bluuebunny/crossref_metadata_2025 huggingface dataset:
Noise estimation in an entanglement distillation protocol
Authors: Maity Ananda G. , Casapao Joshua C. A. , Benchasattabuse Naphan , Hajdusek Michal , Van Meter Rodney , Elkouss David
Published: October 2023

Estimating noise processes is an essential step for practical quantum information processing. Standard estimation tools require consuming valuable quantum resources. Here we ask the question of whether the noise affecting entangled states can be learned solely from the measurement statistics obtained during a distillation protocol. As a first step, we consider states of the Werner form and find that the Werner parameter can be estimated efficiently from the measurement statistics of an idealized distillation protocol. Our proposed estimation method can find application in scenarios where distillation is an unavoidable step.
Learning-based Optimal Quantum Switch Scheduling
Authors: Huang Jiatai , Huang Longbo
Published: October 2023

In this paper, we consider the problem of optimal scheduling for quantum switches with dynamic demand and random entanglement successes. Different from prior results that often focus on (known) fixed entanglement success probabilities, we assume zero prior knowledge about the entanglement success probabilities and allow them to vary from time to time in an adversarial manner. We propose a learning-based algorithm QSSoftMW based on the framework developed in [1], which combines adversarial learning and Lyapunov queue analysis. We show that QSSoftMW is able to automatically adapt to the changing system statistics and ensure quantum switch stability.
Toward Fast Query Serving in Key-Value Store Migration with Approximate Telemetry
Authors: Braverman Alexander , Liu Zaoxing
Published: October 2023

Distributed key-value stores scale data analytical processing by spreading data across nodes. Frequent migration of key-value shards between online nodes is a key technique to react to dynamic workload changes for load balancing and service elasticity. During migration, the data is split between a source and a destination, making it difficult to query the exact location. Existing solutions aiming to provide real-time read and write query capabilities during migration may require querying both source and destination servers, doubling the compute/network resources. In this paper, we explore a simple yet effective measurement approach to track the key-value migration status, in order to improve the query-serving performance under migration. In our preliminary prototype, we use a Bloom filter on the destination server to keep track of individual key-value pairs that have been successfully migrated. For key-value pairs that have yet migrated, the information stored in the Bloom filter enables fast forwarding to the source server without the need to check the database. We prototype this design on a local cluster with Redis deployments. Our preliminary results show that this approximate measurement-based design minimizes query losses during migration.
Enabling Perception-Driven Optimization in Networking
Authors: Cheng Yihua , Zhang Xu , Jiang Junchen
Published: October 2023

Service providers struggle to catch up with the rapid growth in bandwidth and latency demand of Internet videos and other applications. An essential contributor to this resource contention is the assumption that users are equally sensitive to service quality everywhere, so any low-quality incidents must be avoided. However, this assumption is not true. For example, our work and other parallel efforts have shown that more video users can be served with better quality of experience (QoE) if we embrace the fact that the QoE's sensitivity to video quality varies greatly with the video content. To unleash such benefits, the application systems must be driven by not only system measurement data but also user feedback data that capture users' perceptions of service quality. In this short paper, I will highlight some of our recent efforts toward the efficient collection of user feedback and enabling perception-driven optimization for Internet applications.
Supplementary Fig. S1 from Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor–Positive Breast Cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Cañadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: October 2023

Supplementary Fig. S1. Comprehensive analysis of protein expression data in immune and invasive cancer epithelial regions from in various patient cohorts.
Table S3 from LncRNA AGPG Confers Endocrine Resistance in Breast Cancer by Promoting E2F1 Activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: October 2023

Table S3
Figure S4 from LncRNA AGPG Confers Endocrine Resistance in Breast Cancer by Promoting E2F1 Activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: October 2023

Figure S4
Supplementary Figure 5 from Galectin-1 Mediates Chronic STING Activation in Tumors to Promote Metastasis through MDSC Recruitment
Authors: Nambiar Dhanya K. , Viswanathan Vignesh , Cao Hongbin , Zhang Weiruo , Guan Li , Chamoli Manish , Holmes Brittany , Kong Christina , Hildebrand Rachel , Koong Amanda Jeanette , von Eyben Rie , Plevritis Sylvia , Li Lingyin , Giaccia Amato , Engleman Edgar , Le Quynh Thu
Published: October 2023

A. Quantification of phospho-p65 (NF-kb) staining in MOC2 and mEERL WT/KO-Gal1 tumors (N=5 tumors, 3 random microscopic fields per tumor). B. Quantitation of STING mRNA levels in MOC2 and mEERL WT/KO-Gal1 cell lines. C. Immunoblot showing degradation kinetics of STING in LLC and FaDU WT/KD-Gal1 cells at 1, 2, 4h post cycloheximide treatment. D. Magnified images showing co-localization of STING and LAMP1 in MOC2 WT/KO-Gal1 cells. E. Representative images showing low and high IHC staining of STING in oral cavity cancer (Left) and the distribution of negative and positive STING staining in 83 oral cavity cancers on the TMA. F. Kaplan Meier curve showing progression-free survival (calculated as the time from the surgery date until death or progression) of patients based on Gal1 and STING expression in the tumor.
Supplementary Figure 2 from Galectin-1 Mediates Chronic STING Activation in Tumors to Promote Metastasis through MDSC Recruitment
Authors: Nambiar Dhanya K. , Viswanathan Vignesh , Cao Hongbin , Zhang Weiruo , Guan Li , Chamoli Manish , Holmes Brittany , Kong Christina , Hildebrand Rachel , Koong Amanda Jeanette , von Eyben Rie , Plevritis Sylvia , Li Lingyin , Giaccia Amato , Engleman Edgar , Le Quynh Thu
Published: October 2023

