bluuebunny/crossref_metadata_2025 huggingface dataset:
Diminishing productivity and hyperstable harvest in northern Wisconsin walleye fisheries
Authors: Mrnak Joseph T. , Embke H.S. , Wilkinson M.V. , Shaw S.L. , Vander Zanden M.J. , Sass G.G.
Published: August 2024

Managing fisheries in a changing socio-ecological environment may require holistic approaches for identifying and adapting to novel ecosystem dynamics. Using 32 years of Ceded Territory of Wisconsin (CTWI) walleye ( Sander vitreus) data, we estimated production ( P), biomass ( B), biomass turnover ( P/B), yield ( Y), and yield over production ( Y/P) and tested for hyperstability in walleye yield. Most CTWI walleye populations showed low P and B, and Y/P < 1 . Yet, production overharvest ( Y/P > 1) was prevalent among Wisconsin walleye recruitment-based management approaches (natural recruitment (NR), sustained only by stocking, combination). Production, B, and P/B have declined in NR populations, while Y and Y/P have remained constant. Walleye Y was hyperstable along a production gradient among all management approaches and fishery types (i.e., angling only, angling/tribal harvest combined). Diminishing productivity and hyperstable yield may be jointly contributing to observed walleye declines. We classified lakes into management groups of low, moderate, or high vulnerability to harvest based on Y/P and P/B dynamics and identify that harvest may benefit from declines to maintain or increase the adaptive capacity of CTWI walleye.
Gravity’s rainbow effects on higher curvature modification of $$R^{2}$$ inflation
Authors: Yuennan Jureeporn , Channuie Phongpichit , Momeni Davood
Published: August 2024

In this work, we study several extensions of the higher curvature modification of $$R^{2}$$

R
2

inflation in the context of gravity’s rainbow. We modify the $$(R+R^{2})$$

(
R
+

R
2

)

model by adding an $$f_{1}R^3$$

f
1

R
3

-term, an $$f_{2}R^4$$

f
2

R
4

-term, and an $$f_{3}R^{3/2}$$

f
3

R

3
/
2

-term to the original model. We calculate the inflationary observables and confront them using the latest observational bounds from Planck 2018 data. We assume the rainbow function of the form $${\tilde{f}}=1+\left( \frac{H}{M}\right) ^{\lambda }$$

f
~

=
1
+

H
M

λ

with $$\lambda $$
λ
being a rainbow parameter and M a mass-dimensional parameter. We demonstrate that the power spectrum of curvature perturbation relies on the dimensionless coefficient $$f_{i},\,i=1,2,3$$

f
i

,

i
=
1
,
2
,
3

, a rainbow parameter $$\lambda $$
λ
and a ratio H/M. Likewise, the scalar spectral index $$n_s$$

n
s

is affected by both $$f_{i}$$

f
i

and the rainbow parameter. Moreover, the tensor-to-scalar ratio r is solely determined by the rainbow parameter. Interestingly, by ensuring that $$n_s$$

n
s

aligns with the Planck collaboration’s findings at the $$1\sigma $$

1
σ

confidence level, the tensor-to-scalar ratio could reach up to $$r\sim 0.01$$

r
∼
0.01

, which is possibly measurable for detection in forthcoming Stage IV CMB ground experiments and is certainly feasible for future dedicated space missions.
CoFix: Advancing Semi-Supervised Learning with Noisy Label Mitigation Through Sample Selection and Consistent Regularization
Authors: Ma Yexin
Published: August 2024

Deep Neural Networks (DNNs) have revolutionized various fields through their ability to model complex patterns, yet their performance critically hinges on the availability of large-scale, accurately labeled datasets. The costly and time-consuming process of creating such datasets has motivated research into Learning with Noisy Labels (LNL), which aims to reduce reliance on perfect labels. This paper introduces CoFix, an innovative LNL framework that integrates sample selection with semi-supervised learning techniques to address the challenge of noisy labels in training. CoFix employs a Gaussian Mixture Model (GMM) to dynamically segment the training data into clean and noisy subsets, leveraging semi-supervised learning approaches on both. Inspired by the FixMatch algorithm, CoFix refines consistent regularization and pseudo-labeling strategies, enhancing augmentation strategies and temperature sharpening techniques. Additionally, CoFix explores label smoothing to augment the loss function, further refining model performance. Our experiments demonstrate CoFix’s superiority over state-of-the-art methods, achieving significant improvements in fewer training epochs, particularly in lower noise scenarios. The robustness and versatility of CoFix are evident through its consistent performance across various benchmark datasets and noise levels. The contributions of this paper include a novel LNL method with enhanced generalization capability, an investigation into the impact of label smoothing on the loss function, and extensive testing that confirms CoFix’s efficiency and adaptability to different noise levels.
Visual Target Interaction Modeling with Multichannel Data Fusion
Authors: Zhao Mingwei , Cai Changlong , Huang Wenbo , Mu Longtao , Zhang Hao , Yan Lingzhi , Liu Yonghui , Wang Jiaming
Published: August 2024

Facing the demand for accurate, fast, and natural human–computer interaction in the multi-screen control environment, the traditional exchange method of frequent switching control of multi-screen through mouse, keyboard, and other manual methods has problems of low efficiency, weak flexibility, and poor experience. In this paper, we research multi-screen precision control technology based on eye movement to break through the difficulties of precise recognition of human vision under complex environments and poor stability of vision estimation under frequent switching control of multi-screen. This study explores the technology for controlling multiple screens with high precision by tracking eye movements. It overcomes the challenges associated with reliably discerning human visual focus in intricate settings and the instability of visual assessments during rapid transitions between multiple screens. The experimental results of 1143 eye-movement capture tasks are studied, including the accurate recognition technology of human head posture and pupil gaze direction under complex backgrounds, illumination, and different visual field environments, and the theoretical modeling method of multi-screen precise target interaction based on eye-movement is explored. The expression data will be processed using convolutional neural networks, and the dataset will be trained through Python programming and tested on test samples collected by simulated flight crews in the laboratory with an accuracy rate of more than 85%.
Particle Tuned Mass Dampers for Wind-Induced Vibration Control in Supertall Building Tower Crowns
Authors: Lu Zheng , Wang Zhijie , Bao Lianjin , Zhao Xuelian , Zhang Quanwu
Published: August 2024

