bluuebunny/crossref_metadata_2025 huggingface dataset:
From O’Shaughnessy to opportunity: innovating Hepatology Trials in the
UK
Authors: Tavabie Oliver D , Enever Yvanne , Green Daniel , Crisp Helen , Tsochatzis Emmanouil , Gander Amir , Mansour Dina , Hebditch Vanessa , Adams Julie , Ashbourn Adam , Mysko Christopher , Allen Richard , Kent Laura , Maurice James B , Srivastava Ankur , Chauhan Abhishek , Johnston Tom , Ruane Janet , Varni Rebecca , Fletcher Caroline , Sieberhagen Cyril , Hay Gordon , Bretland Giovanna , Corrigan Maggie , Ferraro Francesco , McMahon Riley , Burge Trudie , Ferguson Harry , Jennings Louise , Hogan Brian , Cook Andrew , Jalan Rajiv , Mehta Gautam
Published: July 2024

Developing new treatments that improve outcomes for patients with
decompensated cirrhosis remains an unmet area of clinical need. The UK has a
rich history of being on the forefront of clinical trials for this patient
group. However, there have been challenges in achieving this goal in the
past decade, with several negative studies as well as trials struggling to
achieve recruitment. This has been further exacerbated by the changed
clinical landscape following the COVID-19 pandemic. In response to this, the
O’Shaughnessy report was commissioned to identify potential opportunities to
improve clinical trial performance in the UK. In this review article, we
identify critical areas for the UK hepatology community to collaborate and
develop sustainable partnerships for clinical trial delivery which will
ensure that outcomes are representative, inclusive and
patient-centred.
Assessing the implications of sentinel lymph node removal in cervical cancer: an immunogenetic perspective – a SENTICOL ancillary study
Authors: Thareja Gaurav , Salvioni Anna , Lauzeral-Vizcaino Françoise , Halabi Najeeb , Mery-Lamarche Eliane , Thebault Noemie , Scarlata Clara-Maria , Michelas Marie , Navarro Anne-Sophie , Ferron Gwenaël , Lecuru Fabrice , Mathevet Patrice , Khalifa Jonathan , Ayyoub Maha , Rafii Arash , Martinez Alejandra
Published: July 2024

Background

Cervical cancer’s lymphatic spread primarily begins from the sentinel lymph nodes (SLNs), underlining their pivotal role in disease metastasis. However, these nodes’ immune gene expression profiles and immunoregulation mechanisms have yet to be explored.

Methods

Our study aimed to elucidate the immune cell populations and their roles in the immune gene expression profile of negative SLNs compared with positive SLNs and non-SLNs using Nanostring RNA seq analysis. We performed a principal component analysis on the log2 normalized expression of 685 endogenous genes in the nCounter PanCancer Immune Profiling Panel, followed by an assessment of the differential expression of genes and immune cell type abundance.

Results

We found significant variations in gene expression among the groups, with negative SLNs displaying overexpression of genes related to tumor-infiltrating immune cells, specifically innate cell populations. They also demonstrated the upregulation of genes involved in antigen presentation and T-cell priming. In contrast, positive SLNs were enriched in regulatory networks, suggesting their potential role in immune evasion. A comparison of negative SLNs and non-SLNs revealed increased innate and adaptive immune cell types, underscoring the ongoing T cell response to tumor antigens.

Conclusion

Our findings underscore a specific immunogenetic phenotype profile in negative SLNs, emphasizing their crucial role in the initial anticancer response, immunosurveillance, and the propagation of immune tolerance from the primary cervical tumor. These results highlight the potential of SLNs as a novel target for immunotherapy strategies and underscore the importance of new imaging methods for accurately identifying SLN status without removal. Future investigations are needed to understand further the immunological interplay within SLNs and their influence on cervical cancer progression.
A Relational Graph Convolution Network-Based Smart Risk Recognition Model for Financial Transactions
Authors: Zhang Li , Deng Junmiao
Published: July 2024

The financial transaction relationships between existing entities are complex and diverse. In this situation, traditional risk control methods mainly ignored such complex and implicit relationship characteristics, remaining difficult to cope with complex and ever-changing financial risks. To address this issue, this paper proposes a novel relational graph convolution network (GCN)-based smart risk recognition model for financial transactions. Firstly, the classic GCN is simplified based on spatiotemporal effect. Then, feature extraction is conducted for financial transaction data, and a transformer encoder-based GCN model is proposed for risk recognition. The proposed model in this work is named as graph transformer graph convolutional network (GT-GCN) for short. In addition, fuzzy evaluation method is added into it. Finally, some experiments are conducted on real-world financial transaction data to make validation for the proposed GT-GCN. The research results indicate that the GT-GCN can not only effectively identify risks in financial transactions, but also has high accuracy and predictive ability. The application of GT-GCN to actual datasets also has good scalability and adaptability, and it can be resiliently extended into many other fields.
Image Restoration Technology of Tang Dynasty Tomb Murals Using Adversarial Edge Learning
Authors: Yan Yao , Zhang Rui , He Hao , Lei Tong , Zhang Xusheng , Jiang Chao
Published: July 2024

The city of Xi’an, China houses a vast collection of valuable Tang dynasty (618 AD-907 AD) tomb murals that have experienced various degrees of damage over time due to weathering. This research proposes an adversarial edge learning-based mural restoration technique that provides a fast and accurate automatic repair of the murals. The method uses generative adversarial networks to learn how to repair the edge contour of a damaged mural and restore the missing content. The contour restoration network and mural restoration networks are trained and updated simultaneously to enhance the feature extraction and restoration coordination performance of the network. The experiments were conducted on a self-built Tang dynasty tomb mural painting restoration dataset and compared to several existing algorithms. The proposed algorithm showed a 1.3 increase in peak signal-to-noise ratio (PSNR) and a 1.43% increase in structural similarity (SSIM) value, providing a precise restoration of the structure and contour of the mural content. The algorithm successfully repaired damaged murals with fractures and small missing parts. The suggested method can be useful for both the technical repair and conservation of significant national visual cultural property and the digital restoration of historic murals.
INCEPT: A Framework for Duplicate Posts Classification with Combined Text Representations
Authors: Skenderi Erjon , Huhtamäki Jukka , Laaksonen Salla-Maaria , Stefanidis Kostas
Published: July 2024

