bluuebunny/crossref_metadata_2025 huggingface dataset:
Stroke severity shapes extracellular vesicle profiles and their impact on the cerebral endothelial cells
Authors: Escudero‐Guevara Esthefanny , Sandoval Hermes , Ibáñez Belén , Pino José León , Acurio Jesenia , Troncoso Felipe , Vatish Manu , López Eduardo , Escudero Carlos
Published: January 2025

Ischaemic stroke is a leading cause of death and disability. Circulating extracellular vesicles (EVs) post‐stroke may help brain endothelial cells (BECs) counter ischaemic injury. However data on how EVs from ischaemic stroke patients, considering injury severity, affect these cells are limited. The aims were to characterize the inflammatory and angiogenic components of circulating EVs in acute ischaemic stroke patients, considering stroke severity, and to investigate whether these circulating EVs differentially influence the proangiogenic properties and blood–brain barrier (BBB) integrity of human BECs. Eighteen ischaemic stroke patients (acute phase: 24–48 h) and nine controls matched by age, sex, and blood pressure were studied. Stroke severity was classified as severe (n = 9) or mild (n = 9). Plasma EVs were analysed for size, concentration, and protein markers (CD63, Alix, CD81, TSG101, HSP70), as well as proinflammatory and angiogenic proteins. EV uptake, cell viability, proangiogenic capacity, electrical resistance [TEER (transendothelial electrical resistance)], and dextran‐70 kD permeability were assessed using human brain microvascular endothelial cells (hCMEC/D3). Stroke patients had lower EV concentrations than controls (p = 0.075), with mild‐stroke patients having the smallest EVs. Stroke‐derived EVs had higher levels of interleukin 6 (IL‐6), tumour necrosis factor α (TNF‐α), nitrotyrosine, and vascular endothelial growth factor (VEGF) but lower placental growth factor (PLGF) compared to controls. IL‐6 was higher in mild strokes (p = 0.0025), and VEGF was higher in severe strokes (p = 0.048). EVs from severe‐stroke cases enhanced proangiogenic capacity and minimally disrupted the BBB. Stroke severity influences EV number, size, and composition. EVs from severe strokes may promote BBB restoration and cerebral angiogenesis, suggesting their role in intercellular communication and homeostasis in ischaemic tissue.

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Key points

Ischaemic stroke is one of the leading causes of death worldwide. After an ischaemic stroke several physiological processes are triggered to recover the injured tissue.

Increasing evidence has suggested that extracellular vesicles (EVs) present in the bloodstream could play a role in brain recovery, but their specific impact, especially concerning stroke severity, was unclear.

This study demonstrates that plasma‐derived EVs from first‐ever ischaemic stroke patients have distinctive characteristics and effects over brain angiogenesis and blood–brain barrier (BBB) integrity.

Our study proposes that circulating EVs from patients with severe stroke may carry protective factors to initiate brain endothelial cell recovery after acute episodes.

These findings underscore the role of EVs as potential effectors of BBB recovery and biomarkers in severe ischaemic stroke.
Temporal patterns in Malaysian rainforest soundscapes demonstrated using acoustic indices and deep embeddings trained on time-of-day estimation
Authors: Loo Yen Yi , Lee Mei Yi , Shaheed Samien , Maul Tomas , Clink Dena Jane
Published: January 2025

Rapid urban development impacts the integrity of tropical ecosystems on broad spatiotemporal scales. However, sustained long-term monitoring poses significant challenges, particularly in tropical regions. In this context, ecoacoustics emerges as a promising approach to address this gap. Yet, harnessing insights from extensive acoustic datasets presents its own set of challenges, such as the time and expertise needed to label species information in recordings. Here, this study presents an approach to investigating soundscapes: the use of a deep neural network trained on time-of-day estimation. This research endeavors to (1) provide a qualitative analysis of the temporal variation (daily and monthly) of the soundscape using conventional ecoacoustic indices and deep ecoacoustic embeddings, (2) compare the predictive power of both methods for time-of-day estimation, and (3) compare the performance of both methods for supervised classification and unsupervised clustering to the specific recording site, habitat type, and season. The study's findings reveal that conventional acoustic indices and the proposed deep ecoacoustic embeddings approach exhibit overall comparable performance. This article concludes by discussing potential avenues for further refinement of the proposed method, which will further contribute to understanding of soundscape variation across time and space.
Validation of a three-dimensional model for improving the design of multiple-backscattering ultrasonic sensors
Authors: Reyna Carlos A. B. , Lopes José H. , Franco Ediguer E. , Tsuzuki Marcos S. G. , Buiochi Flávio
Published: January 2025