A. Representative gating strategy for quantification of PMN-MDSCs, M-MDSCs, Ly6C+Mo-MØs, Alveolar macrophages (AMs), Interstitial macrophages (IMs) and myeloid DCs in the lungs of tumor-bearing mice. B. Quantification of PMN-MDSCs (CD11b+Ly6Clo/intLy6G+) in the lungs of MOC2 WT- or KO-Gal1 tumor-bearing mice at matched tumor volumes and of naïve mice. C. Quantitation of CD4+ and CD8+ T cells in MOC2 WT/KO-Gal1 tumor-bearing mice lungs at matched tumor volumes. D. Quantitation of CD8+ T cells in the blood after treatment with either isotype control IgG or anti-mouse CD8a antibody (clone 2.43, BioXCell, 400 μg i.p. twice weekly) in mice bearing MOC2 WT- or KO-Gal1 tumors. E. Quantitation of PMN-MDSCs in the lungs after treatment with either isotype control IgG or anti-mouse CD8a antibody i.p. twice weekly in mice bearing MOC2 WT- or KO-Gal1 tumors. Each dot represents one mouse, and the bar denotes the mean. Student’s t-test (two-tailed) was used to compare the two groups. One-way ANOVA with Tukey’s adjustment was used for comparing multiple treatments to each other. Data are shown as mean+/-SD.
Data from Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Canadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: October 2023

Abstract
Immunotherapies have yet to demonstrate significant efficacy in the treatment of hormone receptor positive (HR+) breast cancer. Given that endocrine therapy (ET) is the primary approach for treating HR+ breast cancer, we investigated the effects of ET on the tumor immune microenvironment (TME) in HR+ breast cancer. Spatial proteomics analysis of primary HR+ breast cancer samples obtained at baseline and after ET from patients enrolled in a neoadjuvant clinical trial (NCT02764541) indicated that ET upregulated B2-microglobulin and influenced the TME in a manner that promotes enhanced immunogenicity. To gain a deeper understanding of the underlying mechanisms, the intrinsic effects of ET on cancer cells were explored, which revealed that ET plays a crucial role in facilitating the chromatin binding of RelA, a key component of the NF-κB complex. Consequently, heightened NF-κB signaling enhanced the response to interferon-gamma, leading to the upregulation of β2-microglobulin and other antigen presentation-related genes. Further, modulation of NF-κB signaling using a SMAC-mimetic in conjunction with ET augmented T-cell migration and enhanced MHC-I specific T-cell mediated cytotoxicity. Remarkably, the combination of ET and SMAC-mimetics, which also block pro-survival effects of NF-κB signaling through the degradation of inhibitors of apoptosis (IAP) proteins, elicited tumor regression through cell-autonomous mechanisms, providing additional support for their combined use in HR+ breast cancer.
Data from Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor–Positive Breast Cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Cañadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: October 2023

Abstract
Immunotherapies have yet to demonstrate significant efficacy in the treatment of hormone receptor–positive (HR+) breast cancer. Given that endocrine therapy (ET) is the primary approach for treating HR+ breast cancer, we investigated the effects of ET on the tumor immune microenvironment (TME) in HR+ breast cancer. Spatial proteomics of primary HR+ breast cancer samples obtained at baseline and after ET from patients enrolled in a neoadjuvant clinical trial (NCT02764541) indicated that ET upregulated β2-microglobulin and influenced the TME in a manner that promotes enhanced immunogenicity. To gain a deeper understanding of the underlying mechanisms, the intrinsic effects of ET on cancer cells were explored, which revealed that ET plays a crucial role in facilitating the chromatin binding of RelA, a key component of the NF-κB complex. Consequently, heightened NF-κB signaling enhanced the response to interferon-gamma, leading to the upregulation of β2-microglobulin and other antigen presentation-related genes. Further, modulation of NF-κB signaling using a SMAC mimetic in conjunction with ET augmented T-cell migration and enhanced MHC-I-specific T-cell–mediated cytotoxicity. Remarkably, the combination of ET and SMAC mimetics, which also blocks prosurvival effects of NF-κB signaling through the degradation of inhibitors of apoptosis proteins, elicited tumor regression through cell autonomous mechanisms, providing additional support for their combined use in HR+ breast cancer.
Significance:
Adding SMAC mimetics to endocrine therapy enhances tumor regression in a cell autonomous manner while increasing tumor immunogenicity, indicating that this combination could be an effective treatment for HR+ patients with breast cancer.
Data from Allosteric Regulation of Switch-II Domain Controls KRAS Oncogenicity
Authors: Yang Moon Hee , Tran Timothy H. , Hunt Bethany , Agnor Rebecca , Johnson Christian W. , Shui Bing , Waybright Timothy J. , Nowak Jonathan A. , Stephen Andrew G. , Simanshu Dhirendra K. , Haigis Kevin M.
Published: October 2023

