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Reconstructing co-dependent cellular crosstalk in lung adenocarcinoma using REMI

Alice Yu, Yuanyuan Li, Irene Li, Christine Yeh, Aaron Chiou, Michael Ozawa, Jonathan Taylor, Sylvia Plevritis,

Cellular crosstalk in tissue microenvironments is fundamental to normal and pathological biological processes. Global assessment of cell-cell interactions (CCI) is not yet technically feasible, but computational efforts to reconstruct these interactions have been proposed. Current computational approaches that identify CCI often make the simplifying assumption that pairwise interactions are independent ... Read more >>

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Editorial Comment.

Nicholas Chakiryan, Alice Yu,

J Urol (The Journal of urology)
[2021, :101097JU000000000000178601]

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Clinical assessment of chemotherapy-induced peripheral neuropathy: a discrete choice experiment of patient preferences.

Alice Yu, Deborah Street, Rosalie Viney, Stephen Goodall, Alison Pearce, Philip Haywood, Marion Haas, Eva Battaglini, David Goldstein, Hannah Timmins, Susanna B Park,

<h4>Purpose</h4>Up to 40% of cancer patients treated with neurotoxic chemotherapies experience chemotherapy-induced peripheral neuropathy (CIPN). Currently, there is no gold standard assessment tool for CIPN and there is little information in the literature on patient preferences for such assessments. This study aims to address this gap by identifying the features ... Read more >>

Support Care Cancer (Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer)
[2021, :]

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Systemic light-chain amyloidosis incidentally diagnosed after subtotal parathyroidectomy and thyroid lobectomy.

Karen Tsai, Alice Chen Yu, Masha J Livhits, Dipti Sajed, Angela M Leung, Dianne S Cheung,

A 74-year-old woman with a history of primary hyperparathyroidism, thyroid nodules, atrial fibrillation and pacemaker placement for sick sinus syndrome presented with fatigue, constipation and persistent lower extremity oedema. She underwent subtotal parathyroidectomy and left thyroid lobectomy. Histopathology revealed amyloidosis affecting the thyroidand parathyroids confirmed by Congo Red Staining with ... Read more >>

BMJ Case Rep (BMJ case reports)
[2021, 14(4):]

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Transmembrane and coiled-coil domain family 3 (TMCC3) regulates breast cancer stem cell and AKT activation.

Ya-Hui Wang, Yu-Tzu Chan, Tsai-Hsien Hung, Jung-Tung Hung, Ming-Wei Kuo, Sheng-Hung Wang, Yenlin Huang, Yu-Ju Lin, Shin-Cheh Chen, Jyh-Cherng Yu, Jen-Chine Wu, John Yu, Alice L Yu,

Cancer stem cells (CSC) play a pivotal role in cancer metastasis and resistance to therapy. Previously, we compared the phosphoproteomes of breast cancer stem cells (BCSCs) enriched subpopulation and non-BCSCs sorted from breast cancer patient-derived xenograft (PDX), and identified a function unknown protein, transmembrane and coiled-coil domain family 3 (TMCC3) ... Read more >>

Oncogene (Oncogene)
[2021, 40(16):2858-2871]

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Segmental Arterial Mediolysis: a rare cause of abdominal pain masquerading as vasculitis.

Caoilfhionn Connolly, Alice Yu, Philip Seo, Julie Paik,

Rheumatology (Oxford) (Rheumatology (Oxford, England))
[2021, :]

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Alcohol Exerts a Shifted U-Shaped Effect on Central Blood Pressure in Young Adults.

Alice Yu, Alexandra B Cooke, Patrick Scheffler, Robert J Doonan, Stella S Daskalopoulou,

<h4>Background</h4>Consumption of 1-2 alcoholic beverages daily has been associated with a lower risk of cardiovascular disease and all-cause mortality in middle-aged and older adults. Central blood pressure has emerged as a better predictor of cardiovascular risk than peripheral blood pressure. However, the effects of habitual alcohol consumption on central blood ... Read more >>

J Gen Intern Med (Journal of general internal medicine)
[2021, :]

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Low Expression of IL-15 and NKT in Tumor Microenvironment Predicts Poor Outcome of MYCN-Non-Amplified Neuroblastoma.