Ultrasonic sensors based on backscattering principles have been developed for various applications involving arbitrary or random scatterer distributions. Although the theory of multiple scattering of waves is well-established, it has not been thoroughly explored in these applications. This work presents a feasible and simplified three-dimensional scattering model to predict the transient response generated by a set of rods positioned in the near field of a 1 MHz water-coupled ultrasonic transducer. The developed algorithm accurately reproduced the received waveform for seven different configurations of scatterers. Additionally, this model was used as the core of a parametric optimization routine to determine the optimal distribution of five rods that maximizes the acoustic energy of the echo signal. The theoretical signals were compared with experimental data, demonstrating good agreement and indicating the feasibility of the method as a design tool for the backscattering sensor.
On the mechanism underlying two distinct types of nonlinear sound absorption trends of porous layers
Authors: Peng Feng
Published: January 2025

Through non-dimensional analysis of the nonlinear sound absorption characteristics of rigid-porous layers, the results indicate that the nonlinear sound absorption trend of a porous layer (PL) at high sound pressure levels (SPLs) mainly depends on the state of flow resistance matching. When a PL is in an under-matched state, the sound absorption coefficient (SAC) will initially rise to a maximum and then gradually decline as SPL increases. Comparatively, when it is in an over-matched state, the SAC will decrease monotonically. In light of this understanding, several guidelines are proposed to improve the sound absorption performance of PLs at high SPLs.
‘I’m not ok, we are not ok’: an exploration into the embodied precarity experienced by disabled people and their family members living in rural South Africa during the COVID-19 pandemic
Authors: Neille Joanne
Published: January 2025

Research suggests that the impact of the COVID-19 pandemic on disabled people was magnified compared with the impact on non-disabled people; however, little is known about the experiences of disabled people living in rural areas, particularly those in the Global South. Disabled people living in rural areas experience significant challenges related to poverty, food insecurity and access to information and healthcare. Data were collected in the Nkomazi East Municipality in Mpumalanga, South Africa. Interviews with two key informants were conducted in English. Eight semistructured interviews were conducted in Siswati with people with disabilities. Five family members of people with disabilities were also interviewed. All data were transcribed and translated into English, then analysed using inductive thematic analysis and interpreted through the lens of corporeal vulnerability. Findings revealed increased isolation, stigma, discrimination and financial and food insecurity during the pandemic, giving rise to a sense of embodied precarity. Access to healthcare was influenced by the presence of gatekeepers and informal triage systems. Experiences were compounded by food supply challenges, limited public transport and the complexities of trying to maintain social distancing, intensifying the experience of social inequality. Findings suggest that the COVID-19 pandemic magnified the experience of oppression and discrimination because of a communal sense of threat to survival. They highlight the need for increased awareness, social support and policy reform in response to the challenges imposed by the pandemic, with a specific focus on basic human rights, including access to information, healthcare and nutrition and ensuring the dignity of all community members. Additional efforts are needed in planning for future healthcare crises to ensure that responses are authentically disability inclusive.
Classroom Application of English Language and Literature Wisdom based on Artificial Intelligence Technology
Authors: Yun Bai
Published: January 2025

In order to improve the ability of intelligent classroom management and dynamic management of English language and literature in streaming media environment, this paper proposes an intelligent classroom application of English language and literature based on artificial intelligence technology. To construct the information interaction resource scheduling and fitness control model of English language and literature smart classroom in streaming media environment, this paper restructures the situation and context information of language application, and extract the course parameter setting information of smart classroom teaching mode. The sparsity feature decomposition is carried out on the personalized assignment set assigned by the smart platform, and the recognition evaluation decision of the smart classroom teaching mode is realized according to the coding results of interactive information features. The control of information interaction is achieved based on the evaluation results concerning the level of classroom participation and the effectiveness of learning. The changes of students’ satisfaction with teaching design and students’ participation in class were analyzed. The operation data were divided into decision-making data and computing resource pool data to achieve intelligent classroom design of English language and literature. The experimental results show that the proposed method has good adaptability in the intelligent classroom design of English language and literature, the level of students’ participation and satisfaction is higher, and the utilization rate of classroom teaching resources is higher.
Vocal Performance Simulation and Training System Optimized by Neural Networks in Virtual Reality Environment
Authors: Zhang Sheng Huan , Cheng Ye
Published: January 2025