Abstract
RAS proteins are GTPases that regulate a wide range of cellular processes. RAS activity is dependent on its nucleotide-binding status, which is modulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP). KRAS can be acetylated at lysine 104 (K104), and an acetylation-mimetic mutation of K104 to glutamine (K104Q) attenuates the in vitro–transforming capacity of oncogenic KRAS by interrupting GEF-induced nucleotide exchange. To assess the effect of this mutation in vivo, we used CRISPR-Cas9 to generate mouse models carrying the K104Q point mutation in wild-type and conditional KrasLSL-G12D alleles. Homozygous animals for K104Q were viable, fertile, and arose at the expected Mendelian frequency, indicating that K104Q is not a complete loss-of-function mutation. Consistent with our previous findings from in vitro studies, however, the oncogenic activity of KRASG12D was significantly attenuated by mutation at K104. Biochemical and structural analysis indicated that the G12D and K104Q mutations cooperate to suppress GEF-mediated nucleotide exchange, explaining the preferential effect of K104Q on oncogenic KRAS. Furthermore, K104 functioned in an allosteric network with M72, R73, and G75 on the α2 helix of the switch-II region. Intriguingly, point mutation of glycine 75 to alanine (G75A) also showed a strong negative regulatory effect on KRASG12D. These data demonstrate that lysine at position 104 is critical for the full oncogenic activity of mutant KRAS and suggest that modulating the sites in its allosteric network may provide a unique therapeutic approach in cancers expressing mutant KRAS.
Significance:
An allosteric network formed by interaction between lysine 104 and residues in the switch-II domain is required for KRAS oncogenicity, which could be exploited for developing inhibitors of the activated oncoprotein.
Data from Single-Cell Characterization of Pulmonary Nodules Implicates Suppression of Immunosurveillance across Early Stages of Lung Adenocarcinoma
Authors: Yanagawa Jane , Tran Linh M. , Salehi-Rad Ramin , Lim Raymond J. , Dumitras Camelia , Fung Eileen , Wallace William D. , Prosper Ashley E. , Fishbein Gregory , Shea Conor , Hong Rui , Kahangi Bitta , Deng John J. , Gower Adam C. , Liu Bin , Campbell Joshua D. , Mazzilli Sarah A. , Beane Jennifer E. , Kadara Humam , Lenburg Marc E. , Spira Avrum E. , Aberle Denise R. , Krysan Kostyantyn , Dubinett Steven M.
Published: October 2023

Abstract
A greater understanding of molecular, cellular, and immunological changes during the early stages of lung adenocarcinoma development could improve diagnostic and therapeutic approaches in patients with pulmonary nodules at risk for lung cancer. To elucidate the immunopathogenesis of early lung tumorigenesis, we evaluated surgically resected pulmonary nodules representing the spectrum of early lung adenocarcinoma as well as associated normal lung tissues using single-cell RNA sequencing and validated the results by flow cytometry and multiplex immunofluorescence (MIF). Single-cell transcriptomics revealed a significant decrease in gene expression associated with cytolytic activities of tumor-infiltrating natural killer and natural killer T cells. This was accompanied by a reduction in effector T cells and an increase of CD4+ regulatory T cells (Treg) in subsolid nodules. An independent set of resected pulmonary nodules consisting of both adenocarcinomas and associated premalignant lesions corroborated the early increment of Tregs in premalignant lesions compared with the associated normal lung tissues by MIF. Gene expression analysis indicated that cancer-associated alveolar type 2 cells and fibroblasts may contribute to the deregulation of the extracellular matrix, potentially affecting immune infiltration in subsolid nodules through ligand–receptor interactions. These findings suggest that there is a suppression of immune surveillance across the spectrum of early-stage lung adenocarcinoma.
Significance:
Analysis of a spectrum of subsolid pulmonary nodules by single-cell RNA sequencing provides insights into the immune regulation and cell–cell interactions in the tumor microenvironment during early lung tumor development.
Data from Abemaciclib is effective in palbociclib-resistant hormone receptor-positive metastatic breast cancers
Authors: Navarro-Yepes Juliana , Kettner Nicole M. , Rao Xiayu , Bishop Cassandra Santaella. , Bui Tuyen N. , Wingate Hannah F. , Singareeka Raghavendra Akshara , Wang Yan , Wang Jing , Sahin Aysegul A. , Meric-Bernstam Funda , Hunt Kelly K. , Damodaran Senthil , Tripathy Debu , Keyomarsi Khandan
Published: October 2023

Abstract
Cyclin-dependent-kinase-4/6 inhibitor (CDK4/6i) plus endocrine therapy (ET) is standard of care for patients with hormone receptor (HR)-positive, HER2-negative metastatic breast cancer (MBC). However, resistance to CDK4/6is plus ET remains a clinical problem with limited therapeutic options following disease progression. Different CDK4/6is might have distinct mechanisms of resistance, and therefore using them sequentially or targeting their differentially altered pathways could delay disease progression. To understand pathways leading to resistance to the CDK4/6is palbociclib and abemaciclib, we generated multiple in vitro models of palbociclib-resistant (PR) and abemaciclib-resistant (AR) cell lines, as well as in vivo patient-derived xenografts (PDX) and ex vivo PDX-derived organoids from patients who progressed on CDK4/6i. PR and AR breast cancer cells exhibited distinct transcriptomic and proteomic profiles that sensitized them to different classes of inhibitors; PR cells upregulated G2/M pathways and responded to abemaciclib, while AR cells upregulated mediators of the oxidative phosphorylation pathway (OXPHOS) and responded to OXPHOS inhibitors. PDX and organoid models derived from palbociclib-resistant breast cancer patients remained responsive to abemaciclib. Resistance to palbociclib while maintaining sensitivity to abemaciclib was associated with pathway-specific transcriptional activity but was not associated with any individual genetic alterations. Lastly, data from a cohort of 52 patients indicated that patients with HR-positive/HER2-negative MBC who progressed on palbociclib-containing regimens can exhibit a meaningful overall clinical benefit from abemaciclib-based therapy when administered after palbociclib. These findings provide the rationale for clinical trials evaluating the benefit of abemaciclib treatment following progression on a prior CDK4/6i.
Supplementary Table S5 from Genome-Scale Methylation Analysis Identifies Immune Profiles and Age Acceleration Associations with Bladder Cancer Outcomes
Authors: Chen Ji-Qing , Salas Lucas A. , Wiencke John K. , Koestler Devin C. , Molinaro Annette M. , Andrew Angeline S. , Seigne John D. , Karagas Margaret R. , Kelsey Karl T. , Christensen Brock C.
Published: October 2023

