bluuebunny/crossref_metadata_2025 huggingface dataset:
Probing late-time annihilations of oscillating asymmetric dark matter via rotation curves of galaxies
Authors: Mamprim Júlia G. , Gambini Guillermo , Arbeletche Luan B. , Olegario Marcos , de Souza Vitor
Published: February 2025

In this paper, we explore the Oscillating Asymmetric Dark Matter (OADM) model to address the core-cusp problem, aiming to resolve the discrepancy between the predictions of the

$$\Lambda \textrm{CDM}$$

Λ
CDM

cosmological model and the observed dark matter profiles in dwarf spheroidal galaxies. The reactivation of dark matter annihilation during the structure formation epoch is possible if there is a small Majorana mass term that breaks the conservation of dark matter particle number, leading to oscillations between dark matter and its antiparticle. We analyzed the effects of the annihilation mechanism in the galaxy rotation curves of the SPARC and LITTLE THINGS catalogs. We searched for the characteristics of the OADM model which best describes the data. Our results show that the OADM model can successfully turn originally cusp-type halos into core-type ones according to our data sample.
Deterministic Ratchet Transport of Impurities in Fluids
Authors: Oliveira Tulio M. , Beims Marcus W. , Manchein Cesar
Published: February 2025

This paper investigates unbiased directed transport, known as the ratchet effect, within a system coupled to a fluid modeled by the bailout embedding technique. The system dynamics under the fluid influence are described by a four-dimensional mapping governed by parameters such as dissipation ([Formula: see text]), ratchet kicking ([Formula: see text]), and the relationship between fluid and particle densities ([Formula: see text]). We explore the behavior of the Ratchet Current (RC) in the parameter spaces [Formula: see text] and [Formula: see text], particularly focusing on the aerosol case ([Formula: see text]). Our findings reveal a complex interplay of parameters, with larger RCs observed for parameter pairs that induce periodic dynamics in the ratchet system. Furthermore, we observe RC reversal as a function of [Formula: see text] and [Formula: see text], and identify coexisting attractors (multistability) at higher [Formula: see text] values. These results shed light on the intriguing phenomenon of directed transport in fluid dynamics, offering insights that may contribute to understanding particle transport in nature, especially in the aerosol regime.
Global regularity and sharp decay for incompressible Oldroyd-B model with only fractional dissipation of stress tensor
Authors: Feng Weixun , Qin Dongdong , Tang Xianhua , Zhu Rui
Published: February 2025

In this paper, we investigate the Cauchy problem for the [Formula: see text]-dimensional ([Formula: see text]) incompressible Oldroyd-B model with only fractional dissipation [Formula: see text], [Formula: see text]. Applying the pure energy argument rather than spectral analysis method, we obtain the small initial data global existence results in critical Besov spaces, and establish the sharp time-decay rates of the global solutions to such model for the case [Formula: see text] and the case [Formula: see text], respectively. In particular, our results include the situation that Oldroyd-B model possesses only stress tensor damping and has no dissipation term.
Mining Repetitive Negative Sequential Patterns With Gap Constraints
Authors: Li Yan , Wang Zhulin , Liu Jing , Guo Lei , Fournier-Viger Philippe , Wu Youxi , Wu Xindong
Published: February 2025

Sequential pattern mining (SPM) with gap constraints (or repetitive SPM or tandem repeat discovery in bioinformatics) can find frequent repetitive subsequences satisfying gap constraints, which are called positive sequential patterns with gap constraints (PSPGs). However, classical SPM with gap constraints cannot find the frequent missing items in the PSPGs. To tackle this issue, this paper explores negative sequential patterns with gap constraints (NSPGs). We propose an efficient NSPG-Miner algorithm that can mine both frequent PSPGs and NSPGs simultaneously. To effectively reduce candidate patterns, we propose a pattern join strategy with negative patterns which can generate both positive and negative candidate patterns at the same time. To calculate the support (frequency of occurrence) of a pattern in each sequence, we explore a NegPair algorithm that employs a key-value pair array structure to deal with the gap constraints and the negative items simultaneously and can avoid redundant rescanning of the original sequence, thus improving the efficiency of the algorithm. To report the performance of NSPG-Miner, 11 competitive algorithms and 11 datasets are employed. The experimental results not only validate the effectiveness of the strategies adopted by NSPG-Miner, but also verify that NSPG-Miner can discover more valuable information than the state-of-the-art algorithms. Algorithms and datasets can be downloaded from
https://github.com/wuc567/Pattern-Mining/tree/master/NSPG-Miner
.
AI Agents Under Threat: A Survey of Key Security Challenges and Future Pathways
Authors: Deng Zehang , Guo Yongjian , Han Changzhou , Ma Wanlun , Xiong Junwu , Wen Sheng , Xiang Yang
Published: February 2025

An Artificial Intelligence (AI) agent is a software entity that autonomously performs tasks or makes decisions based on pre-defined objectives and data inputs. AI agents, capable of perceiving user inputs, reasoning and planning tasks, and executing actions, have seen remarkable advancements in algorithm development and task performance. However, the security challenges they pose remain under-explored and unresolved. This survey delves into the emerging security threats faced by AI agents, categorizing them into four critical knowledge gaps: unpredictability of multi-step user inputs, complexity in internal executions, variability of operational environments, and interactions with untrusted external entities. By systematically reviewing these threats, this article highlights both the progress made and the existing limitations in safeguarding AI agents. The insights provided aim to inspire further research into addressing the security threats associated with AI agents, thereby fostering the development of more robust and secure AI agent applications.
Analysis of Intensive Longitudinal Data: Putting Psychological Processes in Perspective
Authors: Hamaker E.L.
Published: February 2025

Research based on intensive longitudinal data (ILD)—consisting of many repeated measures from one or multiple individuals—is rapidly gaining popularity in psychological science. To appreciate the unique potential of ILD research for clinical psychology, this review begins by examining how our three traditional research approaches fall short when the goal is to investigate processes. It then explores how the analysis of ILD can be used to study a process as it unfolds within a specific person over time but also to study average process features or individual differences therein. By emphasizing the alignment between research questions, data collection, and analytical strategies, the potential of ILD research is further highlighted. It is argued that for future progress it is essential to integrate machine learning and causal inference methods with statistical techniques for ILD and to become more explicit about timescales, time frames, and dynamics in psychological theories.
Review of Ankle and Foot Tendon Transfers, Emphasizing Indications, Anatomy, and Imaging Appearances
Authors: Cantarelli Rodrigues Tatiane , Godoy Ivan Rodrigues Barros , Serfaty Aline , Flores Dyan V.
Published: February 2025