Yu-Mei Liao, Tsai-Hsien Hung, John K Tung, John Yu, Ya-Ling Hsu, Jung-Tung Hung, Alice L Yu,

Immune tumor microenvironment (TME) in neuroblastoma (NBL) contributes to tumor behavior and treatment response. T cells and natural killer (NK) cells have been shown to play important roles in the neuroblastoma TME. However, few reports address the clinical relevance of natural killer T cells (NKTs) and interleukin-15 (IL-15), one of ... Read more >>

J Pers Med (Journal of personalized medicine)
[2021, 11(2):]

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NAD+ depletion by type I interferon signaling sensitizes pancreatic cancer cells to NAMPT inhibition.

Alexandra M Moore, Lei Zhou, Jing Cui, Luyi Li, Nanping Wu, Alice Yu, Soumya Poddar, Keke Liang, Evan R Abt, Stephanie Kim, Razmik Ghukasyan, Nooneh Khachatourian, Kristina Pagano, Irmina Elliott, Amanda M Dann, Rana Riahi, Thuc Le, David W Dawson, Caius G Radu, Timothy R Donahue,

Emerging evidence suggests that intratumoral interferon (IFN) signaling can trigger targetable vulnerabilities. A hallmark of pancreatic ductal adenocarcinoma (PDAC) is its extensively reprogrammed metabolic network, in which nicotinamide adenine dinucleotide (NAD) and its reduced form, NADH, are critical cofactors. Here, we show that IFN signaling, present in a subset of ... Read more >>

Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America)
[2021, 118(8):]

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Long-Term Follow-up of a Phase III Study of ch14.18 (Dinutuximab) + Cytokine Immunotherapy in Children with High-Risk Neuroblastoma: COG Study ANBL0032.

Alice L Yu, Andrew L Gilman, M Fevzi Ozkaynak, Arlene Naranjo, Mitchell B Diccianni, Jacek Gan, Jacquelyn A Hank, Ayse Batova, Wendy B London, Sheena C Tenney, Malcolm Smith, Barry L Shulkin, Marguerite Parisi, Katherine K Matthay, Susan L Cohn, John M Maris, Rochelle Bagatell, Julie R Park, Paul M Sondel,

<h4>Purpose</h4>Previously our randomized phase III trial demonstrated that immunotherapy including dinutuximab, a chimeric anti-GD2 mAb, GM-CSF, and IL2 improved survival for children with high-risk neuroblastoma that had responded to induction and consolidation therapy. These results served as the basis for FDA approval of dinutuximab. We now present long-term follow-up results ... Read more >>

Clin Cancer Res (Clinical cancer research : an official journal of the American Association for Cancer Research)
[2021, 27(8):2179-2189]

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BTK Inhibition Reverses MDSC-Mediated Immunosuppression and Enhances Response to Anti-PDL1 Therapy in Neuroblastoma.

Mehreen Ishfaq, Timothy Pham, Cooper Beaman, Pablo Tamayo, Alice L Yu, Shweta Joshi,

MDSCs are immune cells of myeloid lineage that plays a key role in promoting tumor growth. The expansion of MDSCs in tumor-bearing hosts reduces the efficacy of checkpoint inhibitors and CAR-T therapies, and hence strategies that deplete or block the recruitment of MDSCs have shown benefit in improving responses to ... Read more >>

Cancers (Basel) (Cancers)
[2021, 13(4):]

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Yulink, predicted from evolutionary analysis, is involved in cardiac function.

Ming-Wei Kuo, Hsiu-Hui Tsai, Sheng-Hung Wang, Yi-Yin Chen, Alice L Yu, John Yu,

<h4>Background</h4>The comparative evolutionary genomics analysis was used to study the functions of novel Ka/Ks-predicted human exons in a zebrafish model. The Yulink (MIOS, Entrez Gene: 54,468), a conserved gene from zebrafish to human with WD40 repeats at N-terminus, was identified and found to encode an 875 amino acid in human. ... Read more >>

J Biomed Sci (Journal of biomedical science)
[2021, 28(1):7]

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High B3GALT5 expression confers poor clinical outcome and contributes to tumor progression and metastasis in breast cancer.

Yu-Mei Liao, Ya-Hui Wang, Jung-Tung Hung, Yu-Ju Lin, Yen-Lin Huang, Guo-Shiou Liao, Ya-Ling Hsu, Jen-Chien Wu, Alice L Yu,

<h4>Background</h4>Existence of breast cancer stem cells (BCSCs) is implicated in disease relapse, metastasis, and resistance of treatment. β1,3-Galactosyltransferase 5 (B3GALT5) has been shown to be a pro-survival marker for BCSCs. However, little is known about the prognostic significance of B3GALT5 in breast cancer.<h4>Methods</h4>Paired tissues (tumor part and adjacent non-tumor part) ... Read more >>

Breast Cancer Res (Breast cancer research : BCR)
[2021, 23(1):5]

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B3GALT5 knockout alters gycosphingolipid profile and facilitates transition to human naïve pluripotency.