Supplementary Table S5: The information of optimal CpGs selected by SS-RPMM using the model controlling for Pheno and Hannum age acceleration respectively
Supplementary Table S2 from Genome-Scale Methylation Analysis Identifies Immune Profiles and Age Acceleration Associations with Bladder Cancer Outcomes
Authors: Chen Ji-Qing , Salas Lucas A. , Wiencke John K. , Koestler Devin C. , Molinaro Annette M. , Andrew Angeline S. , Seigne John D. , Karagas Margaret R. , Kelsey Karl T. , Christensen Brock C.
Published: October 2023

Supplementary Table S2: Cox proportional hazards multivariable models for demographic and tumor characteristics of 601 NMIBC patients (For Hannum Age Acceleration)
Supplementary Figure S2 from Genome-Scale Methylation Analysis Identifies Immune Profiles and Age Acceleration Associations with Bladder Cancer Outcomes
Authors: Chen Ji-Qing , Salas Lucas A. , Wiencke John K. , Koestler Devin C. , Molinaro Annette M. , Andrew Angeline S. , Seigne John D. , Karagas Margaret R. , Kelsey Karl T. , Christensen Brock C.
Published: October 2023

Supplementary Figure S2: Blood immune cell profiles, age and age acceleration distribution of three groups assigned by partDSA algorithm in NMIBC patients
Supplementary Figure S1 from Genome-Scale Methylation Analysis Identifies Immune Profiles and Age Acceleration Associations with Bladder Cancer Outcomes
Authors: Chen Ji-Qing , Salas Lucas A. , Wiencke John K. , Koestler Devin C. , Molinaro Annette M. , Andrew Angeline S. , Seigne John D. , Karagas Margaret R. , Kelsey Karl T. , Christensen Brock C.
Published: October 2023

Supplementary Figure S1: The distribution of chronological age, methylation age, age acceleration, and each immune cell profile
Supplementary Table S4 from Sex-Specific Associations between Adiponectin and Leptin Signaling and Pancreatic Cancer Survival
Authors: Babic Ana , Wang Qiao-Li , Lee Alice A. , Yuan Chen , Rifai Nader , Luo Juhua , Tabung Fred K. , Shadyab Aladdin H. , Wactawski-Wende Jean , Saquib Nazmus , Kim Jihye , Kraft Peter , Sesso Howard D. , Buring Julie E. , Giovannucci Edward L. , Manson JoAnn E. , Stampfer Meir J. , Ng Kimmie , Fuchs Charles S. , Wolpin Brian M.
Published: October 2023

Correlation between adipokine levels and select patient characteristics
Supplementary Table S2 from Sex-Specific Associations between Adiponectin and Leptin Signaling and Pancreatic Cancer Survival
Authors: Babic Ana , Wang Qiao-Li , Lee Alice A. , Yuan Chen , Rifai Nader , Luo Juhua , Tabung Fred K. , Shadyab Aladdin H. , Wactawski-Wende Jean , Saquib Nazmus , Kim Jihye , Kraft Peter , Sesso Howard D. , Buring Julie E. , Giovannucci Edward L. , Manson JoAnn E. , Stampfer Meir J. , Ng Kimmie , Fuchs Charles S. , Wolpin Brian M.
Published: October 2023

Association between SNPs in adiponectin receptor genes and pancreatic cancer mortality by sex
Table S1 from Risk of Colorectal Cancer and Colorectal Cancer Mortality Beginning One Year after a Negative Fecal Occult Blood Test, among Screen-Eligible 76- to 85-Year-Olds
Authors: Dalmat Ronit R. , Ziebell Rebecca A. , Kamineni Aruna , Phipps Amanda I. , Weiss Noel S. , Breslau Erica S. , Burnett-Hartman Andrea N. , Corley Douglas A. , Doria-Rose V. Paul , Green Beverly B. , Halm Ethan A. , Levin Theodore R. , Schottinger Joanne E. , Chubak Jessica
Published: October 2023

Table S-1 shows characteristics of screen-eligible patients aged 76-85 years at index date, stratified by healthcare system.
Figure S1 from A Genomic Analysis of Esophageal Squamous Cell Carcinoma in Eastern Africa
Authors: Van Loon Katherine , Mmbaga Elia J. , Mushi Beatrice P. , Selekwa Msiba , Mwanga Ally , Akoko Larry O. , Mwaiselage Julius , Mosha Innocent , Ng Dianna L. , Wu Wei , Silverstein Jordyn , Mulima Gift , Kaimila Bongani , Gopal Satish , Snell Jeff M. , Benz Stephen Charles , Vaske Charles , Sanborn Zack , Sedgewick Andrew J. , Radenbaugh Amie , Newton Yulia , Collisson Eric A.
Published: October 2023

Supplementary Figure S1. Measurement of RNA Quantity and Quality using PAXgene tissue container vs. RNAlater.
Supplementary Table 2 from Association between Outdoor Light at Night and Prostate Cancer in the Health Professionals Follow-up Study
Authors: Chowdhury-Paulino Ilkania M. , Hart Jaime E. , James Peter , Iyer Hari S. , Wilt Grete E. , Booker Benjamin D. , Nethery Rachel C. , Laden Francine , Mucci Lorelei A. , Markt Sarah C.
Published: October 2023