The simulation of vocal performance has emerged as an important means of training singers in a more engaging manner than standard methods of vocal coaching. The purpose of this research is to present a new vocal performance simulation and training system developed using neural networks (NN) in a virtual reality (VR) environment and to improve the training of vocal performance using advanced NN models and VR. For this purpose, the researcher’s audio is primarily to analyze, collect and process samples recording performance as well as specific performers’ training audio-video material. Preprocessing techniques such as noise reduction, and normalization, and applied to prepare the data. Key features like pitch, tone, and breath control were extracted using the Mel-frequency cepstral coefficients (MFCC) algorithm, enabling effective feature representation. We propose the Refined Fruit Fly Optimized Intelligent Long-Short Term Memory (RFF-ILSTM) model, a recurrent neural network (RNN)-based approach optimized for handling sequential vocal data with high precision. The model incorporates the RFF optimization technique in order to enhance the tuning of the LSTM architecture thereby increasing its speed of convergence and training. The information collected was already processed by the proposed framework in an effort to enhance vocal performance simulation. VR integration enhances the enjoyment and effectiveness of the interface as it allows singers to receive immediate feedback as if they were performing in front of an audience. Users engage in performing activities based on 3D images, thereby allowing the practice of different types of vocations without difficulty. Simulation results showed dramatic improvements in terms of ability to control vocals and tones, as well as consistency in performance. The system successfully integrates VR and NN enhancement for an improved, interactive system of training for vocal performances.
Blockchain-Based Supply Chain Management System: Framework Design for Achieving Transparency and Collaboration
Authors: Liu Ailushi , Han Zhaoyun
Published: January 2025

In today’s gradually modest universal marketplaces, effective supply chain management (SCM) is important. Using cutting-edge strategy, contains blockchain, offers more transparency and collaboration in data sharing. This paper suggested an innovative privacy preservation approach for supply chain networks utilizing blockchain technology, employing the novel Foraging Redefined Remora Optimization Algorithm (FR-ROA). The FR-ROA offers the right keys for protecting designated sensitive areas. The encrypted data and the protected key are transmitted from the manufacturer to the supplier through the blockchain network. After distribution, the original data are reconstructed utilizing the same key. The FR-ROA strategy improves search competencies without growing computational difficulty, providing a flexible balance between exploration and exploitation in optimizing supply chain security within blockchain frameworks. We executed our suggested strategy in Python software. The proposed framework is assessed based on correlation coefficient, sanitization efficiency and restoration efficiency parameters. We also performed a comparison valuation with several conventional strategies. The experimental findings illustrate its effectiveness in improving supply chain security associated with conventional strategies.
Time-dependent analysis of Hall current and nth-order reaction in non-Newtonian Casson liquid over an oblique stretching surface
Authors: Srividya K , Shamshuddin MD. , Ram M. Sunder , Salawu S. O.
Published: January 2025

This work undertakes a comprehensive investigation into the behavior of a novel Hall current, a non-uniform heat source/sink, and an nth-order chemical reaction in a three-dimensional (3D) Casson fluid transport towards a tilted stretched device. The research is characterized by its thoroughness, meticulously examining these occurrences. The Rosseland diffusion model, a mathematical framework used to describe the heat transfer process by radiation, was employed. After similarity transformations, the controlling partial differential equations become nonlinearly connected ordinary differential equations. We solve these equations numerically using Runge–Kutta fourth order with the shooting technique. Numerical solutions can be computed for the concentration, temperature, velocity, and Sherwood numbers. The necessary answers are not only analyzed through diagrams but also physical logic. It has been observed that when the hall parameter is increased, the dimensionless velocity field consistently shows an increasing trend. The Sherwood number rises in tandem with an increasing chemical reaction term, whereas the Nusselt number falls in the presence of a rising Casson fluid term. Various investigations validate the results, revealing their high level of accuracy. This investigation highlights the intricate interplay between electromagnetic, chemical, and non-Newtonian fluid dynamics, providing insights critical for optimizing industrial processes involving such fluids. The study’s findings are applicable in polymer processing, bioengineering, and chemical reaction engineering, where precise control of fluid flow and reaction rates is essential.
Factors Influencing Disasters Information-Seeking Behaviour via Social Networking Sites
Authors: Alajmi Bibi M. , Khalil Omar
Published: January 2025

Disasters bring uncertainties and substantial health, economic, social and psychological challenges. Effective management of disasters requires thorough understanding of their causes, nature and consequences. Affected individuals may, therefore, seek instant, trustworthy information from different sources including social networking sites (SNSs). This study investigates what leads individuals to seek disaster information on SNSs. The investigated potential drivers are source credibility, argument quality, self-efficacy, perceived usefulness of information and behavioural intention. The Structural Equation Modelling analysis of 867 responses confirms that source and argument quality, self-efficacy and perceived usefulness are all significant antecedents of behavioural intention, which in turn influences disaster information seeking on SNSs. This study’s empirical findings augment the sparse literature on factors influencing SNS use to source the much-needed information amid the uncertainty and ambiguity of a disaster. Policymakers can establish SNSs as a vital source of catastrophe information by understanding people’s SNS interactions during catastrophes. Our findings may help government authorities and crisis managers integrate SNSs into disaster management and public engagement.
SmartTBD: Smart Tracking for Resource-constrained Object Detection
Authors: Zhou Shihang , Hernandez Alejandra C. , Gomez Clara , Yin Wenjie , Björkman Mårten
Published: January 2025