Dealing with many of the problems related to the quality of textual content online involves identifying similar content. Algorithmic solutions for duplicate content classification typically rely on text vector representation, which maps textual information into a set of features. Ideally, this representation would capture all aspects of the underlying text, including length, word frequencies, syntax, and semantics. While recent advancements in text representation have led to improved performance, a comprehensive approach that explicitly incorporates all text features has not yet been proposed. In this study, we present the INCEPT framework that utilizes multiple representation methods to detect duplicate text pairs, taking advantage of their individual strengths. The core of our approach involves using a stacking ensemble of pairwise vector distance measurements that are computed from multiple text representation methods. A stacking classifier then utilizes these distance scores as input and learns to identify duplicate posts. We assess the proposed framework’s effectiveness in identifying duplicate posts in an online Question and Answer platform. By combining several text representation methods, INCEPT performs well in the duplicate posts classification task. Our experiments demonstrate that specific framework configurations outperform the accuracy scores obtained from individual text representation methods. Therefore, we also infer that no single text representation method can independently capture a text’s features.
Pure-Circuit: Tight Inapproximability for PPAD
Authors: Deligkas Argyrios , Fearnley John , Hollender Alexandros , Melissourgos Themistoklis
Published: July 2024

The current state-of-the-art methods for showing inapproximability in
PPAD
arise from the ɛ-Generalized-Circuit (ɛ-
GCircuit
) problem. Rubinstein (2018) showed that there exists a small unknown constant ɛ for which ɛ-
GCircuit
is
PPAD
-hard, and subsequent work has shown hardness results for other problems in
PPAD
by using ɛ-
GCircuit
as an intermediate problem.

We introduce
Pure-Circuit
, a new intermediate problem for
PPAD
, which can be thought of as ɛ-
GCircuit
pushed to the limit as ɛ → 1, and we show that the problem is
PPAD
-complete. We then prove that ɛ-
GCircuit
is
PPAD
-hard for all ɛ < 1/10 by a reduction from
Pure-Circuit
, and thus strengthen all prior work that has used
GCircuit
as an intermediate problem from the existential-constant regime to the large-constant regime.

We show that stronger inapproximability results can be derived by reducing directly from
Pure-Circuit
. In particular, we prove tight inapproximability results for computing approximate Nash equilibria and approximate well-supported Nash equilibria in graphical games, for finding approximate well-supported Nash equilibria in polymatrix games, and for finding approximate equilibria in threshold games.
MarMot: Metamorphic Runtime Monitoring of Autonomous Driving Systems
Authors: Ayerdi Jon , Iriarte Asier , Valle Pablo , Roman Ibai , Illarramendi Miren , Arrieta Aitor
Published: July 2024

Autonomous driving systems (ADSs) are complex cyber-physical systems (CPSs) that must ensure safety even in uncertain conditions. Modern ADSs often employ deep neural networks (DNNs), which may not produce correct results in every possible driving scenario. Thus, an approach to estimate the confidence of an ADS at runtime is necessary to prevent potentially dangerous situations. In this article we propose
MarMot
, an online monitoring approach for ADSs based on metamorphic relations (MRs), which are properties of a system that hold among multiple inputs and the corresponding outputs. Using domain-specific MRs,
MarMot
estimates the uncertainty of the ADS at runtime, allowing the identification of anomalous situations that are likely to cause a faulty behavior of the ADS, such as driving off the road.

We perform an empirical assessment of
MarMot
with five different MRs, using two different subject ADSs, including a small-scale physical ADS and a simulated ADS. Our evaluation encompasses the identification of both external anomalies, e.g., fog, as well as internal anomalies, e.g., faulty DNNs due to mislabeled training data. Our results show that
MarMot
can identify up to 65% of the external anomalies and 100% of the internal anomalies in the physical ADS, and up to 54% of the external anomalies and 88% of the internal anomalies in the simulated ADS. With these results,
MarMot
outperforms or is comparable to other state-of-the-art approaches, including SelfOracle, Ensemble, and MC Dropout-based ADS monitors.
CoMix: Confronting with Noisy Label Learning with Co-training Strategies on Textual Mislabeling
Authors: Zhao Shu , Zhao Zhuoer , Xu Yangyang , Sun Xiao
Published: July 2024

The existence of noisy labels is inevitable in real-world large-scale corpora. As deep neural networks are notably vulnerable to overfitting on noisy samples, this highlights the importance of the ability of language models to resist noise for efficient training. However, little attention has been paid to alleviating the influence of label noise in natural language processing. To address this problem, we present CoMix, a robust Noise-against training strategy taking advantage of Co-training that deals with textual annotation errors in text classification tasks. In our proposed framework, the original training set is first split into labeled and unlabeled subsets according to a sample partition criteria and then applies label refurbishment on the unlabeled subsets. We implement textual interpolation in hidden space between samples on the updated subsets. Meanwhile, we employ peer diverged networks simultaneously leveraging co-training strategies to avoid the accumulation of confirm bias. Experimental results on three popular text classification benchmarks demonstrate the effectiveness of CoMix in bolstering the network’s resistance to label mislabeling under various noise types and ratios, which also outperforms the state-of-the-art methods.
Multi-Level Fusion for Robust RGBT Tracking via Enhanced Thermal Representation
Authors: Tang Zhangyong , Xu Tianyang , Wu Xiao-Jun , Kittler Josef
Published: July 2024

