bluuebunny/crossref_metadata_2025 huggingface dataset:
Stochastic differential equations with Hölder–Dini drift and driven by α-stable processes
Authors: Tian Rongrong , Wei Jinlong , Duan Jinqiao
Published: September 2024

We prove the Hölder–Dini regularity for a class of fractional Fokker–Planck–Kolmogorov equations. Then, by applying the Itô–Tanaka trick, we obtain the unique strong solvability of time inhomogeneous stochastic differential equations with drift coefficients in [Formula: see text] for [Formula: see text] and driven by [Formula: see text]-stable processes.
Source rocks and petroleum systems of the Hungarian Pannonian Basin
Authors: Badics Balázs , Vető István , Sajgó Csanád , Koncz István
Published: September 2024

In this study, our primary objectives were to describe and assess the potential source rocks in Hungary, focusing on parameters such as lateral extent, thickness and organic richness. We investigated the burial and thermal evolution and timing of petroleum generation. Utilizing a substantial database of 1400 vitrinite reflectance and 6500 total organic carbon/Rock-Eval data, we performed a quantitative assessment of source-rock potential per basin. A 93 000 km
2
3D basin model covering entire Hungary was created. In the Zala North Basin, the Upper Triassic Kössen Marl is the main source rock, charging the Nagylengyel oil fields. Lower–Middle Jurassic sediments in the Mecsek Unit were identified as fair-quality gas-prone source rocks, potentially charging the nitrogen-rich gas fields in the Szolnok Flysch Zone. In the Paleogene Basin, the Lower Oligocene Tard Clay is the best source rock, with additional potential in the Upper Eocene Kosd Fm. and Buda Marl. The Badenian marine shales are the likely source rocks in the Zala South and the Dráva Basin, and in the Somogy Trough. In the Kiskunság area, Karpatian lacustrine, Badenian marine and lower Pannonian Endrőd Marl source rocks charged the known fields, similarly to the Pusztaföldvár High and Békés Basin, and in the Derecske Trough.
Sedimentation cycles, tectonic phases and progradation trends: Late Pannonian deposition in the Drmno Basin, Serbia
Authors: Ninić Anastasia , Životić Dragana , Radivojević Dejan
Published: September 2024

The Drmno Basin is characterized by siliciclastic deposition and coal accumulation during the Late Pannonian and Pliocene, which resulted in the formation of numerous coal seams that lack lateral continuity, challenging traditional research methods. The cyclicity and geometry of the coal seams suggest several phases of peat accumulation, interrupted by the influx of siliciclastic material from the Carpathians. Siliciclastic deposition began in the upper delta plain environment and developed into an alluvial plain with river channels and swamps. The coal seams in the Drmno field within the Kostolac open-cast mine show a northward shift of the peat accumulation centre and, together with the coarsening upward trend in the interburden sediments, indicate a south-northward progradation. Biostratigraphic results confirmed the progradation trend with
Prosodacnomya carbonifera
indicating an age of 7.5–8 Ma in the southern part of the field and with
Prosodacnomya elongata
indicating an age of 7.2 Ma in the northern part. The influence of recent tectonic activity in the peri-Pannonian domain is reflected by the presence of compressional tectonic structures observed in the basin fill.
Reputation Gaming in Crowd Technical Knowledge Sharing
Authors: Mazloomzadeh Iren , Uddin Gias , Khomh Foutse , Sami Ashkan
Published: September 2024

Stack Overflow incentive system awards users with reputation scores to ensure quality. The decentralized nature of the forum may make the incentive system prone to manipulation. This article offers, for the first time, a comprehensive study of the reported types of reputation manipulation scenarios that might be exercised in Stack Overflow and the prevalence of such reputation gamers by a qualitative study of 1,697 posts from meta Stack Exchange sites. We found four different types of reputation fraud scenarios, such as voting rings where communities form to upvote each other repeatedly on similar posts. We developed algorithms that enable platform managers to automatically identify these suspicious reputation gaming scenarios for review. The first algorithm identifies isolated/semi-isolated communities where probable reputation frauds may occur mostly by collaborating with each other. The second algorithm looks for sudden unusual big jumps in the reputation scores of users. We evaluated the performance of our algorithms by examining the reputation history dashboard of Stack Overflow users from the Stack Overflow Web site. We observed that around 60–80% of users flagged as suspicious by our algorithms experienced reductions in their reputation scores by Stack Overflow.
MemoVis: A GenAI-Powered Tool for Creating Companion Reference Images for 3D Design Feedback
Authors: Chen Chen , Nguyen Cuong , Groueix Thibault , Kim Vladimir G. , Weibel Nadir
Published: September 2024

Providing asynchronous feedback is a critical step in the 3D design workflow. A common approach to providing feedback is to pair textual comments with companion reference images, which helps illustrate the gist of text. Ideally, feedback providers should possess 3D and image editing skills to create reference images that can effectively describe what they have in mind. However, they often lack such skills, so they have to resort to sketches or online images that might not match well with the current 3D design. To address this, we introduce
MemoVis
, a text editor interface that assists feedback providers in creating reference images with generative AI driven by the feedback comments. First, a novel real-time viewpoint suggestion feature, based on a vision-language foundation model, helps feedback providers anchor a comment with a camera viewpoint. Second, given a camera viewpoint, we introduce three types of image modifiers based on pre-trained 2D generative models to turn a text comment into an updated version of the 3D scene from that viewpoint. We conducted a within-subjects study with

