela, Arons, Evgeny, Banerji, Versha, Barrientos, Jacqueline, Bhat, Seema A., Blachly, James, Broccoli, Alessandro, Call, Timothy, Dearden, Claire, Dietrich, Sascha, Else, Monica, Epperla, Narendranath, Fagarasanu, Andrei, Falini, Brunangelo, Forconi, Francesco, Gozzetti, Alessandro, Hampel, Paul, Hermel, David J., Iyengar, Sunil, Johnston, James B., Juliusson, Gunnar, Kreitman, Robert J., Lauria, Francesco, Lozanski, Gerard, Oakes, Christopher C., Parikh, Sameer A., Park, Jae, Quest, Graeme, Rai, Kanti, Ravandi, Farhad, Robak, Tadeusz, Rogers, Kerry A., Saven, Alan, Seymour, John F., Tadmor, Tamar, Tallman, Martin S., Tam, Constantine S., Tiacci, Enrico, Troussard, Xavier, Wörmann, Bernhard, Zent, Clive S., Zenz, Thorsten, and Zinzani, Pier Luigi
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- 2024
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291. Scalar Co-SIMP Dark Matter: Models and Sensitivities
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Parikh, Aditya, Smirnov, Juri, Xu, Weishuang Linda, and Zhou, Bei
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High Energy Physics - Phenomenology ,Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
In this work, we present UV completions of the recently proposed number-changing Co-SIMP freeze-out mechanism. In contrast to the standard cannibalistic-type dark matter picture that occurs entirely in the dark sector, the $3\to 2$ process setting the relic abundance in this case requires one Standard Model particle in the initial and final states. This prevents the dark sector from overheating and leads to rich experimental signatures. We generate the Co-SIMP interaction with a dark sector consisting of two scalars, with the mediator coupling to either nucleons or electrons. In either case, \textit{the dark matter candidate is naturally light}: nucleophilic interactions favor the sub-GeV mass range and leptophilic interactions favor the sub-MeV mass range. Viable thermal models in these lighter mass regimes are particularly intriguing to study at this time, as new developments in low-threshold detector technologies will begin probing this region of parameter space. While particles in the sub-MeV regime can potentially impact light element formation and CMB decoupling, we show that a late-time phase transition opens up large fractions of parameter space. These thermal light dark matter models can instead be tested with dedicated experiments. We discuss the viable parameter space in each scenario in light of the current sensitivity of various experimental probes and projected future reach., Comment: 42 pages, 10 figures
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- 2023
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292. Text-To-4D Dynamic Scene Generation
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Singer, Uriel, Sheynin, Shelly, Polyak, Adam, Ashual, Oron, Makarov, Iurii, Kokkinos, Filippos, Goyal, Naman, Vedaldi, Andrea, Parikh, Devi, Johnson, Justin, and Taigman, Yaniv
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
We present MAV3D (Make-A-Video3D), a method for generating three-dimensional dynamic scenes from text descriptions. Our approach uses a 4D dynamic Neural Radiance Field (NeRF), which is optimized for scene appearance, density, and motion consistency by querying a Text-to-Video (T2V) diffusion-based model. The dynamic video output generated from the provided text can be viewed from any camera location and angle, and can be composited into any 3D environment. MAV3D does not require any 3D or 4D data and the T2V model is trained only on Text-Image pairs and unlabeled videos. We demonstrate the effectiveness of our approach using comprehensive quantitative and qualitative experiments and show an improvement over previously established internal baselines. To the best of our knowledge, our method is the first to generate 3D dynamic scenes given a text description.