Due to the limitations of visible (RGB) sensors in challenging scenarios, such as nighttime and foggy environments, the thermal infrared (TIR) modality draws increasing attention as an auxiliary source for robust tracking systems. Currently, the existing methods extract both the RGB and TIR (RGBT) clues in a similar approach, i.e., utilising RGB-pretrained models with or without finetuning, and then aggregate the multi-modal information through a fusion block embedded in a single level. However, the different imaging principles of RGB and TIR data raise questions about the suitability of RGB-pretrained models for thermal data. In this article, it is argued that the modality gap is overlooked, and an alternative training paradigm is proposed for TIR data to ensure consistency between the training and test data, which is achieved by optimising the TIR feature extractor with only TIR data involved. Furthermore, with the goal of making better use of the enhanced thermal representations, a multi-level fusion strategy is inspired by the observation that various fusion strategies at different levels can contribute to a better performance. Specifically, fusion modules at both the feature and decision levels are derived for a comprehensive fusion procedure while the pixel-level fusion strategy is not considered due to the misalignment of multi-modal image pairs. The effectiveness of our method is demonstrated by extensive qualitative and quantitative experiments conducted on several challenging benchmarks. Code will be released at
https://github.com/Zhangyong-Tang/MELT
.
Lidar, Space, and Time in Archaeology: Promises and Challenges
Authors: Inomata Takeshi
Published: July 2024

Airborne lidar (light detection and ranging), which produces three-dimensional models of ground surfaces under the forest canopy, has become an important tool in archaeological research. On a microscale, lidar can lead to a new understanding of building shapes and orientations that were not recognized previously. On a medium scale, it can provide comprehensive views of settlements, cities, and polities and their relationships to the topography. It also facilitates studies of diverse land use practices, such as agricultural fields, roads, and canals. On a macroscale, lidar provides a means to comprehend broad spatial patterns beyond individual sites, including the implications of vacant spaces. A significant challenge for archaeologists is the integration of historical and temporal information in order to contextualize lidar data in the framework of landscape archaeology. In addition, a rapid increase in lidar data presents ethical issues, including the question of data ownership.
Influence of angiotensin II and telmisartan on in vivo high‐resolution renal arterial impedance in rats
Authors: Fukuda Yukiko , Kawada Toru , Kataoka Yasuyuki , Peterson Jon , Saku Keita , Alexander Joe , Sunagawa Kenji
Published: July 2024

This present method of quantifying high-resolution renal arterial impedance could contribute to elucidating the characteristics of renal vasculature influenced by physiological mechanisms, renal diseases, or pharmacological effects. The present findings help construct a lumped-parameter renal hemodynamic model that reflects the influence of angiotensin II.
High-intensity interval versus moderate-intensity continuous cycling training in Parkinson’s disease: a randomized trial
Authors: Kathia Muhammad M. , Duplea Sergiu-Gabriel , Bommarito Julian C. , Hinks Avery , Leake Elira , Shannon Julia , Pitman Jenna , Khangura Pardeep K. , Coates Alexandra M. , Slysz Joshua T. , Katerberg Carlin , McCarthy Devin G. , Beedie Taylor , Malcolm Rhianna , Witton Leslie A. , Connolly Barbara S. , Burr Jamie F. , Vallis Lori Ann , Power Geoffrey A. , Millar Philip J.
Published: July 2024

The optimal exercise prescription to improve cardiorespiratory fitness and disease-related motor symptoms in adults with Parkinson’s disease remains unknown. In a single-center randomized trial consisting of either 10 wk of high-intensity interval training (HIIT) or moderate-intensity continuous training (MICT), we found that both training modes increased V̇o2peak, with a larger clinically meaningful difference following HIIT. Both exercise modes improved motor symptoms and subjective fatigue, whereas HIIT increased the muscular endurance of the knee extensors.
Aloe vera Leaf Extract Reduced BBB Permeability and Improved Neurological Results after Traumatic Brain Injury: The Role of Oxidative Stress
Authors: Khaksari Mohammad , Shahryari Marzieh , Raji-Amirhasani Alireza , Soltani Zahra , Bibak Bahram , Keshavarzi Zakieh , Shakeri Farzaneh
Published: July 2024

Introduction. Recognizing the importance of medicinal plants and the absence of specific medications for traumatic brain injury (TBI) treatment, this study was conducted to evaluate the effects of an aqueous extract of Aloe vera on oxidative stress, blood–brain barrier (BBB) permeability, and neurological scores following TBI. Materials and Methods. Adult male rats were categorized into five groups: sham, TBI, vehicle, low‐dose Aloe vera (LA), and high‐dose Aloe vera (HA). We induced diffuse TBI using the Marmaro model and administered the aqueous Aloe vera leaf extract, as well as vehicle, via intraperitoneal injection half an hour after TBI. Neurological outcomes were assessed both before and several hours after TBI. Additionally, oxidative stress factors were measured 24 hr after TBI, and Evans blue content (a BBB permeability index) was determined 5 hr after TBI in both serum and brain. Results. Both LA and HA reduced the increase in BBB permeability after TBI, with HA having a more pronounced effect than LA. Both Aloe vera doses decreased brain MDA levels, increased brain TAC, and lowered both serum and brain PC levels. The impact of Aloe vera on brain oxidative parameters was more significant than on serum. HA also counteracted the declining effects of TBI on neurological outcomes at 4 and 24 hr post‐TBI. Conclusion. This study suggests that Aloe vera extract may reduce BBB permeability and improve neurological outcomes after TBI by decreasing oxidative factors and increasing antioxidant factors.
Intravitreal Dexamethasone Implant (Ozurdex) for Ocular Toxocariasis
Authors: Zhou Yongwei , Zhen Fangyuan , Wu Jiahui , Wang Shasha , Lu Xiaoyan , Yang Ge , Hu Zhirou , Chen Fei , Li Qiuming , Dong Shuqian
Published: July 2024