Supplementary Table 2. Hazard ratios and 95% confidence intervals for the association between outdoor light at night (LAN) and lethal prostate cancer incidence in HPFS 1986-2016, stratified by urbanicity (urban: >1,000 people/mi2, nonurban: <1,000 people/mi2), PSA screening intensity, and neighborhood socioeconomic status
Supplementary Table 3 from Patterns of Evidence-Based Care for the Diagnosis, Staging, and First-line Treatment of Breast Cancer by Race–Ethnicity: A SEER-Medicare Study
Authors: Herbach Emma L. , Nash Sarah H. , Lizarraga Ingrid M. , Carnahan Ryan M. , Wang Kai , Ogilvie Amy C. , Curran Michaela , Charlton Mary E.
Published: October 2023

Supplementary Table 3 shows adjusted rate ratios for all applicable outcomes stratified by age at diagnosis.
Supplementary Table 5 from Body Composition, Relative Dose Intensity, and Adverse Events among Patients with Colon Cancer
Authors: Cheng En , Caan Bette J. , Cawthon Peggy M. , Evans William J. , Hellerstein Marc K. , Shankaran Mahalakshmi , Nyangau Edna , Campbell Kristin L. , Lee Catherine , Binder Alexandra M. , Meyerhardt Jeffrey A. , Schmitz Kathryn H. , Cespedes Feliciano Elizabeth M.
Published: October 2023

Supplementary Table 5. The Adjusted Associations of Body Composition Measurements (Per SD Increase) with Reduced RDI Counting from the Initiation of First Chemotherapy
Supplementary Table 4 from Body Composition, Relative Dose Intensity, and Adverse Events among Patients with Colon Cancer
Authors: Cheng En , Caan Bette J. , Cawthon Peggy M. , Evans William J. , Hellerstein Marc K. , Shankaran Mahalakshmi , Nyangau Edna , Campbell Kristin L. , Lee Catherine , Binder Alexandra M. , Meyerhardt Jeffrey A. , Schmitz Kathryn H. , Cespedes Feliciano Elizabeth M.
Published: October 2023

Supplementary Table 4. The Adjusted Associations of Body Composition Measurements (Per SD Increase) with Reduced RDI Counting for Each Chemotherapy Agent
Supplementary Table 3 from Body Composition, Relative Dose Intensity, and Adverse Events among Patients with Colon Cancer
Authors: Cheng En , Caan Bette J. , Cawthon Peggy M. , Evans William J. , Hellerstein Marc K. , Shankaran Mahalakshmi , Nyangau Edna , Campbell Kristin L. , Lee Catherine , Binder Alexandra M. , Meyerhardt Jeffrey A. , Schmitz Kathryn H. , Cespedes Feliciano Elizabeth M.
Published: October 2023

Supplementary Table 3. The Adjusted Associations of Scaled Body Composition Measurements (Per SD Increase) with Reduced RDI and Relative Changes (%) in the Number of Moderate and Severe Adverse Events
Supplementary Table 2 from Body Composition, Relative Dose Intensity, and Adverse Events among Patients with Colon Cancer
Authors: Cheng En , Caan Bette J. , Cawthon Peggy M. , Evans William J. , Hellerstein Marc K. , Shankaran Mahalakshmi , Nyangau Edna , Campbell Kristin L. , Lee Catherine , Binder Alexandra M. , Meyerhardt Jeffrey A. , Schmitz Kathryn H. , Cespedes Feliciano Elizabeth M.
Published: October 2023

Supplementary Table 2. Sex-Specific Standard Deviations of Body Composition Measurements (CT SMA, DXA ALM, D3Cr Muscle, CT TAT, and DXA TBF)
Supplemental Table 7 from New-Onset Diabetes after an Obesity-Related Cancer Diagnosis and Survival Outcomes in the Women's Health Initiative
Authors: Karra Prasoona , Hardikar Sheetal , Winn Maci , Anderson Garnet L. , Haaland Benjamin , Krick Benjamin , Thomson Cynthia A. , Shadyab Aladdin , Luo Juhua , Saquib Nazmus , Strickler Howard D. , Chlebowski Rowan , Arthur Rhonda S. , Summers Scott A. , Holland William L. , Jalili Thunder , Playdon Mary C.
Published: October 2023

Supplemental Table 7 provides results for the 6 months lag analysis.
Supplemental Table 5 from New-Onset Diabetes after an Obesity-Related Cancer Diagnosis and Survival Outcomes in the Women's Health Initiative
Authors: Karra Prasoona , Hardikar Sheetal , Winn Maci , Anderson Garnet L. , Haaland Benjamin , Krick Benjamin , Thomson Cynthia A. , Shadyab Aladdin , Luo Juhua , Saquib Nazmus , Strickler Howard D. , Chlebowski Rowan , Arthur Rhonda S. , Summers Scott A. , Holland William L. , Jalili Thunder , Playdon Mary C.
Published: October 2023

Supplemental Table 5 provides effect estimates for the association of incident diabetes and cancer-specific mortality among obesity-related cancer survivors.
Supplemental Table 1 from New-Onset Diabetes after an Obesity-Related Cancer Diagnosis and Survival Outcomes in the Women's Health Initiative
Authors: Karra Prasoona , Hardikar Sheetal , Winn Maci , Anderson Garnet L. , Haaland Benjamin , Krick Benjamin , Thomson Cynthia A. , Shadyab Aladdin , Luo Juhua , Saquib Nazmus , Strickler Howard D. , Chlebowski Rowan , Arthur Rhonda S. , Summers Scott A. , Holland William L. , Jalili Thunder , Playdon Mary C.
Published: October 2023

