bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the UV and IR of a type-II holographic superconductor using a dyonic black hole
Authors: de la Cruz-López Manuel , Herrera-Mendoza Jhony A. , Cartas-Fuentevilla Roberto , Herrera-Aguilar Alfredo
Published: September 2024

In this study, we investigate a type-II holographic superconductor with a perturbative scalar field over a (3 + 1)-dimensional electric and magnetically charged planar AdS black hole. We review the thermodynamical properties of the background relevant for the dual description of the Ginzburg–Landau density of superconducting states, showing that the adoption of a London gauge allows a consistent description of the Abrikosov vortex lattices, typical of type-II superconductors. We further derive a new expression for the upper critical magnetic field as a function of temperature in the grand canonical ensemble, supplementary to the one previously obtained in the canonical ensemble setup. These results confirm that our perturbative scalar field model consistently reproduces the well-known temperature behavior of the upper critical magnetic field according to the Ginzburg–Landau theory and other Abelian–Higgs holographic developments for type-II superconductors. We then continue with an original analysis of the scalar field equation in terms of a Schrödinger potential that led to the observation of bound states, a signal for the condensation of Cooper pairs. These results provide robust evidence for the existence of an IR order parameter near extremality. In view of this, we performed a closer inspection of the IR effective scalar equation in which the geometry adopts a Schwarzschild $$\hbox {AdS}_{2}\times {\mathbb {R}}^{2}$$

AdS
2

×

R

2

structure, finding novel condensed bound states in the IR regime.
ANALYSIS OF ANTI-REFLECTIVE AND SELF-CLEANING COATINGS ON GLASS SUBSTRATES FOR SOLAR PANELS
Authors: SINGH ARVIND KUMAR , KHARB SANDEEP SINGH , Malik ANUP
Published: September 2024

Dust and other environmentally suspended particles deposited on the solar panels reduce the sunlight to photovoltaic cells, reducing the total energy outcome. A dust-reflecting coating keeps a cleaner surface, thus enhancing light absorption and improving the overall energy outcome. This study synthesized the sol–gel of SiO2, MgF2, and TiO2 and made the coating on the glass substrate by SiO[Formula: see text], SiO[Formula: see text], and MgF[Formula: see text] using sol–gel dip coating and spin coating method. Coatings that occurred on the glass sample surfaces were identified by using FTIR analysis. Five of the above six coatings made using different mixtures have increased transmittance than pure glass, while one SiO[Formula: see text] spin coating reduced the transmittance. The minimum water contact angle of 37.69∘ was found on the SiO[Formula: see text] spin-coated surface, and the maximum contact angle was 72.10∘ on the MgF2 dip-coated surface. This shows that the self-cleaning properties in SiO[Formula: see text] spin-coated surfaces are maximum and minimum in MgF2 dip-coated surfaces. The angle found by the test shows that spin coating is a better technique than dip coating for hydrophilic surface coating. This was due to the more homogenous coating on the spin-coated sample surfaces. There was less accumulation of dust found on the coated surfaces compared to non-coated glass sample surfaces.
COMPREHENSIVE INVESTIGATION OF Si ADDITIONS AND NANOCOMPOSITE INHIBITORS ON MICROSTRUCTURE/CORROSION PERFORMANCE OF CAST AX53 ALLOY IN 3.5% NaCl SOLUTION
Authors: ABDELFATAH ALIAA , MOHAMED LAMIAA Z. , EL-HADAD SHIMAA , MOUSSA M. E. , GABER GHALIA A.
Published: September 2024

Magnesium-based AX53 alloy was manufactured by a simple stir-casting method. In addition to the standard alloy constituting elements (Ca, Al), elemental Si was added in (0.1, 0.3, 0.6, and 1.0[Formula: see text]wt.%) during the melting process. SEM and EDX characterized the microstructure and elemental analyses of cast AX53 alloy with/without Si additions, respectively. The effects of Si on the corrosion characteristics of AX53 alloy in 3.5% NaCl have been investigated by weight reduction analysis, potentiodynamic polarization, and electrochemical impedance spectroscopy measurements. The SEM and EDX analyzed the morphology and composition of corrosion products, respectively. Also, the behavior of AX53 alloy with different investigated inhibitors such as nano-TiO2, nano-ZrO2, and mixed nano-(TiO2+ZrO[Formula: see text] was assessed. It was observed that the modification of 0.1% Si AX53 alloy by nano-TiO2 reduces the CR of the alloy. The CR increases with Si additions increasing, generally, the addition of an inhibitor reduces the corrosion rate, and the reductions depend on the type of inhibitor.
p-numerical semigroups with p-symmetric properties, II
Authors: Komatsu Takao
Published: September 2024

Recently, the concept of the [Formula: see text]-numerical semigroup with [Formula: see text]-symmetric properties has been introduced. When [Formula: see text], the classical numerical semigroup with symmetric properties is recovered. In this paper, we further study the [Formula: see text]-numerical semigroup with [Formula: see text]-almost symmetric properties. We also give [Formula: see text]-generalized formulas of Watanabe and Johnson, and introduce [Formula: see text]-Arf numerical semigroup and study its properties.
On What Dark Matter Is and the Non-existence of Dark Energy
Authors: Wang Jian
Published: September 2024

Since the concept of dark matter and dark energy was proposed, it is still unclear what its essence is. This paper will discuss the nature of dark matter and dark energy based on the dualism and its derivative theories or viewpoints. In the process of photon degradation to eight-subphotons in the edge region of sub-galaxy force, the traction force is superimposed on the gravity of adjacent sub-galaxies. Then the so-called dark matter is the dormant generalized photon in space. In addition to the previously known factors, there are three other types of redshift of light waves, namely, low density of space photons, photon degradation and strong light interference. Therefore, it is also concluded that the farther away from the observer, the greater the redshift, without assuming that dark energy drives the expansion of the universe — energy cannot be continuously generated out of thin air.
Cross-linguistic rhythm analysis of Mising and Assamese
Authors: Gogoi Parismita , Sarmah Priyankoo , Prasanna S. R. M.
Published: September 2024

