bluuebunny/crossref_metadata_2025 huggingface dataset:
Quality of skeletal muscles during allogeneic stem-cell transplantation: a pilot study
Authors: Maeda Yusaku , Takao Shoichiro , Morita Shiori , Kondo Shin , Yamashita Michiko , Sumitani Ryohei , Oura Masahiro , Sogabe Kimiko , Takahashi Mamiko , Fujii Shiro , Harada Takeshi , Miki Hirokazu , Abe Masahiro , Nakamura Shingen
Published: October 2024

Objectives

This study investigated the muscle fat fraction (FF) and muscle-related parameters before and after allogeneic hematopoietic stem cell transplantation (HSCT).

Methods

Fat and water signals were derived from the in-phase and out-of-phase MR signal intensities of the pelvis and thigh using the two-point Dixon technique. They were analysed using Synapse Vincent, and muscle quality was evaluated using the FF. The muscle mass was assessed by measuring the thigh and gluteal muscle areas using a manual trace on the MR image. The association between the muscle FF and clinical data was retrospectively determined.

Results

This study included 11 patients (6 males). Their mean age was 42.7 years, and eight had leukaemia. Eight were assessed at a mean of 65.4 days post-HSCT. The hip and thigh skeletal muscle FFs were not significantly different during HSCT. The grip and lower limb muscle strengths decreased significantly after HSCT. Patients with low FFs before transplantation tended to lose muscle strength, and the increase in FF and decrease of muscle strength were correlated.

Conclusions

Muscle strength and quantity decrease during the early phase after HSCT, especially in patients with low FF muscles. Therefore, interventions based on muscle quality and quantity are essential.
Glucagon-like peptide-1 receptor agonists may benefit cardiopulmonary outcomes in patients with COPD
Authors: Yen Fu-Shun , Hsu Chih-Cheng , Wei James Cheng-Chung , Tsai Fuu-Jen , Huang Yuhan , Yu Teng-Shun , Hwu Chii-Min
Published: October 2024

Background

Clinical studies have shown that glucagon-like peptide-1 receptor agonists (GLP-1 RA) can have beneficial effects on cardiopulmonary function. We conducted this longitudinal cohort study to compare the risk of cardiopulmonary outcomes and mortality between GLP-1 RA use and no use in patients with type 2 diabetes (T2D) and chronic obstructive pulmonary disease (COPD).

Methods

The study identified 8060 matched GLP-1 RA users and non-users from Taiwan’s National Health Insurance Research Database from 1 January 2008 to 31 December 2019. Cox proportional hazards models were used to determine the risk of cardiopulmonary outcomes between GLP-1 RA users and non-users.

Results

The mean follow-up time was 2.51 and 2.46 years for GLP-1 RA users and non-users, respectively. In the matched cohorts, GLP-1 RA users had a significantly lower risk of mortality (adjusted HR (aHR) 0.46, 95% CI 0.38 to 0.56), cardiovascular events (aHR 0.73, 95% CI 0.65 to 0.82), non-invasive positive pressure ventilation (aHR 0.66, 95% CI 0.47 to 0.93), invasive mechanical ventilation (aHR 0.64, 95% CI 0.51 to 0.8) and bacterial pneumonia (aHR 0.76, 95% CI 0.65 to 0.88) than GLP-1 RA non-users. The subsequent analyses for various subgroup and medication duration also showed that GLP-1 RA was associated with a significantly lower risk of mortality, cardiovascular events, ventilation support and bacterial pneumonia than non-GLP-1 RA.

Conclusion

This nationwide cohort study showed that GLP-1 RA had a lower risk of cardiopulmonary outcomes and all-cause mortality than non-GLP-1 RA in patients with T2D and COPD. GLP-1 RA may help manage diabetes in people with COPD.
Comparison of surface layers responses under heavy truck loadings on new and rehabilitated pavement with different interface bond conditions
Authors: Al Bacha Marina , Nguyen Mai-Lan , Hornych Pierre , Chupin Olivier , Blanc Juliette , Chapeleau Xavier
Published: October 2024

The integrity and functionality of road pavements are vital for ensuring safe and efficient transportation networks. However, surface layers are prone to various forms of deterioration. This study investigates the responses of two pavement structures—one newly constructed and one rehabilitated—under traffic loading, through experimental tests conducted on an accelerated pavement testing facility and numerical simulations using the Viscoroute©2.0 software. Focus is placed on surface layer behaviour, with an emphasis on understanding the behaviour of interfaces between the asphalt layers. The findings show that the new pavement structure exhibits good bonding and continuous strain distribution, while the rehabilitated pavement structure exhibits partial sliding at the interface and strain discontinuity. For the new pavement structure, the strains are well predicted using a bonded interface, while for the rehabilitated pavement structure, the strains are predicted using a thin elastic interface layer with a low elastic modulus.
An Efficient Clustered N-Tier Computing Scheme for Large-Scale IoT-Enabled Healthcare Environments
Authors: Alblehai Fahad , Gafar Manal , Said Omar
Published: October 2024

Recently, Internet of Things (IoT) technology has become popular and applicable in different fields. The exchangeable data through IoT systems are extremely huge. This poses a great challenge in constructing a scalable and reliable computing scheme for IoT environments. Therefore, an efficient computing scheme for an IoT-enabled healthcare environment was proposed in this paper. The computing scheme idea was based on the use of cloud, fog, mist and edge computing strategies after dividing their resources into N-tiers. For easy management, these tiers were clustered depending on their geographical distribution. The number of tiers for each computing strategy dynamically changed depending on the computing load. Each tier had its own capabilities. Therefore, selecting a computing strategy and its tier was achieved regarding the data requirements and the specs of each computing resource. To evaluate the proposed computing scheme, a network simulator package (NS-3) was used to construct a simulation for the IoT-enabled healthcare environment and the computing scheme. Most simulation results of our computing scheme were compared with the cloud/fog/mist, cloud/fog and cloud computing schemes. Finally, the simulation results proved that the proposed computing scheme outperformed the performance of other traditional computing schemes regarding the following performance metrics: Delay, utilization, energy consumption, beneficial users and different healthcare organization complexities.
Influence of Spatially Varied Soil Property on Train-Induced Soil-to-Column Vibration Transmission
Authors: Tu Desi , Tao Ziyu , Zheng Bokai , Zou Chao , Hu Jiahao
Published: October 2024