Supplemental Table 1 provides demographic characteristics for the included and excluded participants in the study.
Supplementary Table S3 from Prediagnostic Prescription Antibiotics Use and Survival in Patients with Colorectal Cancer: A Swedish National Register-Based Study
Authors: Lu Sai San Moon , Rutegård Martin , Ahmed Maghfoor , Häggström Christel , Gylfe Åsa , Harlid Sophia , Van Guelpen Bethany
Published: October 2023

Supplementary Table S3: Characteristics of stage I-III colorectal cancer patients by limiting the antibiotics use to a 4.5-year period before colorectal cancer diagnosis
Supplementary Table S2 from Prediagnostic Prescription Antibiotics Use and Survival in Patients with Colorectal Cancer: A Swedish National Register-Based Study
Authors: Lu Sai San Moon , Rutegård Martin , Ahmed Maghfoor , Häggström Christel , Gylfe Åsa , Harlid Sophia , Van Guelpen Bethany
Published: October 2023

Supplementary Table S2: Reported number of defined daily doses (DDD) for specific antibiotics
Supplementary Table S1 from Prediagnostic Prescription Antibiotics Use and Survival in Patients with Colorectal Cancer: A Swedish National Register-Based Study
Authors: Lu Sai San Moon , Rutegård Martin , Ahmed Maghfoor , Häggström Christel , Gylfe Åsa , Harlid Sophia , Van Guelpen Bethany
Published: October 2023

Supplementary Table S1: Classification of antibiotics types and indications
Table S5 from Dietary Fish and n-3 Polyunsaturated Fatty Acid Consumption, and Renal Cell Carcinoma Risk in Japan: The Japan Public Health Center-Based Prospective Study
Authors: Takahashi Michiko , Sobue Tomotaka , Zha Ling , Kitamura Tetsuhisa , Iwasaki Motoki , Inoue Manami , Yamaji Taiki , Tsugane Shoichiro , Sawada Norie
Published: October 2023

Supplementary Table S5. Risk of RCC based on the energy-adjusted dietary intakes of fish and n-3 PUFA for each detection method.
Table S1 from Dietary Fish and n-3 Polyunsaturated Fatty Acid Consumption, and Renal Cell Carcinoma Risk in Japan: The Japan Public Health Center-Based Prospective Study
Authors: Takahashi Michiko , Sobue Tomotaka , Zha Ling , Kitamura Tetsuhisa , Iwasaki Motoki , Inoue Manami , Yamaji Taiki , Tsugane Shoichiro , Sawada Norie
Published: October 2023

Supplementary Table S1. Details of RCC cases based on method of diagnosis.
Data from Patterns of Evidence-Based Care for the Diagnosis, Staging, and First-line Treatment of Breast Cancer by Race–Ethnicity: A SEER-Medicare Study
Authors: Herbach Emma L. , Nash Sarah H. , Lizarraga Ingrid M. , Carnahan Ryan M. , Wang Kai , Ogilvie Amy C. , Curran Michaela , Charlton Mary E.
Published: October 2023

AbstractBackground:
Racial and ethnic disparities in guideline-recommended breast cancer treatment are well documented, however studies including diagnostic and staging procedures necessary to determine treatment indications are lacking. The purpose of this study was to characterize patterns in delivery of evidence-based services for the diagnosis, clinical workup, and first-line treatment of breast cancer by race–ethnicity.
Methods:
SEER-Medicare data were used to identify women diagnosed with invasive breast cancer between 2000 and 2017 at age 66 or older (n = 2,15,605). Evidence-based services included diagnostic procedures (diagnostic mammography and breast biopsy), clinical workup (stage and grade determination, lymph node biopsy, and HR and HER2 status determination), and treatment initiation (surgery, radiation, chemotherapy, hormone therapy, and HER2-targeted therapy). Poisson regression was used to estimate rate ratios (RR) and 95% confidence intervals (CI) for each service.
Results:
Black and American Indian/Alaska Native (AIAN) women had significantly lower rates of evidence-based care across the continuum from diagnostics through first-line treatment compared to non-Hispanic White (NHW) women. AIAN women had the lowest rates of HER2-targeted therapy and hormone therapy initiation. While Black women also had lower initiation of HER2-targeted therapy than NHW, differences in hormone therapy were not observed.
Conclusions:
Our findings suggest patterns along the continuum of care from diagnostic procedures to treatment initiation may differ across race–ethnicity groups.
Impact:
Efforts to improve delivery of guideline-concordant treatment and mitigate racial–ethnic disparities in healthcare and survival should include procedures performed as part of the diagnosis, clinical workup, and staging processes.
Data from Association between Outdoor Light at Night and Prostate Cancer in the Health Professionals Follow-up Study
Authors: Chowdhury-Paulino Ilkania M. , Hart Jaime E. , James Peter , Iyer Hari S. , Wilt Grete E. , Booker Benjamin D. , Nethery Rachel C. , Laden Francine , Mucci Lorelei A. , Markt Sarah C.
Published: October 2023