The objective of the current study is to explore a quantitative frequency domain technique to evaluate rhythm in spontaneous speech data of 19 native speakers of Mising and Assamese, two low-resourced languages spoken in Assam, North-East India. The concept of analyzing speech rhythm using amplitude modulation (AM) low-frequency (LF) spectrum, also known as rhythm formant analysis (RFA), is initially put forth by Gibbon and Li [
17
]. We propose three features from rhythm formants of the LF spectrum and also explore discrete cosine transform (DCT)–based characterization of the retrieved LF spectrum. We aim to distinguish the rhythm of Assamese and two Mising dialects, namely Pagro and Delu, with the aid of machine learning techniques fed with the derived features as input. We have observed that the features are efficient in classifying Assamese vs Pagro and Assamese vs Delu with an accuracy of 92.73% and 91.15%, respectively. The experimental analysis further reveals that Assamese is rhythmically closer to Delu than Pagro.
Complexities in the Implementation and Maintenance of Integrated Pest Management in Potato
Authors: Gao Yulin , Alyokhin Andrei , Prager Sean M. , Reitz Stuart , Huseth Anders
Published: September 2024

Integrated pest management (IPM) is an educated and systematic effort to use multiple control techniques to reduce pest damage to economically acceptable levels while minimizing negative environmental impacts. Although its benefits are widely acknowledged, IPM is not universally practiced by farmers. Potato farming, which produces one of the most important staple crops in the world, provides a good illustration of the issues surrounding IPM adoption. Potatoes are attacked by a complex of insect pests that can inflict catastrophic crop losses. Potato production has gone through the processes of consolidation and intensification, which are linked to increased pest problems, particularly selection for insecticide-resistant pest populations. While use of insecticides remains the most common method of pest control in potatoes, other techniques, including crop rotation and natural enemies, are also available. In addition, there are effective monitoring techniques for many potato pests. However, reliable economic thresholds are often lacking. Potato ecosystems are complex and diverse; therefore, the knowledge necessary for developing ecologically based pest management is not easily obtained or transferable. Furthermore, potato systems change with the arrival of new pest species and the evolution of existing pests. Modern technological advances, such as remote sensing and molecular biotechnology, are likely to improve potato IPM. However, these tools are not going to solve all problems. IPM is not just about integrating different techniques; it is also about integrating the efforts and concerns of all stakeholders. The collaboration of farmers and scientists in agricultural research is needed to foster the development of IPM systems that are appropriate for grower implementation and thus more likely to be adopted. Additional emphasis also needs to be placed on the fact that not only does IPM decrease degradation of the environment, but it also improves the economic well-being of its practitioners.
Status of the World's Soils
Authors: Smith Pete , Poch Rosa M. , Lobb David A. , Bhattacharyya Ranjan , Alloush Ghiath , Eudoxie Gaius D. , Anjos Lúcia H.C. , Castellano Michael , Ndzana Georges M. , Chenu Claire , Naidu Ravi , Vijayanathan Jeyanny , Muscolo Adele M. , Studdert Guillermo A. , Eugenio Natalia Rodriguez , Calzolari M. Costanza , Amuri Nyambilila , Hallett Paul
Published: September 2024

Healthy soils contribute to a wide range of ecosystem services and virtually all of the UN Sustainable Development Goals, but most of the world's soil resources are in only fair, poor, or very poor condition, and conditions are getting worse in more cases than they are improving. A total of 33% of all soils are moderately to highly degraded as a result of erosion, loss of organic matter, poor nutrient balance, salinization and alkalinization, contamination, acidification, loss of biodiversity, sealing, compaction, and poor water status. Best management practices are available to limit or mitigate threats to soil health, and many of them mitigate multiple soil threats. In many regions of the world, policies or initiatives to protect or enhance the status of soils are in place, and they need to be strengthened and enforced. The Food and Agriculture Organisation will publish its second comprehensive assessment of the status of the world's soils in 2025, and this review provides an interim update on world soil status and offers an accessible overview of the topic.
How Does the Ocean Melt Antarctic Ice Shelves?
Authors: Rosevear Madelaine G. , Gayen Bishakhdatta , Vreugdenhil Catherine A. , Galton-Fenzi Benjamin K.
Published: September 2024

The present-day state and future of the Antarctic Ice Sheet depend on the rate at which the ocean melts its fringing ice shelves. Ocean heat must cross many physical and dynamical barriers to melt ice shelves, with the last of these being the ice–ocean boundary layer. This review summarizes the current understanding of ice–ocean boundary-layer dynamics, focusing on recent progress from laboratory experiments, turbulence-resolving numerical simulations, novel observations, and the application to large-scale simulations. The complex interplay between buoyant meltwater and external processes such as current shear leads to the emergence of several melting regimes that we describe, as well as freezing processes. The remaining challenges include developing new parameterizations for large-scale ice–ocean models based on recent advances and understanding the coevolution of melt and basal topography.
Machine Replacement: A Mind-Role Fit Perspective
Authors: Yam Kai Chi , Eng Alexander , Gray Kurt
Published: September 2024