The proximity of residential areas to traffic corridors has raised concerns among researchers regarding train-induced vibrations. Experimental studies have consistently shown variations in train-induced vibrations, which can be attributed to uncertainties and randomness in both the vibration source and propagation path. This study aims to investigate the influence factors and quantify their contributions to train-induced vibration variations through a comprehensive field measurement campaign and numerical simulations using random finite element models. During the field measurements, vibrations were recorded at the ground surface and the column base for a total of 53 passbys of the same type of metro train on parallel rail lines. Variations in train-induced vibrations caused by the source-to-receiver distance and spatially varied soil properties were analyzed and compared. Specifically, the investigation focused on the spatial variation of soil properties including elastic modulus, density and damping ratio in the topsoil and the second layer of clay, while simultaneously considering the influence of spatial variations of all three soil properties on the transmission of train-induced vibrations from the surface soil to the structural columns. Understanding these variations is crucial for the probabilistic assessment of building serviceability during train passbys. The findings of this research provide valuable insights for probabilistic prediction and evaluation of building vibration comfort.
Experiments for the Assessment of the Probabilistic Multistage Algorithm for Damage Detection in Flat and Curved CFRP Panels
Authors: Perfetto Donato , Polverino Antonio , De Luca Alessandro , Lamanna Giuseppe
Published: October 2024

The Probabilistic Multistage (PM) algorithm was developed by authors for identifying and localizing damages in isotropic plates. More specifically, PM algorithm consists of a fully automated probabilistic damage imaging methodology based on ultrasonic guided wave propagation and a 5-sensor array working in a pitch-catch approach. The algorithm processes the gathered data in three steps to identify key features associated with damage. The aim of this work is to assess the effectiveness of the PM algorithm on more complex structures. Specifically, the study investigates three cases of study, made of Carbon Fiber Reinforced Plastic (CFRP) composite, characterized by different geometries and layups. The algorithm is initially tested on panels with artificial damage in the form of a Teflon disk located in a specific location between the middle laminae of the panels, which is used to replicate the effect of delamination. In order to expand the experimental dataset without incurring additional costs or waste, new damage conditions are simulated by adding masses on the upper surface of the panels. Each plate is investigated considering three different damage sizes and 16 different damage locations. The proposed algorithm successfully detects damages both within and outside the sensor network. The PM algorithm produces a clear damage positioning map and a positioning (probabilistic field) range for the identified damage. This information can be used to assist operators in conducting inspections more efficiently by focusing on the highlighted areas, which may potentially lead to reduced maintenance and repair expenses.
Solving for the Thermal Vibration Behaviors of Functionally Graded Stepped Conical Curved Plates with Point Connection Conditions
Authors: Guo Chenchen , Wang Qingshan , Liu Tao , Qin Bin
Published: October 2024

This paper proposed a degree-of-freedom reduction model for the rapid and unified solution of the modal and steady-state response behavior of functionally graded stepped conical curved plates with point connections under thermal environments. Within the framework of the first-order shear deformation theory, the two-dimensional spectral Chebyshev method and the fixed interface modal synthesis method were combined to derive the degree-of-freedom reduction model for functionally graded conical curved plates under thermal environments. Each reduction model was assembled considering external load excitations. Virtual springs were used to equivalently handle the coupling interface forces and point connection interface forces, further establishing a thermal vibration response analysis model for functionally graded stepped conical curved plates with point connections. In numerical examples, this degree-of-freedom reduction model was compared with experimental results and overall finite element results, validating the accuracy of the model and the advantages of rapid solution. Additionally, this degree-of-freedom reduction model was applied to quickly analyze the effects of material parameters and point connection parameters on the thermal steady-state response of the structure, providing a theoretical basis for the environmental adaptability design, verification, and evaluation of such structures.
Engel condition of composition of generalized derivations in prime rings
Authors: Dhara Basudeb
Published: October 2024

Let [Formula: see text] be a prime ring, [Formula: see text] a noncentral Lie ideal of [Formula: see text] and [Formula: see text] the extended centroid of [Formula: see text], where [Formula: see text] is the Utumi quotient ring of [Formula: see text]. Suppose that [Formula: see text] are two nonzero generalized derivations of [Formula: see text]. Recently, [Dhara et al., Engel conditions of generalized derivations on left ideals and Lie ideals in prime rings, Comm. Algebra 48(1) (2020) 154–167] studied the case [Formula: see text] for all [Formula: see text], where [Formula: see text] is a derivation (which is independent of [Formula: see text]) and [Formula: see text] fixed positive integers and obtained the structure of [Formula: see text] and the ring [Formula: see text]. [Liu, An Engel condition with two generalized derivations on Lie ideals of prime rings, J. Algebra and Its Applications, 22(5) (2023) 2350115] studied a similar identity replacing derivation [Formula: see text] with another generalized derivation [Formula: see text]. Recently, [Pandey, Pair of generalized derivations on Lie ideals in prime rings, Asian-European J. Math. 16(1) (2022) 2350002] studied an identity considering composition of mapping, that is [Formula: see text] for all [Formula: see text].