This study aimed to evaluate the efficacy and safety of intravitreal dexamethasone implants in the treatment of ocular toxocariasis (OT). A retrospective analysis was performed on 6 cases in which laboratory tests diagnosed OT. All patients were administered with intravitreal dexamethasone implants with or without vitrectomy. The average follow‐up time was 19.7 months. All operated eyes achieved anatomic success, and all patients’ visual acuity was improved. Five of these six had a visual acuity of 20/100, and three had final acuity of 20/40 or even better. Intravitreal dexamethasone implants can be used to treat different types of OT, which not only effectively control inflammation and improve the patient’s vision but also reduce the use of systemic glucocorticoids.
Health Services for Young Adults with Stroke: A Service Mapping Study over Two Australian States
Authors: Giummarra Melita J. , Power Emma , Stolwyk Renerus , Crotty Maria , Parsons Brooke , Lannin Natasha A.
Published: July 2024

Despite increased incidence of stroke in young adulthood across the world, young adults report significant difficulties finding services with the expertise and experience to meet their needs. This service mapping study sought to identify and characterise the availability, accessibility, and accommodation of services to meet the needs of young adults (aged 18–44 years) with stroke in two Australian states. Methods. Relevant clinical, rehabilitation, and allied health services were systematically identified from previous publications; the National Health Service Directory; professional association “find a provider” listings; and Stroke Foundation service lists. Desktop audit (n = 465 services) and key informant interviews (n = 321 services) were used to collect service design and delivery characteristics; level of experience, confidence, and willingness to work with young adults with stroke; and accommodation of communication impairments. Results. Most services (85%) were in major cities or inner regional areas. No services worked solely with young adults with stroke; however, several reported having relevant expertise, training, experience, and programmes to provide neurological rehabilitation to meet the needs of young adults with stroke. Reported willingness (91.0%) to work with young adults with stroke was high, but only 57.0% were very confident to do so. Most services with neurorehabilitation expertise addressed psychosocial recovery needs (e.g., emotional adjustment and relationships) as well as functional recovery, but few supported return‐to‐driving, peer support, and sensory processing disturbances. Further gaps were the use of accessible communication materials in only 50.2% of services, and staff had completed communication training at only 60.4% of services. Conclusion. Findings highlight that while expert neurorehabilitation services exist, they are not sufficiently available, accessible, or accommodating of the needs of young adults with stroke. There remains a need to improve access to services where clinicians have the skills to meet the rehabilitation needs of young adults with stroke in Australia.
Supplementary Table 2 from CRISPR–Cas9 Screening Identifies KRAS-Induced COX2 as a Driver of Immunotherapy Resistance in Lung Cancer
Authors: Boumelha Jesse , de Castro Andrea , Bah Nourdine , Cha Hongui , de Carné Trécesson Sophie , Rana Sareena , Tomaschko Mona , Anastasiou Panayiotis , Mugarza Edurne , Moore Christopher , Goldstone Robert , East Phil , Litchfield Kevin , Lee Se-Hoon , Molina-Arcas Miriam , Downward Julian
Published: July 2024

Supplementary Table S2. Antibodies used for FACS analysis of mouse tumors
Supplementary Figure 9 from CRISPR–Cas9 Screening Identifies KRAS-Induced COX2 as a Driver of Immunotherapy Resistance in Lung Cancer
Authors: Boumelha Jesse , de Castro Andrea , Bah Nourdine , Cha Hongui , de Carné Trécesson Sophie , Rana Sareena , Tomaschko Mona , Anastasiou Panayiotis , Mugarza Edurne , Moore Christopher , Goldstone Robert , East Phil , Litchfield Kevin , Lee Se-Hoon , Molina-Arcas Miriam , Downward Julian
Published: July 2024

Supplementary Figure 9. Oncogenic KRAS drives tumor-intrinsic expression of COX-2 in LUAD
Supplementary Figure 7 from CRISPR–Cas9 Screening Identifies KRAS-Induced COX2 as a Driver of Immunotherapy Resistance in Lung Cancer
Authors: Boumelha Jesse , de Castro Andrea , Bah Nourdine , Cha Hongui , de Carné Trécesson Sophie , Rana Sareena , Tomaschko Mona , Anastasiou Panayiotis , Mugarza Edurne , Moore Christopher , Goldstone Robert , East Phil , Litchfield Kevin , Lee Se-Hoon , Molina-Arcas Miriam , Downward Julian
Published: July 2024

Supplementary Figure 7. Genetic loss of COX-2 signaling synergizes with ICB
Fig. S6 from Metabolic Reprogramming Is an Initial Step in Pancreatic Carcinogenesis That Can Be Targeted to Inhibit Acinar-to-Ductal Metaplasia
Authors: Neuß Thorsten , Chen Min-Chun , Wirges Nils , Usluer Sinem , Oellinger Rupert , Lier Svenja , Dudek Michael , Madl Tobias , Jastroch Martin , Steiger Katja , Schmitz Werner , Einwächter Henrik , Schmid Roland M.
Published: July 2024

Glutaminolysis is dispensable for ADM
Figure 4 from CRISPR–Cas9 Screening Identifies KRAS-Induced COX2 as a Driver of Immunotherapy Resistance in Lung Cancer
Authors: Boumelha Jesse , de Castro Andrea , Bah Nourdine , Cha Hongui , de Carné Trécesson Sophie , Rana Sareena , Tomaschko Mona , Anastasiou Panayiotis , Mugarza Edurne , Moore Christopher , Goldstone Robert , East Phil , Litchfield Kevin , Lee Se-Hoon , Molina-Arcas Miriam , Downward Julian
Published: July 2024

