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5. Spectral Roll-off Points Variations: Exploring Useful Information in Feature Maps by Its Variations

Author

Yu, Yunkai, You, Yuyang, Yang, Zhihong, Liu, Guozheng, Li, Peiyao, Yang, Zhicheng, and Shan, Wenjing

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Useful information (UI) is an elusive concept in neural networks. A quantitative measurement of UI is absent, despite the variations of UI can be recognized by prior knowledge. The communication bandwidth of feature maps decreases after downscaling operations, but UI flows smoothly after training due to lower Nyquist frequency. Inspired by the low-Nyqusit-frequency nature of UI, we propose the use of spectral roll-off points (SROPs) to estimate UI on variations. The computation of an SROP is extended from a 1-D signal to a 2-D image by the required rotation invariance in image classification tasks. SROP statistics across feature maps are implemented as layer-wise useful information estimates. We design sanity checks to explore SROP variations when UI variations are produced by variations in model input, model architecture and training stages. The variations of SROP is synchronizes with UI variations in various randomized and sufficiently trained model structures. Therefore, SROP variations is an accurate and convenient sign of UI variations, which promotes the explainability of data representations with respect to frequency-domain knowledge., Comment: 11 pages, 5 figures. This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible

Published
2021

17. A Phase II Clinical Trial of TRC105 (Anti-Endoglin Antibody) in Adults With Advanced/Metastatic Urothelial Carcinoma

Author

Apolo, Andrea B., Karzai, Fatima H., Trepel, Jane B., Alarcon, Sylvia, Lee, Sunmin, Lee, Min-Jung, Tomita, Yusuke, Cao, Liang, Yu, Yunkai, Merino, Maria J., Madan, Ravi A., Parnes, Howard L., Steinberg, Seth M., Rodriguez, Beatriz Walter, Seon, Ben K., Gulley, James L., Arlen, Philip M., Dawson, Nancy A., Figg, William D., and Dahut, William L.

Published
2017
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18. Supplementary Figure from Cabozantinib plus Nivolumab Phase I Expansion Study in Patients with Metastatic Urothelial Carcinoma Refractory to Immune Checkpoint Inhibitor Therapy

Author

Girardi, Daniel M., primary, Niglio, Scot A., primary, Mortazavi, Amir, primary, Nadal, Rosa, primary, Lara, Primo, primary, Pal, Sumanta K., primary, Saraiya, Biren, primary, Cordes, Lisa, primary, Ley, Lisa, primary, Ortiz, Olena Sierra, primary, Cadena, Jacqueline, primary, Diaz, Carlos, primary, Bagheri, Hadi, primary, Redd, Bernadette, primary, Steinberg, Seth M., primary, Costello, Rene, primary, Chan, Keith S., primary, Lee, Min-Jung, primary, Lee, Sunmin, primary, Yu, Yunkai, primary, Gurram, Sandeep, primary, Chalfin, Heather J., primary, Valera, Vladimir, primary, Figg, William D., primary, Merino, Maria, primary, Toubaji, Antoun, primary, Streicher, Howard, primary, Wright, John J., primary, Sharon, Elad, primary, Parnes, Howard L., primary, Ning, Yang-Min, primary, Bottaro, Donald P., primary, Cao, Liang, primary, Trepel, Jane B., primary, and Apolo, Andrea B., primary

Published
2023
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19. Supplementary Data from Evaluation of KRAS Mutations, Angiogenic Biomarkers, and DCE-MRI in Patients with Advanced Non–Small-Cell Lung Cancer Receiving Sorafenib

Author

Kelly, Ronan J., primary, Rajan, Arun, primary, Force, Jeremy, primary, Lopez-Chavez, Ariel, primary, Keen, Corrine, primary, Cao, Liang, primary, Yu, Yunkai, primary, Choyke, Peter, primary, Turkbey, Baris, primary, Raffeld, Mark, primary, Xi, Liqiang, primary, Steinberg, Seth M., primary, Wright, John J., primary, Kummar, Shivaani, primary, Gutierrez, Martin, primary, and Giaccone, Giuseppe, primary