Ruey-Jen Lin, Ming-Wei Kuo, Bei-Chia Yang, Hsiu-Hui Tsai, Kowa Chen, Jing-Rong Huang, Yun-Shien Lee, Alice L Yu, John Yu,

Conversion of human pluripotent stem cells from primed to naïve state is accompanied by altered transcriptome and methylome, but glycosphingolipid (GSL) profiles in naïve human embryonic stem cells (hESCs) have not been systematically characterized. Here we showed a switch from globo-(SSEA-3, SSEA-4, and Globo H) and lacto-series (fucosyl-Lc4Cer) to neolacto-series ... Read more >>

Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America)
[2020, 117(44):27435-27444]

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COVID-19 in Canada: A self-assessment and review of preparedness and response.

Alice Yu, Sophia Prasad, Adebisi Akande, Andreea Murariu, Serena Yuan, Sylvia Kathirkamanathan, Myles Ma, Sarah Ladha,

J Glob Health (Journal of global health)
[2020, 10(2):0203104]

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Sialylation of CD55 by ST3GAL1 Facilitates Immune Evasion in Cancer.

Wen-Der Lin, Tan-Chi Fan, Jung-Tung Hung, Hui-Ling Yeo, Sheng-Hung Wang, Chu-Wei Kuo, Kay-Hooi Khoo, Li-Mei Pai, John Yu, Alice L Yu,

Altered glycosylations, which are associated with expression and activities of glycosyltransferases, can dramatically affect the function of glycoproteins and modify the behavior of tumor cells. ST3GAL1 is a sialyltransferase that adds sialic acid to core 1 glycans, thereby terminating glycan chain extension. In breast carcinomas, overexpression of ST3GAL1 promotes tumorigenesis ... Read more >>

Cancer Immunol Res (Cancer immunology research)
[2021, 9(1):113-122]

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Patient factors predict complications after partial nephrectomy: validation and calibration of the Preoperative Risk Evaluation for Partial Nephrectomy (PREP) score.

Melissa J Huynh, Ye Wang, Mugdha Joshi, Ross Krasnow, Alice X Yu, Matthew Mossanen, Benjamin I Chung, Steven L Chang,

<h4>Objectives</h4>To develop and validate the Preoperative Risk Evaluation for Partial Nephrectomy (PREP) score to predict the probability of major postoperative complications after partial nephrectomy (PN) based on patient comorbidities.<h4>Patients and methods</h4>The Premier Healthcare Database was used to identify patients who had undergone elective PN. Through review of International Classification of ... Read more >>

BJU Int (BJU international)
[2021, 127(3):369-374]

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Targeting glycosphingolipids for cancer immunotherapy.

John Yu, Jung-Tung Hung, Sheng-Hung Wang, Jing-Yan Cheng, Alice L Yu,

Aberrant expression of glycosphingolipids (GSLs) is a unique feature of cancer and stromal cells in tumor microenvironments. Although the impact of GSLs on tumor progression remains largely unclear, anticancer immunotherapies directed against GSLs are attracting growing attention. Here, we focus on GD2, a disialoganglioside expressed in tumors of neuroectodermal origin, ... Read more >>

FEBS Lett (FEBS letters)
[2020, 594(22):3602-3618]

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One Algorithm May Not Fit All: How Selection Bias Affects Machine Learning Performance.

Alice C Yu, John Eng,

Machine learning (ML) algorithms have demonstrated high diagnostic accuracy in identifying and categorizing disease on radiologic images. Despite the results of initial research studies that report ML algorithm diagnostic accuracy similar to or exceeding that of radiologists, the results are less impressive when the algorithms are installed at new hospitals ... Read more >>

Radiographics (Radiographics : a review publication of the Radiological Society of North America, Inc)
[2020, 40(7):1932-1937]

Cited: 1 time

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Patient perceptions of autologous serum eye drops for severe dry eye disease.

Alice T Yu, Graham A Lee, Stephen Vincent, Peter Shah,

Clin Exp Ophthalmol (Clinical & experimental ophthalmology)
[2020, 48(8):1109-1111]

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Can AI outperform a junior resident? Comparison of deep neural network to first-year radiology residents for identification of pneumothorax.