This study aims to investigate the performance of Particle Tuned Mass Damper (PTMD) in mitigating wind-induced vibrations in tower crown structures, providing findings to tower crowns with hinged boundary conditions in supertall buildings. A multi-degree-of-freedom (MDOF) model of the tower crown and a PTMD model based on the discrete element method (DEM) are established and validated. The intermediate story is a suitable choice for arranging damping devices in hinged tower crown structures. By analyzing the vibration response of the tower crown structure with PTMD under wind excitation, the study reveals the vibration mitigation effects of PTMD and the particle energy dissipation mechanism. The results indicate that the vibration reduction ratios of peak displacement and acceleration for the tower crown are 12.29% and 14.53%, respectively. Field test experiment shows its effectiveness from another perspective. Additionally, the energy dissipation between particles is the primary method of energy dissipation during collisions, accounting for approximately 80% of the total dissipated energy. Furthermore, the wide tuning frequency band characteristic of PTMD is examined through experimental testing, and its damping performance is compared with traditional Tuned Mass Damper (TMD) and Multiple Tuned Mass Damper (MTMD). Finally, the research findings, limitations, and potential impacts are discussed. This study contributes to advancing the development of tower crowns and their vibration reduction technology.
Almost Ricci solitons on weakly Ricci symmetric perfect fluid spacetime
Authors: Yadav Akhilesh , Saxena Tarun
Published: August 2024

The aim of this paper is to study geometrical aspects of an almost Ricci soliton on [Formula: see text] perfect fluid spacetime obeying Einstein’s field equation. Among others, we first find the soliton constant and cosmological constant in terms of scalar curvature and potential vector field in [Formula: see text] perfect fluid spacetime. Next, we discuss some physical phenomena related to dust fluid, dark fluid, and radiation era in [Formula: see text] perfect fluid spacetime admitting an almost Ricci soliton with potential vector field as solenoidal vector field and basic vector field [Formula: see text] under matter collineation condition. Further, we find an inequality for soliton constant when [Formula: see text] perfect fluid spacetime obeys the timelike convergence condition. Finally, we obtain some results in a [Formula: see text] perfect fluid spacetime whose metric represents an almost Ricci soliton when basic vector field and potential vector field both are torseforming vector field [Formula: see text]. Also, for such spacetime we find the soliton constant in terms of cosmological constant, gravitational constant, energy density, and isotropic pressure. We also provide an example of [Formula: see text] spacetime whose metric represents an almost Ricci soliton.
Analyzing the quantum corrected adS spherically symmetric black holes with phantom global monopoles for thermal properties
Authors: Rasheed Bilal , Ditta Allah , Naseer Tayyab , Javed Faisal , Mustafa G.
Published: August 2024

In this paper, we investigate the quantum corrected black hole’s thermodynamic properties in this paper. To assess the local and global thermodynamic stability, we compute a number of indicators such as the geometric mass, heat capacity, Hawking temperature, thermodynamic temperature, Gibbs free energy, and energy emission. The fundamental law of thermodynamics determines the temperature of the black hole. Our results ensure the overall thermal stability of the black hole solution. Our results for Gibbs free energy and heat capacity show the phase transition behavior of the black hole.
Viability of reconstructed bouncing cosmologies in f(T,𝒯 ) gravity
Authors: Azhar Nadeem
Published: August 2024

Cosmological reconstruction is a powerful technique in modified gravity invented to find the analogy of different cosmological epochs in modified gravity. In this paper, I present the modified holographic reconstruction scheme for [Formula: see text] theory of gravity where [Formula: see text] and [Formula: see text] are the torsion scalar and trace of energy–momentum tensor in the context of flat FRW universe. For this reconstruction, I consider Hubble horizon as an infrared cutoff and focus on a particular model [Formula: see text] (a correction to the teleparallel action depending on the matter content). Within this framework, I consider both the power law scale factor as well as the well-established cosmological bouncing scenario. Further, I explore various gravitational Lagrangians that can be reconstructed to yield analytical solution for symmetric, superbounce, oscillatory, singular bounce and matter bounce settings. The viability of these reconstructed models is then assessed through the EoS parameter [Formula: see text] and the [Formula: see text] plane [Formula: see text]. Notably, all the results align well with recent observational data.
Classical and quantum cosmology in Weyl integrable gravity: A Noether symmetry approach
Authors: Das Dipanjana , Hembrom Shriton , Bhaumik Roshni , Chakraborty Subenoy
Published: August 2024

The paper deals with an extensive study of Weyl integrable gravity theory in the background of flat FLRW space-time model, considering both classical and quantum cosmology. Noether symmetry approach has been used not only to simplify the evolution equations but also to obtain analytic solution from them. The classical solution has been analyzed from observational view point. Finally, canonical quantization programme has been complemented by the Noether symmetry analysis.
Life-Cycle Cost Assessment of the Base-Isolated-Reinforced Concrete Structure
Authors: Wang Hao , Guo Xiaoxia , Luo Chao , Zhao Jun , Feng Huaiping
Published: August 2024