In this paper, we consider the situation containing composition of mappings as well as Engel condition, that is, [Formula: see text] for all [Formula: see text], where [Formula: see text] are fixed integers and then obtain the nature of mappings [Formula: see text], [Formula: see text] and the ring [Formula: see text].
Contrastive Clustering Learning for Multi-Behavior Recommendation
Authors: Lan Wei , Zhou Guoxian , Chen Qingfeng , Wang Wenguang , Pan Shirui , Pan Yi , Zhang Shichao
Published: October 2024

Increasing multiple behavior recommendation models have achieved great successes. However, many models do not consider commonalities and differences between behaviors and data sparsity of the target behavior. This article proposes a novel multi-behavior recommendation model based on contrastive clustering learning (MBRCC). Specifically, the graph convolutional network (GCN) is employed to obtain the embeddings of users and items, respectively. Then, three kinds of tasks (including behavior-level embedding, instance-level embedding, and cluster-level embedding) are designed to optimize the embeddings of users and items. In behavior-level embedding, we design an adaptive parameter learning strategy to analyze the impact of auxiliary behaviors on the target behavior. Then, the embeddings of users for each behavior are weighted to obtain the final embeddings of users. In instance-level embedding, we employ contrastive learning to analyze the instances of user and item for mitigating the issue of data sparsity. In cluster-level embedding, we design a new cluster contrastive learning method to capture the similarity between groups of user and item. Finally, we combine these three tasks to improve the quality of the embeddings of users and items. We conduct extensive experiments on three real-world datasets and experimental results indicate that the MBRCC remarkably outperforms numerous existing recommendation models.
Spatial Transcriptomics of the Respiratory System
Authors: Megas Stathis , Wilbrey-Clark Anna , Maartens Aidan , Teichmann Sarah A. , Meyer Kerstin B.
Published: October 2024

Over the last decade, single-cell genomics has revealed remarkable heterogeneity and plasticity of cell types in the lungs and airways. The challenge now is to understand how these cell types interact in three-dimensional space to perform lung functions, facilitating airflow and gas exchange while simultaneously providing barrier function to avoid infection. An explosion in novel spatially resolved gene expression technologies, coupled with computational tools that harness machine learning and deep learning, now promise to address this challenge. Here, we review the most commonly used spatial analysis workflows, highlighting their advantages and limitations, and outline recent developments in machine learning and artificial intelligence that will augment how we interpret spatial data. Together these technologies have the potential to transform our understanding of the respiratory system in health and disease, and we showcase studies in lung development, COVID-19, lung cancer, and fibrosis where spatially resolved transcriptomics is already providing novel insights.
Statistics in Phonetics
Authors: Tavakoli Shahin , Matteo Beatrice , Pigoli Davide , Chodroff Eleanor , Coleman John , Gubian Michele , Renwick Margaret E.L. , Sonderegger Morgan
Published: October 2024

Phonetics is the scientific field concerned with the study of how speech is produced, heard, and perceived. It abounds with data, such as acoustic speech recordings, neuroimaging data, or articulatory data. In this article, we provide an introduction to different areas of phonetics (acoustic phonetics, sociophonetics, speech perception, articulatory phonetics, speech inversion, sound change, and speech technology), an overview of the statistical methods for analyzing their data, and an introduction to the signal processing methods commonly applied to speech recordings. A major transition in the statistical modeling of phonetic data has been the shift from fixed effects to random effects regression models, the modeling of curve data (for instance, via generalized additive mixed models or functional data analysis methods), and the use of Bayesian methods. This shift has been driven in part by the increased focus on large speech corpora in phonetics, which has arisen from machine learning methods such as forced alignment. We conclude by identifying opportunities for future research.
Diagnostic Accuracy of Screening Contrast-enhanced Mammography for Women with Extremely Dense Breasts at Increased Risk of Breast Cancer
Authors: Nissan Noam , Comstock Christopher E. , Sevilimedu Varadan , Gluskin Jill , Mango Victoria L. , Hughes Mary , Ochoa-Albiztegui R. Elena , Sung Janice S. , Jochelson Maxine S.
Published: October 2024

Compared with low-energy imaging, contrast-enhanced mammography depicted 11 additional cancers in asymptomatic women with extremely dense breasts and showed higher sensitivity but lower specificity, with specificity improving at follow-up examinations.
Detecting Cellular Microstructural Changes of Liver Fibrosis with Time-Dependent Diffusion MRI
Authors: Zhang Lijie , Long Xi , Chen Leqing , Han Xiaoyu , Zhang Xiaoxiao , Sun Peng , Yang Yuhan , Fan Jun , Wang Jiazheng , Lei Ziqiao , Liang Bin , Liu Xiaoming , Shi Heshui
Published: October 2024

Time-dependent diffusion MRI can be used to effectively evaluate liver fibrosis grading, potentially enabling noninvasive assessment of treatment efficacy and facilitating personalized clinical treatment.
Formal degree programs in physiology promote careers of clinical scientists and benefit basic science departments
Authors: Joshua Irving , Polk Hiram C. , Macleod Anne , Eichenberger R. Maurice , Gardner Sarah A. , Schuschke Dale , Galandiuk Susan
Published: October 2024

Physiologists may play critical roles in the development of clinician-scientists who aspire to an academic career. The complexity of contemporary biomedical science and economic matters regarding postgraduate education pose real conundrums. We report a more than 22-year follow-up of surgical trainees pursuing bench laboratory science experience through a collaboration between a physiology postgraduate program and a surgical researcher program within a single public medical school. The sources and resources include selection, funding, physiology classroom work, and laboratory studies with personal involvement by faculty that have seldom been recorded, especially with longer term career outcomes. These selected PhD candidates have subsequently pursued several lines of activity, many with distinguished careers and major influences upon future generations of academic surgeons.
A Review of Electronic Early Warning Systems for Acute Kidney Injury
Authors: Wang Xiangxiang , Bian Zhixiang , Zhu Rui , Chen Shunjie
Published: October 2024