Understanding the anatomy, indications, and expected imaging features of an ankle or foot tendon transfer, coupled with basic knowledge of joint axes and force couples, aids in construction of a meaningful and relevant radiologic report and in appropriate treatment selection and follow-up.
Transforming Medical Education: Leveraging Large Language Models to Enhance PBL - A Proof-of-Concept Study
Authors: Arain Shoukat Ali , Akhund Shahid Akhtar , Barakzai Muhammad Abrar , Meo Sultan Ayoub
Published: February 2025

The alignment of learning materials with the learning objectives (LOs) is critical for successfully implementing the Problem-Based Learning (PBL) curriculum. This study investigated the capabilities of Gemini Advanced, a large language model (LLM), in creating clinical vignettes that align with LOs, and comprehensive tutor guides. This study used a faculty-written clinical vignette about diabetes mellitus for third-year medical students. We submitted the LOs and the associated clinical vignette and tutor guide to the LLM to evaluate their alignment and generate new versions. Four faculty members compared both versions using a structured questionnaire. The mean evaluation scores for original and LLM-generated versions are reported. The LLM identified new triggers for the clinical vignette to align it better with the LOs. Moreover, it restructured the tutor guide for better organization and flow and included thought-provoking questions. The medical information provided by the LLM was scientifically appropriate and accurate. LLM-generated clinical vignette scored higher (3.0 vs. 1.25) for the alignment with the LOs. However, the original version scored better for being educational-level appropriate (2.25 vs. 1.25) and adhering to PBL design (2.50 vs. 1.25). The LLM-generated tutor guide scored higher for better flow (3.0 vs. 1.25), comprehensive and relevant content (2.75 vs. 1.50) and thought-provoking questions (2.25 vs. 1.75). However, LLM-generated learning material lacked visual elements. In conclusion, this study demonstrated that Gemini could align and improve PBL learning materials. By leveraging the potential of LLMs while acknowledging their limitations, medical educators can create innovative and effective learning experiences for future physicians.
Drinking pattern and sex modulate the impact of ethanol consumption on the mouse gut microbiome
Authors: Silva Carla B P , Nascimento-Silva Edson Alexandre , Zaramela Lívia Soares , da Costa Bruno Ruiz Brandão , Rodrigues Vanessa Fernandes , De Martinis Bruno Spinosa , Carlos Daniela , Tostes Rita C
Published: February 2025

Background: Gut microbiota impacts host homeostasis and diseases. Chronic plus binge ethanol consumption has been linked to increased injuries than chronic or binge ethanol intake alone. We hypothesized that distinct shapes in gut microbiota composition are induced by chronic, binge and the association of these treatments, thereby affecting host functions and contributing to sex-based differences in alcohol use disorders.

Methods: Male and female C57BL/6J mice were submitted to chronic, binge or chronic plus binge ethanol feeding. DNA was extracted from fecal microbiota, followed by analysis of the V3-V4 region of the 16S rRNA gene and sequencing on an Illumina platform. Gut microbiome analysis was performed using QIIME v2022.2.0. Functional profiling of the gut microbiome was performed using PICRUSt2.

Results: Ethanol differentially affected the gut microbiota of female and male mice. Decreased alpha diversity was observed in male and female mice from the chronic plus binge and chronic groups, respectively. The genera Faecalibaculum, Lachnospiraceae and Alistipes were identified as major potential biomarkers for gut dysbiosis induced by ethanol consumption. In addition, ethanol-induced gut dysbiosis altered several metabolic pathways.

Conclusion: Ethanol consumption modifies the mouse gut microbiome in a drinking pattern- and sex-dependent manner, potentially leading to different susceptibility to ethanol-related diseases. Chronic plus binge ethanol intake induces a more pronounced gut dysbiosis in male mice. Conversely, chronic ethanol is linked to a greater degree of gut dysbiosis in female mice. The changed gut microbiome may be potentially targeted to prevent, mitigate, or treat alcohol use disorders.
Effects of Dietary Supplement of Probiotic Enterococcus faecium on Intestinal Microbiota and Barrier Structure, Immune Function, and Antioxidant Capacity of Soft‐Shelled Turtle Pelodiscus sinensis
Authors: Zhang Yu , Lu Yang , Zhang Yi , Niu Cuijuan
Published: February 2025

Enterococcus faecium inhabits animal gastrointestinal tracts and has been demonstrated to benefit livestock and poultry, but its effects on soft‐shelled turtles remain unexplored. The present work investigates the effects of probiotic E. faecium on intestinal microbiota and barrier structure, immune function, and antioxidant capacity of the soft‐shelled turtle. Twenty‐four juvenile Pelodiscus sinensis were divided into two groups: control (fed a basal diet) and treatment (fed a diet supplemented with E. faecium, 3.3 × 108 CFU/g feed), over a period of 6 weeks. We found that E. faecium did not promote the growth of turtles at the present feeding level, but the treatment resulted in significant alterations in the intestinal microbial community structure, with increased abundance of Enterococcus, Romboutsia, and Clostridium_sensu_stricto_1, and a reduction in Aeromonas (p  < 0.05). E. faecium notably enhanced villus height/crypt depth, villus width, and villus density in the intestine. The treatment group exhibited a 1.50‐fold increase in goblet cells count and a 1.18‐fold higher in the muscular layer thickness compared to the control group. E. faecium also improved the immune function, with an increase in the ratio of plasma neutrophils and lymphocytes to the total number of leukocytes after feeding probiotics, and upregulation of the levels of toll‐like receptor 4 (TLR 4), lysozyme, interleukin 1β (IL‐1β), tumor necrosis factor α (TNF‐α), and immunoglobulin A (IgA) in the intestine, as well as the level of hepatic immunoglobulin M (IgM). Additionally, E. faecium supplementation boosted antioxidant capabilities, including a significant increase in catalase (CAT) and glutathione peroxidase (GPx) activity and reduced glutathione (GSH) levels in the intestine and GSH levels in the spleen. Our study demonstrates the beneficial effects of supplemental E. faecium on the intestine and overall health of soft‐shelled turtles, particularly in enhancing their immune function and antioxidant capacity.
Novel AC–AC Converter Design for High‐Efficiency Wireless Electric Vehicle Charging Systems
Authors: Tightiz Lilia , Al-Shibli Wedad Khamis
Published: February 2025