With the growing demand for video analysis on mobile devices, object tracking has demonstrated to be a suitable assistance to object detection under the Tracking-By-Detection (TBD) paradigm for reducing computational overhead and power demands. However, performing TBD with fixed hyper-parameters leads to computational inefficiency and ignores perceptual dynamics, as fixed setups tend to run suboptimally, given the variability of scenarios. In this article, we propose SmartTBD, a scheduling strategy for TBD based on multi-objective optimization of accuracy-latency metrics. SmartTBD is a novel deep reinforcement learning based scheduling architecture that computes appropriate TBD configurations in video sequences to improve the speed and detection accuracy. This involves a challenging optimization problem due to the intrinsic relation between the video characteristics and the TBD performance. Therefore, we leverage video characteristics, frame information, and the past TBD results to drive the optimization problem. Our approach surpasses baselines with fixed TBD configurations and recent research, achieving accuracy comparable to pure detection while significantly reducing latency. Moreover, it enables performance analysis of tracking and detection in diverse scenarios. The method is proven to be generalizable and highly practical in common video analytics datasets on resource-constrained devices.
Unified and Split Symbolic Execution for Exposing Semantic Differences
Authors: Liang Hongliang , Yin Luming , Hu Wenying , Li Yuxiang , Shen Wuwei
Published: January 2025

Software evolution is an important activity during a software development life cycle. Understanding semantic differences between two versions of a software system is a crucial yet challenging task, especially in many safety critical sectors. Consequently, various techniques have been proposed to check semantic differences between a program and its evolution. But, many current techniques are still far from being satisfactory in terms of the accuracy and efficiency. In this paper, we propose a novel framework, called

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, which can efficiently and effectively generate the minimal number of test cases that reveal as many semantic differences across two versions as possible. Specifically, given a unified control flow graph that denotes two versions of a program,

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executes as many common nodes as possible and leaves execution of non-common nodes separately in a single concolic execution instance. We evaluate

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on 86 pairs of C programs from four benchmarks, and experimental results show that

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can efficiently and effectively generate test cases demonstrating the semantic differences across two versions, with better performance than six baseline tools.
Virtual Migrations and Meta-Innovations: Update Struggle in No Man's Sky
Authors: Nielsen Daniel
Published: January 2025

No Man's Sky, developed by Hello Games, is renowned for its vast universe of infinite exploration, and a truly unique player experience, yet its trajectory has been shaped by a series of updates to meet the initial promises set in early pre-release marketing. Previous research on update resistance in games suggests that player reactions to game updates resemble player-developer negotiation, as these reactions often lead to some kind of recourse on the side of the publishers and developers. This study investigates how the Galactic Hub Project (GHP) community's responses—such as virtual migrations and the use of cryptocurrency HubCoin—illustrate a shift from negotiations to tactics of survival, as most community members have come to accept the conditions of disruptive exploits and updates. This case study highlights how meta innovations in game cultures reflect player reactions to a power struggle between producers and audiences, calling for closer examination of the socio-technical dynamics that shape game cultures.
Traditional Authorities Around the World: Toward a Better Understanding of their De Facto Power, Downward Accountability, and State Recognition
Authors: Baldwin Kate
Published: January 2025

Research in political science on traditional authorities has advanced quickly in the past decade, highlighting the diversity of these institutions and how variation among them affects political outcomes. However, existing research often fails to distinguish between three distinct attributes of these institutions: their de facto power, their downward accountability to the communities they lead, and their recognition by the state. This review demonstrates the importance of these conceptual distinctions by showing that they are empirically distinct concepts, that they have separate causes, and that they have different political effects. In particular, existing research shows that powerful traditional authorities increase collective action to provide local public goods, but state recognition of traditional institutions is important for improving conflict resolution, and their own downward accountability conditions their effect on the accountability of elected representatives.
Combining Distributed Electrochemical Measurements with a Semi-Empirical Model to Identify Local Variations in Overpotentials for PEM Water Electrolyzers
Authors: Roy Anirban , Roenning Frida Helena Helena , Aaron Douglas , Zhang Feng-Yuan , Mench Matthew M
Published: January 2025