Acute kidney injury (AKI) is characterized by impaired renal function that can result in irreversible severe renal impairment or lifelong dependence on renal replacement therapy in some cases. Early intervention can significantly slow down the progression of AKI and reduce mortality. In recent years, electronic early warning systems for patients with AKI have been gaining attention as a potential clinical decision‐support option. This paper presents a review of the application of electronic early warning systems for AKI from four aspects: development process, types of output, influencing factors, and system evaluation.
Three‐Dimensional Numerical Simulation of Fracture Extension in Conglomerate Fracturing Considering Pore‐Fracture Seepage and Study of Influencing Factors
Authors: Xu Zehao , Zhao Haiyang , Liu Xiangjun , Liang Lixi , Luo Pandeng
Published: October 2024

The nonhomogeneity of conglomerate in terms of organization and the complexity of fracture extension make the design and effective implementation of fracturing in conglomerate reservoirs challenging. Considering the limitations of physical experiments and two‐dimensional (2D) numerical modeling, this paper adopts the continuum‐discontinue element method (CDEM) to carry out numerical simulation of three‐dimensional (3D) conglomerate fracturing considering pore‐fracture seepage. By introducing multiple parameters to quantify the correlation between fracture geometry, fracture complexity, and damage mode, the evolution mechanism of fracture morphology under the influence of multiple factors is systematically investigated. The results show that the numerical simulation experiments can control the variables well, but the random distribution of gravel leads to the unpredictability of fracture extension, and the concluding patterns obtained still show large fluctuations. The high permeability of the gravel promotes the development of gravel‐penetrating fractures but has less effect on the overall morphology of the fractures. High‐strength gravel promotes the development of branching fractures in the initiation phase, which acts as a barrier to expanding fractures, and the most complex fracture development occurs when the gravel strength is approximately 4–5 times that of the matrix. In the weakly cemented state, fracture development around the gravel contributes to the shear failure of the conglomerate, but the strength of the cemented interface has no obvious control on the overall fracture morphology. The correlation between gravel content and conglomerate damage mode is significant, with the highest degree of fracture complexity occurring when the gravel content is approximately 30%. Stress differential is the most significant controlling factor affecting fracture morphology, followed by minimum principal stress. When the stress difference reaches 8 MPa, the fracture morphology begins to stabilize, and too high a stress difference will cause the phenomenon that the fracture stops expanding, affecting the fracturing effect. A high level of minimum stress promotes tensile failure in conglomerate, and the scale and complexity of fracture decrease. High injection displacement promotes branch fracture development and reduces the effect of in situ stress on fracture extension, and too high a displacement leads to inhibition of main fracture development.
Supplementary Table 1 from A Prime-Boost Vaccination Approach Induces Lung Resident Memory CD8+ T Cells Derived from Central Memory T Cells That Prevent Tumor Lung Metastasis
Authors: Xu Haoran , Yue Ming , Zhou Runhong , Wang Pui , Wong Michael Yik-Chun , Wang Jinlin , Huang Huarong , Chen Bohao , Mo Yufei , Tam Rachel Chun-Yee , Zhou Biao , Du Zhenglong , Huang Haode , Liu Li , Tan Zhiwu , Yuen Kwok-Yung , Song Youqiang , Chen Honglin , Chen Zhiwei
Published: October 2024

qPCR primer list
Supplementary Figure 7 from A Prime-Boost Vaccination Approach Induces Lung Resident Memory CD8+ T Cells Derived from Central Memory T Cells That Prevent Tumor Lung Metastasis
Authors: Xu Haoran , Yue Ming , Zhou Runhong , Wang Pui , Wong Michael Yik-Chun , Wang Jinlin , Huang Huarong , Chen Bohao , Mo Yufei , Tam Rachel Chun-Yee , Zhou Biao , Du Zhenglong , Huang Haode , Liu Li , Tan Zhiwu , Yuen Kwok-Yung , Song Youqiang , Chen Honglin , Chen Zhiwei
Published: October 2024

Characterization of circulating genes across tissues and vaccination groups
Raw data from NAT10 Phase Separation Regulates YTHDF1 Splicing to Promote Gastric Cancer Progression
Authors: Liu Songyi , Lin Chunlin , Lin Xiang , Lin Penghang , He Ruofan , Pan Xiaoyu , Lin Yan , Ye Jianxin , Zhu Guangwei
Published: October 2024

Raw data
Figure S1-S17 from NAT10 Phase Separation Regulates YTHDF1 Splicing to Promote Gastric Cancer Progression
Authors: Liu Songyi , Lin Chunlin , Lin Xiang , Lin Penghang , He Ruofan , Pan Xiaoyu , Lin Yan , Ye Jianxin , Zhu Guangwei
Published: October 2024

Supplementary Figures
Supplementary Table 1 from CCN6 Suppresses Metaplastic Breast Carcinoma by Antagonizing Wnt/β-Catenin Signaling to Inhibit EZH2-Driven EMT
Authors: Gonzalez Maria E. , Brophy Bryce , Eido Ahmad , Leonetti Adele E. , Djomehri Sabra I. , Augimeri Giuseppina , Carruthers Nicholas J. , Cavalcante Raymond G. , Giordano Francesca , Andò Sebastiano , Nesvizhskii Alexey I. , Fearon Eric R. , Kleer Celina G.
Published: October 2024