Electric vehicle (EV) batteries may now be conveniently charged with wireless chargers. These systems are prized for their dependability and security in a range of weather scenarios. Generally speaking, there are two kinds of EV wireless charging systems: static (for parked cars) and dynamic (for moving cars). Traditionally, EV chargers have parts like a high‐frequency direct current (DC)–alternating current (AC) converter that usually requires intricate cabling and an AC–DC converter that aids in power quality management. In these systems, a process called as “transformation” occurs when energy moves from a main component—the power source—to a secondary component—the vehicle’s receiver. Eliminating physical connections, such wires and charging outlets on the car, improves convenience and lessens wear and tear on the charger. This is another advantage of wireless chargers over plug‐in varieties. In this study, we investigate a novel design that substitutes a single integrated AC–AC converter on the input side for the conventional AC–DC and DC–AC converters. This creative solution lowers the demand on power switches while raising voltage levels, which not only makes the system simpler but also more efficient. To further reduce the voltage stress on these switches, we additionally employ a multilevel diode clamp inverter, which not only helps to reduce the size of the switches but also greatly increases the efficiency of the system. To validate the performance of this new converter, we provide data from the laboratory as well as simulation results.
Performance Investigation of a Cabin Thermal Management System for Electric Vehicles Based on R290 Refrigerant
Authors: Zhao Jiahao , Luo Zihao , Zhang Yifei , Yakubu Abubakar Unguwanrimi , Ye Xuanhong , Jiang Qi , Xiong Shusheng , Xia Chenbo
Published: February 2025

Electric vehicle (EV) thermal management systems (TMSs) face a critical challenge in adopting environmentally friendly refrigerants, essential for adaptability, thermal safety, driving range optimization, and passenger comfort across wide temperature ranges. This study investigates the use of R290, a low‐cost and environmentally friendly refrigerant, in a secondary‐loop‐based TMS. A system test bench was established to validate the system performance experimentally, and a comparison was made with the system using R134a. The experimental results show that the R290 charge amount is approximately 50% of that of R134a. Under low‐temperature heating condition (0°C), R290 demonstrates significant performance advantages, with heating capacity and coefficient of performance (COP) increasing by up to 67.6% and 36%, respectively, compared to R134a. At extremely low temperatures (−20°C), R290 achieves a COP of 1.24, further showcasing its superior heating performance. Under high‐temperature cooling conditions (35 and 43°C), R290 exhibits slightly lower cooling capacity compared to R134a; however, its performance remains sufficient to meet the operational requirements of a TMS. In summary, the proposed TMS using R290 as the refrigerant demonstrates excellent performance and promising potential for application in EVs across a wide range of operating conditions.
Biomass Production of Azolla microphylla in Rainwater Solution of Coconut Husk
Authors: Jaroenchai Chutinan
Published: February 2025

The present work reports the use of rainwater solution of coconut husk (CCH) as growth media of Azolla microphylla in Thailand. A series of seven experiments were conducted to test the hypothesis that water solution of CCH may be used as growth media of A. microphylla for biomass production. The media treatments of the seven experiments consisted of tap water (TW), rainwater (RW), fertile soil (S), water buffalo manure (M), and CCH depending on experimental conditions. TW and RW were used as media or solvent in the media treatments tested in this study. The fern was grown on the media in 23 L containers under a greenhouse covered with 60% black shade cloth and biomass at least four weeks of growth was evaluated. The results showed that the fern had four to five times greater biomass after four and 12 weeks of growth in the medium RW. The fern had 14‐time greater biomass after four weeks of growth in the media RW solutions of CCH at 10:1–10:9 by volume. Biomass tended to be greater in the media RW solutions of CCH than the medium RW. Biomass was small in the media TW solutions of CCH. To conclude, RW solutions of CCH at 10:1–10:9 by volume can be used as growth media of A. microphylla for biomass production.
A Class of Higher‐Order Collocation Scheme for the Integral Equation of the Convolution Type
Authors: Alsahlanee M. , Darania P. , Pishbin S.
Published: February 2025

Auto convolution Volterra integral equations (ACVIEs) are the particular form of non‐standard integral equations arising in mathematical modeling processes and the computation of certain functions. In this paper, a novel class of multistep collocation methods (NM‐SCMs) is constructed in order to find a higher‐order method is constructed for the numerical solution of this kind of the ACVIEs. We analyze the convergence of this method and determine the order of convergence. Also, 1‐SCMs and M‐SCMs are applied to solve this equation numerically.
Supplemental Figure 8 from Intra- and Extrahepatic Cholangiocarcinomas Display Differing Sensitivities to NK Cell Lysis and Modulate NK Cell Function through Shared and Distinct Pathways
Authors: Nguyen Ngan , Henrich Ian C.
Published: February 2025

Figure S8. Difference in relative immune abundance between NKHigh and NKLow eCCA patients.
Supplemental Figure 6 from Intra- and Extrahepatic Cholangiocarcinomas Display Differing Sensitivities to NK Cell Lysis and Modulate NK Cell Function through Shared and Distinct Pathways
Authors: Nguyen Ngan , Henrich Ian C.
Published: February 2025

Figure S6. Inhibition of NK cytotoxicity across different healthy human NK donors.
Supplemental Figure 2 from Intra- and Extrahepatic Cholangiocarcinomas Display Differing Sensitivities to NK Cell Lysis and Modulate NK Cell Function through Shared and Distinct Pathways
Authors: Nguyen Ngan , Henrich Ian C.
Published: February 2025