Published
2023
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20. Supplemental Data legends from Phase I and Preliminary Phase II Study of TRC105 in Combination with Sorafenib in Hepatocellular Carcinoma

Author

Duffy, Austin G., primary, Ma, Chi, primary, Ulahannan, Susanna V., primary, Rahma, Osama E., primary, Makarova-Rusher, Oxana, primary, Cao, Liang, primary, Yu, Yunkai, primary, Kleiner, David E., primary, Trepel, Jane, primary, Lee, Min-Jung, primary, Tomita, Yusuke, primary, Steinberg, Seth M., primary, Heller, Theo, primary, Turkbey, Baris, primary, Choyke, Peter L., primary, Peer, Cody J., primary, Figg, William D., primary, Wood, Brad J., primary, and Greten, Tim F., primary

Published
2023
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21. Supplementary Table 1 from Phase I and Preliminary Phase II Study of TRC105 in Combination with Sorafenib in Hepatocellular Carcinoma

Author

Duffy, Austin G., primary, Ma, Chi, primary, Ulahannan, Susanna V., primary, Rahma, Osama E., primary, Makarova-Rusher, Oxana, primary, Cao, Liang, primary, Yu, Yunkai, primary, Kleiner, David E., primary, Trepel, Jane, primary, Lee, Min-Jung, primary, Tomita, Yusuke, primary, Steinberg, Seth M., primary, Heller, Theo, primary, Turkbey, Baris, primary, Choyke, Peter L., primary, Peer, Cody J., primary, Figg, William D., primary, Wood, Brad J., primary, and Greten, Tim F., primary

Published
2023
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22. Supplementary Data from Cabozantinib plus Nivolumab Phase I Expansion Study in Patients with Metastatic Urothelial Carcinoma Refractory to Immune Checkpoint Inhibitor Therapy

Author

Girardi, Daniel M., primary, Niglio, Scot A., primary, Mortazavi, Amir, primary, Nadal, Rosa, primary, Lara, Primo, primary, Pal, Sumanta K., primary, Saraiya, Biren, primary, Cordes, Lisa, primary, Ley, Lisa, primary, Ortiz, Olena Sierra, primary, Cadena, Jacqueline, primary, Diaz, Carlos, primary, Bagheri, Hadi, primary, Redd, Bernadette, primary, Steinberg, Seth M., primary, Costello, Rene, primary, Chan, Keith S., primary, Lee, Min-Jung, primary, Lee, Sunmin, primary, Yu, Yunkai, primary, Gurram, Sandeep, primary, Chalfin, Heather J., primary, Valera, Vladimir, primary, Figg, William D., primary, Merino, Maria, primary, Toubaji, Antoun, primary, Streicher, Howard, primary, Wright, John J., primary, Sharon, Elad, primary, Parnes, Howard L., primary, Ning, Yang-Min, primary, Bottaro, Donald P., primary, Cao, Liang, primary, Trepel, Jane B., primary, and Apolo, Andrea B., primary

Published
2023
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23. Supplementary Figure 2 from Phase I and Preliminary Phase II Study of TRC105 in Combination with Sorafenib in Hepatocellular Carcinoma

Author

Duffy, Austin G., primary, Ma, Chi, primary, Ulahannan, Susanna V., primary, Rahma, Osama E., primary, Makarova-Rusher, Oxana, primary, Cao, Liang, primary, Yu, Yunkai, primary, Kleiner, David E., primary, Trepel, Jane, primary, Lee, Min-Jung, primary, Tomita, Yusuke, primary, Steinberg, Seth M., primary, Heller, Theo, primary, Turkbey, Baris, primary, Choyke, Peter L., primary, Peer, Cody J., primary, Figg, William D., primary, Wood, Brad J., primary, and Greten, Tim F., primary