Seismic isolation structures have excellent seismic mitigation effects, but implementing isolation measures may increase the initial cost of the structure. This paper presents a method to calculate the seismic loss and assess the life-cycle cost of isolated structures, which is convenient for owners to make decisions. The life-cycle cost assessment model is divided into two parts: initial cost assessment and seismic loss assessment over life-cycle period. Among them, the assessment method of the isolation layer is proposed, including the cost assessment of isolation bearings and dampers. The assessment method of seismic loss considers direct loss, indirect loss, casualties and integrating casualties into a unified assessment system. Direct loss includes building loss, indirect loss includes rental loss, relocation loss, income loss, personal property loss and business inventory loss. The seismic loss model is associated with seismic damage probability, which is obtained through seismic vulnerability and seismic probability risk assessment. The 8-story base-isolated-reinforced concrete structure illustrates the feasibility of the life-cycle-cost assessment model. The example shows that the initial cost of the isolated structure exceeds that of the nonisolated structure, however, the rental loss, income loss, personal property loss and casualties are much lower than those of nonisolated structures. The income loss of the isolated structure is the maximum proportion in life-cycle cost, and the casualty loss is the minimum proportion in the seismic loss, due to its excellent seismic mitigation effects.
Revolutionizing Mental Health Counseling with Serenity: An Emotion-Detecting Chatbot
Authors: Khan Tauseef , Parida Sagar Mousam , Swain Sankalpa , Mishra Abhishek , Dawal Gaurav , Mohanty Sachi Nandan , Ijaz Khan M.
Published: August 2024

Mental health counseling is a significant challenge in contemporary society, primarily due to issues such as cost, stigma, fear, and limited availability. Emotions play a crucial role in conveying information in this context, making emotion detection essential for a deeper understanding of an individual’s mental well-being. Utilizing generative machine learning models in mental health counseling could potentially lower barriers to access and improve outcomes. This paper proposes the development of a deep learning-based emotion-detecting chatbot named Serenity. The approach involves combining a pre-trained deep neural model, RoBERTa, with a multi-resolution adversarial model, EmpDG, to enhance the accuracy of detected emotions and generate more empathetic responses. RoBERTa has been trained on a dataset of thousands of tweets from Twitter. Additionally, an interactive adversarial learning framework is introduced to leverage user feedback and assess the emotional perceptivity of generated responses in dialogues. The study aims to demonstrate that a machine learning-based mental health chatbot like Serenity has the potential to serve as an effective complement to traditional human counselors.
ICA-CRMAS: Intelligent Context-Awareness Approach for Citation Recommendation based on Multi-Agent System
Authors: Degha Houssem Eddine , Laallam Fatima Zohra
Published: August 2024

Navigating the ever-expanding sea of scientific literature presents a daunting challenge for researchers seeking relevant and up-to-date information. Traditional citation recommendation systems, while well-intentioned, often fall short due to their limited focus on text-based features and lack of contextual awareness. In this article, we introduce the ICA-CRMAS (Intelligent Context-Aware Approach for Citation Recommendation based on Multi-Agent System), an intelligent system that leverages the power of deep learning, semantic analysis, and multimodal learning to overcome these limitations. ICA-CRMAS goes beyond the surface, delving into the rich tapestry of information within academic papers, including figures, which often hold vital contextual clues. By weaving this contextual data directly into its recommendation models, ICA-CRMAS generates highly personalized and relevant suggestions. This comprehensive approach unlocks enhanced accuracy, diversity, and serendipity, enabling researchers to effectively discover papers aligning with their interests and research objectives. ICA-CRMAS illuminates its reasoning. Instead of opaque suggestions, the system provides clear explanations that justify and illustrate recommended citations. This transparency builds user confidence, allowing researchers to critically engage with and trust the system’s recommendations. Evaluation experiments conducted on real-world academic datasets demonstrate that ICA-CRMAS outperforms existing approaches across various metrics. it surpassing its closest competitor by a margin of 7.53 on accuracy, 6.07% on MRR and by 5.87 on Recall. User feedback further reinforces its effectiveness, with an Overall System Usability Scale (SUS) score of 76.73, exceeding benchmark scores for comparable systems.
A Systematic Review of Digital Twin Technology for Home Care
Authors: Zafar Raja Omman , Rybarczyk Yves , Borg Johan
Published: August 2024

The concept of digital twin has captured significant attention in recent years, and its potential application within the domain of home care has been explored in several studies. This review endeavors to provide a comprehensive overview of digital twin technology and its applications in the realm of home care, delineating the key attributes and challenges entailed in their implementation. A systematic search was conducted across five databases, namely ACM digital library, IEEE Xplore, PubMed, Scopus, and Web of Science. Findings from forty-five included articles were categorized employing a systematic approach, highlighting the technology's deployment in remote older adults’ care monitoring, health issue prediction and personalized treatment planning. Furthermore, this review identified the challenges of integrating digital twins into the home care sector. Despite recognition of its potential, there is a distinct lack in the literature of in-depth studies specifically exploring the implementation of digital twin technology in home care, highlighting the need for further research.
Automated Generation of Modular Assurance Cases with the System Assurance Reference Model
Authors: Wardziński Andrzej , Jarzębowicz Aleksander
Published: August 2024

Assurance cases are structured arguments used to demonstrate specific system properties such as safety or security. They are used in many industrial sectors including automotive, aviation and medical devices. Assurance cases are usually divided into modules which address goals allocated to specific system properties, components, functions, modes of operation or environmental conditions. Depending on the system and assurance process characteristics, assurance case modules may follow shared argument templates. The templates refer to the system, process or environment attributes, described collectively as an assurance case context and stored in external context models. Our goal is to manage all contextual relations at the level of assurance case templates and instantiated arguments with the use of a generic System Assurance Reference Model (SARM). We describe its structure and demonstrate how it can be used to automatically generate assurance case modules, based on templates and context models. The article also presents a prototype tool, SARMER, which implements the SARM model and enables automatic data flow between models and assurance cases. The use of SARM and the SARMER tool is illustrated with an example of a component-based system and a modular assurance case to demonstrate that allocated contracts are satisfied for each component.
Prospects for Disease Slowing in Parkinson Disease
Authors: Menozzi Elisa , Schapira Anthony H.V.
Published: August 2024