A segmented cell and PCB approach was used to demonstrate an advanced technique for measuring and understanding the electrochemical behavior of PEM water electrolyzers. By employing a semi-empirical model, discrete modes of overpotential and their spatial distributions were identified in an operating cell. Distributed area-specific resistance (DASR measurements indicate that local dehydration of the polymer electrolyte membrane is the primary driver of increased polarization, behaving similarly to mass transport-limited currents at low flow rates due to ineffective gas-phase bubble removal. To improve quantification, the overall ohmic overpotential is divided into background (ηOhm,b) and mass transport-coupled (ηOhm,mt) components. Two types of anode diffusion media, a baseline PTL and a thin foil liquid/gas diffusion layer (LGDL), were examined. The results show significant variations in ηOhm,b and highlight that ineffective bubble removal leads to pronounced local dehydration. The effect of cell temperature on various overpotentials was also examined. Negligible differences in diffusion overpotential were observed when comparing PEWE performance using the PTL and LGDL, despite major differences in two-phase fluid transport within each diffusion media. This underscores the critical role of the catalyst layer's micro-porous structure in diffusion processes. The study highlights the complex nature and intricacies of mass transport limitations within PEWEs.
Cobalt-Content-Dependent Performance Trade-Off in PtxCo Alloy Catalysts for Fuel Cells
Authors: Li Shuai , Tong Lei , Sun Zi-Ang , Ma Chang-Song , Zhang Le , Song Tian-Wei , Liang Hai-Wei
Published: January 2025

Carbon-supported PtxCo alloy nanoparticles are among the most effective cathode catalysts for proton exchange membrane fuel cells (PEMFCs). However, cobalt leaching from the catalyst into the electrode ionomer negatively impacts cell performance. While this leaching has traditionally been associated with PEMFC operation, recent studies show that it also occurs during electrode fabrication. In this study, we investigated how the cobalt content in PtxCo catalysts influences cobalt leaching during electrode fabrication and its impact on initial cell performance. We identified a cobalt-content-dependent trade-off between performance at low and high current densities, where higher cobalt content enhances low-current density performance but deteriorates high-current density performance. By a comprehensive set of electrochemical and physical characterizations, we showed that increasing cobalt content in PtxCo catalysts with a similar particle size results in higher cobalt leaching during electrode fabrication, which in turn elevates mass transport resistance and thus degrades the high-current-density performance. On the other hand, a higher cobalt content also induces more pronounced compressive strain, which enhances the kinetic performance at low-current density regions.
Long‐Term Outcomes of Surgical Decompression in Treating Calcifying Odontogenic Cyst Associated With Compound Odontoma: A 9‐Year Follow‐Up Case Report and Literature Review
Authors: Alarcón Álvaro , Barison Rodrigo , Martínez Benjamín , González Sergio
Published: January 2025

A calcifying odontogenic cyst (COC) is a cystic lesion originating from odontogenic epithelium, exhibiting ameloblastomatous features and containing focal accumulations of ghost cells. The standard treatment for COC typically involves enucleation followed by surgical curettage. However, if the cyst is large or closely associated with anatomical structures, decompression may be considered as a preliminary step before enucleation. A 12‐year‐old male patient presented with swelling in the anterior mandibular region. Radiological assessment revealed an extensive radiolucent area crossing the mandibular midline, accompanied by radiopaque areas within the lesion. The diagnosis of COC associated with compound odontoma was confirmed. The treatment plan involved decompression, followed by enucleation. After over 9 years of follow‐up, the patient showed satisfactory and effective outcomes, with no signs of recurrence. This therapeutic approach minimizes the morbidity and cost associated with extensive and invasive reconstructive surgeries.
Proactively Seeking Feedback From Diverse Networks: A Weekly Diary Study on Nurses’ Work Engagement and Task Performance
Authors: Wan Li , Liu Jiakun , Wang Huatian , Li Kongqi
Published: January 2025