Here we review work examining reactions to machines replacing humans in both professional and personal domains. Using a mind-role fit perspective, we synthesize findings across several decades of research spanning multiple disciplines to suggest the types and trends for how people will respond to machines replacing humans. We propose that as intelligent machines have evolved to possess “minds,” their range of replacement and the scope of people's reactions to this replacement increase. Additionally, we suggest that people's reactions to machine replacement depend on the fit between the perceived mind of the machine and their ideal conception of the mind deemed suitable for that particular role. Our review organizes the literature on machine replacement into three distinct phases: the pre-2000s era, characterized by the perception of machines as mindless tools; the 2000s, which explored the extent to which machines are perceived as possessing minds; and the 2010s, marked by the proliferation of artificial intelligence and the emergence of reactions such as algorithm aversion and appreciation. This review suggests that our mind-role fit perspective is influenced by three key factors: how an individual in the machine interaction is involved in or affected by the introduction of intelligent machines, the characteristics of the machine itself, and the nature of the task the machine is intended to perform.
Indole-3-Carbinol Upconversion with Copper Oxide Nanoparticles Supported Graphitic Carbon Nitride: A Sustainable Approach
Authors: Rodrigues Roopa Margaret , Varghese Anitha
Published: September 2024

Electro-organic chemistry offers a sustainable and efficient approach to organic synthesis by utilizing electrochemical processes. This field has gained significant attention due to its potential for minimizing waste, reducing energy consumption, and enabling selective transformations. Herein, we report the development of a graphitic carbon nitride-coated carbon fiber electrode modified with electropolymerized amino-2-thiazole and electrodeposited Cu2O nanoparticles from copper nitrate trihydrate for the oxidation of Indole-3-carbinol (IC). Scanning electron microscopy, X-ray diffraction analysis, and X-ray photoelectron spectroscopy studies were carried out to characterize the developed electrode. Cyclic voltammetry, electrochemical impedance spectroscopy, and bulk electrolysis techniques were employed for the electrochemical studies. The enhanced electrochemical activity of the Cu2O-pAT-GCN-TCFP electrode compared to the individual GCN and polymer electrode was studied using electrochemical characterization, which revealed a 3-fold increase in the current response for Cu2O-pAT-GCN-TCFP (0.0011 A) compared to the bare electrode. The reaction was carried out using an aqueous carbonate buffer solution as an electrolyte via bulk electrolysis at a set potential of 0.82 V. The product obtained was isolated by column chromatography to obtain a yield of 74% and characterized by proton nuclear magnetic resonance (1H NMR) spectroscopy. Additionally, the Cu2O-pAT-GCN-TCFP electrode was studied for its stability, reproducibility, and selectivity.
A Realist Evaluation of Mechanisms and Contexts for Facilitating the Implementation of Supported Self‐Management in Community Stroke Care (The IMPETUS Study)
Authors: Kidd Lisa , Brown Julie , Mason Helen , Quinn Terry , Gallacher Katie I. , Jones Fiona , Fisher Rebecca , Lebedis Therese , Barber Mark , Brennan Katrina , Gilmour Betty , Fraser Colin , Mooney Patricia , Taggart Audrey
Published: September 2024

The past decade has seen a growing recognition of the role of supported self‐management in the provision of long‐term care and support for stroke survivors in primary and community care. However, its implementation and delivery across different contexts and models of community stroke care is inconsistent and patchy. This realist evaluation explored how and in which circumstances supported self‐management is enacted and delivered within community stroke rehabilitation. Specifically, the study aimed to identify and explore contexts, mechanisms, and outcomes related to the delivery of collaborative supported self‐management. It comprised a realist synthesis, Q‐methodology study, and realist‐informed interviews and focus groups with stroke survivors (n = 20), community‐based stroke practitioners (n = 20), and community service delivery managers/clinical leads (n = 8) in stroke. The findings revealed that delivering supported self‐management effectively and consistently in community stroke rehabilitation starts with embedding the ethos of collaborative supported self-management across staff, teams, and the organisation and involves collaborative relationships with stroke survivors that aim to build trust, confidence, and resilience. The findings identified specific mechanisms and facilitatory and inhibitory contexts that influence how well this is enacted and achieved in practice. A realist approach in this study is novel and has helped to generate new insights and perspectives how and when supported self‐management approaches work in community stroke rehabilitation. The findings expand on and complement existing research on the efficacy of supported self‐management in stroke and are of clinical importance for informing how collaborative, relational supported self‐management approaches can be implemented, personalised, and tailored to people’s needs and evaluated within current healthcare systems.
Desempeño financiero de Pymes en Chile: estilos de toma de decisiones del CEO
Authors: Jorquera Castro Rosario Del Pilar
Published: September 2024

Este artículo se centra en la influencia de los estilos de toma de decisiones del Gerente-Dueño (CEO) y el desempeñofinanciero de las Pymes en Chile. Aplicando un cuestionario a una muestra de 185 Pymes chilenas en 2017 se encontróque el género femenino del CEO incide positivamente en el desempeño de la empresa. Al indagar si las característicassociodemográficas, rasgos de personalidad y estilos de toma de decisiones del Gerente-Dueño(CEO) se relacionan conel desempeño de la firma, hay evidencia estadísticamente significativa sólo de ciertos estilos de toma de decisiones queinciden en el desempeño de las Pymes. Los resultados confirman la importancia de reducir las brechas de género en lasempresas para que las autoridades implementen políticas públicas enfocadas en la incorporación de mujeres en la altadirección.
Supplementary Figures 1 through 6 from RETRACTED: PHGDH Expression Is Required for Mitochondrial Redox Homeostasis, Breast Cancer Stem Cell Maintenance, and Lung Metastasis
Authors: Samanta Debangshu , Park Youngrok , Andrabi Shaida A. , Shelton Laura M. , Gilkes Daniele M. , Semenza Gregg L.
Published: September 2024