Published
2023
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25. Supplementary Figure 1 from Phase I and Preliminary Phase II Study of TRC105 in Combination with Sorafenib in Hepatocellular Carcinoma

Author

Duffy, Austin G., primary, Ma, Chi, primary, Ulahannan, Susanna V., primary, Rahma, Osama E., primary, Makarova-Rusher, Oxana, primary, Cao, Liang, primary, Yu, Yunkai, primary, Kleiner, David E., primary, Trepel, Jane, primary, Lee, Min-Jung, primary, Tomita, Yusuke, primary, Steinberg, Seth M., primary, Heller, Theo, primary, Turkbey, Baris, primary, Choyke, Peter L., primary, Peer, Cody J., primary, Figg, William D., primary, Wood, Brad J., primary, and Greten, Tim F., primary

Published
2023
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34. Systemic immune changes accompany combination treatment with immunotoxin LMB ‐100 and nab‐paclitaxel

Author

Pegna, Guillaume Joe, primary, Lee, Min‐Jung, additional, Peer, Cody J., additional, Ahmad, Mehwish I., additional, Venzon, David J., additional, Yu, Yunkai, additional, Yuno, Akira, additional, Steinberg, Seth M., additional, Cao, Liang, additional, Figg, William D., additional, Donahue, Renee N., additional, Hassan, Raffit, additional, Pastan, Ira, additional, Trepel, Jane B., additional, and Alewine, Christine, additional

Published
2022
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38. Cixutumumab for patients with recurrent or refractory advanced thymic epithelial tumours: a multicentre, open-label, phase 2 trial

Author

Rajan, Arun, Carter, Corey A, Berman, Arlene, Cao, Liang, Kelly, Ronan J, Thomas, Anish, Khozin, Sean, Chavez, Ariel Lopez, Bergagnini, Isabella, Scepura, Barbara, Szabo, Eva, Lee, Min-Jung, Trepel, Jane B, Browne, Sarah K, Rosen, Lindsey B, Yu, Yunkai, Steinberg, Seth M, Chen, Helen X, Riely, Gregory J, and Giaccone, Giuseppe

Published
2014
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39. Evidence of solvent-mediated proton transfer during H2O2 activation in titanosilicate-catalyzed oxidation systems.

Author

Yu, Yunkai, Wang, Jianhao, Fang, Nan, Chen, Zhen, Liu, Dongxu, Liu, Yueming, and He, Mingyuan

Abstract

The catalytic performance of titanosilicates involving hydrogen peroxide (H2O2) as the oxidant is strongly influenced by the solvents. Until now, there is still a lack of a universal principle that can guide the choice of a solvent. Herein, the kinetics of H2O2 activation catalyzed by various titanosilicates in different solvents is investigated, and an isokinetic compensation effect is concluded. This indicates that the solvent participates in the H2O2 activation process for the formation of a Ti–OOH species. Additionally, the results of isotopically labeled infrared spectra preliminarily confirm that the solvent acts as the mediator to promote the proton transfer during the H2O2 activation process. The catalytic activities of a series of TS-1 catalysts toward 1-hexene epoxidation are compared, which include Ti(OSi)3OH species with a range of densities but a constant total Ti content. This reveals that the solvent effect is closely related to the Ti active sites of these TS-1 catalysts. Based on these results, a principle for the rational choice of solvent for this catalytic process is proposed. ROH is found to be the mediator for Ti(OSi)4 sites, and methanol, which has a strong proton-donating ability, is the best solvent for these sites. However, for the Ti(OSi)3OH sites, water (H2O) is the mediator, and a weaker hydrogen bonding between H2O molecules promotes proton transfer more effectively. The solvent influences the catalytic performance by perturbing the hydrogen bonds between the H2O molecules, and aprotic acetonitrile, which has a strong ability to break the hydrogen bonding network between H2O molecules, is the best solvent for Ti(OSi)3OH sites. This study provides experimental evidence that the solvent promotes the catalytic performance of titanosilicates by assisting the proton transfer during the catalytic H2O2 activation process, which will pave the way toward the rational choice of solvent for the titanosilicate-catalyzed oxidation systems. [ABSTRACT FROM AUTHOR]

Published
2023
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42. Systemic immune changes accompany combination treatment with immunotoxin LMB‐100 and nab‐paclitaxel.