Figure S2. NKp46 is differentially regulated between NK-92MI and primary human NK cells.
Supplemental Figure 1 from Intra- and Extrahepatic Cholangiocarcinomas Display Differing Sensitivities to NK Cell Lysis and Modulate NK Cell Function through Shared and Distinct Pathways
Authors: Nguyen Ngan , Henrich Ian C.
Published: February 2025

Figure S1. Correlation of other immune lineages with CCA outcome and NK cytotoxicity toward CCA after co-culture.
Kindlin-2-mediated hematopoiesis remodeling regulates triple-negative breast cancer immune evasion
Authors: Wang Wei , Chaudhary Rahul , Szpendyk Justin , El Khalki Lamyae , Yousafzai Neelum Aziz , Chan Ricky , Desai Amar , Sossey-Alaoui Khalid
Published: February 2025

Triple-negative breast cancer (TNBC) presents significant clinical challenges due to its limited treatment options and aggressive behavior, often associated with poor prognosis. This study focuses on Kindlin-2, an adaptor protein, and its role in TNBC progression, particularly in hematopoiesis-mediated immune evasion. TNBC tumors expressing high levels of Kindlin-2 induce a notable reshaping of hematopoiesis, promoting expansion of myeloid cells in bone marrow (BM) and spleen. This shift correlated with increased levels of neutrophils and monocytes in tumor-bearing mice over time. Conversely, genetic knockout of Kindlin-2 mitigated this myeloid bias and fostered T cell infiltration within the tumor microenvironment, indicating Kindlin-2's pivotal role in immune modulation. Further investigations revealed that Kindlin-2 deficiency led to reduced expression of PD-L1, a critical immune checkpoint inhibitor, in TNBC tumors. This molecular change sensitized Kindlin-2-deficient tumors to host anti-tumor immune responses, resulting in enhanced tumor suppression in immune-competent mouse models. Single-cell RNA sequencing, bulk RNA-seq, and immunohistochemistry data supported these findings by highlighting enriched immune-related pathways and increased infiltration of immune cells in Kindlin-2-deficient tumors. Therapeutically, targeting PD-L1 in Kindlin-2-expressing TNBC tumors effectively inhibited tumor growth, akin to the effects observed with genetic Kindlin-2 knockout or PD-L1-KO. Our data underscore Kindlin-2 as a promising therapeutic target in combination with immune checkpoint blockade to bolster anti-tumor immunity and counteract resistance mechanisms typical of TNBC and other immune evasive solid tumors. Implications: Kindlin-2 regulates tumor immune evasion through the systemic modulation of hematopoiesis and PD-L1 expression, which warrants therapeutic targeting of Kindlin-2 in TNBC patients.
Supplementary Table S5 from The UBA1–STUB1 Axis Mediates Cancer Immune Escape and Resistance to Checkpoint Blockade
Authors: Bao Yi , Cruz Gabriel , Zhang Yuping , Qiao Yuanyuan , Mannan Rahul , Hu Jing , Yang Fan , Gondal Mahnoor , Shahine Miriam , Kang Sarah , Mahapatra Somnath , Chu Alec , Choi Jae Eun , Yu Jiali , Lin Heng , Miner Stephanie J. , Robinson Dan R. , Wu Yi-Mi , Zheng Yang , Cao Xuhong , Su Fengyun , Wang Rui , Hosseini Noshad , Cieslik Marcin , Kryczek Ilona , Vaishampayan Ulka , Zou Weiping , Chinnaiyan Arul M.
Published: February 2025

Supplementary Table S5. Data from the CRISPR screen in Myc-CaP cells treated with TAK-243 + IFN-γ.
Supplementary Table 7 from CTR-FAPI PET Enables Precision Management of Medullary Thyroid Carcinoma
Authors: Kong Ziren , Li Zhu , Cui Xi-Yang , Wang Jian , Xu Mengxin , Liu Yang , Chen Junyi , Ni Song , Zhang Zongmin , Fan Xiaowei , Huang Jiazhao , Lin Yansong , Sun Yuning , He Yuqin , Lin Xinfeng , Meng Tianyu , Li Han , Song Yixuan , Peng Boshizhang , An Changming , Gao Chenyan , Li Nan , Liu Chen , Zhu Yiming , Yang Zhi , Liu Zhibo , Liu Shaoyan
Published: February 2025

Tumor uptake stratified by calcitonin levels
Supplementary Table 6 from CTR-FAPI PET Enables Precision Management of Medullary Thyroid Carcinoma
Authors: Kong Ziren , Li Zhu , Cui Xi-Yang , Wang Jian , Xu Mengxin , Liu Yang , Chen Junyi , Ni Song , Zhang Zongmin , Fan Xiaowei , Huang Jiazhao , Lin Yansong , Sun Yuning , He Yuqin , Lin Xinfeng , Meng Tianyu , Li Han , Song Yixuan , Peng Boshizhang , An Changming , Gao Chenyan , Li Nan , Liu Chen , Zhu Yiming , Yang Zhi , Liu Zhibo , Liu Shaoyan
Published: February 2025

Tumor uptake in lesions avid on both imaging
Supplementary Table 4 from CTR-FAPI PET Enables Precision Management of Medullary Thyroid Carcinoma
Authors: Kong Ziren , Li Zhu , Cui Xi-Yang , Wang Jian , Xu Mengxin , Liu Yang , Chen Junyi , Ni Song , Zhang Zongmin , Fan Xiaowei , Huang Jiazhao , Lin Yansong , Sun Yuning , He Yuqin , Lin Xinfeng , Meng Tianyu , Li Han , Song Yixuan , Peng Boshizhang , An Changming , Gao Chenyan , Li Nan , Liu Chen , Zhu Yiming , Yang Zhi , Liu Zhibo , Liu Shaoyan
Published: February 2025

