A Large-Scale Vision-Language Dataset Derived from Open Scientific Literature to Advance Biomedical Generalist AI

Authors: Lozano, Alejandro, Sun, Min Woo, Burgess, James, Nirschl, Jeffrey J., Polzak, Christopher, Zhang, Yuhui, Chen, Liangyu, Gu, Jeffrey, Lopez, Ivan, Aklilu, Josiah, Rau, Anita, Katzer, Austin Wolfgang, Chiu, Collin, Zohar, Orr, Wang, Xiaohan, Song, Alfred Seunghoon, Chia-Chun, Chiang, Tibshirani, Robert, Yeung-Levy, Serena

Subject Terms: Computer Science - Computation and Language, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2503.22727

MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research

Authors: Burgess, James, Nirschl, Jeffrey J, Bravo-Sánchez, Laura, Lozano, Alejandro, Gupte, Sanket Rajan, Galaz-Montoya, Jesus G., Zhang, Yuhui, Su, Yuchang, Bhowmik, Disha, Coman, Zachary, Hasan, Sarina M., Johannesson, Alexandra, Leineweber, William D., Nair, Malvika G, Yarlagadda, Ridhi, Zuraski, Connor, Chiu, Wah, Cohen, Sarah, Hansen, Jan N., Leonetti, Manuel D, Liu, Chad, Lundberg, Emma, Yeung-Levy, Serena

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence, Computer Science - Computation and Language, Computer Science - Machine Learning, Quantitative Biology - Cell Behavior

Access URL: http://arxiv.org/abs/2503.13399

BIOMEDICA: An Open Biomedical Image-Caption Archive, Dataset, and Vision-Language Models Derived from Scientific Literature

Authors: Lozano, Alejandro, Sun, Min Woo, Burgess, James, Chen, Liangyu, Nirschl, Jeffrey J, Gu, Jeffrey, Lopez, Ivan, Aklilu, Josiah, Katzer, Austin Wolfgang, Chiu, Collin, Rau, Anita, Wang, Xiaohan, Zhang, Yuhui, Song, Alfred Seunghoon, Tibshirani, Robert, Yeung-Levy, Serena

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Computation and Language

Access URL: http://arxiv.org/abs/2501.07171

Revisiting Active Learning in the Era of Vision Foundation Models

Authors: Gupte, Sanket Rajan, Aklilu, Josiah, Nirschl, Jeffrey J., Yeung-Levy, Serena

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2401.14555

Rapid Deployment of Whole Slide Imaging for Primary Diagnosis in Surgical Pathology at Stanford Medicine: Responding to Challenges of the COVID-19 Pandemic

Authors: Rojansky, Rebecca, Jhun, Iny, Dussaq, Alex M., Chirieleison, Steven M., Nirschl, Jeffrey J., Born, Don, Fralick, Jennifer, Hetherington, William, Kerr, Alison M., Lavezo, Jonathan

Source: Archives of pathology & laboratory medicine. 147(3):359-367

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN631431572&indx=1&recIds=ETOCRN631431572

Creatine transport and pathological changes in creatine transporter deficient mice

Authors: Wawro, Adam M., Gajera, Chandresh R., Baker, Steven A., Nirschl, Jeffrey J., Vogel, Hannes, Montine, Thomas J.

Source: Journal of inherited metabolic disease. 44(4):939-948

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100127368028.0x000001&indx=1&recIds=ETOCvdc_100127368028.0x000001

A vision–language foundation model for precision oncology

Authors: Xiang, Jinxi, Wang, Xiyue, Zhang, Xiaoming, Xi, Yinghua, Eweje, Feyisope, Chen, Yijiang, Li, Yuchen, Bergstrom, Colin, Gopaulchan, Matthew, Kim, Ted, Yu, Kun-Hsing, Willens, Sierra, Olguin, Francesca Maria, Nirschl, Jeffrey J., Neal, Joel, Diehn, Maximilian, Yang, Sen, Li, Ruijiang

Source: Nature; 20250101, Issue: Preprints p1-10, 10p

Kinesin-3 Responds to Local Microtubule Dynamics to Target Synaptic Cargo Delivery to the Presynapse

Authors: Guedes-Dias, Pedro, Nirschl, Jeffrey J., Abreu, Nohely, Tokito, Mariko K., Janke, Carsten, Magiera, Maria M., Holzbaur, Erika L.F.

Source: In Current Biology 21 January 2019 29(2):268-282

Amyotrophic lateral sclerosis-linked mutations increase the viscosity of liquid-like TDP-43 RNP granules in neurons

Authors: Gopal, Pallavi P., Nirschl, Jeffrey J., Klinman, Eva, Holzbaur, Erika L. F.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2017 Mar . 114(12), E2466-E2475.

Access URL: https://www.jstor.org/stable/26480218

α-Tubulin Tyrosination and CLIP-170 Phosphorylation Regulate the Initiation of Dynein-Driven Transport in Neurons

Authors: Nirschl, Jeffrey J., Magiera, Maria M., Lazarus, Jacob E., Janke, Carsten, Holzbaur, Erika L.F.