The increasing prevalence of Parkinson disease (PD) highlights the need to develop interventions aimed at slowing or halting its progression. As a result of sophisticated disease modeling in preclinical studies, and refinement of specific clinical/genetic/pathological profiles, our understanding of PD pathogenesis has grown over the years, leading to the identification of several targets for disease modification. This has translated to the development of targeted therapies, many of which have entered clinical trials. Nonetheless, up until now, none of these treatments have satisfactorily shown disease-modifying effects in PD. In this review, we present the most up-to-date disease-modifying pharmacological interventions in the clinical trial pipeline for PD. We focus on agents that have reached more advanced stages of clinical trials testing, highlighting both positive and negative results, and critically reflect on strengths, weaknesses, and challenges of current disease-modifying therapeutic avenues in PD.
Leg cycling efficiency is unaltered in healthy aging regardless of sex or training status
Authors: Duong Justin J. , Leija Robert G. , Osmond Adam D. , Arevalo Jose A. , Brooks George A.
Published: August 2024

Muscular power is reduced, but the efficiency of movement is unaltered in healthy aging.
Bibliometric Analysis of the Role of Occludin in the Pathogenesis of Stroke
Authors: Urasheva Zhanylsyn U. , Kabdrakhmanova Gulnar B. , Yermagambetova Aigul P. , Utegenova Aigerim B. , Seitmaganbetova Nazgul A. , Aliyev Ondassyn M. , Kurmangaliyeva Saulesh S. , Kenzhina Nazym K. , Kurmambayev Yergen Z. , Khamidulla Alima A.
Published: August 2024

Over the past decade, there has been a notable surge in research dedicated to unraveling the intricate role of tight junction proteins in blood–brain barrier (BBB) damage associated with ischemic stroke. This bibliometric analysis explores the expansive landscape of occludin research, a key tight junction protein, during the years 2000–2023, shedding light on the global scientific contributions, collaborations, and emerging trends in this critical area of stroke pathogenesis. China and the United States emerge as significant contributors, underscoring their prominence in advancing our understanding of tight junction proteins. Occludin, identified as a linchpin in regulating BBB integrity, proves to be a pivotal player, with implications extending to the diagnosis of hemorrhagic transformation in ischemic stroke. This study identifies occludin as a potential biomarker, offering promise for early diagnosis and paving the way for novel diagnostic strategies. The analysis highlights the necessity for a more comprehensive exploration of tight junction proteins, including occludin and claudin‐5, particularly in the context of acute cerebral ischemia. The unique healthcare landscape in Kazakhstan adds urgency to the call for further scientific research in this region, emphasizing the need for tailored investigations to address specific regional challenges. This comprehensive overview not only delineates the current state of occludin research but also signals the direction for future investigations. The identified knowledge gaps and emerging trends provide a roadmap for researchers and policymakers alike, with implications for both scientific discourse and clinical practice. Moving forward, a deeper understanding of tight junction proteins, informed by the insights gleaned from this study, holds the potential to shape targeted therapeutic interventions and diagnostic strategies, ultimately contributing to advancements in global stroke care.
Design of Interdisciplinary Operation Mechanism in Universities Considering Management Policy Constraints: A Multiagent Simulation Model
Authors: Fan Shu
Published: August 2024

Innovation is an important guarantee for maintaining national competitiveness and promoting social productivity, and it has a strong driving force for national and social development. At present, interdisciplinary research is widely used as a mechanism for innovation to solve complex problems, and universities are important subjects of innovation activities. Therefore, how to design the interdisciplinary operation mechanism in universities is of great significance to improving innovation productivity. This paper focuses on the design of interdisciplinary research management policies. By using a multiagent simulation model describing the university interdisciplinary research process, the useful management policies are determined by comparing the evolution results of the interdisciplinary research process under different management policy constraints. The simulation results show that (1) scientific research output and cooperation in interdisciplinary research of universities can be promoted by dynamic allocation policies, (2) interdisciplinary research performance can be increased by setting a proper number of research directions in universities, (3) the presence of teachers with high efficiency coefficient and high initial scientific research output will not negatively affect scientific research output and fairness of interdisciplinary research, and (4) high‐level research output can be increased by setting proper rewards for high‐level tasks in interdisciplinary research. The work of this paper can provide a basis for interdisciplinary research management policy design from a new theoretical perspective.
Figure S4 from Estrogen Induces LCAT to Maintain Cholesterol Homeostasis and Suppress Hepatocellular Carcinoma Development
Authors: He Wenzhi , Wang Min , Zhang Xuechun , Wang Yilan , Zhao Dongli , Li Wenhua , Lei Fang , Peng Min , Zhang Zhonglin , Yuan Yufeng , Huang Zan
Published: August 2024

Supplementary Figure 4
Table S1 from HDAC Inhibition Increases CXCL12 Secretion to Recruit Natural Killer Cells in Peripheral T-cell Lymphoma
Authors: Zhu Jiayan , Wang Feng , Wang Lining , Dai Bo , Xu Guilin , Zhao Luyao , Jiang Huimin , Gao Wenhui , Zhang Tingting , Zhao Chenxi , Li Yun-Xuan , Hu Jiong , Li Ke
Published: August 2024

Supplementary Table S1. Patient characteristics of GSE58445
Supplementary Table S2 from HTS384 NCI60: The Next Phase of the NCI60 Screen
Authors: Kunkel Mark W. , Coussens Nathan P. , Morris Joel , Taylor Ronald C. , Dexheimer Thomas S. , Jones Eric M. , Doroshow James H. , Teicher Beverly A.
Published: August 2024