Supplementary Figure S1. Analysis of G6PD mRNA expression. Supplementary Figure S2. Analysis of MCF-7 Subclones. Supplementary Figure S3. Effect of PHGDH knockdown on cell growth. Supplementary Figure S4. Effect of carboplatin on cell viability. Supplementary Figure S5. Effect of doxorubicin treatment. Supplementary Figure S6. Clinical correlates.
Supplementary Table S3 from Multistate Gene Cluster Switches Determine the Adaptive Mitochondrial and Metabolic Landscape of Breast Cancer
Authors: Menegollo Michela , Bentham Robert B. , Henriques Tiago , Ng Seow Q. , Ren Ziyu , Esculier Clarinde , Agarwal Sia , Tong Emily T.Y. , Lo Clement , Ilangovan Sanjana , Szabadkai Zorka , Suman Matteo , Patani Neill , Ghanate Avinash , Bryson Kevin , Stein Robert C. , Yuneva Mariia , Szabadkai Gyorgy
Published: September 2024

Supplementary Table S3
Supplementary Data from Ku70 Binding to YAP Alters PARP1 Ubiquitination to Regulate Genome Stability and Tumorigenesis
Authors: Shu Yinyin , Jin Xiaoni , Ji Mintao , Zhang Zhisen , Wang Xiuxiu , Liang Haisheng , Lu Shuangshuang , Dong Shuai , Lin Yiping , Guo Yuhan , Zhuang Qiuyu , Wang Yuhong , Lei Zhe , Guo Lingchuan , Meng Xuanyu , Zhou Guangming , Zhang Wensheng , Chang Lei
Published: September 2024

Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S7, Figure S8
Data from Targeting the TRIM14/USP14 Axis Enhances Immunotherapy Efficacy by Inducing Autophagic Degradation of PD-L1
Authors: Liu Di , Li Mengqiu , Zhao Zhiyao , Zhou Liang , Zhi Feng , Guo Zhiyong , Cui Jun
Published: September 2024

Abstract
Immunotherapy has greatly improved cancer treatment in recent years by harnessing the immune system to target cancer cells. The first immunotherapeutic agent approved by the FDA was IFNα. Treatment with IFNα can lead to effective immune activation and attenuate tumor immune evasion, but persistent treatment has been shown to elicit immunosuppressive effects. Here, we identified an autophagy-dependent mechanism by which IFNα triggers tumor immune evasion by upregulating PD-L1 to suppress the antitumor activity of CD8+ T cells. Mechanistically, IFNα increased the transcription of TRIM14, which recruited the deubiquitinase USP14 to inhibit the autophagic degradation of PD-L1. USP14 removed K63-linked ubiquitin chains from PD-L1, impairing its recognition by the cargo receptor p62 (also known as SQSTM1) for subsequent autophagic degradation. Combining the USP14 inhibitor IU1 with IFNα and anti-CTLA4 treatment effectively suppressed tumor growth without significant toxicity. This work suggests a strategy for targeting selective autophagy to abolish PD-L1-mediated cancer immune evasion.

Significance: IFNα-induced TRIM14 transcription suppresses antitumor immunity by recruiting USP14 to inhibit autophagic degradation of PD-L1, indicating that targeting this axis could be an effective immunotherapeutic approach for treating cancer.
Figure S10 from HPN328, a Trispecific T Cell–Activating Protein Construct Targeting DLL3-Expressing Solid Tumors
Authors: Molloy Mary E. , Aaron Wade H. , Barath Manasi , Bush Mabel C. , Callihan Evan C. , Carlin Kevin , Cremin Michael , Evans Thomas , Guerrero Maria G. , Hemmati Golzar , Hundal Avneel S. , Lao Llewelyn , Laurie Payton , Lemon Bryan D. , Lin S.J. , O’Rear Jessica , Patnaik Purbasa , Sotelo Rocha Sony , Santiago Linda , Strobel Kathryn L. , Valenzuela Laura B. , Wu Chi-Heng , Yu Stephen , Yu Timothy Z. , Anand Banmeet S. , Law Che-Leung , Sun Liping L. , Wesche Holger , Austin Richard J.
Published: September 2024

TDCC co-cultures show no T cell activation in the presence DLL3 negative tumor cell line.
Supplementary Table 3 from Prognostic Significance of SASP-Related Gene Signature of Radiation Therapy in Head and Neck Squamous Cell Carcinoma
Authors: Lee Min Kyeong , Woo Seon Rang , Noh Joo Kyung , Min Soonki , Kong Moonkyoo , Lee Young Chan , Ko Seong-Gyu , Eun Young-Gyu
Published: September 2024

Supplementary Table 3
Figure S1 from IL-15/IL-15Rα-Fc-Fusion Protein XmAb24306 Potentiates Activity of CD3 Bispecific Antibodies through Enhancing T-Cell Expansion
Authors: Li Ji , Clark Robyn , Slaga Dionysos , Avery Kendra , Liu Ke , Schubbert Suzanne , Varma Rajat , Chiang Eugene , Totpal Klara , Bernett Matthew J. , Holder Patrick G. , Junttila Teemu T.
Published: September 2024

Supplementary figure S1 shows the proliferation activity of surrogate mIL-15-Fc
Data from Prognostic Significance of SASP-Related Gene Signature of Radiation Therapy in Head and Neck Squamous Cell Carcinoma
Authors: Lee Min Kyeong , Woo Seon Rang , Noh Joo Kyung , Min Soonki , Kong Moonkyoo , Lee Young Chan , Ko Seong-Gyu , Eun Young-Gyu
Published: September 2024