Paul H Yi, Tae Kyung Kim, Alice C Yu, Bradford Bennett, John Eng, Cheng Ting Lin,

<h4>Purpose</h4>To (1) develop a deep learning system (DLS) using a deep convolutional neural network (DCNN) for identification of pneumothorax, (2) compare its performance to first-year radiology residents, and (3) evaluate the ability of a DLS to augment radiology residents by detecting missed pneumothoraces.<h4>Methods</h4>This was a retrospective study performed in September ... Read more >>

Emerg Radiol (Emergency radiology)
[2020, 27(4):367-375]

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Globo H-KLH vaccine adagloxad simolenin (OBI-822)/OBI-821 in patients with metastatic breast cancer: phase II randomized, placebo-controlled study.

Chiun-Sheng Huang, Alice L Yu, Ling-Ming Tseng, Louis W C Chow, Ming-Feng Hou, Sara A Hurvitz, Richard B Schwab, James L Murray, Hsien-Kun Chang, Hong-Tai Chang, Shin-Cheh Chen, Sung-Bae Kim, Jung-Tung Hung, Shir-Hwa Ueng, Su-Hua Lee, Chwen-Cheng Chen, Hope S Rugo,

<h4>Purpose</h4>This randomized, double-blind, placebo-controlled, parallel-group, phase II trial assessed the efficacy and safety of adagloxad simolenin (OBI-822; a Globo H epitope covalently linked to keyhole limpet hemocyanin (KLH)) with adjuvant OBI-821 in metastatic breast cancer (MBC).<h4>Methods</h4>At 40 sites in Taiwan, USA, Korea, India, and Hong Kong, patients with MBC of ... Read more >>

J Immunother Cancer (Journal for immunotherapy of cancer)
[2020, 8(2):]

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How personalized are benefit and harm results of randomized trials? A systematic review.

Alice Yu, Yaanu Jeyakumar, Mei Wang, Justin Lee, Maura Marcucci, Anne Holbrook,

<h4>Objectives</h4>This study aimed to review the degree of personalization of benefit and harm in the reporting of recent high-profile randomized controlled trials (RCTs) involving pharmacological interventions.<h4>Study design and setting</h4>This study is a systematic review of RCTs published between 2012 and 2017 with at least one intervention evaluating drug therapy and ... Read more >>

J Clin Epidemiol (Journal of clinical epidemiology)
[2020, 126:17-25]

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A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk.

Andrew J Gentles, Angela Bik-Yu Hui, Weiguo Feng, Armon Azizi, Ramesh V Nair, Gina Bouchard, David A Knowles, Alice Yu, Youngtae Jeong, Alborz Bejnood, Erna Forgó, Sushama Varma, Yue Xu, Amanda Kuong, Viswam S Nair, Rob West, Matt van de Rijn, Chuong D Hoang, Maximilian Diehn, Sylvia K Plevritis,

<h4>Background</h4>Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway.<h4>Result</h4>To develop a deeper understanding of the interactions between ... Read more >>

Genome Biol (Genome biology)
[2020, 21(1):107]

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Irinotecan, Temozolomide, and Dinutuximab With GM-CSF in Children With Refractory or Relapsed Neuroblastoma: A Report From the Children's Oncology Group.

Rajen Mody, Alice L Yu, Arlene Naranjo, Fan F Zhang, Wendy B London, Barry L Shulkin, Marguerite T Parisi, Sabah-E-Noor Servaes, Mitchell B Diccianni, Jacquelyn A Hank, Mildred Felder, Jennifer Birstler, Paul M Sondel, Shahab Asgharzadeh, Julia Glade-Bender, Howard Katzenstein, John M Maris, Julie R Park, Rochelle Bagatell,

<h4>Purpose</h4>The combination of irinotecan, temozolomide, dintuximab, and granulocyte-macrophage colony-stimulating factor (I/T/DIN/GM-CSF) demonstrated activity in patients with relapsed/refractory neuroblastoma in the randomized Children's Oncology Group ANBL1221 trial. To more accurately assess response rate and toxicity, an expanded cohort was nonrandomly assigned to I/T/DIN/GM-CSF.<h4>Patients and methods</h4>Patients were eligible at first relapse or ... Read more >>

J Clin Oncol (Journal of clinical oncology : official journal of the American Society of Clinical Oncology)
[2020, 38(19):2160-2169]

Cited: 3 times

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