Detection rate of patients with calcitonin >2000 pg/ml
Supplementary Figure S9 from The UBA1–STUB1 Axis Mediates Cancer Immune Escape and Resistance to Checkpoint Blockade
Authors: Bao Yi , Cruz Gabriel , Zhang Yuping , Qiao Yuanyuan , Mannan Rahul , Hu Jing , Yang Fan , Gondal Mahnoor , Shahine Miriam , Kang Sarah , Mahapatra Somnath , Chu Alec , Choi Jae Eun , Yu Jiali , Lin Heng , Miner Stephanie J. , Robinson Dan R. , Wu Yi-Mi , Zheng Yang , Cao Xuhong , Su Fengyun , Wang Rui , Hosseini Noshad , Cieslik Marcin , Kryczek Ilona , Vaishampayan Ulka , Zou Weiping , Chinnaiyan Arul M.
Published: February 2025

Supplementary Figure S9. UBA1 inactivation upregulates interferon signaling in vivo.
Supplementary Figure S4 from The UBA1–STUB1 Axis Mediates Cancer Immune Escape and Resistance to Checkpoint Blockade
Authors: Bao Yi , Cruz Gabriel , Zhang Yuping , Qiao Yuanyuan , Mannan Rahul , Hu Jing , Yang Fan , Gondal Mahnoor , Shahine Miriam , Kang Sarah , Mahapatra Somnath , Chu Alec , Choi Jae Eun , Yu Jiali , Lin Heng , Miner Stephanie J. , Robinson Dan R. , Wu Yi-Mi , Zheng Yang , Cao Xuhong , Su Fengyun , Wang Rui , Hosseini Noshad , Cieslik Marcin , Kryczek Ilona , Vaishampayan Ulka , Zou Weiping , Chinnaiyan Arul M.
Published: February 2025

Supplementary Figure S4. UBA1 inhibition synergizes with anti-PD-1 therapy to control tumor growth.
Supplementary Figure S3 from The UBA1–STUB1 Axis Mediates Cancer Immune Escape and Resistance to Checkpoint Blockade
Authors: Bao Yi , Cruz Gabriel , Zhang Yuping , Qiao Yuanyuan , Mannan Rahul , Hu Jing , Yang Fan , Gondal Mahnoor , Shahine Miriam , Kang Sarah , Mahapatra Somnath , Chu Alec , Choi Jae Eun , Yu Jiali , Lin Heng , Miner Stephanie J. , Robinson Dan R. , Wu Yi-Mi , Zheng Yang , Cao Xuhong , Su Fengyun , Wang Rui , Hosseini Noshad , Cieslik Marcin , Kryczek Ilona , Vaishampayan Ulka , Zou Weiping , Chinnaiyan Arul M.
Published: February 2025

Supplementary Figure S3. UBA1 diminishes intratumoral functional T cells.
Supplementary Table 1 from CTR-FAPI PET Enables Precision Management of Medullary Thyroid Carcinoma
Authors: Kong Ziren , Li Zhu , Cui Xi-Yang , Wang Jian , Xu Mengxin , Liu Yang , Chen Junyi , Ni Song , Zhang Zongmin , Fan Xiaowei , Huang Jiazhao , Lin Yansong , Sun Yuning , He Yuqin , Lin Xinfeng , Meng Tianyu , Li Han , Song Yixuan , Peng Boshizhang , An Changming , Gao Chenyan , Li Nan , Liu Chen , Zhu Yiming , Yang Zhi , Liu Zhibo , Liu Shaoyan
Published: February 2025

Baseline characteristics of the enrolled patients
Supplementary Figure 2 from CTR-FAPI PET Enables Precision Management of Medullary Thyroid Carcinoma
Authors: Kong Ziren , Li Zhu , Cui Xi-Yang , Wang Jian , Xu Mengxin , Liu Yang , Chen Junyi , Ni Song , Zhang Zongmin , Fan Xiaowei , Huang Jiazhao , Lin Yansong , Sun Yuning , He Yuqin , Lin Xinfeng , Meng Tianyu , Li Han , Song Yixuan , Peng Boshizhang , An Changming , Gao Chenyan , Li Nan , Liu Chen , Zhu Yiming , Yang Zhi , Liu Zhibo , Liu Shaoyan
Published: February 2025

Lesion uptake of [18F]FDG and [68Ga]Ga-CTR-FAPI
Supplementary Tables 1-8 from Predisposition Footprints in the Somatic Genome of Wilms Tumors
Authors: Treger Taryn D. , Wegert Jenny , Wenger Anna , Coorens Tim H.H. , Al-Saadi Reem , Kemps Paul G. , Kennedy Jonathan , Parks Conor , Anderson Nathaniel D. , Hodder Angus , Letunovska Aleksandra , Jung Hyunchul , Ogbonnah Toochi , Trinh Mi K. , Lee-Six Henry , Morcrette Guillaume , van den Heuvel-Eibrink Marry M. , Drost Jarno , van Boxtel Ruben , Bertrums Eline J.M. , Goemans Bianca F. , Antoniou Evangelia , Reinhardt Dirk , Streitenberger Heike , Ziegler Barbara , Bartram Jack , Hutchinson John C. , Vujanic Gordan M. , Vokuhl Christian , Chowdhury Tanzina , Furtwängler Rhoikos , Graf Norbert , Pritchard-Jones Kathy , Gessler Manfred , Behjati Sam
Published: February 2025

Contains Supplementary Tables 1-8. Supplementary Table 1 shows characteristics of discovery cohort. Supplementary Table 2 shows genes included in predisposition analysis. Supplementary Table 3 shows evidence underlying novel predispositions. Supplementary Table 4 shows variants that would be detectable by current clinical assays. Supplementary Table 5 shows substitutions and indels. Supplementary Table 6 shows rearrangements. Supplementary Table 7 shows 10,000 most variable probes. Supplementary Table 8 shows differentially expressed genes.
Supplementary Figures 1-9 from Predisposition Footprints in the Somatic Genome of Wilms Tumors
Authors: Treger Taryn D. , Wegert Jenny , Wenger Anna , Coorens Tim H.H. , Al-Saadi Reem , Kemps Paul G. , Kennedy Jonathan , Parks Conor , Anderson Nathaniel D. , Hodder Angus , Letunovska Aleksandra , Jung Hyunchul , Ogbonnah Toochi , Trinh Mi K. , Lee-Six Henry , Morcrette Guillaume , van den Heuvel-Eibrink Marry M. , Drost Jarno , van Boxtel Ruben , Bertrums Eline J.M. , Goemans Bianca F. , Antoniou Evangelia , Reinhardt Dirk , Streitenberger Heike , Ziegler Barbara , Bartram Jack , Hutchinson John C. , Vujanic Gordan M. , Vokuhl Christian , Chowdhury Tanzina , Furtwängler Rhoikos , Graf Norbert , Pritchard-Jones Kathy , Gessler Manfred , Behjati Sam
Published: February 2025