COX2 inhibition enhances the efficacy of immunotherapy. A, Surface expression [mean fluorescence intensity (MFI)] of CD86 (left) and MHC II (right) on CD11b+ macrophages and CD11c+ macrophages in KPAR tumors treated for 7 days with 30 mg/kg celecoxib. B–D, Percentage of Arg1+ CD11b+ macrophages (B), quantification of M1/M2 macrophages (C), and frequency of CD69+ CD8+ T cells (D) in KPAR tumors treated as shown in A. E, Kaplan–Meier survival of mice treated intraperitoneally with 200 μg anti-PD1 and/or daily oral gavage of 30 mg/kg celecoxib after orthotopic transplantation of KPAR cells. Daily celecoxib treatment was initiated on day 7 and anti-PD1 began on day 10 and was administered twice weekly for a maximum of 3 weeks. Data from two independent experiments, n = 15–16 per group. Analysis of survival curves was carried out using the log-rank (Mantel–Cox) test. F, Quantification of CD8+ T cells by IHC in KPAR tumors treated for 7 days with celecoxib and/or anti-PD1. G, CD8+ T-cell phenotypes in KPAR tumors treated as shown in F. Tcm, central memory CD8+ T cells (CD44+CD62L+); Tem, effector memory CD8+ T cells (CD44+CD62L−). H, mRNA expression by qPCR of antitumor immunity genes in KPAR tumors treated as shown in F. Data are represented as mean ± SEM (A–D and F–H), n = 5–10 per group. Samples were analyzed using unpaired, two-tailed Student t test (A–D), one-way ANOVA, FDR 0.05 (F and H), or two-way ANOVA, FDR 0.05 (G). ns, not significant; *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.
Supplementary Data from IL1R2 Blockade Alleviates Immunosuppression and Potentiates Anti-PD-1 Efficacy in Triple-Negative Breast Cancer
Authors: Xia Jie , Zhang Lixing , Peng Xilei , Tu Juchuanli , Li Siqin , He Xueyan , Li Fengkai , Qiang Jiankun , Dong Haonan , Deng Qiaodan , Liu Cuicui , Xu Jiahui , Zhang Rui , Liu Quentin , Hu Guohong , Liu Chong , Jiang Yi-Zhou , Shao Zhi-Ming , Chen Ceshi , Liu Suling
Published: July 2024

Table S4
Figure S7 from IL1R2 Blockade Alleviates Immunosuppression and Potentiates Anti-PD-1 Efficacy in Triple-Negative Breast Cancer
Authors: Xia Jie , Zhang Lixing , Peng Xilei , Tu Juchuanli , Li Siqin , He Xueyan , Li Fengkai , Qiang Jiankun , Dong Haonan , Deng Qiaodan , Liu Cuicui , Xu Jiahui , Zhang Rui , Liu Quentin , Hu Guohong , Liu Chong , Jiang Yi-Zhou , Shao Zhi-Ming , Chen Ceshi , Liu Suling
Published: July 2024

Supplementary Figure S7
Table S2 from HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer
Authors: Gnanapragasam Ansley , Kirbizakis Eftyhios , Li Anna , White Kyle H. , Mortenson Katelyn L. , Cavalcante de Moura Juliana , Jawhar Wajih , Yan Yifei , Falter Reilly , Russett Colleen , Giannias Betty , Camilleri-Broët Sophie , Bertos Nicholas , Cools-Lartigue Jonathan , Garzia Livia , Sangwan Veena , Ferri Lorenzo , Zhang Xiaoyang , Bailey Swneke D.
Published: July 2024

ldSNVs for each GWAS index SNV (r2 ≥ 0.8)
Figure S4 from HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer
Authors: Gnanapragasam Ansley , Kirbizakis Eftyhios , Li Anna , White Kyle H. , Mortenson Katelyn L. , Cavalcante de Moura Juliana , Jawhar Wajih , Yan Yifei , Falter Reilly , Russett Colleen , Giannias Betty , Camilleri-Broët Sophie , Bertos Nicholas , Cools-Lartigue Jonathan , Garzia Livia , Sangwan Veena , Ferri Lorenzo , Zhang Xiaoyang , Bailey Swneke D.
Published: July 2024

The rs147518036 SNV genotypes for the gastric cancer cell lines.
Table S3 from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Table S3. ASPSCR1::TFE3 proximal proteins identified by BioID.
Table S2 from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Table S2. H3K27ac ChIP-seq samples.
Figure S9 from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Figure S9. H3K27ac ChIP-seq, input and gene expression of VEGFA
Figure S5 from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Figure S5. H3K27ac and ASPSCR1::TFE3 overlap in ASPS
Figure S17 from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Figure S17. Expression of ASPS-associated genes following drug treatment
Figure S13 from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Figure S13. ATAC-seq profiles at regions of reduced DNA accessibility following dTAG13 treatment.
Figure S12 from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Figure S12. ASPS ATAC-seq TSS and enhancer profiles.
Figure S11 from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Figure S11. ASPS model evaluation.
Dataset S3 from ACSM1 and ACSM3 Regulate Fatty Acid Metabolism to Support Prostate Cancer Growth and Constrain Ferroptosis
Authors: Shrestha Raj K. , Nassar Zeyad D. , Hanson Adrienne R. , Iggo Richard , Townley Scott L. , Dehairs Jonas , Mah Chui Y. , Helm Madison , Alizadeh-Ghodsi Mohammadreza , Pickering Marie , Ghesquière Bart , Watt Matthew J. , Quek Lake-Ee , Hoy Andrew J. , Tilley Wayne D. , Swinnen Johannes V. , Butler Lisa M. , Selth Luke A.
Published: July 2024