Abstract
In this study, we developed and validated the clinical significance of senescence-associated secretory phenotype (SASP)-related gene signature and explored its association with radiation therapy (RT) in patients with head and neck squamous cell carcinoma (HNSCC). First, we searched the three published review literature associated with SASP and selected all 81 genes to develop SASP-related gene signature. Then, 81 SASP-related genes were adapted to gene expression dataset from The Cancer Genome Atlas (TCGA). Patients with HNSCC of TCGA were classified into clusters 1 and 2 via unsupervised clustering according to SASP-related gene signature. Kaplan–Meier plot survival analysis showed that cluster 1 had a poorer prognosis than cluster 2 in 5-year overall survival and recurrence-free survival. Similarly, cluster 1 showed a worse prognosis than cluster 2 in three validation cohorts (E-MTAB-8588, FHCRC, and KHU). Cox proportional hazards regression observed that the SASP-related signature was an independent prognostic factor for patients with HNSCC. We also established a nomogram using a relevant clinical parameter and a risk score. Time-dependent receiver operating characteristic analysis was carried out to assess the accuracy of the prognostic risk model and nomogram. Senescence SASP-related gene signature was associated with the response to RT. Therefore, subsequent, in vitro experiments further validated the association between SASP-related gene signature and RT in HNSCC. In conclusion, we developed a SASP-related gene signature, which could predict survival of patients with HNSCC, and this gene signature provides new clinical evidence for the accurate diagnosis and targeted RT of HNSCC.
Data from A Senescence-Mimicking (Senomimetic) VEGFR TKI Side Effect Primes Tumor Immune Responses via IFN/STING Signaling
Authors: Dolan Melissa , Shi Yuhao , Mastri Michalis , Long Mark D. , McKenery Amber , Hill James W. , Vaghi Cristina , Benzekry Sebastien , Barbi Joseph , Ebos John M.L.
Published: September 2024

Abstract
Tyrosine kinase inhibitors (TKIs) that block the vascular endothelial growth factor receptors (VEGFRs) not only disrupt tumor angiogenesis but also have many unexpected side effects that impact tumor cells directly. This includes the induction of molecular markers associated with senescence, a form of cellular aging that typically involves growth arrest. We have shown that VEGFR TKIs can hijack these aging programs by transiently inducting senescence markers (SMs) in tumor cells to activate senescence-associated secretory programs that fuel drug resistance. Here we show that these same senescence-mimicking (“senomimetic”) VEGFR TKI effects drive an enhanced immunogenic signaling that, in turn, can alter tumor response to immunotherapy. By using a live cell sorting method to detect β-galactosidase, a commonly used SM, we found that subpopulations of SM-expressing (SM+) tumor cells have heightened IFN signaling and increased expression of IFN-stimulated genes (ISGs). These ISGs increase under the control of the STimulator of the INterferon Gene (STING) signaling pathway, which we found could be directly activated by several VEGFR TKIs. TKI-induced SM+ cells could stimulate or suppress CD8 T-cell activation depending on host–tumor cell contact while tumors grown from SM+ cells were more sensitive to PDL1 inhibition in vivo, suggesting that offsetting immune-suppressive functions of SM+ cells can improve TKI efficacy overall. Our findings may explain why some (but not all) VEGFR TKIs improve outcomes when combined with immunotherapy and suggest that exploiting senomimetic drug side effects may help identify TKIs that uniquely “prime” tumors for enhanced sensitivity to PDL1-targeted agents.
Supplementary Table S3 from miR-497 Target Gene Regulatory Network in Angiosarcoma
Authors: Benton Annaleigh , Moriarty Noah M. , Terwilliger Emma , Liu Bozhi , Murphy Ant , Maluvac Hannah , Shu Mae , Gartenhaus Lauren E. , Janson Nimod D. , Pfeffer Claire M. , Utturkar Sagar M. , Parkinson Elizabeth I. , Lanman Nadia A. , Hanna Jason A.
Published: September 2024

Primers for pre-miR-497, 3` UTR cloning of miR-497 target genes, and VAT1 knockdown constructs.
Figure S4 from Clinically Relevant Humanized Mouse Models of Metastatic Prostate Cancer Facilitate Therapeutic Evaluation
Authors: Kostlan Raymond J. , Phoenix John T. , Budreika Audris , Ferrari Marina G. , Khurana Neetika , Choi Jae E. , Juckette Kristin , Mahapatra Somnath , McCollum Brooke L. , Moskal Russell , Mannan Rahul , Qiao Yuanyuan , Vander Griend Donald J. , Chinnaiyan Arul M. , Kregel Steven
Published: September 2024

Metastasis by 22Rv1 to the spleen in huNOG and huNOG-EXL mice.
Supplementary Figure S1 from miR-497 Target Gene Regulatory Network in Angiosarcoma
Authors: Benton Annaleigh , Moriarty Noah M. , Terwilliger Emma , Liu Bozhi , Murphy Ant , Maluvac Hannah , Shu Mae , Gartenhaus Lauren E. , Janson Nimod D. , Pfeffer Claire M. , Utturkar Sagar M. , Parkinson Elizabeth I. , Lanman Nadia A. , Hanna Jason A.
Published: September 2024

Validation of microRNA mimic transfection in cell line panel.
Figure S1 from Clinically Relevant Humanized Mouse Models of Metastatic Prostate Cancer Facilitate Therapeutic Evaluation
Authors: Kostlan Raymond J. , Phoenix John T. , Budreika Audris , Ferrari Marina G. , Khurana Neetika , Choi Jae E. , Juckette Kristin , Mahapatra Somnath , McCollum Brooke L. , Moskal Russell , Mannan Rahul , Qiao Yuanyuan , Vander Griend Donald J. , Chinnaiyan Arul M. , Kregel Steven
Published: September 2024