Contains Supplementary Figures 1-9. Supplementary Figure 1 shows age of diagnosis of children and indel burden and rearrangement burden for tumours from predisposed children versus those with sporadic disease. Supplementary Figure 2 shows genomic evidence for novel predispositions. Supplementary Figure 3 shows global methylation patterns. Supplementary Figure 4 shows differential gene expression. Supplementary Figure 5 shows mutational signatures. Supplementary Figure 6 shows histological subtypes across predispositions and across somatic drivers. Supplementary Figure 7 shows polyclonal versus clonal enrichment of 11p LOH in normal kidneys. Supplementary Figure 8 shows phylogenies in children with multiple neoplasms and either WT1 or TRIM28 predispositions. Supplementary Figure 9 shows phylogenies in children with non WT1/ non TRIM28 predispositions or sporadic disease.
Supplementary Table S4 from Glioblastoma Cortical Organoids Recapitulate Cell-State Heterogeneity and Intercellular Transfer
Authors: Mangena Vamsi , Chanoch-Myers Rony , Sartore Rafaela , Paulsen Bruna , Gritsch Simon , Weisman Hannah , Hara Toshiro , Breakefield Xandra O. , Breyne Koen , Regev Aviv , Chung Kwanghun , Arlotta Paola , Tirosh Itay , Suvà Mario L.
Published: February 2025

Supplementary Table S4 shows gene sets defining malignant (mouse) programs in mouse-human (m005) mixed-species GCOs.
Supplementary Table S3 from Glioblastoma Cortical Organoids Recapitulate Cell-State Heterogeneity and Intercellular Transfer
Authors: Mangena Vamsi , Chanoch-Myers Rony , Sartore Rafaela , Paulsen Bruna , Gritsch Simon , Weisman Hannah , Hara Toshiro , Breakefield Xandra O. , Breyne Koen , Regev Aviv , Chung Kwanghun , Arlotta Paola , Tirosh Itay , Suvà Mario L.
Published: February 2025

Supplementary Table S3 shows gene sets defining malignant programs in human GCOs.
Supplementary Figure S5 from Glioblastoma Cortical Organoids Recapitulate Cell-State Heterogeneity and Intercellular Transfer
Authors: Mangena Vamsi , Chanoch-Myers Rony , Sartore Rafaela , Paulsen Bruna , Gritsch Simon , Weisman Hannah , Hara Toshiro , Breakefield Xandra O. , Breyne Koen , Regev Aviv , Chung Kwanghun , Arlotta Paola , Tirosh Itay , Suvà Mario L.
Published: February 2025

Supplementary Figure S5 describes extracellular vesicle mediated intercellular transfer in GCOs, related to Figure 5.
Supplementary Table 4 from Tumor-Intrinsic Kinome Landscape of Pancreatic Cancer Reveals New Therapeutic Approaches
Authors: Xu Yi , Peng Xianlu L. , East Michael P. , McCabe Ian C. , Stroman Grace C. , Jenner Madison R. , Chan Priscilla S. , Morrison Ashley B. , Shen Emily C. , Hererra Silvia G. , Joisa Chinmaya U. , Rashid Naim U. , Iuga Alina C. , Gomez Shawn M. , Miller-Phillips Lisa , Boeck Stefan , Heinemann Volker , Haas Michael , Ormanns Steffen , Johnson Gary L. , Yeh Jen Jen
Published: February 2025

Supplementary Table 4.RASH_ACCEPT_stats
Supplementary Table 3 from Tumor-Intrinsic Kinome Landscape of Pancreatic Cancer Reveals New Therapeutic Approaches
Authors: Xu Yi , Peng Xianlu L. , East Michael P. , McCabe Ian C. , Stroman Grace C. , Jenner Madison R. , Chan Priscilla S. , Morrison Ashley B. , Shen Emily C. , Hererra Silvia G. , Joisa Chinmaya U. , Rashid Naim U. , Iuga Alina C. , Gomez Shawn M. , Miller-Phillips Lisa , Boeck Stefan , Heinemann Volker , Haas Michael , Ormanns Steffen , Johnson Gary L. , Yeh Jen Jen
Published: February 2025

Supplementary Table 3.ttest_basalclassical
Supplementary Table 2 from Tumor-Intrinsic Kinome Landscape of Pancreatic Cancer Reveals New Therapeutic Approaches
Authors: Xu Yi , Peng Xianlu L. , East Michael P. , McCabe Ian C. , Stroman Grace C. , Jenner Madison R. , Chan Priscilla S. , Morrison Ashley B. , Shen Emily C. , Hererra Silvia G. , Joisa Chinmaya U. , Rashid Naim U. , Iuga Alina C. , Gomez Shawn M. , Miller-Phillips Lisa , Boeck Stefan , Heinemann Volker , Haas Michael , Ormanns Steffen , Johnson Gary L. , Yeh Jen Jen
Published: February 2025

Supplementary Table 2.limma_kinomeclusters
Supplementary Figures S1-S8 from DNAJB1-PRKACA Fusion Drives Fibrolamellar Liver Cancer through Impaired SIK Signaling and CRTC2/p300-Mediated Transcriptional Reprogramming
Authors: Gritti Ilaria , Wan Jinkai , Weeresekara Vajira , Vaz Joel M. , Tarantino Giuseppe , Bryde Tenna Holgersen , Vijay Vindhya , Kammula Ashwin V. , Kattel Prabhat , Zhu Songli , Vu Phuong , Chan Marina , Wu Meng-Ju , Gordan John D. , Patra Krushna C. , Silveira Vanessa S. , Manguso Robert T. , Wein Marc N. , Ott Christopher J. , Qi Jun , Liu David , Sakamoto Kei , Gujral Taranjit S. , Bardeesy Nabeel
Published: February 2025