Aggregate correlations of compound pairs grouped by target for 91 targets with more than a single representative compound
Supplementary Figure S5 from HTS384 NCI60: The Next Phase of the NCI60 Screen
Authors: Kunkel Mark W. , Coussens Nathan P. , Morris Joel , Taylor Ronald C. , Dexheimer Thomas S. , Jones Eric M. , Doroshow James H. , Teicher Beverly A.
Published: August 2024

Correlation plots agents targeting BRAF, MEK or ERK.
Figure S1 from HTS384 NCI60: The Next Phase of the NCI60 Screen
Authors: Kunkel Mark W. , Coussens Nathan P. , Morris Joel , Taylor Ronald C. , Dexheimer Thomas S. , Jones Eric M. , Doroshow James H. , Teicher Beverly A.
Published: August 2024

Diagram outlining processing of assay data
Supplementary Videos legend from Human 3D Ovarian Cancer Models Reveal Malignant Cell–Intrinsic and –Extrinsic Factors That Influence CAR T-cell Activity
Authors: Joy Joash D. , Malacrida Beatrice , Laforêts Florian , Kotantaki Panoraia , Maniati Eleni , Manchanda Ranjit , Annibaldi Alessandro , Hopkins Sarah , Garrobo-Calleja Ianire , Gautrot Julien , Balkwill Frances R.
Published: August 2024

Legend for supplementary videos 1-6
Supplementary Table 1 from Human 3D Ovarian Cancer Models Reveal Malignant Cell–Intrinsic and –Extrinsic Factors That Influence CAR T-cell Activity
Authors: Joy Joash D. , Malacrida Beatrice , Laforêts Florian , Kotantaki Panoraia , Maniati Eleni , Manchanda Ranjit , Annibaldi Alessandro , Hopkins Sarah , Garrobo-Calleja Ianire , Gautrot Julien , Balkwill Frances R.
Published: August 2024

Fluorophore-conjugated antibodies used for flow cytometry.
Supplementary Figure 3 from Human 3D Ovarian Cancer Models Reveal Malignant Cell–Intrinsic and –Extrinsic Factors That Influence CAR T-cell Activity
Authors: Joy Joash D. , Malacrida Beatrice , Laforêts Florian , Kotantaki Panoraia , Maniati Eleni , Manchanda Ranjit , Annibaldi Alessandro , Hopkins Sarah , Garrobo-Calleja Ianire , Gautrot Julien , Balkwill Frances R.
Published: August 2024

Impaired death receptor signaling in malignant cells caused resistance to CAR-T cell cytotoxicity.
Figure 6 from Human 3D Ovarian Cancer Models Reveal Malignant Cell–Intrinsic and –Extrinsic Factors That Influence CAR T-cell Activity
Authors: Joy Joash D. , Malacrida Beatrice , Laforêts Florian , Kotantaki Panoraia , Maniati Eleni , Manchanda Ranjit , Annibaldi Alessandro , Hopkins Sarah , Garrobo-Calleja Ianire , Gautrot Julien , Balkwill Frances R.
Published: August 2024

Inhibition of TGFβ signaling reduced ECM density and stimulated CAR T-cell activity in G164/FB gels. A, M3C, COL1A1, and FN1 staining and quantification of G164/FB gels treated with TGFβR inhibitor (TGFβR inhi). Scale bar, 50 μm. B, TWOMBLI analysis showing the heatmaps and %HDM for M3C, COL1A1, and fibronectin (FN1) in G164/FB gels treated with TGFβR inhibitor. Scale bar, 100 μm. C, Number of CD3+ CAR T cells at the peripheral and core regions of G164/FB collagen gels treated with TGFβR inhibitor. Two different CAR T-cell and FB donors were used for this experiment. D, Heatmaps generated using Definiens Tissue Studio showing the distribution of CAR T cells in G164/FB collagen gels treated with TGFβR inhibitor. Representative images from two/three gels per two replicates. Scale bar, 500 μm. E, IHC staining and quantification for caspase-3 (Casp3) on G164/FB gels treated with TGFβR inhibitor. Scale bar, 50 μm. F, Expression of FAP on G164/FB gels treated with TGFβR inhibitor. Scale bar, 50 μm. G, Behavior of CAR T cells in G164/FB gels treated with TGFβR inhibitor. Representative images from three repeats. Blue, FN1; green, CAR T cells; red, EpCAM. Scale bar, 50 μm. Speed and length of movement of migrating (vehicle, 83; TGFβR inhibitor, 62) CAR T cells. H, Number of CD3+ (left) and Casp3+ (right) on G164/FB gels treated with TGFβR inhibitor and aCCL2. A–C, E, F, and H, Data plotted as mean ± SD of two/three gels per two replicates. Statistics performed using unpaired t test (A, B, and F) and two-way ANOVA (C, E, and H).
Supplementary Table S6 from Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Authors: Keller Patricia J. , Adams Elizabeth J. , Wu Rentian , Côté Alexandre , Arora Shilpi , Cantone Nico , Meyer Rosana , Mertz Jennifer A. , Gehling Victor , Cui Jike , Stuckey Jacob I. , Khanna Avinash , Zhao Feng , Chen Zehua , Yu Ziyang , Cummings Richard T. , Taimi Mohammed , Lakhani Nehal J. , Rasco Drew , Gutierrez Martin , Duska Linda , Devitt Michael , Rippley Ronda , Levell Julian , Truong Jennifer , Wang Jing , Sun Kaiming , Trojer Patrick
Published: August 2024