Quantification of metabolites by mass spectrometry
Supplementary Table 3 from A Multimodal Drug–Diet–Immunotherapy Combination Restrains Melanoma Progression and Metastasis
Authors: Oatman Nicole , Gawali Mruniya V. , Congrove Sunny , Cáceres Román , Sukumaran Abitha , Gupta Nishtha , Murugesan Narmadha , Arora Priyanka , Subramanian Srividhya , Choi Kwangmin , Abdel-Malek Zalfa , Reisz Julie A. , Stephenson Daniel , Amaravadi Ravi , Desai Pankaj , D’Alessandro Angelo , Komurov Kakajan , Dasgupta Biplab
Published: July 2024

Supplementary Table 3
Supplementary Fig 5 from A Multimodal Drug–Diet–Immunotherapy Combination Restrains Melanoma Progression and Metastasis
Authors: Oatman Nicole , Gawali Mruniya V. , Congrove Sunny , Cáceres Román , Sukumaran Abitha , Gupta Nishtha , Murugesan Narmadha , Arora Priyanka , Subramanian Srividhya , Choi Kwangmin , Abdel-Malek Zalfa , Reisz Julie A. , Stephenson Daniel , Amaravadi Ravi , Desai Pankaj , D’Alessandro Angelo , Komurov Kakajan , Dasgupta Biplab
Published: July 2024

Supplementary Fig 5
Figure S3 from ACSM1 and ACSM3 Regulate Fatty Acid Metabolism to Support Prostate Cancer Growth and Constrain Ferroptosis
Authors: Shrestha Raj K. , Nassar Zeyad D. , Hanson Adrienne R. , Iggo Richard , Townley Scott L. , Dehairs Jonas , Mah Chui Y. , Helm Madison , Alizadeh-Ghodsi Mohammadreza , Pickering Marie , Ghesquière Bart , Watt Matthew J. , Quek Lake-Ee , Hoy Andrew J. , Tilley Wayne D. , Swinnen Johannes V. , Butler Lisa M. , Selth Luke A.
Published: July 2024

ACSM3 protein levels are elevated in prostate cancer.
Figure S12 from ACSM1 and ACSM3 Regulate Fatty Acid Metabolism to Support Prostate Cancer Growth and Constrain Ferroptosis
Authors: Shrestha Raj K. , Nassar Zeyad D. , Hanson Adrienne R. , Iggo Richard , Townley Scott L. , Dehairs Jonas , Mah Chui Y. , Helm Madison , Alizadeh-Ghodsi Mohammadreza , Pickering Marie , Ghesquière Bart , Watt Matthew J. , Quek Lake-Ee , Hoy Andrew J. , Tilley Wayne D. , Swinnen Johannes V. , Butler Lisa M. , Selth Luke A.
Published: July 2024

Targeting ACSM1 or ACSM3 does not induce apoptosis of prostate cancer cells.
Data from HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer
Authors: Gnanapragasam Ansley , Kirbizakis Eftyhios , Li Anna , White Kyle H. , Mortenson Katelyn L. , Cavalcante de Moura Juliana , Jawhar Wajih , Yan Yifei , Falter Reilly , Russett Colleen , Giannias Betty , Camilleri-Broët Sophie , Bertos Nicholas , Cools-Lartigue Jonathan , Garzia Livia , Sangwan Veena , Ferri Lorenzo , Zhang Xiaoyang , Bailey Swneke D.
Published: July 2024

Abstract
Genome-wide association studies (GWAS) have identified more than a hundred single nucleotide variants (SNV) associated with the risk of gastroesophageal cancer (GEC). The majority of the identified SNVs map to noncoding regions of the genome. Uncovering the causal SNVs and genes they modulate could help improve GEC prevention and treatment. Herein, we used HiChIP against histone 3 lysine 27 acetylation (H3K27ac) to simultaneously annotate active promoters and enhancers, identify the interactions between them, and detect nucleosome-free regions (NFR) harboring potential causal SNVs in a single assay. The application of H3K27ac HiChIP in GEC relevant models identified 61 potential functional SNVs that reside in NFRs and interact with 49 genes at 17 loci. The approach led to a 67% reduction in the number of SNVs in linkage disequilibrium at these 17 loci, and at 7 loci, a single putative causal SNV was identified. One SNV, rs147518036, located within the promoter of the UDP-glucuronate decarboxylase 1 (UXS1) gene, seemed to underlie the GEC risk association captured by the rs75460256 index SNV. The rs147518036 SNV creates a GABPA DNA recognition motif, resulting in increased promoter activity, and CRISPR‐mediated inhibition of the UXS1 promoter reduced the viability of the GEC cells. These findings provide a framework that simplifies the identification of potentially functional regulatory SNVs and target genes underlying risk-associated loci. In addition, the study implicates increased expression of the enzyme UXS1 and activation of its metabolic pathway as a predisposition to gastric cancer, which highlights potential therapeutic avenues to treat this disease.

Significance: Epigenomic footprinting using a histone posttranslational modification targeted 3D genomics methodology elucidates functional noncoding sequence variants and their target genes at cancer risk loci.
Data from ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs
Authors: Sicinska Ewa , Kola Vijaya S.R. , Kerfoot Joseph A. , Taddei Madeleine L. , Al-Ibraheemi Alyaa , Hsieh Yi-Hsuan , Church Alanna J. , Landesman-Bollag Esther , Landesman Yosef , Hemming Matthew L.
Published: July 2024

Abstract
Alveolar soft part sarcoma (ASPS) is a rare mesenchymal malignancy driven by the ASPSCR1::TFE3 fusion. A better understanding of the mechanisms by which this oncogenic transcriptional regulator drives cancer growth is needed to help identify potential therapeutic targets. In this study, we characterized the transcriptional and chromatin landscapes of ASPS tumors and preclinical models, identifying the essential role of ASPSCR1::TFE3 in tumor cell viability by regulating core transcriptional programs involved in cell proliferation, angiogenesis, and mitochondrial biology. ASPSCR1::TFE3 directly interacted with key epigenetic regulators at enhancers and promoters to support ASPS-associated transcription. Among the effector programs driven by ASPSCR1::TFE3, cell proliferation was driven by high levels of cyclin D1 expression. Disruption of cyclin D1/CDK4 signaling led to a loss of ASPS proliferative capacity, and combined inhibition of CDK4/6 and angiogenesis halted tumor growth in xenografts. These results define the ASPS oncogenic program, reveal mechanisms by which ASPSCR1::TFE3 controls tumor biology, and identify a strategy for therapeutically targeting tumor cell–intrinsic vulnerabilities.