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- 2023
293. Reversing The Twenty Questions Game
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Parikh, Parth and Gupta, Anisha
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Computer Science - Computation and Language - Abstract
Twenty questions is a widely popular verbal game. In recent years, many computerized versions of this game have been developed in which a user thinks of an entity and a computer attempts to guess this entity by asking a series of boolean-type (yes/no) questions. In this research, we aim to reverse this game by making the computer choose an entity at random. The human aims to guess this entity by quizzing the computer with natural language queries which the computer will then attempt to parse using a boolean question answering model. The game ends when the human is successfully able to guess the entity of the computer's choice., Comment: 14 pages, 9 figures, 2 tables, This paper is a graduate course project for North Carolina State University, written for the Natural Language Processing class in Fall 2021. The paper was submitted to and graded by Dr. Munindar P. Singh
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- 2023
294. Transfer learning for conflict and duplicate detection in software requirement pairs
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Malik, Garima, Yildirim, Savas, Cevik, Mucahit, Bener, Ayse, and Parikh, Devang
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Computer Science - Software Engineering ,Computer Science - Machine Learning - Abstract
Consistent and holistic expression of software requirements is important for the success of software projects. In this study, we aim to enhance the efficiency of the software development processes by automatically identifying conflicting and duplicate software requirement specifications. We formulate the conflict and duplicate detection problem as a requirement pair classification task. We design a novel transformers-based architecture, SR-BERT, which incorporates Sentence-BERT and Bi-encoders for the conflict and duplicate identification task. Furthermore, we apply supervised multi-stage fine-tuning to the pre-trained transformer models. We test the performance of different transfer models using four different datasets. We find that sequentially trained and fine-tuned transformer models perform well across the datasets with SR-BERT achieving the best performance for larger datasets. We also explore the cross-domain performance of conflict detection models and adopt a rule-based filtering approach to validate the model classifications. Our analysis indicates that the sentence pair classification approach and the proposed transformer-based natural language processing strategies can contribute significantly to achieving automation in conflict and duplicate detection
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- 2023
295. Adaptive Fine-tuning for Multiclass Classification over Software Requirement Data
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Yildirim, Savas, Cevik, Mucahit, Parikh, Devang, and Basar, Ayse
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Computer Science - Software Engineering - Abstract
The analysis of software requirement specifications (SRS) using Natural Language Processing (NLP) methods has been an important study area in the software engineering field in recent years. Especially thanks to the advances brought by deep learning and transfer learning approaches in NLP, SRS data can be utilized for various learning tasks more easily. In this study, we employ a three-stage domain-adaptive fine-tuning approach for three prediction tasks regarding software requirements, which improve the model robustness on a real distribution shift. The multi-class classification tasks involve predicting the type, priority and severity of the requirement texts specified by the users. We compare our results with strong classification baselines such as word embedding pooling and Sentence BERT, and show that the adaptive fine-tuning leads to performance improvements across the tasks. We find that an adaptively fine-tuned model can be specialized to particular data distribution, which is able to generate accurate results and learns from abundantly available textual data in software engineering task management systems.
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- 2023
296. Measuring the effect of newborn screening on survival after haematopoietic cell transplantation for severe combined immunodeficiency: a 36-year longitudinal study from the Primary Immune Deficiency Treatment Consortium.