List of gene names corresponding to 132 tulmimetostat upregulated genes in responder versus non responder cell lines
Supplementary Table S3 from Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Authors: Keller Patricia J. , Adams Elizabeth J. , Wu Rentian , Côté Alexandre , Arora Shilpi , Cantone Nico , Meyer Rosana , Mertz Jennifer A. , Gehling Victor , Cui Jike , Stuckey Jacob I. , Khanna Avinash , Zhao Feng , Chen Zehua , Yu Ziyang , Cummings Richard T. , Taimi Mohammed , Lakhani Nehal J. , Rasco Drew , Gutierrez Martin , Duska Linda , Devitt Michael , Rippley Ronda , Levell Julian , Truong Jennifer , Wang Jing , Sun Kaiming , Trojer Patrick
Published: August 2024

Table listing experimentally determined compound binding affinities for EZH2 and EZH1 containing PRC2 protein complexes
Figure S5 from Extracellular Vesicles Containing circMYBL1 Induce CD44 in Adenoid Cystic Carcinoma Cells and Pulmonary Endothelial Cells to Promote Lung Metastasis
Authors: Fu Min , Gao Qian , Xiao Mian , Li Rui-Feng , Sun Xin-Yi , Li Sheng-Lin , Peng Xin , Ge Xi-Yuan
Published: August 2024

Figure S5
Supplementary Table S1 from Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Authors: Keller Patricia J. , Adams Elizabeth J. , Wu Rentian , Côté Alexandre , Arora Shilpi , Cantone Nico , Meyer Rosana , Mertz Jennifer A. , Gehling Victor , Cui Jike , Stuckey Jacob I. , Khanna Avinash , Zhao Feng , Chen Zehua , Yu Ziyang , Cummings Richard T. , Taimi Mohammed , Lakhani Nehal J. , Rasco Drew , Gutierrez Martin , Duska Linda , Devitt Michael , Rippley Ronda , Levell Julian , Truong Jennifer , Wang Jing , Sun Kaiming , Trojer Patrick
Published: August 2024

Table with cell line information including source and RRID
Supplementary Materials and Methods from Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Authors: Keller Patricia J. , Adams Elizabeth J. , Wu Rentian , Côté Alexandre , Arora Shilpi , Cantone Nico , Meyer Rosana , Mertz Jennifer A. , Gehling Victor , Cui Jike , Stuckey Jacob I. , Khanna Avinash , Zhao Feng , Chen Zehua , Yu Ziyang , Cummings Richard T. , Taimi Mohammed , Lakhani Nehal J. , Rasco Drew , Gutierrez Martin , Duska Linda , Devitt Michael , Rippley Ronda , Levell Julian , Truong Jennifer , Wang Jing , Sun Kaiming , Trojer Patrick
Published: August 2024

Additional method information to describe technical aspects of the experiments described in this manuscript
Supplementary Figure S7 from Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Authors: Keller Patricia J. , Adams Elizabeth J. , Wu Rentian , Côté Alexandre , Arora Shilpi , Cantone Nico , Meyer Rosana , Mertz Jennifer A. , Gehling Victor , Cui Jike , Stuckey Jacob I. , Khanna Avinash , Zhao Feng , Chen Zehua , Yu Ziyang , Cummings Richard T. , Taimi Mohammed , Lakhani Nehal J. , Rasco Drew , Gutierrez Martin , Duska Linda , Devitt Michael , Rippley Ronda , Levell Julian , Truong Jennifer , Wang Jing , Sun Kaiming , Trojer Patrick
Published: August 2024

In cancer patients tulmimetostat plasma exposure levels correlate with PRC2 target gene expression changes in peripheral blood.
Supplementary Figure S6 from Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Authors: Keller Patricia J. , Adams Elizabeth J. , Wu Rentian , Côté Alexandre , Arora Shilpi , Cantone Nico , Meyer Rosana , Mertz Jennifer A. , Gehling Victor , Cui Jike , Stuckey Jacob I. , Khanna Avinash , Zhao Feng , Chen Zehua , Yu Ziyang , Cummings Richard T. , Taimi Mohammed , Lakhani Nehal J. , Rasco Drew , Gutierrez Martin , Duska Linda , Devitt Michael , Rippley Ronda , Levell Julian , Truong Jennifer , Wang Jing , Sun Kaiming , Trojer Patrick
Published: August 2024

Tulmimetostat demonstrates superior level of tumor PRC2 target gene inducon and correlation with efficacy in a bladder cancer xenograft mouse model.
Supp_Fig_S1-S19 from The DNA Methyltransferase Inhibitor 5-Aza-4′-thio-2′-Deoxycytidine Induces C>G Transversions and Acute Lymphoid Leukemia Development
Authors: Bertoli Ryan M. , Chung Yang Jo , Difilippantonio Michael J. , Wokasch Anthony , Marasco Madison R.B. , Klimaszewski Haley , Gammell Susannah , Zhu Yuelin J. , Walker Robert L. , Cao Dengchao , Khanna Ajay , Walter Matthew J. , Doroshow James H. , Meltzer Paul S. , Aplan Peter D.
Published: August 2024

Supp_Fig_S1-S19
Supplementary Figure S3 from Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Authors: Keller Patricia J. , Adams Elizabeth J. , Wu Rentian , Côté Alexandre , Arora Shilpi , Cantone Nico , Meyer Rosana , Mertz Jennifer A. , Gehling Victor , Cui Jike , Stuckey Jacob I. , Khanna Avinash , Zhao Feng , Chen Zehua , Yu Ziyang , Cummings Richard T. , Taimi Mohammed , Lakhani Nehal J. , Rasco Drew , Gutierrez Martin , Duska Linda , Devitt Michael , Rippley Ronda , Levell Julian , Truong Jennifer , Wang Jing , Sun Kaiming , Trojer Patrick
Published: August 2024

Tulmimetostat increases PRC2-repressed gene expression in ARID1A mutant bladder cancer cells. (
Supplementary Tables from Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression
Authors: Meng Xiaoyan , Zheng Yang , Zhang Lingfang , Liu Peipei , Liu Zhonglong , He Yue
Published: August 2024