Supplementary Figure S1: Validation of the specificity of the p-SIK Ser343 antibody. Supplementary Figure S2. PKAfus inactivates SIKs to support tumor cell growth in vitro and in vivo. Supplementary Figure S3. PKAfus reprograms transcription by inactivating SIK and stimulating CRTC2. Supplementary Figure S4. CRTC2/CREB mediates transcriptional regulation downstream of PKAfu. Supplementary Figure S5. CRTC2/CREB supports tumor cell growth downstream of PKAfus. Supplementary Figure S6. Primary FLC tumors show deregulation of SIK/CRTC2- controlled genes. Supplementary Figure S7. PKAfus driven tumors are sensitive to p300 inhibition. Supplementary Figure S8. PKAfus driven tumors are sensitive to p300 inhibition.
Supplementary Table S5 from Copper Drives Remodeling of Metabolic State and Progression of Clear Cell Renal Cell Carcinoma
Authors: Bischoff Megan E. , Shamsaei Behrouz , Yang Juechen , Secic Dina , Vemuri Bhargav , Reisz Julie A. , D’Alessandro Angelo , Bartolacci Caterina , Adamczak Rafal , Schmidt Lucas , Wang Jiang , Martines Amelia , Venkat Jahnavi , Tcheuyap Vanina Toffessi , Biesiada Jacek , Behrmann Catherine A. , Vest Katherine E. , Brugarolas James , Scaglioni Pier Paolo , Plas David R. , Patra Krushna C. , Gulati Shuchi , Landero Figueroa Julio A. , Meller Jarek , Cunningham John T. , Czyzyk-Krzeska Maria F.
Published: February 2025

Gene signatures in scRNA-seq analysis
Supplementary Figure S2 from Copper Drives Remodeling of Metabolic State and Progression of Clear Cell Renal Cell Carcinoma
Authors: Bischoff Megan E. , Shamsaei Behrouz , Yang Juechen , Secic Dina , Vemuri Bhargav , Reisz Julie A. , D’Alessandro Angelo , Bartolacci Caterina , Adamczak Rafal , Schmidt Lucas , Wang Jiang , Martines Amelia , Venkat Jahnavi , Tcheuyap Vanina Toffessi , Biesiada Jacek , Behrmann Catherine A. , Vest Katherine E. , Brugarolas James , Scaglioni Pier Paolo , Plas David R. , Patra Krushna C. , Gulati Shuchi , Landero Figueroa Julio A. , Meller Jarek , Cunningham John T. , Czyzyk-Krzeska Maria F.
Published: February 2025

Cu regulates metabolism and CuCOX is necessary for Cu-induced tumor growth.
Data from Copper Drives Remodeling of Metabolic State and Progression of Clear Cell Renal Cell Carcinoma
Authors: Bischoff Megan E. , Shamsaei Behrouz , Yang Juechen , Secic Dina , Vemuri Bhargav , Reisz Julie A. , D’Alessandro Angelo , Bartolacci Caterina , Adamczak Rafal , Schmidt Lucas , Wang Jiang , Martines Amelia , Venkat Jahnavi , Tcheuyap Vanina Toffessi , Biesiada Jacek , Behrmann Catherine A. , Vest Katherine E. , Brugarolas James , Scaglioni Pier Paolo , Plas David R. , Patra Krushna C. , Gulati Shuchi , Landero Figueroa Julio A. , Meller Jarek , Cunningham John T. , Czyzyk-Krzeska Maria F.
Published: February 2025

Abstract
Copper (Cu) is a cofactor of cytochrome c oxidase (CuCOX), indispensable for aerobic mitochondrial respiration. This study reveals that advanced clear cell renal cell carcinomas (ccRCC) accumulate Cu, allocating it to CuCOX. Using a range of orthogonal approaches, including metabolomics, lipidomics, isotope-labeled glucose and glutamine flux analysis, and transcriptomics across tumor samples, cell lines, xenografts, and patient-derived xenograft models, combined with genetic and pharmacologic interventions, we explored the role of Cu in ccRCC. Elevated Cu levels stimulate CuCOX biogenesis, providing bioenergetic and biosynthetic benefits that promote tumor growth. This effect is complemented by glucose-dependent glutathione production, which facilitates detoxification and mitigates Cu–H2O2 toxicity. Single-cell RNA sequencing and spatial transcriptomics reveal increased oxidative metabolism, altered glutathione and Cu metabolism, and diminished hypoxia-inducible transcription factor activity during ccRCC progression. Thus, Cu drives an integrated oncogenic remodeling of bioenergetics, biosynthesis, and redox homeostasis, fueling ccRCC growth, which can be targeted for new therapeutic approaches.
Significance:
The work establishes a requirement for glucose-dependent coordination between energy production and redox homeostasis, which is fundamental for the survival of cancer cells that accumulate Cu and contributes to tumor growth.
Strengthening Asian/Asian American, Native Hawaiian, and Pacific Islander Leadership in Cancer Research
Authors: Wu Lawrence W. , Moy Ryan H. ,   the AACR AANHPI Task Force, Bhardwaj Nina , Cho Kathleen , Feng Gen-Sheng , Kim Edward S. , Lei Ming , Liu Edison T. , Maitra Anirban , Mori Motomi , Ng Irene O.L. , Oshima Masanobu , Pao William , Park Ben Ho , Ramalingam Suresh , Rha Sun Young , Ryeom Sandra W. , Shaw Alice T. , Siu Lillian L. , Suri Anil K. , Tan Daniel S. , Tanabe Kenneth K. , Ueno Naoto T. , Verma Sunil , Wong Kwok-Kin , Wu Catherine J. , Wu Hong , Yang James Chih-Hsin
Published: February 2025

Individuals in the United States from Asian and Asian American, Native Hawaiian, and Pacific Islander (AANHPI) backgrounds face a distinct set of cancer-related disparities. In this study, in conjunction with the American Association for Cancer Research Asian/AANHPI Task Force, we highlight the unique disparities faced by AANHPI patients and professionals, and we offer actionable recommendations on how to strengthen AANHPI leadership in cancer research.
A Material Transfer Agreement between Glioblastoma and Normal Brain Cells
Authors: Shakya Sajina , Hubert Christopher G. , Lathia Justin D.
Published: February 2025

Tumor cells communicate with normal cells in various ways, typically leading to the exploitation of resources of the normal cells by tumor cells for their benefit. In this issue, Mangena and colleagues use three-dimensional organoid models to show the transfer of GFP and mRNA from malignant glioblastoma to nonmalignant cells in cerebral organoid models; this transfer is facilitated by extracellular vesicles and possibly tunneling nanotubes, demonstrating how nonmalignant cells in the tumor microenvironment can be exploited by neighboring malignant cells.