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Thakar, Monica, Logan, Brent, Puck, Jennifer, Dunn, Elizabeth, Buckley, Rebecca, Cowan, Morton, OReilly, Richard, Kapoor, Neena, Satter, Lisa, Pai, Sung-Yun, Heimall, Jennifer, Chandra, Sharat, Ebens, Christen, Chellapandian, Deepak, Williams, Olatundun, Burroughs, Lauri, Saldana, Blachy, Rayes, Ahmad, Madden, Lisa, Chandrakasan, Shanmuganathan, Bednarski, Jeffrey, DeSantes, Kenneth, Cuvelier, Geoffrey, Teira, Pierre, Gillio, Alfred, Eissa, Hesham, Knutsen, Alan, Goldman, Frederick, Aquino, Victor, Shereck, Evan, Moore, Theodore, Caywood, Emi, Lugt, Mark, Rozmus, Jacob, Broglie, Larisa, Yu, Lolie, Shah, Ami, Andolina, Jeffrey, Liu, Xuerong, Parrott, Roberta, Dara, Jasmeen, Prockop, Susan, Martinez, Caridad, Kapadia, Malika, Jyonouchi, Soma, Sullivan, Kathleen, Bleesing, Jack, Chaudhury, Sonali, Petrovic, Aleksandra, Keller, Michael, Quigg, Troy, Parikh, Suhag, Shenoy, Shalini, Seroogy, Christine, Rubin, Tamar, Decaluwe, Hélène, Routes, John, Torgerson, Troy, Leiding, Jennifer, Pulsipher, Michael, Kohn, Donald, Griffith, Linda, Haddad, Elie, Dvorak, Christopher, and Notarangelo, Luigi
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Humans ,Infant ,Newborn ,Graft vs Host Disease ,Hematopoietic Stem Cell Transplantation ,Longitudinal Studies ,Neonatal Screening ,Proportional Hazards Models ,Severe Combined Immunodeficiency - Abstract
BACKGROUND: Severe combined immunodeficiency (SCID) is fatal unless durable adaptive immunity is established, most commonly through allogeneic haematopoietic cell transplantation (HCT). The Primary Immune Deficiency Treatment Consortium (PIDTC) explored factors affecting the survival of individuals with SCID over almost four decades, focusing on the effects of population-based newborn screening for SCID that was initiated in 2008 and expanded during 2010-18. METHODS: We analysed transplantation-related data from children with SCID treated at 34 PIDTC sites in the USA and Canada, using the calendar time intervals 1982-89, 1990-99, 2000-09, and 2010-18. Categorical variables were compared by χ2 test and continuous outcomes by the Kruskal-Wallis test. Overall survival was estimated by the Kaplan-Meier method. A multivariable analysis using Cox proportional hazards regression models examined risk factors for HCT outcomes, including the variables of time interval of HCT, infection status and age at HCT, trigger for diagnosis, SCID type and genotype, race and ethnicity of the patient, non-HLA-matched sibling donor type, graft type, GVHD prophylaxis, and conditioning intensity. FINDINGS: For 902 children with confirmed SCID, 5-year overall survival remained unchanged at 72%-73% for 28 years until 2010-18, when it increased to 87% (95% CI 82·1-90·6; n=268; p=0·0005). For children identified as having SCID by newborn screening since 2010, 5-year overall survival was 92·5% (95% CI 85·8-96·1), better than that of children identified by clinical illness or family history in the same interval (79·9% [69·5-87·0] and 85·4% [71·8-92·8], respectively [p=0·043]). Multivariable analysis demonstrated that the factors of active infection (hazard ratio [HR] 2·41, 95% CI 1·56-3·72; p