This is a supplementary Table
Table S1 from Hypoxic Memory Mediates Prolonged Tumor-Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression
Authors: Iriondo Oihana , Mecenas Desirea , Li Yilin , Chin Christopher R. , Thomas Amal , Moriarty Aidan , Marker Rebecca , Wang Yiru J. , Hendrick Haley , Amzaleg Yonatan , Ortiz Veronica , MacKay Matthew , Dickerson Amber , Lee Grace , Harotoonian Sevana , Benayoun Bérénice A. , Smith Andrew , Mason Christopher E. , Roussos Torres Evanthia T. , Klotz Remi , Yu Min
Published: October 2024

List of genes downregulated in BRx68 cells grown in hypoxia for 8 weeks
Data from Proteomic Profiling of Serum Extracellular Vesicles Identifies Diagnostic Signatures and Therapeutic Targets in Breast Cancer
Authors: Xu Ganfei , Huang Rui , Wumaier Reziya , Lyu Jiacheng , Huang Minjing , Zhang Yaya , Chen Qingjian , Liu Wenting , Tao Mengyu , Li Junjian , Tao Zhonghua , Yu Bo , Xu Erxiang , Wang Lingfeng , Yu Guoying , Gires Olivier , Zhou Lei , Zhu Wei , Ding Chen , Wang Hongxia
Published: October 2024

Abstract
Analysis of extracellular vesicles (EV) is a promising noninvasive liquid biopsy approach for breast cancer detection, prognosis, and therapeutic monitoring. A comprehensive understanding of the characteristics and proteomic composition of breast cancer–specific EVs from human samples is required to realize the potential of this strategy. In this study, we applied a mass spectrometry–based, data-independent acquisition proteomic approach to characterize human serum EVs derived from patients with breast cancer (n = 126) and healthy donors (n = 70) in a discovery cohort and validated the findings in five independent cohorts. Examination of the EV proteomes enabled the construction of specific EV protein classifiers for diagnosing breast cancer and distinguishing patients with metastatic disease. Of note, TALDO1 was found to be an EV biomarker of distant metastasis of breast cancer. In vitro and in vivo analysis confirmed the role of TALDO1 in stimulating breast cancer invasion and metastasis. Finally, high-throughput molecular docking and virtual screening of a library consisting of 271,380 small molecules identified a potent TALDO1 allosteric inhibitor, AO-022, which could inhibit breast cancer migration in vitro and tumor progression in vivo. Together, this work elucidates the proteomic alterations in the serum EVs of breast cancer patients to guide the development of improved diagnosis, monitoring, and treatment strategies.

Significance: Characterization of the proteomic composition of circulating extracellar vesicles in breast cancer patients identifies signatures for diagnosing primary and metastatic tumors and reveals tumor-promoting cargo that can be targeted to improve outcomes.
A Prime-Boost Vaccination Approach Induces Lung Resident Memory CD8+ T Cells Derived from Central Memory T Cells That Prevent Tumor Lung Metastasis
Authors: Xu Haoran , Yue Ming , Zhou Runhong , Wang Pui , Wong Michael Yik-Chun , Wang Jinlin , Huang Huarong , Chen Bohao , Mo Yufei , Tam Rachel Chun-Yee , Zhou Biao , Du Zhenglong , Huang Haode , Liu Li , Tan Zhiwu , Yuen Kwok-Yung , Song Youqiang , Chen Honglin , Chen Zhiwei
Published: October 2024

Memory T cells play a key role in immune protection against cancer. Vaccine-induced tissue-resident memory T (TRM) cells in the lung have been shown to protect against lung metastasis. Identifying the source of lung TRM cells can help to improve strategies, preventing tumor metastasis. Here, we found that a prime-boost vaccination approach using intramuscular DNA vaccine priming, followed by intranasal live-attenuated influenza-vectored vaccine (LAIV) boosting induced higher frequencies of lung CD8+ TRM cells compared with other vaccination regimens. Vaccine-induced lung CD8+ TRM cells, but not circulating memory T cells, conferred significant protection against metastatic melanoma and mesothelioma. Central memory T (TCM) cells induced by the DNA vaccination were major precursors of lung TRM cells established after the intranasal LAIV boost. Single-cell RNA sequencing analysis indicated that transcriptional reprogramming of TCM cells for differentiation into TRM cells in the lungs started as early as day 2 post the LAIV boost. Intranasal LAIV altered the mucosal microenvironment to recruit TCM cells via CXCR3-dependent chemotaxis and induced CD8+ TRM-associated transcriptional programs. These results identified TCM cells as the source of vaccine-induced CD8+ TRM cells that protect against lung metastasis.

Significance: Prime-boost vaccination shapes the mucosal microenvironment and reprograms central memory T cells to generate lung resident memory T cells that protect against lung metastasis, providing insights for the optimization of vaccine strategies.
Supplementary Table S4 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Clinical features of the patients included in the SU2C identification cohort.
Supplementary Table S2 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

List of up-regulated genes identified by differential gene expression when comparing NSCLC with pathogenic KEAP1-NFE2L2 mutations (OncoKB) versus wild-type samples in the TCGA NSCLC study.
Supplementary Table S1 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

List of up-regulated genes identified by differential gene expression when comparing KEAP1-NFE2L2-mutant and wild-type NSCLC in the TCGA study.
Supplementary Figure S5 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 5. KEAPness and the tumor immune microenvironment (TIME) in the TCGA NSCLC study
Supplementary Figure S9 from Targeting the Dendritic Cell-Secreted Immunoregulatory Cytokine CCL22 Alleviates Radioresistance
Authors: Bugno Jason , Wang Liangliang , Yu Xianbin , Cao Xuezhi , Wang Jiaai , Huang Xiaona , Yang Kaiting , Piffko Andras , Chen Katherine , Luo Stephen Y. , Naccasha Emile , Hou Yuzhu , Fu Sherry , He Chuan , Fu Yang-xin , Liang Hua L. , Weichselbaum Ralph R.
Published: October 2024