Representative histology of subcutaneous tumor, bone and liver metastasis of 22Rv1 cells in huNOG mice.
Figure 3 from Clinically Relevant Humanized Mouse Models of Metastatic Prostate Cancer Facilitate Therapeutic Evaluation
Authors: Kostlan Raymond J. , Phoenix John T. , Budreika Audris , Ferrari Marina G. , Khurana Neetika , Choi Jae E. , Juckette Kristin , Mahapatra Somnath , McCollum Brooke L. , Moskal Russell , Mannan Rahul , Qiao Yuanyuan , Vander Griend Donald J. , Chinnaiyan Arul M. , Kregel Steven
Published: September 2024

Activated T-cell immune profile in huNOG tumors. A, Gating strategy employed to determine T-cell activation status. B, Total percentage of CD45+ cells acquired from tumor tissue harvesting split between the intact control, castrated vehicle, and castrated with enzalutamide treatment. C, Percentage of CD3+ cells observed in the total CD45+ population. D, Percentage of CD3+ cells showing IFNγ expression via intracellular staining. E, Measurement of the percentage of CD4+ cells expressing IFNγ harvested from the spleen. F, Measurement of CD8+ cells expressing IFNγ from the spleen. G, Spleen bioluminescent metastasis signal quantification.
Data from MLLT6/ATF2 Axis Restrains Breast Cancer Progression by Driving DDIT3/4 Expression
Authors: Yu Qing , Zhao Jiayi , Yang Anli , Li Xiangxin
Published: September 2024

Abstract
Epigenetic deregulation is strongly associated with tumor progression. The identification of natural tumor suppressors to overcome cancer metastasis is urgent for cancer therapy. We investigate whether myeloid/lymphoid or mixed-lineage leukemia translocated (MLLT) family members contribute to breast cancer progression and found that high MLLT6 expression predicted a better prognosis and that gradually decreased MLLT6 expression was accompanied by breast cancer malignancy. MLLT6 was downregulated by hypoxia-induced enrichment of DNMT1 at the MLLT6 promoter. The results of in vitro functional experiments indicated that MLLT6 depletion promoted colony formation and cell migration, probably by hampering apoptosis. RNA profiling revealed that the apoptotic pathway was downregulated following stable knockdown of MLLT6. DNA damage-inducible transcript 3/4 (DDIT3/4) were among the top 10 downregulated genes and may have expression patterns similar to that of MLLT6. Restoring DDIT3/4 expression in cells with MLLT6 depletion blocked colony formation and cell migration and attenuated the successful colonization of breast cancer cells in vivo. We also determined that the transcription factor activating transcription factor 2 is a binding partner of MLLT6 and participates in the MLLT6/ATF2 axis, which was reinforced by inhibition of AKT signaling, in turn inducing DDIT3/4 expression by establishing an active chromatin structure at the DDIT3/4 gene promoters. As MLLT6 promotes breast cancer cell apoptosis by inducing DDIT3/4 expression during metastasis, it could be a novel tumor suppressor.

Implications: Control of MLLT6 expression via inhibition of PI3K/AKT kinase activity is a potential therapeutic approach for the management of metastatic breast cancer.
Supplemental Figure 3 from Diet Modulates the Gut Microbiome, Metabolism, and Mammary Gland Inflammation to Influence Breast Cancer Risk
Authors: Arnone Alana A. , Wilson Adam S. , Soto-Pantoja David R. , Cook Katherine L.
Published: September 2024

Supplemental Figure 3: A. Individual filter components of mammary gland fluorescent images DAPI, CD68-FITC, CD80-PE, and overlay. B. Quantification of periductal Gram-positive bacteria-laden cells in the mammary glands of mice fed differing diets. C. Gram-positive bacteria in mammary gland tissue do not colocalize with macrophages in lard diet-fed animals.
Supplementary Figure S6 from CHD2 Regulates Neuron–Glioma Interactions in Pediatric Glioma
Authors: Zhang Xu , Duan Shoufu , Apostolou Panagiota E. , Wu Xiaoping , Watanabe Jun , Gallitto Matthew , Barron Tara , Taylor Kathryn R. , Woo Pamelyn J. , Hua Xu , Zhou Hui , Wei Hong-Jian , McQuillan Nicholas , Kang Kyung-Don , Friedman Gregory K. , Canoll Peter D. , Chang Kenneth , Wu Cheng-Chia , Hashizume Rintaro , Vakoc Christopher R. , Monje Michelle , McKhann Guy M. , Gogos Joseph A. , Zhang Zhiguo
Published: September 2024

FOSL1 colocalizes with CHD2 to regulate cell viability and gene expression.
Figure S2 from MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer
Authors: Meena Jitendra K. , Wang Jarey H. , Neill Nicholas J. , Keough Dianne , Putluri Nagireddy , Katsonis Panagiotis , Koire Amanda M. , Lee Hyemin , Bowling Elizabeth A. , Tyagi Siddhartha , Orellana Mayra , Dominguez-Vidaña Rocio , Li Heyuan , Eagle Kenneth , Danan Charles , Chung Hsiang-Ching , Yang Andrew D. , Wu William , Kurley Sarah J. , Ho Brian M. , Zoeller Joseph R. , Olson Calla M. , Meerbrey Kristen L. , Lichtarge Olivier , Sreekumar Arun , Dacso Clifford C. , Guddat Luke W. , Rejman Dominik , Hocková Dana , Janeba Zlatko , Simon Lukas M. , Lin Charles Y. , Pillon Monica C. , Westbrook Thomas F.
Published: September 2024