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- 2023
297. Health Disparity Curricula for Ophthalmology Residents: Current Landscape, Barriers, and Needs.
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Carvajal, Nicole, Lopez, Justin, Ahmad, Tessnim, Maru, Johsias, Seitzman, Gerami, Padmanabhan, Sriranjani, Parikh, Neeti, and Ramanathan, Saras
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Health disparities ,residency programs curriculum - Abstract
Background Social determinants of health play a critical role in visual health outcomes. Yet, there exists no structured curriculum for ophthalmology residents to identify and address health disparities relevant to eye care or no a standard assessment of health disparities education within ophthalmology residency programs. This study aims to characterize current health disparity curricula in ophthalmology residency programs in the United States, determine resident confidence in addressing health disparities in the clinical setting, and identify perceived barriers and needs of program directors (PDs) and residents in this area. Design This was a cross-sectional survey study. Methods A closed-ended questionnaire with comments was distributed to the Accreditation Council for Graduate Medical Education-accredited ophthalmology residency PDs and residents in April 2021 and May 2022. The questionnaire solicited characteristics of any existing health disparity curricula, PD and resident perceptions of these curricula, and residents experience with and confidence in addressing health disparities in the delivery of patient care. Results In total, 29 PDs and 96 residents responded. Sixty-six percent of PDs stated their program had a formal curriculum compared to fifty-three percent of residents. Forty-one percent of PDs and forty-one percent of residents stated their program places residents in underserved care settings for more than 50% of their training. Most residents (72%) were confident in recognizing health disparities. Sixty-six percent were confident in managing care in the face of disparities and fifty-nine percent felt they know how to utilize available resources. Residents were most concerned with the lack of access to resources to help patients. Forty-five percent of PDs felt the amount of time dedicated to health disparities education was adequate. Forty-nine percent of residents reported they felt the amount of training they received on health disparities to be adequate. The top barrier to curriculum development identified by PDs was the availability of trained faculty to teach. Time in the curriculum was a major barrier identified by residents. Conclusions Roughly half of ophthalmology residency programs who responded had a health disparity curriculum; however, both PDs and residents felt inadequate time is dedicated to such education. National guidance on structured health disparity curricula for ophthalmology residents may be warranted as a next step.
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- 2023
298. An atlas of healthy and injured cell states and niches in the human kidney.
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Lake, Blue, Menon, Rajasree, Winfree, Seth, Hu, Qiwen, Ferreira, Ricardo, Kalhor, Kian, Barwinska, Daria, Otto, Edgar, Ferkowicz, Michael, Diep, Dinh, Plongthongkum, Nongluk, Knoten, Amanda, Urata, Sarah, Mariani, Laura, Naik, Abhijit, Eddy, Sean, Zhang, Bo, Wu, Yan, Salamon, Diane, Williams, James, Wang, Xin, Balderrama, Karol, Hoover, Paul, Murray, Evan, Marshall, Jamie, Noel, Teia, Vijayan, Anitha, Hartman, Austin, Chen, Fei, Waikar, Sushrut, Rosas, Sylvia, Wilson, Francis, Palevsky, Paul, Kiryluk, Krzysztof, Sedor, John, Toto, Robert, Parikh, Chirag, Kim, Eric, Satija, Rahul, Greka, Anna, Macosko, Evan, Kharchenko, Peter, Gaut, Joseph, Hodgin, Jeffrey, Eadon, Michael, Dagher, Pierre, El-Achkar, Tarek, Kretzler, Matthias, Jain, Sanjay, and Zhang, Kun
- Subjects
Humans ,Cell Nucleus ,Gene Expression Profiling ,Kidney ,Kidney Diseases ,Transcriptome ,Single-Cell Analysis ,Case-Control Studies ,Imaging ,Three-Dimensional - Abstract
Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.