Supplementary Table1,5-6
Supplementary Table4 from Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression
Authors: Meng Xiaoyan , Zheng Yang , Zhang Lingfang , Liu Peipei , Liu Zhonglong , He Yue
Published: August 2024

Supplementary Table4
Supplementary Table3 from Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression
Authors: Meng Xiaoyan , Zheng Yang , Zhang Lingfang , Liu Peipei , Liu Zhonglong , He Yue
Published: August 2024

Supplementary Table3
Supplementary Table2 from Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression
Authors: Meng Xiaoyan , Zheng Yang , Zhang Lingfang , Liu Peipei , Liu Zhonglong , He Yue
Published: August 2024

Supplementary Table2
Supplementary Figures and Legends from Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression
Authors: Meng Xiaoyan , Zheng Yang , Zhang Lingfang , Liu Peipei , Liu Zhonglong , He Yue
Published: August 2024

Supplementary Figures and Legends
Figure S8 from Allysine-Targeted Molecular MRI Enables Early Prediction of Chemotherapy Response in Pancreatic Cancer
Authors: Ma Hua , Esfahani Shadi A. , Krishna Shriya , Ataeinia Bahar , Zhou Iris Y. , Rotile Nicholas J. , Weigand-Whittier Jonah , Boice Avery T. , Liss Andrew S. , Tanabe Kenneth K. , Caravan Peter
Published: August 2024

Figure S8. Quantification of manganese content in the PANC1 tumor 60 minutes post-injection of MnL3. MnL3 exhibited significantly higher tumor uptake in PANC1 tumors treated with one dose of FOLFIRINOX compared to the untreated mice (0.1 mmol/kg, i.v., 60 min p.i., n = 4 for each group, Student’s t-test, two-tailed, *P<0.05).
Figure S6 from Allysine-Targeted Molecular MRI Enables Early Prediction of Chemotherapy Response in Pancreatic Cancer
Authors: Ma Hua , Esfahani Shadi A. , Krishna Shriya , Ataeinia Bahar , Zhou Iris Y. , Rotile Nicholas J. , Weigand-Whittier Jonah , Boice Avery T. , Liss Andrew S. , Tanabe Kenneth K. , Caravan Peter
Published: August 2024

Figure S6. Quantification of manganese content in the PDAC6 tumor 60 minutes post-injection of MnL3. MnL3 (0.1 mmol/kg, i.v., 60 min p.i.) exhibited significantly higher tumor uptake at 3 days (P = 0.05) and 7 days (P = 0.04) after initiation of FOLFIRINOX treatment compared to the untreated tumor (One-way ANOVA with Tukey’s post hoc test, *P<0.05, ns, not significant. n = 6 for day 0 and day 3, n = 5 for day 7).
Figure S2 from Allysine-Targeted Molecular MRI Enables Early Prediction of Chemotherapy Response in Pancreatic Cancer
Authors: Ma Hua , Esfahani Shadi A. , Krishna Shriya , Ataeinia Bahar , Zhou Iris Y. , Rotile Nicholas J. , Weigand-Whittier Jonah , Boice Avery T. , Liss Andrew S. , Tanabe Kenneth K. , Caravan Peter
Published: August 2024

Figure S2. Mass spectra of MnL4 before and after incubation with butyraldehyde. (A) MS spectrum of MnL4. [M + H]+ calcd for [C25H39MnN6O7], 590.2; found 590.0. (B) MnL4 did not react with butyraldehyde at pH 7.4 (PBS). [M + H]+ calcd for [C25H39MnN6O7], 590.2; found 590.0). (C) MnL4 did not react with butyraldehyde at pH 6.5 (PBS). [M + H]+ calcd for [C25H39MnN6O7], 590.2; found 590.0).
Data from Comprehensive Target Engagement by the EZH2 Inhibitor Tulmimetostat Allows for Targeting of ARID1A Mutant Cancers
Authors: Keller Patricia J. , Adams Elizabeth J. , Wu Rentian , Côté Alexandre , Arora Shilpi , Cantone Nico , Meyer Rosana , Mertz Jennifer A. , Gehling Victor , Cui Jike , Stuckey Jacob I. , Khanna Avinash , Zhao Feng , Chen Zehua , Yu Ziyang , Cummings Richard T. , Taimi Mohammed , Lakhani Nehal J. , Rasco Drew , Gutierrez Martin , Duska Linda , Devitt Michael , Rippley Ronda , Levell Julian , Truong Jennifer , Wang Jing , Sun Kaiming , Trojer Patrick
Published: August 2024

Abstract
Recurrent somatic mutations in the BRG1/BRM-associated factor (BAF) chromatin remodeling complex subunit ARID1A occur frequently in advanced urothelial, endometrial, and ovarian clear cell carcinomas, creating an alternative chromatin state that may be exploited therapeutically. The histone methyltransferase EZH2 has been previously identified as targetable vulnerability in the context of ARID1A mutations. In this study, we describe the discovery of tulmimetostat, an orally available, clinical stage EZH2 inhibitor, and it elucidates the aspects of its application potential in ARID1A mutant tumors. Tulmimetostat administration achieved efficacy in multiple ARID1A mutant bladder, ovarian, and endometrial tumor models and improved cisplatin response in chemotherapy-resistant models. Consistent with its comprehensive and durable level of target coverage, tulmimetostat demonstrated greater efficacy than other PRC2-targeted inhibitors at comparable or lower exposures in a bladder cancer xenograft mouse model. Tulmimetostat mediated extensive changes in gene expression, in addition to a profound reduction in global H3K27me3 levels in tumors. Phase I clinical pharmacokinetic and pharmacodynamic data indicated that tulmimetostat exhibits durable exposure and profound target engagement. Importantly, a tulmimetostat controlled gene expression signature identified in whole blood from a cohort of 32 patients with cancer correlated with tulmimetostat exposure, representing a pharmacodynamic marker for the assessment of target coverage for PRC2-targeted agents in the clinic. Collectively, these data suggest that tulmimetostat has the potential to achieve clinical benefit in solid tumors as a monotherapy but also in combination with chemotherapeutic agents, and may be beneficial in various indications with recurrent ARID1A mutations.

