Amy Ly
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View article: Methylation-based signature to distinguish indolent and aggressive prostate cancer
Methylation-based signature to distinguish indolent and aggressive prostate cancer Open
Prostate cancer management faces significant challenges in distinguishing indolent from aggressive disease, particularly since most patients are intermediate-risk and therefore hinders the ability to recommend standardized treatment recomm…
View article: Identification of distinct cDC2 subpopulations that direct microbiota-specific T cell differentiation
Identification of distinct cDC2 subpopulations that direct microbiota-specific T cell differentiation Open
How the complex network of intestinal antigen presenting cells (APCs) instructs CD4 + T cell responses against the microbiota remains unclear. Here, we use Labeling Immune Partnerships by SorTagging Intercellular Contacts (LIPSTIC) to char…
View article: International expert panel’s potentially inappropriate prescribing cascades (PIPC) list
International expert panel’s potentially inappropriate prescribing cascades (PIPC) list Open
Purpose Prescribing cascades contribute to potentially inappropriate prescribing, especially among older adults. With the prescribing cascade framework maturation, it is important to distinguish potentially inappropriate from potentially a…
View article: Pediatric Hematology–Oncology Provider Attitudes and Beliefs About the Use of Acupuncture for Their Patients
Pediatric Hematology–Oncology Provider Attitudes and Beliefs About the Use of Acupuncture for Their Patients Open
Background/Objectives: Children with cancer suffer due to the underlying disease and prescribed cancer-directed therapies, and non-pharmacologic modalities may offer improved symptom control without additional medications. We sought to eli…
View article: PEARL: A Phase Ib/II Biomarker Study of Adding Radiation Therapy to Pembrolizumab Before Neoadjuvant Chemotherapy in Human Epidermal Growth Factor Receptor 2–Negative Breast Cancer
PEARL: A Phase Ib/II Biomarker Study of Adding Radiation Therapy to Pembrolizumab Before Neoadjuvant Chemotherapy in Human Epidermal Growth Factor Receptor 2–Negative Breast Cancer Open
PURPOSE To assess safety and immune biomarkers after preoperative radiation therapy (RT) and anti-PD1 therapy in breast cancer. MATERIALS AND METHODS A phase I/IIb trial of pembrolizumab with RT was conducted in patients with triple-negati…
View article: Doing more with less: integrating small biopsies in cytology practice
Doing more with less: integrating small biopsies in cytology practice Open
Cytopathologists are at the forefront of specimen acquisition during many different procedures while providing rapid on site evaluation (ROSE). This has added pressure to cytopathologists as more and more ancillary testing is being request…
View article: Mapping and characterization of structural variation in 17,795 human genomes
Mapping and characterization of structural variation in 17,795 human genomes Open
A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and re…
View article: Training pathologists to assess stromal tumour‐infiltrating lymphocytes in breast cancer synergises efforts in clinical care and scientific research
Training pathologists to assess stromal tumour‐infiltrating lymphocytes in breast cancer synergises efforts in clinical care and scientific research Open
A growing body of research supports stromal tumour‐infiltrating lymphocyte (TIL) density in breast cancer to be a robust prognostic and predicive biomarker. The gold standard for stromal TIL density quantitation in breast cancer is patholo…
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View article: Reproducible Reporting of the Collection and Evaluation of Annotations for Artificial Intelligence Models
Reproducible Reporting of the Collection and Evaluation of Annotations for Artificial Intelligence Models Open
This work puts forth and demonstrates the utility of a reporting framework for collecting and evaluating annotations of medical images used for training and testing artificial intelligence (AI) models in assisting detection and diagnosis. …
View article: Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer
Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer Open
Recent advances in the field of immuno‐oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response…
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View article: Initial interactions with the <scp>FDA</scp> on developing a validation dataset as a medical device development tool
Initial interactions with the <span>FDA</span> on developing a validation dataset as a medical device development tool Open
Quantifying tumor‐infiltrating lymphocytes (TILs) in breast cancer tumors is a challenging task for pathologists. With the advent of whole slide imaging that digitizes glass slides, it is possible to apply computational models to quantify …
View article: INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA
INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA Open
Motivation Backsplicing of RNA results in circularized rather than linear transcripts, known as circular RNA (circRNA). A recently discovered and poorly understood subset of circRNAs that are composed of multiple genes, termed fusion-deriv…
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No abstract is available for this article.
View article: Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer
Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer Open
Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized method for descr…
View article: Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer
Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer Open
The clinical significance of the tumor‐immune interaction in breast cancer is now established, and tumor‐infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple‐negative (estrogen recep…
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No abstract is available for this article.
View article: Regulation of RNA methylation by therapy treatment, promotes tumor survival
Regulation of RNA methylation by therapy treatment, promotes tumor survival Open
Our data previously revealed that chemosurviving cancer cells translate specific genes. Here, we find that the m6A-RNA-methyltransferase, METTL3, increases transiently in chemotherapy-treated breast cancer and leukemic cells in vitro and i…
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No abstract is available for this article.
View article: Data from PTEN Loss Mediates Clinical Cross-Resistance to CDK4/6 and PI3Kα Inhibitors in Breast Cancer
Data from PTEN Loss Mediates Clinical Cross-Resistance to CDK4/6 and PI3Kα Inhibitors in Breast Cancer Open
The combination of CDK4/6 inhibitors with antiestrogen therapies significantly improves clinical outcomes in ER-positive advanced breast cancer. To identify mechanisms of acquired resistance, we analyzed serial biopsies and rapid autopsies…