Figure S2 shows MYC-induced cell death in MYC-ER HMECs with DIS3L, EXOSC2, EXOSC8 and DIS3 knockdown, expression of DIS3L, EXOSC2, EXOSC8 and DIS3 upon knockdown, and MYC-induced EU incorporation in MYC-hyperactivated conditions.
Supplemental Figure S6 from D3S-001, a KRAS G12C Inhibitor with Rapid Target Engagement Kinetics, Overcomes Nucleotide Cycling, and Demonstrates Robust Preclinical and Clinical Activities
Authors: Zhang Jing , Lim Sun Min , Yu Mi Ra , Chen Cheng , Wang Jia , Wang Wenqian , Rui Haopeng , Lu Jingtao , Lu Shun , Mok Tony , Chen Zhi Jian , Cho Byoung Chul
Published: September 2024

Supplemental Figure S6 shows baseline mutation landscape of the 10 colorectal cancer PDX models
Table S5 from A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation
Authors: Yaeger Rona , McKean Meredith A. , Haq Rizwan , Beck J. Thaddeus , Taylor Matthew H. , Cohen Jonathan E. , Bowles Daniel W. , Gadgeel Shirish M. , Mihalcioiu Catalin , Papadopoulos Kyriakos P. , Diamond Eli L. , Sturtz Keren B. , Feng Gang , Drescher Stefanie K. , Reddy Micaela B. , Sengupta Bhaswati , Maity Arnab K. , Brown Suzy A. , Singh Anurag , Brown Eric N. , Baer Brian R. , Wong Jim , Mou Tung-Chung , Wu Wen-I , Kahn Dean R. , Gadal Sunyana , Rosen Neal , Gaudino John J. , Lee Patrice A. , Hartley Dylan P. , Rothenberg S. Michael
Published: September 2024

Table S5. Preliminary mutation analysis
Figure S2 from A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation
Authors: Yaeger Rona , McKean Meredith A. , Haq Rizwan , Beck J. Thaddeus , Taylor Matthew H. , Cohen Jonathan E. , Bowles Daniel W. , Gadgeel Shirish M. , Mihalcioiu Catalin , Papadopoulos Kyriakos P. , Diamond Eli L. , Sturtz Keren B. , Feng Gang , Drescher Stefanie K. , Reddy Micaela B. , Sengupta Bhaswati , Maity Arnab K. , Brown Suzy A. , Singh Anurag , Brown Eric N. , Baer Brian R. , Wong Jim , Mou Tung-Chung , Wu Wen-I , Kahn Dean R. , Gadal Sunyana , Rosen Neal , Gaudino John J. , Lee Patrice A. , Hartley Dylan P. , Rothenberg S. Michael
Published: September 2024

Figure S2. Crystal structures of BRAF kinase domain with PF-07799933 or encorafenib.
Supplementary Table 3 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

KLHL6 proteomics
Supplementary Figure S14 from Molecular Determinants of Sensitivity to Polatuzumab Vedotin in Diffuse Large B-Cell Lymphoma
Authors: Corcoran Sean R. , Phelan James D. , Choi Jaewoo , Shevchenko Galina , Fenner Rachel E. , Yu Xin , Scheich Sebastian , Hsiao Tony , Morris Vivian M. , Papachristou Evangelia K. , Kishore Kamal , D’Santos Clive S. , Ji Yanlong , Pittaluga Stefania , Wright George W. , Urlaub Henning , Pan Kuan-Ting , Oellerich Thomas , Muppidi Jagan , Hodson Daniel J. , Staudt Louis M.
Published: September 2024

Inhibition of neddylation increases expression of BCR subunits
Supplementary Table S4 from Efficacy of the Allosteric MEK Inhibitor Trametinib in Relapsed and Refractory Juvenile Myelomonocytic Leukemia: a Report from the Children’s Oncology Group
Authors: Stieglitz Elliot , Lee Alex G. , Angus Steven P. , Davis Christopher , Barkauskas Donald A. , Hall David , Kogan Scott C. , Meyer Julia , Rhodes Steven D. , Tasian Sarah K. , Xuei Xiaoling , Shannon Kevin , Loh Mignon L. , Fox Elizabeth , Weigel Brenda J.
Published: September 2024