Significance: The EZH2 inhibitor tulmimetostat achieves comprehensive target inhibition in ARID1A mutant solid tumor models and cancer patients that can be assessed with a pharmacodynamic gene signature in peripheral blood.
Data from Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression
Authors: Meng Xiaoyan , Zheng Yang , Zhang Lingfang , Liu Peipei , Liu Zhonglong , He Yue
Published: August 2024

Abstract
Metabolic reprogramming is a hallmark of cancer. In addition to metabolic alterations in the tumor cells, multiple other metabolically active cell types in the tumor microenvironment (TME) contribute to the emergence of a tumor-specific metabolic milieu. Here, we defined the metabolic landscape of the TME during the progression of head and neck squamous cell carcinoma (HNSCC) by performing single-cell RNA sequencing on 26 human patient specimens, including normal tissue, precancerous lesions, early stage cancer, advanced-stage cancer, lymph node metastases, and recurrent tumors. The analysis revealed substantial heterogeneity at the transcriptional, developmental, metabolic, and functional levels in different cell types. SPP1+ macrophages were identified as a protumor and prometastatic macrophage subtype with high fructose and mannose metabolism, which was further substantiated by integrative analysis and validation experiments. An inhibitor of fructose metabolism reduced the proportion of SPP1+ macrophages, reshaped the immunosuppressive TME, and suppressed tumor growth. In conclusion, this work delineated the metabolic landscape of HNSCC at a single-cell resolution and identified fructose metabolism as a key metabolic feature of a protumor macrophage subpopulation.

Significance: Fructose and mannose metabolism is a metabolic feature of a protumor and prometastasis macrophage subtype and can be targeted to reprogram macrophages and the microenvironment of head and neck squamous cell carcinoma.
Supplemental Figure 4 from Age-Specific Cancer Mortality in the US During the COVID-19 Pandemic, March to December 2020
Authors: Shiels Meredith S. , Haque Anika T. , Freedman Neal D. , Kim Hae-Rin , Berrington de González Amy , Albert Paul S.
Published: August 2024

Supplemental Figure 4. Adjusted rate ratios comparing colorectal cancer death rates during the COVID-19 period (March-December 2020) to the pre–COVID-19 period (January 2011-February 2020) by month by age group. Points represent adjusted rate ratios and lines represent 95% confidence intervals. Models adjusted for linear calendar time in months, and seasonal patterns with sine and cosine terms.
Supplementary Table S8 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms
Authors: Davidson Natalie R. , Barnard Mollie E. , Hippen Ariel A. , Campbell Amy , Johnson Courtney E. , Way Gregory P. , Dalley Brian K. , Berchuck Andrew , Salas Lucas A. , Peres Lauren C. , Marks Jeffrey R. , Schildkraut Joellen M. , Greene Casey S. , Doherty Jennifer A.
Published: August 2024

Balanced accuracy comparing subtype labels from K-means and PrOTYPE for each subtype
Supplementary Table S6 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms
Authors: Davidson Natalie R. , Barnard Mollie E. , Hippen Ariel A. , Campbell Amy , Johnson Courtney E. , Way Gregory P. , Dalley Brian K. , Berchuck Andrew , Salas Lucas A. , Peres Lauren C. , Marks Jeffrey R. , Schildkraut Joellen M. , Greene Casey S. , Doherty Jennifer A.
Published: August 2024

SchildkrautW metadata
Supplementary Figure S6 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms
Authors: Davidson Natalie R. , Barnard Mollie E. , Hippen Ariel A. , Campbell Amy , Johnson Courtney E. , Way Gregory P. , Dalley Brian K. , Berchuck Andrew , Salas Lucas A. , Peres Lauren C. , Marks Jeffrey R. , Schildkraut Joellen M. , Greene Casey S. , Doherty Jennifer A.
Published: August 2024

Gene set venn diagram
Supplementary Figure S3 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms
Authors: Davidson Natalie R. , Barnard Mollie E. , Hippen Ariel A. , Campbell Amy , Johnson Courtney E. , Way Gregory P. , Dalley Brian K. , Berchuck Andrew , Salas Lucas A. , Peres Lauren C. , Marks Jeffrey R. , Schildkraut Joellen M. , Greene Casey S. , Doherty Jennifer A.
Published: August 2024

Evaluation of read quality in Schildkraut datasets
Supplementary Figure S13 from Molecular Subtypes of High-Grade Serous Ovarian Cancer across Racial Groups and Gene Expression Platforms
Authors: Davidson Natalie R. , Barnard Mollie E. , Hippen Ariel A. , Campbell Amy , Johnson Courtney E. , Way Gregory P. , Dalley Brian K. , Berchuck Andrew , Salas Lucas A. , Peres Lauren C. , Marks Jeffrey R. , Schildkraut Joellen M. , Greene Casey S. , Doherty Jennifer A.
Published: August 2024

Immune infiltration violin plots
Table S5 from Genetic Risk of Second Malignant Neoplasm after Childhood Cancer Treatment: A Systematic Review
Authors: Ducos Claire , Aba Naïla , Rosselli Filippo , Fresneau Brice , Al Ahmad Nachar Baraah , Zidane Monia , de Vathaire Florent , Benhamou Simone , Haddy Nadia
Published: August 2024

Table S5 summarizes the reasons behind the exclusion of 15 articles following the review of their full texts.