Author

Pegna, Guillaume Joe, Lee, Min‐Jung, Peer, Cody J., Ahmad, Mehwish I., Venzon, David J., Yu, Yunkai, Yuno, Akira, Steinberg, Seth M., Cao, Liang, Figg, William D., Donahue, Renee N., Hassan, Raffit, Pastan, Ira, Trepel, Jane B., and Alewine, Christine

Subjects
CAPILLARY leak syndrome, T cells, CD38 antigen, CD8 antigen, REGULATORY T cells
Abstract

LMB‐100 is a novel immune‐conjugate (immunotoxin) that targets mesothelin. A phase 1/2 clinical trial was conducted (NCT02810418) with primary objectives assessing the safety and efficacy of LMB‐100 ± nab‐paclitaxel. Participant blood samples were analyzed for changes in serum cytokines and circulating immune cell subsets associated with response or toxicity. On Arm A, participants (n = 20) received standard 30‐minute LMB‐100 infusion with nab‐paclitaxel. Although clinical efficacy was observed, the combination caused intolerable capillary leak syndrome (CLS), a major toxicity of unclear etiology that affects many immunotoxin drugs. Participants developing CLS experienced rapid elevations in IFNγ and IL‐8 compared to those without significant CLS, along with midcycle increases in Ki‐67‐ CD4 T cells that were CD38, HLA‐DR, or TIM3 positive. Additionally, a strong increase in activated CD4 and CD8 T cells and a concurrent decrease in Tregs were seen in the single Arm A patient achieving a partial response. In Arm B, administration of single agent LMB‐100 to participants (n = 20) as a long infusion given over 24–48 h was investigated based on pre‐clinical data that this format could reduce CLS. An optimal dose and schedule of long infusion LMB‐100 were identified, but no clinical efficacy was observed even in patients receiving LMB‐100 in combination with nab‐paclitaxel. Despite this, both Arm A and B participants experienced increases in specific subsets of proliferating CD4 and CD8 T cells following Cycle 1 treatment. In summary, LMB‐100 treatment causes systemic immune activation. Inflammatory and immune changes that accompany drug associated CLS were characterized for the first time. [ABSTRACT FROM AUTHOR]

Published
2023
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44. Cabozantinib plus Nivolumab Phase I Expansion Study in Patients with Metastatic Urothelial Carcinoma Refractory to Immune Checkpoint Inhibitor Therapy

Author

Girardi, Daniel M., primary, Niglio, Scot A., additional, Mortazavi, Amir, additional, Nadal, Rosa, additional, Lara, Primo, additional, Pal, Sumanta K., additional, Saraiya, Biren, additional, Cordes, Lisa, additional, Ley, Lisa, additional, Ortiz, Olena Sierra, additional, Cadena, Jacqueline, additional, Diaz, Carlos, additional, Bagheri, Hadi, additional, Redd, Bernadette, additional, Steinberg, Seth M., additional, Costello, Rene, additional, Chan, Keith S., additional, Lee, Min-Jung, additional, Lee, Sunmin, additional, Yu, Yunkai, additional, Gurram, Sandeep, additional, Chalfin, Heather J., additional, Valera, Vladimir, additional, Figg, William D., additional, Merino, Maria, additional, Toubaji, Antoun, additional, Streicher, Howard, additional, Wright, John J., additional, Sharon, Elad, additional, Parnes, Howard L., additional, Ning, Yang-Min, additional, Bottaro, Donald P., additional, Cao, Liang, additional, Trepel, Jane B., additional, and Apolo, Andrea B., additional

Published
2022
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