Feedback‐seeking behavior has been found to have positive impacts on nurses’ mental health. However, we still lack knowledge on how and under what conditions feedback‐seeking behavior can enhance nurses’ work engagement and task performance on a weekly basis. Based on weak ties theory and information processing theory, this study aimed to investigate the positive relationship between weekly feedback‐seeking behavior, nurses’ work engagement, and task performance. In addition, we explored the moderating roles of contacts’ closeness and contacts’ functional background diversity. Using a 4‐week survey with 368 nurses (totaling 1472 observations), we generally confirmed our hypotheses. The results of the multilevel regression analysis revealed that the positive relationship between weekly feedback‐seeking behavior and work engagement was stronger for those who had higher levels of contacts’ functional background diversity and that the positive relationship between weekly feedback‐seeking behavior and task performance was stronger for those who had lower levels of contacts’ closeness. In summary, taking a network characteristic perspective, we highlight that contacts’ closeness and functional background diversity can significantly influence the nurses’ feedback‐seeking process on a weekly basis. These findings enhance our understanding of how feedback‐seeking behavior can be leveraged to promote positive work outcomes for nurses.
Supplementary Table S1-S14 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Table S1. Patient characteristics. Table S2. Patients-level clinical treatment and outcome details. Table S3. Mutations detected in patient cell-free DNA by EnhanceAR-Seq. Table S4. Copy number alterations detected in patient cell-free DNA by EnhanceAR-Seq. Table S5. Structural variations detected in patient cell-free DNA by EnhanceAR-Seq. Table S6. Cox regression for progression-free survival with baseline covariates including altered AR enhancer detected in pre-treatment plasma. Table S7. Cox regression for overall survival with baseline covariates including altered AR enhancer in pre-treatment samples. Table S8. Clinical characteristics of the metastatic prostate cancer cohort. Table S9. Patient plasma cell-free DNA methylation sequencing metrics. Table S10. Hypomethylated DMRs in AR/enhancer altered lethal mCRPC patients. Table S11. Hypermethylated DMRs in AR/enhancer altered lethal mCRPC patients. Table S12. Central coverage of transcription factor binding sites (TFBSs) for most accessible transcription factors in AR/enhancer altered lethal mCRPC. Table S13. Central coverage of transcription factor binding sites (TFBSs) for least accessible transcription factors in AR/enhancer altered lethal mCRPC. Table S14. Multivariate Cox regression for progression-free survival.
Figure 5 from Chemotherapy Drives Tertiary Lymphoid Structures That Correlate with ICI-Responsive TCF1+CD8+ T Cells in Metastatic Ovarian Cancer
Authors: Lanickova Tereza , Hensler Michal , Kasikova Lenka , Vosahlikova Sarka , Angelidou Artemis , Pasulka Josef , Griebler Hannah , Drozenova Jana , Mojzisova Katerina , Vankerckhoven Ann , Laco Jan , Ryska Ales , Dundr Pavel , Kocian Roman , Cibula David , Brtnicky Tomas , Skapa Petr , Jacob Francis , Kovar Marek , Praznovec Ivan , McNeish Iain A. , Halaska Michal J. , Rob Lukas , Coosemans An , Orsulic Sandra , Galluzzi Lorenzo , Spisek Radek , Fucikova Jitka
Published: January 2025

NACT-mediated progenitor TCF1+PD1+CD8+ T-cell phenotype associates with effector cytotoxic functions within metastatic HGSOC. A–C, Representative dot plot (A) and box plot (B) showing percentage of TIM-3+PD1+CD8+ T cells and GZMB+CD8+ T cells within native pTME and mTME of chemo-naïve and treated HGSOC as determined by flow cytometry. Box plots: lower quartile, median, upper quartile; whiskers, minimum, maximum. Statistical significance was calculated by the Mann–Whitney test. P values are indicated. C, Marker heatmap dot plots obtained after t-SNE and showing the relative expression of the indicated marker in the different phenotypic clusters within mTME of chemo-naïve and treated HGSOS as determined by flow cytometry. D, Design of experimental and sequencing workflow in 11 patients with HGSOC before and after NACT. scRNAseq was performed on dissociated solid tumor specimens using 10× Genomics Chromium platform. E and F, Uniform manifold approximation and projection (UMAP) plot of all cells (n = 51,476) passing the quality control, colored by type of therapy (E) and cell type (F). G and H, TILs projections (G) and predicted subtype frequencies (H) in biopsies from patients with chemo-naïve and treated HGSOC. CM, central memory; EM, effector memory; MAIT, mucosal-associated invariant T cells; PTEX, progenitor exhausted T cells; TEMRA, terminally exhausted T cells; TEX, exhausted T cells. I and J, Radar plot showing percentage of CD8+ T cells expressing respective T-cell marker (KLRB1, TCF7, CCR7, IL7R, LMNA, FGFBP2, XCL1, CD200, CRTAM, TOX, PDCD1, HAVCR2, and GNLY; I) and UMAP showing expression of PDCD1, HAVCR2 and TCF7 in CD4+ and CD8+ T-cell clusters in chemo-naïve and treated HGSOC samples (study cohort 5; J), as determined by scRNA-seq. (Panel D created with BioRender.com.)
Supplementary Figure S6 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Supplementary Figure S6. Kaplan–Meier survival analysis of the 43-patient mCRPC cohort that also underwent genome-wide EM-seq, according to (A,B) AR/enhancer alteration status and (C,D) median-split ichorCNA-based median tumor fraction. p values were calculated by the log-rank test and hazard ratios (HRs) by the Mantel-Haenszel method. cfDNA, cell-free DNA; mCRPC; metastatic castration-resistant prostate cancer.
Supplementary Figure S5 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Supplementary Figure S5. Kaplan-Meier survival analysis based on plasma collected prior to first-line androgen receptor-signaling inhibitor (ARSI) treatment in 63 mCRPC patients according to (A,B) PTEN copy number loss status in cfDNA, (C,D) PTEN copy number loss or mutation in cfDNA, and (E,F) alteration in AR/Enhancer or PTEN in cfDNA. p values were calculated by the log-rank test and hazard ratios (HRs) by the Mantel-Haenszel method. cfDNA, cell-free DNA; mCRPC; metastatic castration-resistant prostate cancer.
Supplementary Figure S4 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Supplementary Figure S4. Summary of alterations in biologically relevant pathways found in pre-ARSI plasma cell-free DNA of 63 metastatic castration-resistant prostate cancer patients. ARSI, androgen receptor-signaling inhibitors.
Supplementary Data1 from Germline DNA Damage Repair Variants and Prognosis of Patients with High-Risk or Metastatic Prostate Cancer
Authors: Stopsack Konrad H. , Vijai Joseph , Conry Michael , Berchuck Jacob E. , Kemel Yelena , Vasselman Samantha E. , Freeman Dory A. , Lee Gwo-Shu M. , Mandelker Diana , Solit David B. , Morris Michael J. , Penney Kathryn L. , Abida Wassim , Offit Kenneth , Mucci Lorelei A. , Kantoff Philip W. , Pomerantz Mark M.
Published: January 2025