AbstractBackground:
Circadian disruption is a potential risk factor for advanced prostate cancer, and light at night (LAN) exposure may disrupt circadian rhythms. We evaluated whether outdoor LAN increases the risk of prostate cancer.
Methods:
We prospectively followed 49,148 participants in the Health Professionals Follow-up Study from 1986 through 2016. We estimated baseline and cumulative time-varying outdoor LAN with ∼1 km2 resolution using data from the US Defense Meteorological Satellite Program's Operational Linescan System, which was assigned to participants’ geocoded addresses. Participants reside in all 50 U.S. states and reported a work or home address. We used multivariable Cox models to estimate HRs and 95% confidence intervals (CI) for the association between outdoor LAN and risk of overall (7,175 cases) and fatal (915 cases) prostate cancer adjusting for individual and contextual factors.
Results:
There was no association between the interquartile range increase in cumulative LAN and total (HR, 1.02; 95% CI, 0.98–1.06) or fatal (HR, 1.05; 95% CI, 0.96–1.15) prostate cancer in adjusted models. However, there was a positive association between baseline LAN and total prostate cancer among non-movers (HR, 1.06; 95% CI, 1.00–1.14) including among highly screened participants (HR, 1.11; 95% CI, 1.01–1.23).
Conclusions:
There was a suggestive positive association between baseline outdoor LAN and total prostate cancer. Additional studies with different measures of outdoor LAN and in more diverse populations are necessary.
Impact:
To our knowledge, this is the first longitudinal cohort study exploring the relationship between outdoor LAN and prostate cancer.
Data from Germline Mutations in 12 Genes and Risk of Ovarian Cancer in Three Population-Based Cohorts
Authors: Kotsopoulos Joanne , Hathaway Cassandra A. , Narod Steven A. , Teras Lauren R. , Patel Alpa V. , Hu Chunling , Yadav Siddhartha , Couch Fergus J. , Tworoger Shelley S.
Published: October 2023

AbstractBackground:
With the widespread use of multigene panel genetic testing, population-based studies are necessary to accurately assess penetrance in unselected individuals. We evaluated the prevalence of germline pathogenic or likely pathogenic variants (mutations) in 12 cancer-predisposition genes and associations with ovarian cancer risk in three population-based prospective studies [Nurses’ Health Study (NHS), NHSII, Cancer Prevention Study II].
Methods:
We included women with epithelial ovarian or peritoneal cancer (n = 776) and controls who were alive and had at least one intact ovary at the time of the matched case diagnosis (n = 1,509). Germline DNA was sequenced for mutations in 12 genes. Conditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) for ovarian cancer risk by mutation status.
Results:
The mutation frequency across all 12 genes was 11.2% in cases and 3.3% in controls (P < 0.0001). BRCA1 and BRCA2 were the most frequently mutated (3.5% and 3.8% of cases and 0.3% and 0.5% of controls, respectively) and were associated with increased ovarian cancer risk [OR, BRCA1 = 12.38; 95% confidence interval (CI) = 4.72–32.45; OR, BRCA2 = 9.18; 95% CI = 3.98–21.15]. Mutation frequencies for the other genes were ≤1.0% and only PALB2 was significantly associated with risk (OR = 5.79; 95% CI = 1.09–30.83). There was no difference in survival for women with a BRCA germline mutation versus no mutation.
Conclusions:
Further research is needed to better understand the role of other mutations in ovarian cancer among unselected populations.
Impact:
Our data support guidelines for germline genetic testing for BRCA1 and BRCA2 among women diagnosed with epithelial ovarian cancer; testing for PALB2 may be warranted.
Data from A Genomic Analysis of Esophageal Squamous Cell Carcinoma in Eastern Africa
Authors: Van Loon Katherine , Mmbaga Elia J. , Mushi Beatrice P. , Selekwa Msiba , Mwanga Ally , Akoko Larry O. , Mwaiselage Julius , Mosha Innocent , Ng Dianna L. , Wu Wei , Silverstein Jordyn , Mulima Gift , Kaimila Bongani , Gopal Satish , Snell Jeff M. , Benz Stephen Charles , Vaske Charles , Sanborn Zack , Sedgewick Andrew J. , Radenbaugh Amie , Newton Yulia , Collisson Eric A.
Published: October 2023

AbstractBackground:
Esophageal squamous cell carcinoma (ESCC) comprises 90% of all esophageal cancer cases globally and is the most common histology in low-resource settings. Eastern Africa has a disproportionately high incidence of ESCC.
Methods:
We describe the genomic profiles of 61 ESCC cases from Tanzania and compare them to profiles from an existing cohort of ESCC cases from Malawi. We also provide a comparison to ESCC tumors in The Cancer Genome Atlas (TCGA).
Results:
We observed substantial transcriptional overlap with other squamous histologies via comparison with TCGA PanCan dataset. DNA analysis revealed known mutational patterns, both genome-wide as well as in genes known to be commonly mutated in ESCC. TP53 mutations were the most common somatic mutation in tumors from both Tanzania and Malawi but were detected at lower frequencies than previously reported in ESCC cases from other settings. In a combined analysis, two unique transcriptional clusters were identified: a proliferative/epithelial cluster and an invasive/migrative/mesenchymal cluster. Mutational signature analysis of the Tanzanian cohort revealed common signatures associated with aging and cytidine deaminase activity (APOBEC) and an absence of signature 29, which was previously reported in the Malawi cohort.
Conclusions:
This study defines the molecular characteristics of ESCC in Tanzania, and enriches the Eastern African dataset, with findings of overall similarities but also some heterogeneity across two unique sites.
Impact:
Despite a high burden of ESCC in Eastern Africa, investigations into the genomics in this region are nascent. This represents the largest comprehensive genomic analysis ESCC from sub-Saharan Africa to date.
Data from Changes in Geographic Variation and Socioeconomic Inequalities in Esophageal Cancer Mortality in China, 1973–2017
Authors: Ran Xianhui , Zheng Rongshou , Zeng Hongmei , Zhang Siwei , Sun Kexin , Han Bingfeng , Wang Shaoming , Chen Ru , Li Li , Wei Wenqiang , He Jie
Published: October 2023