Supplementary Figure S9. Changes in gene expression associated with ISG + cDC2 among sequencing results
Supplementary Figure S7 from Targeting the Dendritic Cell-Secreted Immunoregulatory Cytokine CCL22 Alleviates Radioresistance
Authors: Bugno Jason , Wang Liangliang , Yu Xianbin , Cao Xuezhi , Wang Jiaai , Huang Xiaona , Yang Kaiting , Piffko Andras , Chen Katherine , Luo Stephen Y. , Naccasha Emile , Hou Yuzhu , Fu Sherry , He Chuan , Fu Yang-xin , Liang Hua L. , Weichselbaum Ralph R.
Published: October 2024

Supplementary Figure S7. Characterization of tumor cDC populations in Batf3-/- mice and effect of αCCL22 or Treg depletion on the radiation response
Supplementary Figure S4 from Targeting the Dendritic Cell-Secreted Immunoregulatory Cytokine CCL22 Alleviates Radioresistance
Authors: Bugno Jason , Wang Liangliang , Yu Xianbin , Cao Xuezhi , Wang Jiaai , Huang Xiaona , Yang Kaiting , Piffko Andras , Chen Katherine , Luo Stephen Y. , Naccasha Emile , Hou Yuzhu , Fu Sherry , He Chuan , Fu Yang-xin , Liang Hua L. , Weichselbaum Ralph R.
Published: October 2024

Supplementary Figure S4. Human expression of FOXP3 with RT and correlation with a Human DC_Ccl22 Homolog Score among TCGA cohorts
Supplemental Figure S2 from Genomic Profiling to Contextualize the Results of Intervention for Smoldering Multiple Myeloma
Authors: Kazandjian Dickran , Diamond Benjamin , Papadimitriou Marios , Hill Elizabeth , Sklavenitis-Pistofidis Romanos , Ziccheddu Bachisio , Blaney Patrick , Chojnacka Monika , Durante Michael , Maclachlan Kylee , Young Ryan , Usmani Saad , Davies Faith , Getz Gad , Ghobrial Irene , Korde Neha , Morgan Gareth , Maura Francesco , Landgren Ola
Published: October 2024

Supplemental Figure S2. Mutational Signatures Landscape of NDMM.
Supplementary Tables S1-S3 from Early Detection of Malignant and Premalignant Peripheral Nerve Tumors Using Cell-Free DNA Fragmentomics
Authors: Sundby R. Taylor , Szymanski Jeffrey J. , Pan Alexander C. , Jones Paul A. , Mahmood Sana Z. , Reid Olivia H. , Srihari Divya , Armstrong Amy E. , Chamberlain Stacey , Burgic Sanita , Weekley Kara , Murray Béga , Patel Sneh , Qaium Faridi , Lucas Andrea N. , Fagan Margaret , Dufek Anne , Meyer Christian F. , Collins Natalie B. , Pratilas Christine A. , Dombi Eva , Gross Andrea M. , Kim AeRang , Chrisinger John S.A. , Dehner Carina A. , Widemann Brigitte C. , Hirbe Angela C. , Chaudhuri Aadel A. , Shern Jack F.
Published: October 2024

Supplemental Table 1. Participant characteristics. Supplemental Table 2. MPNST patient characteristics. Supplemental Table 3. Details of all sequencing libraries in this study.
Supplemental Table 1 from Abiraterone, Olaparib, or Abiraterone + Olaparib in First-Line Metastatic Castration-Resistant Prostate Cancer with DNA Repair Defects (BRCAAway)
Authors: Hussain Maha , Kocherginsky Masha , Agarwal Neeraj , Adra Nabil , Zhang Jingsong , Paller Channing J. , Picus Joel , Reichert Zachery R. , Szmulewitz Russell Z. , Tagawa Scott T. , Kuzel Timothy M. , Bazzi Latifa A. , Daignault-Newton Stephanie , Whang Young E. , Dreicer Robert , Stephenson Ryan D. , Rettig Matthew B. , Shevrin Daniel , Gerke Travis , Chinnaiyan Arul M. , Antonarakis Emmanuel S.
Published: October 2024

Supplemental Table 1. Treatment Modifications.
Supplemental Figure 2 from Abiraterone, Olaparib, or Abiraterone + Olaparib in First-Line Metastatic Castration-Resistant Prostate Cancer with DNA Repair Defects (BRCAAway)
Authors: Hussain Maha , Kocherginsky Masha , Agarwal Neeraj , Adra Nabil , Zhang Jingsong , Paller Channing J. , Picus Joel , Reichert Zachery R. , Szmulewitz Russell Z. , Tagawa Scott T. , Kuzel Timothy M. , Bazzi Latifa A. , Daignault-Newton Stephanie , Whang Young E. , Dreicer Robert , Stephenson Ryan D. , Rettig Matthew B. , Shevrin Daniel , Gerke Travis , Chinnaiyan Arul M. , Antonarakis Emmanuel S.
Published: October 2024

Supplemental Figure 2. Outcomes for primary and exploratory arms.
Supplementary Figure S7 from Pharmacologic Inhibition of EIF4A Blocks NRF2 Synthesis to Prevent Osteosarcoma Metastasis
Authors: Lizardo Michael M. , Hughes Christopher , Huang Yue Z. , Shyp Taras , Delaidelli Alberto , Zhang Hai-Feng , Shaool Sol Snir , Renner Annalena F. , Burwag Farez , Sayles Leanne C. , Lee Alex G. , Sweet-Cordero Alejandro , Sorensen Poul H.
Published: October 2024