Source: In Cell Reports 22 March 2016 14(11):2637-2652

Chapter 13 - Live-cell imaging of retrograde transport initiation in primary neurons

Authors: Nirschl, Jeffrey J., Holzbaur, Erika L.F.

Source: In Methods in Cell Biology 2016 131:269-276

Orientation-invariant autoencoders learn robust representations for shape profiling of cells and organelles.

Authors: Burgess, James, Nirschl, Jeffrey J., Zanellati, Maria-Clara, Lozano, Alejandro, Cohen, Sarah, Yeung-Levy, Serena

Source: Nature Communications; 2/3/2024, Vol. 15 Issue 1, p1-14, 14p

Subject Terms: CELL morphology, ORGANELLES, CYTOLOGY, IMAGE analysis, OUTLIER detection, VISUAL cryptography

CDC42BPA::BRAF represents a novel fusion in desmoplastic infantile ganglioglioma/desmoplastic infantile astrocytoma.

Authors: Barros Guinle, Maria Isabel, Nirschl, Jeffrey J, Xing, Yao Lulu, Nettnin, Ella A, Arana, Sophia, Feng, Zhi-Ping, Nasajpour, Emon, Pronina, Anna, Garcia, Cesar A, Grant, Gerald A, Vogel, Hannes, Yeom, Kristen W, Prolo, Laura M, Petritsch, Claudia K

Source: Neuro-Oncology Advances; Jan-Dec2024, Vol. 6 Issue 1, p1-7, 7p

TDP43 pathology in chronic traumatic encephalopathy retinas.

Authors: Phansalkar, Ragini, Goodwill, Vanessa S., Nirschl, Jeffrey J., De Lillo, Chiara, Choi, Jihee, Spurlock, Elizabeth, Coughlin, David G., Pizzo, Donald, Sigurdson, Christina J., Hiniker, Annie, Alvarez, Victor E., Mckee, Ann C., Lin, Jonathan H.

Source: Acta Neuropathologica Communications; 9/22/2023, Vol. 11 Issue 1, p1-10, 10p

Subject Terms: CHRONIC traumatic encephalopathy, INTERNEURONS, RETINA, AUTOPSY, PATHOLOGY, BRAIN diseases, RETINAL degeneration

LC3 Binding to the Scaffolding Protein JIP1 Regulates Processive Dynein-Driven Transport of Autophagosomes

Authors: Fu, Meng-meng, Nirschl, Jeffrey J., Holzbaur, Erika L.F.

Source: Developmental cell. 29(5):577-590

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100066102598.0x000001&indx=1&recIds=ETOCvdc_100066102598.0x000001

Lipid Rafts Assemble Dynein Ensembles

Authors: Nirschl, Jeffrey J., Ghiretti, Amy E., Holzbaur, Erika L.F.

Source: In Trends in Biochemical Sciences May 2016 41(5):393-394

A deep-learning classifier identifies patients with clinical heart failure using whole-slide images of H&E tissue.

Authors: Nirschl, Jeffrey J.¹, Janowczyk, Andrew² axm788@case.edu, Peyster, Eliot G.³, Frank, Renee⁴, Margulies, Kenneth B.³, Feldman, Michael D.⁴, Madabhushi, Anant²

Source: PLoS ONE. 4/3/2018, Vol. 13 Issue 4, p1-16. 16p.

Subject Terms: *HEART failure, *PUBLIC health, *ARTIFICIAL neural networks, *DIABETIC retinopathy, *HEART cancer

A rare neuromyelitis optica mimic: Primary CNS histiocytic sarcoma.

Authors: Rogawski, David S¹ (AUTHOR), Nirschl, Jeffrey J² (AUTHOR), McDonald, Jamie¹ (AUTHOR), Nie, Esther¹ (AUTHOR), Schwartz, Nicholas U¹ (AUTHOR), Vogel, Hannes² (AUTHOR), Scott, Brian J¹ (AUTHOR), Gold, Carl A¹ (AUTHOR), Kipp, Lucas B¹ (AUTHOR) lkipp@stanford.edu

Source: Multiple Sclerosis Journal. Sep2022, Vol. 28 Issue 10, p1651-1654. 4p.

Subject Terms: *NEUROMYELITIS optica, *MYELITIS, *RETICULUM cell sarcoma, *CENTRAL nervous system, *MAGNETIC resonance imaging

Chapter 8 - Deep Learning Tissue Segmentation in Cardiac Histopathology Images

Authors: Nirschl, Jeffrey J., Janowczyk, Andrew, Peyster, Eliot G., Frank, Renee, Margulies, Kenneth B., Feldman, Michael D., Madabhushi, Anant

Source: In Deep Learning for Medical Image Analysis 2017:179-195

Actin cables and comet tails organize mitochondrial networks in mitosis.

Authors: Moore, Andrew S., Coscia, Stephen M., Simpson, Cory L., Ortega, Fabian E., Wait, Eric C., Heddleston, John M., Nirschl, Jeffrey J., Obara, Christopher J., Guedes-Dias, Pedro, Boecker, C. Alexander, Chew, Teng-Leong, Theriot, Julie A., Lippincott-Schwartz, Jennifer, Holzbaur, Erika L. F.

Source: Nature; 3/25/2021, Vol. 591 Issue 7851, p659-664, 6p