Anonymized variant calls
Supplementary Table S3 from BRAF Deletion in Adult Patients with Langerhans Cell Histiocytosis Correlates with Multisystem Disease and Poor Outcomes
Authors: Lang Min , Chang Long , Cai Hao , Lin He , Liu Zheng-zheng , Duan Ming-hui , Zhou Dao-bin , Cao Xin-xin
Published: January 2025

Supplementary Table S3. The coexistence of MAPK/PI3K pathway mutations discovered by NGS.
Supplementary Table S2 from BRAF Deletion in Adult Patients with Langerhans Cell Histiocytosis Correlates with Multisystem Disease and Poor Outcomes
Authors: Lang Min , Chang Long , Cai Hao , Lin He , Liu Zheng-zheng , Duan Ming-hui , Zhou Dao-bin , Cao Xin-xin
Published: January 2025

Supplementary Table S2. Mutations of adult patients with LCH.
Supplementary Table S9 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Clinical characteristics of patients according to the anti-inflammatory TCM treatment in DLRI high risk patients in the internal validation set 2 after propensity score matching.
Supplementary Table S7 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Subgroup analysis of the association between DLRI risk groups and disease-free survival in other clinical characteristics in the internal validation set 2.
Supplementary Table S5 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Univariate CoxPH regression analysis of DLRI risk groups and other clinical characteristics in the internal validation set 2.
Supplementary Table S10 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Clinical characteristics of patients according to the anti-inflammatory TCM treatment in DLRI high risk patients in the internal validation set 2 after propensity score matching.
Supplementary Table S1 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Comparison of clinical characteristics for the internal validation set 2 patients with different DLRI risk groups.
Supplementary Table S1 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Gene set enrichment analysis on Hallmark gene sets, comparing 89Zr-trastuzumab classes “high” (positive normalized enrichment score – NES) and “low” (negative NES).
Supplementary Figure S5 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Levels of stroma (%) according to ZrT class (dichotomized into “high” and “low”), and metabolic response
Supplementary Figure S3 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Deep learning radiomic feature selection and the establishment of DLRI using the LASSO logistic regression model.
Supplementary Figure S1 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Examples of the four classes of HER2-PET/CT uptake.
Supplementary Table S2 from Phase II Study of Palbociclib in Patients with Tumors with CDK4 or CDK6 Amplification: Results from the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol Z1C
Authors: O’Hara Mark H. , Jegede Opeyemi , Dickson Mark A. , DeMichele Angela M. , Piekarz Richard , Gray Robert J. , Wang Victoria , McShane Lisa M. , Rubinstein Lawrence V. , Patton David R. , Williams P. Mickey , Hamilton Stanley R. , Onitilo Adedayo , Tricoli James V. , Conley Barbara A. , Arteaga Carlos L. , Harris Lyndsay N. , O’Dwyer Peter J. , Chen Alice P. , Flaherty Keith T.
Published: January 2025

Representativeness of Study Participants
Supplementary Table S1 from Phase II Study of Palbociclib in Patients with Tumors with CDK4 or CDK6 Amplification: Results from the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol Z1C
Authors: O’Hara Mark H. , Jegede Opeyemi , Dickson Mark A. , DeMichele Angela M. , Piekarz Richard , Gray Robert J. , Wang Victoria , McShane Lisa M. , Rubinstein Lawrence V. , Patton David R. , Williams P. Mickey , Hamilton Stanley R. , Onitilo Adedayo , Tricoli James V. , Conley Barbara A. , Arteaga Carlos L. , Harris Lyndsay N. , O’Dwyer Peter J. , Chen Alice P. , Flaherty Keith T.
Published: January 2025