Fig. S7. CR-1-31B modulates the antioxidant response in metastatic OS cells
Supplementary Figure S11 from Pharmacologic Inhibition of EIF4A Blocks NRF2 Synthesis to Prevent Osteosarcoma Metastasis
Authors: Lizardo Michael M. , Hughes Christopher , Huang Yue Z. , Shyp Taras , Delaidelli Alberto , Zhang Hai-Feng , Shaool Sol Snir , Renner Annalena F. , Burwag Farez , Sayles Leanne C. , Lee Alex G. , Sweet-Cordero Alejandro , Sorensen Poul H.
Published: October 2024

Fig. S11. Down-modulation of NRF2 in metastatic MG63.3 cells inhibits adaptation to oxidative stress and metastatic capacity.
Supplementary Table S1 from Redirecting B7-H3.CAR T Cells to Chemokines Expressed in Osteosarcoma Enhances Homing and Antitumor Activity in Preclinical Models
Authors: Talbot Lindsay J. , Chabot Ashley , Ross Aaron B. , Beckett Alexandra , Nguyen Phuong , Fleming Andrew , Chockley Peter J. , Shepphard Heather , Wang Jian , Gottschalk Stephen , DeRenzo Christopher
Published: October 2024

Chemokine ligands and growth factors assessed by RNA-seq.
Supplementary Figure S3 from Redirecting B7-H3.CAR T Cells to Chemokines Expressed in Osteosarcoma Enhances Homing and Antitumor Activity in Preclinical Models
Authors: Talbot Lindsay J. , Chabot Ashley , Ross Aaron B. , Beckett Alexandra , Nguyen Phuong , Fleming Andrew , Chockley Peter J. , Shepphard Heather , Wang Jian , Gottschalk Stephen , DeRenzo Christopher
Published: October 2024

CXCR.B7-H3.CAR Transduced T cell data
Supplementary Table S2 from Update on Recommendations for Surveillance for Children with Predisposition to Hematopoietic Malignancy
Authors: Maese Luke D. , Wlodarski Marcin W. , Kim Sun Young , Bertuch Alison A. , Bougeard Gaelle , Chang Vivian Y. , Godley Lucy A. , Khincha Payal P. , Kuiper Roland P. , Lesmana Harry , McGee Rose B. , McReynolds Lisa J. , Meade Julia , Plon Sharon E. , Savage Sharon A. , Scollon Sarah R. , Scott Hamish S. , Walsh Michael F. , Nichols Kim E. , Porter Christopher C.
Published: October 2024

Additional resources
Supplementary Figure 9 from Colorectal Cancer Recurrence Prediction Using a Tissue-Free Epigenomic Minimal Residual Disease Assay
Authors: Nakamura Yoshiaki , Tsukada Yuichiro , Matsuhashi Nobuhisa , Murano Tatsuro , Shiozawa Manabu , Takahashi Yusuke , Oki Eiji , Goto Masahiro , Kagawa Yoshinori , Kanazawa Akiyoshi , Ohta Takashi , Ouchi Akira , Bando Hideaki , Uchigata Hiroshi , Notake Chiemi , Ikematsu Hiroaki , Yoshino Takayuki
Published: October 2024

Supplementary Figure 9. Risk of recurrence based on ctDNA detection early on adjuvant chemotherapy in patients with stage II or higher CRC.
Supplementary Figure 7 from Colorectal Cancer Recurrence Prediction Using a Tissue-Free Epigenomic Minimal Residual Disease Assay
Authors: Nakamura Yoshiaki , Tsukada Yuichiro , Matsuhashi Nobuhisa , Murano Tatsuro , Shiozawa Manabu , Takahashi Yusuke , Oki Eiji , Goto Masahiro , Kagawa Yoshinori , Kanazawa Akiyoshi , Ohta Takashi , Ouchi Akira , Bando Hideaki , Uchigata Hiroshi , Notake Chiemi , Ikematsu Hiroaki , Yoshino Takayuki
Published: October 2024

Supplementary Figure 7. Risk of recurrence based on ctDNA detection 28 days post-surgery by pathologic stage.
Supplementary Table S6 from The Innate Immune Landscape of dMMR/MSI Cancers Predicts the Outcome of Nivolumab Treatment: Results from the Drug Rediscovery Protocol
Authors: Zeverijn Laurien J. , Geurts Birgit S. , Battaglia Thomas W. , van Berge Henegouwen Jade M. , de Wit Gijs F. , Hoes Louisa R. , van der Wijngaart Hanneke , van der Noort Vincent , Roepman Paul , de Leng Wendy W.J. , Jansen Anne M.L. , Chalabi Myriam , van Herpen Carla M.L. , Devriese Lot A. , Erdkamp Frans L.G. , Labots Mariette , de Jonge Maja J.A. , Kerver Emile D. , Bins Adriaan D. , Leek Lindsay V.M. , Notohardjo Jessica C.L. , van den Eertwegh Alfonsus J.M. , Wessels Lodewyk F.A. , Verheul Henk M.W. , Gelderblom Hans , van de Haar Joris , Voest Emile E.
Published: October 2024

Supplementary Table S6. Baseline characteristics of all included patients, regardless of evaluability according to protocol definition.
Supplementary Figure 5 from Colorectal Cancer Recurrence Prediction Using a Tissue-Free Epigenomic Minimal Residual Disease Assay
Authors: Nakamura Yoshiaki , Tsukada Yuichiro , Matsuhashi Nobuhisa , Murano Tatsuro , Shiozawa Manabu , Takahashi Yusuke , Oki Eiji , Goto Masahiro , Kagawa Yoshinori , Kanazawa Akiyoshi , Ohta Takashi , Ouchi Akira , Bando Hideaki , Uchigata Hiroshi , Notake Chiemi , Ikematsu Hiroaki , Yoshino Takayuki
Published: October 2024