- Published
- 2023
299. Timing and Predictors of Recanalization After Anticoagulation in Cerebral Venous Thrombosis.
- Author
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Salehi Omran, Setareh, Shu, Liqi, Chang, Allison, Parikh, Neal, Zubair, Adeel, Simpkins, Alexis, Heldner, Mirjam, Hakim, Arsany, Kasab, Sami, Nguyen, Thanh, Klein, Piers, Goldstein, Eric, Vedovati, Maria, Paciaroni, Maurizio, Liebeskind, David, Yaghi, Shadi, and Cutting, Shawna
- Subjects
Cerebral veins ,Sinus thrombosis ,intracranial ,Stroke ,Vascular disease - Abstract
BACKGROUND AND PURPOSE: Vessel recanalization after cerebral venous thrombosis (CVT) is associated with favorable outcomes and lower mortality. Several studies examined the timing and predictors of recanalization after CVT with mixed results. We aimed to investigate predictors and timing of recanalization after CVT. METHODS: We used data from the multicenter, international AntiCoagulaTION in the Treatment of Cerebral Venous Thrombosis (ACTION-CVT) study of consecutive patients with CVT from January 2015 to December 2020. Our analysis included patients that had undergone repeat venous neuroimaging more than 30 days after initiation of anticoagulation treatment. Prespecified variables were included in univariate and multivariable analyses to identify independent predictors of failure to recanalize. RESULTS: Among the 551 patients (mean age, 44.4±16.2 years, 66.2% women) that met inclusion criteria, 486 (88.2%) had complete or partial, and 65 (11.8%) had no recanalization. The median time to first follow-up imaging study was 110 days (interquartile range, 60-187). In multivariable analysis, older age (odds ratio [OR], 1.05; 95% confidence interval [CI], 1.03-1.07), male sex (OR, 0.44; 95% CI, 0.24-0.80), and lack of parenchymal changes on baseline imaging (OR, 0.53; 95% CI, 0.29-0.96) were associated with no recanalization. The majority of improvement in recanalization (71.1%) occurred before 3 months from initial diagnosis. A high percentage of complete recanalization (59.0%) took place within the first 3 months after CVT diagnosis. CONCLUSION: Older age, male sex, and lack of parenchymal changes were associated with no recanalization after CVT. The majority recanalization occurred early in the disease course suggesting limited further recanalization with anticoagulation beyond 3 months. Large prospective studies are needed to confirm our findings.
- Published
- 2023
300. Multicenter Long-Term Follow-Up of Allogeneic Hematopoietic Cell Transplantation with Omidubicel: A Pooled Analysis of Five Prospective Clinical Trials.
- Author
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Lin, Chenyu, Schwarzbach, Aurelie, Sanz, Jaime, Montesinos, Pau, Stiff, Patrick, Parikh, Suhag, Brunstein, Claudio, Cutler, Corey, Lindemans, Caroline, Hanna, Rabi, Koh, Liang, Jagasia, Madan, Valcarcel, David, Maziarz, Richard, Keating, Amy, Hwang, William, Rezvani, Andrew, Karras, Nicole, Fernandes, Juliana, Rocha, Vanderson, Badell, Isabel, Ram, Ron, Schiller, Gary, Volodin, Leonid, Walters, Mark, Hamerschlak, Nelson, Cilloni, Daniela, Frankfurt, Olga, McGuirk, Joseph, Kurtzberg, Joanne, Sanz, Guillermo, Simantov, Ronit, and Horwitz, Mitchell
- Subjects
Allogeneic stem cell transplantation ,Clinical trial ,Cord blood ,Ex vivo expansion ,Long-term follow-up ,Humans ,Follow-Up Studies ,Prospective Studies ,Hematopoietic Stem Cell Transplantation ,Disease-Free Survival ,Multicenter Studies as Topic - Abstract
Omidubicel is an umbilical cord blood (UCB)-derived ex vivo-expanded cellular therapy product that has demonstrated faster engraftment and fewer infections compared with unmanipulated UCB in allogeneic hematopoietic cell transplantation. Although the early benefits of omidubicel have been established, long-term outcomes remain unknown. We report on a planned pooled analysis of 5 multicenter clinical trials including 105 patients with hematologic malignancies or sickle cell hemoglobinopathy who underwent omidubicel transplantation at 26 academic transplantation centers worldwide. With a median follow-up of 22 months (range, .3 to 122 months), the 3-year estimated overall survival and disease-free survival were 62.5% and 54.0%, respectively. With up to 10 years of follow-up, omidubicel showed durable trilineage hematopoiesis. Serial quantitative assessments of CD3+, CD4+, CD8+, CD19+, CD116+CD56+, and CD123+ immune subsets revealed median counts remaining within normal ranges through up to 8 years of follow-up. Secondary graft failure occurred in 5 patients (5%) in the first year, with no late cases reported. One case of donor-derived myeloid neoplasm was reported at 40 months post-transplantation. This was also observed in a control arm patient who received only unmanipulated UCB. Overall, omidubicel demonstrated stable trilineage hematopoiesis, immune competence, and graft durability in extended follow-up.
- Published
- 2023
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