Significance: The ASPSCR1::TFE3 fusion propels the growth of alveolar soft part sarcoma  by activating transcriptional programs that regulate proliferation, angiogenesis, mitochondrial biogenesis, and differentiation and can be therapeutically targeted to improve treatment.
Data from The Circadian Clock Component RORA Increases Immunosurveillance in Melanoma by Inhibiting PD-L1 Expression
Authors: Liu Dandan , Wei Benliang , Liang Long , Sheng Yue , Sun Shengjie , Sun Xing , Li Maohua , Li Haobo , Yang Chaoying , Peng Yuanliang , Xie Yifang , Wen Chengcai , Chen Lu , Liu Xionghao , Chen Xiang , Liu Hong , Liu Jing
Published: July 2024

Abstract
Circadian clock perturbation frequently occurs in cancer and facilitates tumor progression by regulating malignant growth and shaping the immune microenvironment. Emerging evidence has indicated that clock genes are disrupted in melanoma and linked to immune escape. Herein, we found that the expression of retinoic acid receptor–related orphan receptor-α (RORA) is downregulated in melanoma patients and that patients with higher RORA expression have a better prognosis after immunotherapy. Additionally, RORA was significantly positively correlated with T-cell infiltration and recruitment. Overexpression or activation of RORA stimulated cytotoxic T-cell–mediated antitumor responses. RORA bound to the CD274 promoter and formed an inhibitory complex with HDAC3 to suppress PD-L1 expression. In contrast, the DEAD-box helicase family member DDX3X competed with HDAC3 for binding to RORA, and DDX3X overexpression promoted RORA release from the suppressive complex and thereby increased PD-L1 expression to generate an inhibitory immune environment. The combination of a RORA agonist with an anti-CTLA4 antibody synergistically increased T-cell antitumor immunity in vivo. A score based on the combined expression of HDAC3, DDX3X, and RORA correlated with immunotherapy response in melanoma patients. Together, this study elucidates a mechanism of clock component–regulated antitumor immunity, which will help inform the use of immunotherapy and lead to improved outcomes for melanoma patients receiving combined therapeutic treatments.

Significance: RORA forms a corepressor complex to inhibit PD-L1 expression and activate antitumor T-cell responses, indicating that RORA is a potential target and predictive biomarker to improve immunotherapy response in melanoma patients.
Earliest Metabolic Changes Associated with the Initiation of Pancreatic Cancer
Authors: Storz Peter
Published: July 2024

Pancreatic cancer is usually detected at a late stage, when tumors have already metastasized; therefore, it has a poor prognosis with a 5-year survival rate of 11% to 12%. A key to targeting this high mortality is to develop methods for detecting the disease at a stage in which it is still local to the pancreas. However, this needs a better understanding of the events that govern pancreatic cancer oncogenesis. In this issue of Cancer Research, Neuß and colleagues report metabolic changes associated with acinar-to-ductal metaplasia (ADM), an initiating event that leads to the formation of precursor lesions for pancreatic ductal adenocarcinoma (PDAC). Their findings reveal a switch to aerobic glycolysis, increased c-MYC signaling, and increased serine metabolism as driving factors for the ADM process. These findings are important as they demonstrate that metabolic changes that drive the proliferation and metastasis of full-blown PDAC begin in the earliest lesions. The data not only provide insights into how PDAC develops but also a potential explanation for previously described findings, such as circulating lesion cells can be detected even when no carcinoma in situ is present. In summary, this article is highly relevant for furthering our understanding of how metabolic reprogramming drives the earliest events leading to PDAC development and could lay the groundwork for developing methods for early detection or intervention.

See related article by Neuß et al., p. 2297
Is There a Mathematician on Board?
Authors: Fertig Elana J.
Published: July 2024

As convergence science is emerging as a theme in cancer research, scientists from diverse backgrounds, including mathematics, are increasingly entering our research community. The captain of a Southwest Airlines flight recently paged in jest for a mathematician to help support fuel calculations that would enable a flight to arrive safely at the American Association for Cancer Research (AACR) Annual Meeting, epitomizing the need for well-trained mathematicians to address pressing problems. Here, we summarize the roles mathematicians can play in cancer research and the support needed to facilitate their entry into the cancer research field. The inclusion of scientific diversity across quantitative and engineering disciplines is critical for advancing the understanding and treatment of cancer.
Supplementary Table S1 from Minimal Residual Disease using a Plasma-Only Circulating Tumor DNA Assay to Predict Recurrence of Metastatic Colorectal Cancer Following Curative Intent Treatment
Authors: Parikh Aparna R. , Chee Bryant H. , Tsai Jill , Rich Thereasa A. , Price Kristin S. , Patel Sonia A. , Zhang Li , Ibrahim Faaiz , Esquivel Mikaela , Van Seventer Emily E. , Jarnagin Joy X. , Raymond Victoria M. , Corvera Carlos U. , Hirose Kenzo , Nakakura Eric K. , Corcoran Ryan B. , Van Loon Katherine , Atreya Chloe E.
Published: July 2024