Supplementary Figure 5. RFI based on ctDNA detection at each surveillance time point in patients with stage II or higher CRC.
Supplementary Figure 3 from Colorectal Cancer Recurrence Prediction Using a Tissue-Free Epigenomic Minimal Residual Disease Assay
Authors: Nakamura Yoshiaki , Tsukada Yuichiro , Matsuhashi Nobuhisa , Murano Tatsuro , Shiozawa Manabu , Takahashi Yusuke , Oki Eiji , Goto Masahiro , Kagawa Yoshinori , Kanazawa Akiyoshi , Ohta Takashi , Ouchi Akira , Bando Hideaki , Uchigata Hiroshi , Notake Chiemi , Ikematsu Hiroaki , Yoshino Takayuki
Published: October 2024

Supplementary Figure 3. Swimmer plots.
Supplementary Table S3 from The Innate Immune Landscape of dMMR/MSI Cancers Predicts the Outcome of Nivolumab Treatment: Results from the Drug Rediscovery Protocol
Authors: Zeverijn Laurien J. , Geurts Birgit S. , Battaglia Thomas W. , van Berge Henegouwen Jade M. , de Wit Gijs F. , Hoes Louisa R. , van der Wijngaart Hanneke , van der Noort Vincent , Roepman Paul , de Leng Wendy W.J. , Jansen Anne M.L. , Chalabi Myriam , van Herpen Carla M.L. , Devriese Lot A. , Erdkamp Frans L.G. , Labots Mariette , de Jonge Maja J.A. , Kerver Emile D. , Bins Adriaan D. , Leek Lindsay V.M. , Notohardjo Jessica C.L. , van den Eertwegh Alfonsus J.M. , Wessels Lodewyk F.A. , Verheul Henk M.W. , Gelderblom Hans , van de Haar Joris , Voest Emile E.
Published: October 2024

Supplementary Table S3. Baseline characteristics and clinical outcome data of evaluable dMMR/MSI patients treated with nivolumab in high tumor mutational load cohort.
Supplementary Figure S3 from The Innate Immune Landscape of dMMR/MSI Cancers Predicts the Outcome of Nivolumab Treatment: Results from the Drug Rediscovery Protocol
Authors: Zeverijn Laurien J. , Geurts Birgit S. , Battaglia Thomas W. , van Berge Henegouwen Jade M. , de Wit Gijs F. , Hoes Louisa R. , van der Wijngaart Hanneke , van der Noort Vincent , Roepman Paul , de Leng Wendy W.J. , Jansen Anne M.L. , Chalabi Myriam , van Herpen Carla M.L. , Devriese Lot A. , Erdkamp Frans L.G. , Labots Mariette , de Jonge Maja J.A. , Kerver Emile D. , Bins Adriaan D. , Leek Lindsay V.M. , Notohardjo Jessica C.L. , van den Eertwegh Alfonsus J.M. , Wessels Lodewyk F.A. , Verheul Henk M.W. , Gelderblom Hans , van de Haar Joris , Voest Emile E.
Published: October 2024

Supplementary Figure S3. Association between immune marker gene expression and clinical benefit to ICB.
Supplementary Data1 from Elacestrant in ER+, HER2− Metastatic Breast Cancer with ESR1-Mutated Tumors: Subgroup Analyses from the Phase III EMERALD Trial by Prior Duration of Endocrine Therapy plus CDK4/6 Inhibitor and in Clinical Subgroups
Authors: Bardia Aditya , Cortés Javier , Bidard François-Clément , Neven Patrick , Garcia-Sáenz José , Aftimos Phillipe , O’Shaughnessy Joyce , Lu Janice , Tonini Giulia , Scartoni Simona , Paoli Alessandro , Binaschi Monica , Wasserman Tomer , Kaklamani Virginia
Published: October 2024

Supplemental figures 1-3; Supplemental tables 1-15
Data from Biomarker Analyses Investigating Disease Biology and Associations with Outcomes in the JAVELIN Merkel 200 Trial of Avelumab in Metastatic Merkel Cell Carcinoma
Authors: D’Angelo Sandra P. , Lebbé Céleste , Nghiem Paul , Brohl Andrew S. , Mrowiec Thomas , Leslie Trent , Georges Sara , Güzel Gülseren , Shah Parantu
Published: October 2024

AbstractPurpose:
Avelumab (anti–PD-L1) became the first approved treatment for metastatic Merkel cell carcinoma (mMCC) based on results from the phase II JAVELIN Merkel 200 trial. In this study, we report exploratory biomarker analyses from the trial.
Patients and Methods:
Patients with mMCC (n = 88) with or without prior first-line chemotherapy received avelumab 10 mg/kg every 2 weeks. We conducted analyses on somatic mutations, mutational signatures, and tumor mutational burden using paired whole-exome sequencing. Additionally, we examined gene and gene set expression, immune content from RNA sequencing profiles, as well as tumor PD-L1 and CD8 statuses from IHC and CD8 status from digital pathology.
Results:
Tumors positive for Merkel cell polyomavirus (MCPyV) were characterized by an absence of driver mutations and a low tumor mutational burden, consistent with previous studies. A novel MCPyV-specific host gene expression signature was identified. MCPyV+ tumors had increased levels of immunosuppressive M2 macrophages in the tumor microenvironment, which seemed to correlate with PD-L1 expression; high CD8+ T-cell density in these tumors did not predict response to avelumab. Conversely, in patients with MCPyV− tumors, higher CD8+ T-cell density seemed to be associated with response to avelumab. Mutations in several genes were associated with treatment outcomes. Compared with tumors sampled before chemotherapy, tumors sampled after chemotherapy had downregulated gene signatures for immune responses, including reduced expression of IFNγ-related pathways. Levels of activated dendritic cells in responding patients were higher in patients assessed after versus before chemotherapy.
Conclusions:
Exploratory analyses provide insights into mMCC biology and potential associations with response to avelumab. Chemotherapy seems to negatively modulate the immune microenvironment.