Changes in MIB binding ordered by p value (unpaired t-tests of log2LFQ).
Supplementary Table S6 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Table S6: SIDP results in T47D grown in white media (-E2) media. S6.1-3: the tables follow the same structure of S3.1-3.
Supplementary Table S3 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Table S3: SIDP results in MCF7 grown in full (red; +E2) media. S3.1: results of the differential abundance analysis for the positive controls and the non-targeting sgRNAs (as indicated in the genome_partition field). For each sgRNA, an identifier, the pool, and the results from the edgeR analysis are shown. Average abundance of the sgRNA at day 7 and 21 post infection is indicated as logCPM (counts per million). The log2-fold changes (log2FC) between day 21 and 7, and between day 21 and the initial library, are indicated, along with the FDR (Benjamini-corrected p-value). Two further fields indicate whether the sgRNA was identified as showing a significant increase in frequency (IF; FDR <= 0.05 and linear fold-change >= 1.5) or decrease (DF; FDR <= 0.05 and linear fold-change <= -1.5). S3.2: like S3.1 but listing the results for the sgRNAs targeting the genomic regions of interest. Hg38 coordinates are also included in this case. S3.3: summary of the results at the level of each SID region. For each region, hg38 coordinates are listed, along with the symbol of the nearest gene, and the distance to its TSS in bp (positive or negative values indicate the region is either downstream or upstream the TSS, respectively). The table then indicates whether the region was selected as a gene promoter, putative enhancer, or putative insulator. The number of sgRNAs targeting the enlarged region (indicated coordinates +- 1 kbp), is followed by information on the overlapping sgRNAs that scored significantly, separately for DF and IF. In both cases, the total number of significant guides, the corresponding fraction, and the FDR and log2FC of the highest scoring sgRNA are reported. A column indicating significance of one or more sgRNAs is also provided. S3.4: enriched terms in the set of genes close to the regions showing scoring sgRNAs, separately for the DF and the IF sets. For each group, hallmark sets showing a p-value <= 0.05 are included in the table. Statistics of the hyper-geometric test are shown, along with the total number and identity of the overlapping genes. S3.5: overlap between the regions identified in our +E2 MCF7 SIDP assay and previously published screens in breast cancer cell lines (marcotte: Marcotte et al. 2012; fei: Fei at al. 2019; Korkmaz: Korkmaz et al. 2019; ggg: Rui Lopes et al. 2020).
Supplementary Table S19 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Table S19: Overlap between regions with excess of functional alterations. The regions considered in these overlaps are highlighted in table S13.1. S19.1: overlap with noncoding drivers identified by PCAWG (as listed in Supplementary Table 5 of Rheinbay et al. 2020). S19.2: overlap with regulatory mutations from breast cancer samples, as identified by HMF (as listed in Supplementary Table 5 of Dietlein et al. 2022). S19.3: overlap with noncoding mutational hotspots identified by HMF (as listed in Supplementary Table 21 of Dietlein et al. 2022). S19.4: overlap with genes associated with mutation events in non-coding regions from previous studies, as annotated by HMF (as listed in Supplementary Table 22 of Dietlein et al. 2022).
Supplementary Table S1 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Table S1: Regions defined by SID (Systematic Identification of epigenetically Defined loci). For each region (hg38 genomic coordinates including chromosome, starting, and ending positions), the table indicates whether the region was selected as a gene promoter, putative enhancer, or putative insulator. Whether the region is covered by designed oligo baits for SIDV profiling, and the number of sgRNAs targeting the region in SIDP, are also indicated.
Supplementary Figure S2 from A Functional Survey of the Regulatory Landscape of Estrogen Receptor–Positive Breast Cancer Evolution
Authors: Barozzi Iros , Slaven Neil , Canale Eleonora , Lopes Rui , Amorim Monteiro Barbosa Inês , Bleu Melusine , Ivanoiu Diana , Pacini Claudia , Mensa’ Emanuela , Chambers Alfie , Bravaccini Sara , Ravaioli Sara , Győrffy Balázs , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio Giacomo , Magnani Luca
Published: September 2024

Supplementary Figure 2. SIDP identifies Cis Regulatory regions in T47D with high reproducibility.
Supplementary Figure S11 from Identification of Clonal Hematopoiesis Driver Mutations through In Silico Saturation Mutagenesis
Authors: Demajo Santiago , Ramis-Zaldivar Joan E. , Muiños Ferran , Grau Miguel L. , Andrianova Maria , López-Bigas Núria , González-Pérez Abel
Published: September 2024

Fitness of recurrent somatic mutations in UKB
Gene-Specific Machine Learning Models to Classify Driver Mutations in Clonal Hematopoiesis
Authors: Arends Christopher M. , Jaiswal Siddhartha
Published: September 2024

There is no general consensus on the set of mutations capable of driving the age-related clonal expansions in hematopoietic stem cells known as clonal hematopoiesis, and current variant classifications typically rely on rules derived from expert knowledge. In this issue of Cancer Discovery, Damajo and colleagues trained and validated machine learning models without prior knowledge of clonal hematopoiesis driver mutations to classify somatic mutations in blood for 12 genes in a purely data-driven way.

See related article by Demajo et al., p. 1717 (9).
If You Build It, Patients with Rare Cancers Will Come: A Successful Clinical Trial in Relapsed and Refractory JMML
Authors: Ben-Crentsil Nana Adjoa , Padron Eric
Published: September 2024

Juvenile myelomonocytic leukemia (JMML) is a rare pediatric hematologic malignancy with a high relapse rate and a poor prognosis hallmarked by RAS pathway mutations. Stieglitz and colleagues conducted a phase II clinical trial using the MEK inhibitor trametinib to treat patients with relapsed and refractory juvenile myelomonocytic leukemia and observed an objective response rate of 50% and an overall survival of 80% after 4 years.

See related article by Stieglitz et al., p. 1590 (4) .
Table 2 from Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features
Authors: Wijetunga N. Ari , Gessner Kathryn H. , Kanchi Krishna , Moore Jay A. , Fleischmann Zoe , Jin Dexter X. , Frampton Garrett M. , Sturdivant Michael , Repka Michael , Sud Shivani , Corcoran David L. , Galsky Matthew D. , Milowsky Matthew I. , Wobker Sara E. , Kim William Y. , Rose Tracy L. , Damrauer Jeffrey S.
Published: September 2024

Summary of clinical variables within the radiation therapy cohort, grouped by latency.
Supplementary Table S3 from Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features
Authors: Wijetunga N. Ari , Gessner Kathryn H. , Kanchi Krishna , Moore Jay A. , Fleischmann Zoe , Jin Dexter X. , Frampton Garrett M. , Sturdivant Michael , Repka Michael , Sud Shivani , Corcoran David L. , Galsky Matthew D. , Milowsky Matthew I. , Wobker Sara E. , Kim William Y. , Rose Tracy L. , Damrauer Jeffrey S.
Published: September 2024

Supplementary Table S3
Supplementary Table S2 from Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features
Authors: Wijetunga N. Ari , Gessner Kathryn H. , Kanchi Krishna , Moore Jay A. , Fleischmann Zoe , Jin Dexter X. , Frampton Garrett M. , Sturdivant Michael , Repka Michael , Sud Shivani , Corcoran David L. , Galsky Matthew D. , Milowsky Matthew I. , Wobker Sara E. , Kim William Y. , Rose Tracy L. , Damrauer Jeffrey S.
Published: September 2024

Supplementary Table S2