AbstractBackground:
Geographic variability in esophageal cancer has been reported in China, but data are lacking at the local level. We aimed to investigate changes in disparities in esophageal cancer–related mortality among Chinese counties and whether county-level socioeconomic status was associated with this variation.
Methods:
We used data from a nationwide survey and population-based cancer registries to calculate esophageal cancer–related mortality rates for 782 Chinese counties for the periods of 1973–1975 and 2015–2017. We performed hotspot analysis to identify spatial clusters. We used a multivariable negative binomial regression model to estimate the associations between county-level socioeconomic factors and mortality.
Results:
From 1973–1975 to 2015–2017, the age-standardized esophageal cancer–related mortality rate decreased from 27 to 8 per 100,000 person-years in China. By county, 577 (74%) of 782 counties experienced decreasing mortality. Geographic disparities in mortality substantially narrowed, with the gap in mortality rates between 90th and 10th percentile counties decreasing from 55 per 100,000 person-years in 1973–1975 to 16 in 2015–2017. However, clusters of elevated rates persisted across north-central China. Rurality [adjusted mortality rate ratio (MRR) 1.15; 95% confidence interval (CI), 1.10–1.21], per capita gross domestic product (adjusted MRR, 0.95; 95% CI, 0.91–0.98), and percentage of people with a high-school diploma (adjusted MRR, 0.86; 95% CI, 0.84–0.87) in a county were significantly associated esophageal cancer–related mortality rates.
Conclusions:
China has made substantial progress in reducing esophageal cancer–related mortality and disparities, but the intercounty differences remain large.
Impact:
Continued efforts are needed to address the geographical and socioeconomic disparities in esophageal cancer.
Data from Urine pH and Risk of Bladder Cancer in Northern New England
Authors: Fischer Alexander H. , Wong Jason YY. , Baris Dalsu , Koutros Stella , Karagas Margaret R. , Schwenn Molly , Johnson Alison , Alguacil Juan , Silverman Debra T. , Rothman Nathaniel
Published: October 2023

Abstract
Background:
Acidic urine pH is associated with rapid hydrolysis of N-glucuronide conjugates of aromatic amines into metabolites that may undergo metabolism in the bladder lumen to form mutagenic DNA adducts. We previously reported that consistently acidic urine was associated with increased bladder cancer risk in a hospital-based case-control study in Spain. Here, we conducted a separate study in northern New England to replicate these findings.
Methods:
In a large, population-based case-control study conducted in Maine, New Hampshire, and Vermont, we examined bladder cancer risk in relation to consistent urine pH, measured twice daily by participants over four consecutive days using dipsticks. In parallel, we collected spot urine samples and conducted laboratory measurements of urinary acidity using a pH meter. Unconditional logistic regression was used to estimate associations, adjusting for age, gender, race, Hispanic status, and state. Analyses were further stratified by smoking status.
Results:
Among 616 urothelial carcinoma cases and 897 controls, urine pH consistently≤6.0 was associated with increased bladder cancer risk (Odds Ratio(OR)=1.27; 95% Confidence Interval(CI)=1.02-1.57), with the effect limited to ever-smokers. These findings were supported by analyses of a spot urine, with statistically significant exposure-response relationships for bladder cancer risk overall (p-trend=5.1x10-3) and among ever-smokers (p-trend=1.2x10-3).
Conclusions:
Consistent with a previous study in Spain, our findings suggest that acidic urine pH is associated with increased bladder cancer risk.
Impact:
Our findings align with experimental results showing that acidic urine pH, which is partly modifiable by lifestyle factors, is linked to hydrolysis of acid-labile conjugates of carcinogenic aromatic amines.
Data from Genome-scale methylation analysis identifies immune profiles and age acceleration associations with bladder cancer outcomes
Authors: Chen Ji-Qing , Salas Lucas A. , Wiencke John K. , Koestler Devin C. , Molinaro Annette M. , Andrew Angeline S. , Seigne John D. , Karagas Margaret R. , Kelsey Karl T. , Christensen Brock C.
Published: October 2023

Abstract
Background: Immune profiles have been associated with bladder cancer outcomes and may have clinical applications for prognosis. However, associations of detailed immune cell subtypes with patient outcomes remain underexplored and may contribute crucial prognostic information for better managing bladder cancer recurrence and survival.

Methods: Bladder cancer case peripheral blood DNA methylation was measured using the Illumina HumanMethylationEPIC array. Extended cell-type deconvolution quantified twelve immune cell-type proportions, including memory, naïve T and B cells, and granulocyte subtypes. DNA methylation clocks determined biological age. Cox proportional hazard models tested associations of immune cell profiles and age acceleration with bladder cancer outcomes. The partDSA algorithm discriminated 10-year overall survival groups from clinical variables and immune cell profiles, and a semi-supervised recursively partitioned mixture model with DNA methylation data was applied to identify a classifier for 10-year overall survival.

Results: Higher CD8T memory cell proportions were associated with better overall survival (HR=0.95, 95% CI=0.93-0.98), while higher NLR (HR=1.36, 95% CI=1.23-1.50), CD8T naïve (HR=1.21, 95% CI=1.04-1.41), neutrophil (HR=1.04, 95% CI=1.03-1.06) proportions, and age acceleration (HR =1.06, 95% CI=1.03-1.08) were associated with worse overall survival in bladder cancer patients. partDSA and SS-RPMM classified five groups of subjects with significant differences in overall survival.

Conclusions: We identified associations between immune cell subtypes and age acceleration with bladder cancer outcomes.

Impact: The findings of this study suggest that bladder cancer outcomes are associated with specific methylation-derived immune cell-type proportions and age acceleration, and these factors could be potential prognostic biomarkers.