Supplementary Table S1. Patient deidentified record ID by analysis. Description of the patient record IDs used per analysis to be cross-referenced with the swimmer plot in Figure 2.
Supplemental Table 2 from Phase II Clinical Trial of Intravenous Levothyroxine to Mitigate Pharyngocutaneous Fistula in Euthyroid Patients Undergoing Salvage Laryngectomy
Authors: Heft Neal Molly E. , Haring Catherine T. , Bellile Emily , Jaffe Craig C. , Shuman Andrew G. , Chinn Steven B. , Stucken Chaz L. , Malloy Kelly M. , Casper Keith A. , Prince Mark E.P. , Chepeha Douglas B. , Rosko Andrew J. , Spector Matthew E.
Published: July 2024

Supplemental Table 2: Initial tumor and nodal staging for patients stratified by post-operative thyroid status, fistula, and fistula requiring OR. Fischer’s exact test was used to compare each group.
Supplementary Table S7 from Biomarker Identification and Risk Prediction Model Development for Differentiated Thyroid Carcinoma Lung Metastasis Based on Primary Lesion Proteomics
Authors: Peng Xiaoqi , Zhao Hongbo , Ye Lijuan , Hou Fei , Yi Zihan , Ren Yanxin , Lu Lin , Chen Fukun , Lv Juan , Wang Yinghui , Cai Haolin , Zheng Xihua , Yang Qing , Chen Ting
Published: July 2024

Table S7. Validation results of candidate hub proteins by PRM, among which 17 hub proteins are statistically significant
Supplementary Table S5 from Plasma Metabolic Profiles-Based Prediction of Induction Chemotherapy Efficacy in Nasopharyngeal Carcinoma: Results of a Bidirectional Clinical Trial
Authors: Tang Tingxi , Zhou Zhenhua , Chen Min , Li Nan , Sun Jianda , Chen Zekai , Xiao Ting , Wang Xiaoqing , Zhang Longshan , Wang Yingqiao , Zhang Hanbin , Zheng Xiuting , Chen Bei , Ye Feng , Guan Jian
Published: July 2024

Supplementary Table S5 Hyperparameters for each model
Supplementary Table S1 from Plasma Metabolic Profiles-Based Prediction of Induction Chemotherapy Efficacy in Nasopharyngeal Carcinoma: Results of a Bidirectional Clinical Trial
Authors: Tang Tingxi , Zhou Zhenhua , Chen Min , Li Nan , Sun Jianda , Chen Zekai , Xiao Ting , Wang Xiaoqing , Zhang Longshan , Wang Yingqiao , Zhang Hanbin , Zheng Xiuting , Chen Bei , Ye Feng , Guan Jian
Published: July 2024

Supplementary Table S1 List of all sub-classes of Lipoproteins in plasma
Supplementary Material S1 from Biomarker Identification and Risk Prediction Model Development for Differentiated Thyroid Carcinoma Lung Metastasis Based on Primary Lesion Proteomics
Authors: Peng Xiaoqi , Zhao Hongbo , Ye Lijuan , Hou Fei , Yi Zihan , Ren Yanxin , Lu Lin , Chen Fukun , Lv Juan , Wang Yinghui , Cai Haolin , Zheng Xihua , Yang Qing , Chen Ting
Published: July 2024

KEGG Analysis Table of Differential Proteins
Supplementary Figure S6 from Biomarker Identification and Risk Prediction Model Development for Differentiated Thyroid Carcinoma Lung Metastasis Based on Primary Lesion Proteomics
Authors: Peng Xiaoqi , Zhao Hongbo , Ye Lijuan , Hou Fei , Yi Zihan , Ren Yanxin , Lu Lin , Chen Fukun , Lv Juan , Wang Yinghui , Cai Haolin , Zheng Xihua , Yang Qing , Chen Ting
Published: July 2024

Figure S6. Specific performance of the 3 risk prediction models for lung metastasis in DTC.
Supplementary Figure S3 from Plasma Metabolic Profiles-Based Prediction of Induction Chemotherapy Efficacy in Nasopharyngeal Carcinoma: Results of a Bidirectional Clinical Trial
Authors: Tang Tingxi , Zhou Zhenhua , Chen Min , Li Nan , Sun Jianda , Chen Zekai , Xiao Ting , Wang Xiaoqing , Zhang Longshan , Wang Yingqiao , Zhang Hanbin , Zheng Xiuting , Chen Bei , Ye Feng , Guan Jian
Published: July 2024

Supplementary Figure S3. Confusion matrices and Metric for 4 models
Supplementary Figure S3 from Biomarker Identification and Risk Prediction Model Development for Differentiated Thyroid Carcinoma Lung Metastasis Based on Primary Lesion Proteomics
Authors: Peng Xiaoqi , Zhao Hongbo , Ye Lijuan , Hou Fei , Yi Zihan , Ren Yanxin , Lu Lin , Chen Fukun , Lv Juan , Wang Yinghui , Cai Haolin , Zheng Xihua , Yang Qing , Chen Ting
Published: July 2024

Figure S3. Unsupervised clustering analysis of all samples using the expression profiles of the differentially expressed proteins.
Supplementary Figure S2 from Biomarker Identification and Risk Prediction Model Development for Differentiated Thyroid Carcinoma Lung Metastasis Based on Primary Lesion Proteomics
Authors: Peng Xiaoqi , Zhao Hongbo , Ye Lijuan , Hou Fei , Yi Zihan , Ren Yanxin , Lu Lin , Chen Fukun , Lv Juan , Wang Yinghui , Cai Haolin , Zheng Xihua , Yang Qing , Chen Ting
Published: July 2024

Figure S2. Principal component analysis of patients in LMDTC (M) group and NMDTC (NM) group.