See related article by Mangena et al., p. 299
Blocking WNT7A Enhances MHC-I Antigen Presentation and Enhances the Effectiveness of Immune Checkpoint Blockade Therapy
Authors: Sun Jiazheng , Wang Pin , Yi Ziying , Wu Yushen , Wei Yuxian , Fang Huiying , Song Daqiang , Chen Yuru , Du Huimin , Huang Jing , Li Qin , Yang Dejuan , Ren Guosheng , Li Hongzhong
Published: February 2025

The limited infiltration of CD8+ T cells in tumors hampers the effectiveness of T cell–based immunotherapy, yet the mechanisms that limit tumor infiltration by CD8+ T cells remain unclear. Through bulk RNA sequencing of human tumors, we identified a strong correlation between WNT7A expression and reduced CD8+ T-cell infiltration. Further investigation demonstrated that inhibiting WNT7A substantially enhanced MHC-I expression on tumor cells. Mechanistically, WNT7A inhibition inactivated the Wnt/β-catenin signaling pathway and thus resulted in reduced physical interaction between β-catenin and p65 in the cytoplasm, which increased the nuclear translocation of p65 and activated the NF-κB pathway, ultimately promoting the transcription of genes encoding MHC-I molecules. We found that our lead compound, 1365-0109, disrupted the protein–protein interaction between WNT7A and its receptor FZD5, resulting in the upregulation of MHC-I expression. In murine tumor models, both genetic and pharmaceutical suppression of WNT7A led to increased MHC-I levels on tumor cells, and consequently enhanced the infiltration and functionality of CD8+ T cells, which bolstered antitumor immunity and improved the effectiveness of immune checkpoint blockade therapy. These findings have elucidated the intrinsic mechanisms of WNT7A-induced immune suppression, suggesting that therapeutic interventions targeting WNT7A hold promise for enhancing the efficacy of immunotherapy.
Mehr Behandlungen, aber nicht weniger Angst- und affektive Störungen: Warum? Sieben Hypothesen und ihre Bewertung
Authors: Ormel Johan , Emmelkamp Paul M.G.
Published: February 2025
Stuttering: Our Current Knowledge, Research Opportunities, and Ways to Address Critical Gaps
Authors: Chang Soo-Eun , Below Jennifer E. , Chow Ho Ming , Guenther Frank H. , Hampton Wray Amanda M. , Jackson Eric S. , Max Ludo , Neef Nicole E. , SheikhBahaei Shahriar , Shekim Lana , Tichenor Seth E. , Walsh Bridget , Watkins Kate E. , Yaruss J. Scott , Bernstein Ratner Nan
Published: February 2025

Our understanding of the neurobiological bases of stuttering remains limited, hampering development of effective treatments that are informed by basic science. Stuttering affects more than 5% of all preschool-age children and remains chronic in approximately 1% of adults worldwide. As a condition that affects a most fundamental human ability to engage in fluid and spontaneous verbal communication, stuttering can have substantial psychosocial, occupational, and educational impacts on those who are affected. This article summarizes invited talks and breakout sessions that were held in June 2023 as part of a 2-day workshop sponsored by the US National Institute on Deafness and Other Communication Disorders. The workshop encompassed topics including neurobiology, genetics, speech motor control, cognitive, social, and emotional impacts, and intervention. Updates on current research in these areas were summarized by each speaker, and critical gaps and priorities for future research were raised, and then discussed by participants. Research talks were followed by smaller, moderated breakout sessions intended to elicit diverse perspectives, including on the matter of defining therapeutic targets for stuttering. A major concern that emerged following participant discussion was whether priorities for treatment in older children and adults should focus on targeting core speech symptoms of stuttering, or on embracing effective communication regardless of whether the speaker exhibits overt stuttering. This article concludes with accumulated convergent points endorsed by most attendees on research and clinical priorities that may lead to breakthroughs with substantial potential to contribute to bettering the lives of those living with this complex speech disorder.
Observing the impact of meal consumption on limb occlusion pressure in Indian female collegiates
Authors: Hariramani M. , Singh G. , Kothiyal S. , Navjyot T. , Sharma N. , Kaur S. , Majhi R. , Prathap G.D.
Published: February 2025

Blood flow resistance training (BFRT), characterised by low load, short duration, and high-efficiency exercises, has gained popularity among coaches, athletes, and health enthusiasts. Proper application of a compressible cuff, determined by limb occlusion pressure (LOP), is essential for effective BFRT. LOP is influenced by several factors, including limb size, length, temperature, blood pressure, and location. The objective of the study was to observe the variance in LOP, before and after meal consumption, in Indian female collegiate and to find the correlation between LOP and other variables. 93 female collegiate athletes participated in this study. LOP of the lower limb was measured pre- and post-meal using a hand-held Doppler, cuff inflator, and occlusion cuff. Data analysis was performed using IBM SPSS version 21. The mean LOP before meals was 66.99 mmHg (95% CI: 57.38-84.98 mmHg) with a median of 260.00 mmHg (interquartile range: 230.00-300.00 mmHg). Post-meal, the mean LOP increased to 69.98 mmHg (95% CI: 58.91-77.74 mmHg), with a median of 230.00 mmHg (interquartile range: 180.00-260.00 mmHg). A significant decrease in LOP after a meal was observed (Z-score: −7.67, ). Higher weight correlated positively with pre-meal LOP (rho = 0.261, ), and BMI also showed a positive correlation with pre-meal LOP (rho = 0.340, ). In conclusion, meal consumption significantly reduces LOP in Indian female collegiates. Additionally, weight and BMI positively correlate with pre-meal LOP, highlighting the need to consider body composition in LOP studies.