Patient Characteristics of the Eligible and Treated Population (n=38)
Supplementary Table S4 from CD40 Agonist on Patient-Derived Xenograft Mice for the Treatment of B-Cell Acute Lymphoblastic Leukemia
Authors: Bellaye Pierre-Simon , Georgievski Aleksandra , Ballerini Paola , Bouslama Boutheina , Richard Corentin , Boidot Romain , Chevreux Guillaume , Legros Véronique , Guy Julien , Racine Jessica , Collin Bertrand , Garrido Carmen , Quéré Ronan
Published: January 2025

Supplementary Table S4. Flow cytometry analysis of specific markers expressed by B-ALL PDX cells.
Supplementary Table S1 from CD40 Agonist on Patient-Derived Xenograft Mice for the Treatment of B-Cell Acute Lymphoblastic Leukemia
Authors: Bellaye Pierre-Simon , Georgievski Aleksandra , Ballerini Paola , Bouslama Boutheina , Richard Corentin , Boidot Romain , Chevreux Guillaume , Legros Véronique , Guy Julien , Racine Jessica , Collin Bertrand , Garrido Carmen , Quéré Ronan
Published: January 2025

Supplementary Table S1. Cytogenetic and immunophenotyping of B-ALL primary samples used to generate B-ALL PDX models.
Supplementary Table S9 from Intestinal Subtype as a Biomarker of Response to Neoadjuvant Immunochemotherapy in Locally Advanced Gastric Adenocarcinoma: Insights from a Prospective Phase II Trial
Authors: Wang Lei , Sun Mengting , Li Jinyang , Wan Linghong , Tan Yuting , Tian Shuoran , Hou Yongying , Wu Linyu , Peng Ziyi , Hu Xiao , Zhang Qihua , Huang Zening , Han Mengyi , Peng Shiyin , Pan Yuwei , Ren Yuanfeng , Zhang Mengsi , Chen Dongfeng , Liu Qin , Li Xianfeng , Qin Zhong-yi , Xiang Junyv , Li Mengxia , Zhu Jianwu , Chen Qiyue , Luo Huiyan , Wang Shunan , Wang Tao , Li Fan , Bian Xiu-wu , Wang Bin
Published: January 2025

Representativeness of Study Participants
Supplementary Figure S9 from CD40 Agonist on Patient-Derived Xenograft Mice for the Treatment of B-Cell Acute Lymphoblastic Leukemia
Authors: Bellaye Pierre-Simon , Georgievski Aleksandra , Ballerini Paola , Bouslama Boutheina , Richard Corentin , Boidot Romain , Chevreux Guillaume , Legros Véronique , Guy Julien , Racine Jessica , Collin Bertrand , Garrido Carmen , Quéré Ronan
Published: January 2025

Supplementary Figure S9. Combination of CD40 agonist and chemotherapy significantly reduces B-ALL development in PDX mice.
Supplementary Figure S5 from CD40 Agonist on Patient-Derived Xenograft Mice for the Treatment of B-Cell Acute Lymphoblastic Leukemia
Authors: Bellaye Pierre-Simon , Georgievski Aleksandra , Ballerini Paola , Bouslama Boutheina , Richard Corentin , Boidot Romain , Chevreux Guillaume , Legros Véronique , Guy Julien , Racine Jessica , Collin Bertrand , Garrido Carmen , Quéré Ronan
Published: January 2025

Supplementary Figure S5. The CD40 agonist does not bind to mouse immune cells in vivo.
Supplementary Figure S4 from Intestinal Subtype as a Biomarker of Response to Neoadjuvant Immunochemotherapy in Locally Advanced Gastric Adenocarcinoma: Insights from a Prospective Phase II Trial
Authors: Wang Lei , Sun Mengting , Li Jinyang , Wan Linghong , Tan Yuting , Tian Shuoran , Hou Yongying , Wu Linyu , Peng Ziyi , Hu Xiao , Zhang Qihua , Huang Zening , Han Mengyi , Peng Shiyin , Pan Yuwei , Ren Yuanfeng , Zhang Mengsi , Chen Dongfeng , Liu Qin , Li Xianfeng , Qin Zhong-yi , Xiang Junyv , Li Mengxia , Zhu Jianwu , Chen Qiyue , Luo Huiyan , Wang Shunan , Wang Tao , Li Fan , Bian Xiu-wu , Wang Bin
Published: January 2025

Marker genes for immune and stromal cell subtypes