\(14\)

feedback providers, demonstrating the effectiveness of MemoVis. The quality and explicitness of the companion images were evaluated by another eight participants with prior 3D design experience.
MVLevelDB
+
: Meeting Relative Consistency Requirements of Temporal Queries in Sensor Stream Databases
Authors: Lam Kam-Yiu , Zhao Xiaofei , Zhu Chunjiang , Kuo Tei-Wei
Published: September 2024

Ensuring relative consistency in executing temporal queries to access real-time sensor data streams maintained in a database is a challenging problem, particularly when data transmission delays are lengthy and highly variable. Due to the unordered arrivals of sensor data, the databases may contain numerous open data versions (ODVs) with undefined validity intervals. Accessing ODVs may violate the relative consistency requirements of temporal queries, resulting in incorrect results. Although the Re-execution with Every Update (REU) method can resolve this issue, it may introduce heavy re-execution costs and significant delays in query completion. In this article, we study the problem of retrieving data items with temporal consistency requirements in a multi-data-stream database. To balance response time and meet the relative consistency requirements of queries, we introduce an enhanced REU mechanism called Re-Execution with Deadline (RED). Moreover, we propose a novel optional mechanism called Backward Execution Option (BEO) for temporal queries to achieve relative consistency in their execution with quick results by relaxing the data freshness constraints. By combining RED with BEO, we formulate the Repeated BEO (RBEO) to further reduce the query response time. We extend the timestamped key-value store MVLevelDB into MVLevelDB
+
to implement the proposed mechanisms. To reduce the query re-execution cost as required in RED and REU, we designed the Query Pool with Execution State (QpES) mechanism to achieve relative consistency in query execution with lower checking overhead and only one re-execution. We conducted extensive evaluation experiments on MVLevelDB
+
using benchmark programs to illustrate their performance characteristics on handling temporal queries in the modeled IoT system.
Bimetallic MOFs-Based Electrodes for the Simultaneous Electrochemical Detection of Epinephrine and Nor-Epinephrine
Authors: Soosaimanickam Charlin , Murugavel Kathiresan , Alwarappan Subbiah
Published: September 2024

We designed a bi-metallic Co-Ni/BTC/4,4′-BiPy metal organic frameworks (MOFs) as an electrode material for the electrochemical detection of epinephrine and nor-epinephrine. The bi-metallic MOFs were synthesized by a solvothermal method. Following this, the bimetallic MOFs were modified with BTC and amine rich 4,4′-BiPy to improve charge transfer kinetics through non-covalent π–π interaction. This modified electrode was employed as a sensing platform for the simultaneous electrochemical detection of epinephrine and nor-epinephrine. The MOFs modified platform exhibited a 10–50 μM linear range with a limit of detection of 0.724 μM ± 0.128 (N = 3) and 0.815 μM ± 0.124 (N = 3), a sensitivity of 0.583 and 0.505 μA μM−1 cm−2 corresponding to epinephrine and nor-epinephrine detection. Finally, the electrochemical sensor was tested in blood and urine samples spiked with known concentrations of epinephrine and nor-epinephrine. Results confirmed the usefulness of the proposed platform for the detection of epinephrine and nor-epinephrine in clinical samples.
ZrO2 Nanofiber-Based Molecular Imprinted Electrochemical Sensor for Detection of Ampicillin
Authors: Sun Yiwei , Shao Fenjuan , Luo Yuting , Wang Haoxiang , He Yuyang , Sun Liying , Xu Dongpo
Published: September 2024

An efficient molecularly-imprinted electrochemical sensor for the detection of ampicillin was prepared using polypyrrole tetracycline polymer modified with ZrO2 nanofibers. The ZrO2 nanofibers prepared by electrostatic spinning increased the surface area of the electrode with the binding sites of the electropolymerized membrane. The ampicillin sensor with polypyrrole as the functional monomer was able to specifically bind ampicillin molecules and detect ampicillin in various types of samples. In this study, cyclic voltammetry and differential pulse voltammetry were used to evaluate the electrochemical performance of ZrO2-MIP. Under the optimized conditions, the detection limit of this sensor was 0.397 nM, the detection range was 0.5 ∼ 500 nM, and the R2 reached 0.998. It has good selectivity, reproducibility, and stability, and achieves the AMP detection of the milk of the actual samples, which has a good prospect of application.
Digital Image Correlation for Assessment of Bridges’ Technical State and Remaining Resource
Authors: Kopiika Nadiia , Blikharskyy Yaroslav
Published: September 2024

Bridges enable communications and transportation of goods nationally and internationally, underpinning economic and social activities, and thus they are pylons of our prosperity and mobility. Bridges worldwide are constantly subjected to physical wear, ageing, deterioration, hazards, environmental influences, and increased loading. Loss of performance and functionality of bridge structures would have a crucial impact on overall infrastructural resilience and would cause significant negative economic and social consequences. Monitoring their behaviour for different loading conditions relies on accurate estimations of the stress‐strain state of various critical components and remaining capacities. These activities are of high importance for better planning and lifespan prolongation, that is, the extension of their service life and prevention of unforeseen collapses, in line with sustainability principles of well‐informed maintenance. In many cases, access to the structure is limited or even impossible, which causes the need for the deployment of remote and contactless methods. One such innovative technique, which has recently attracted attention in scientific and practical applications, is the digital image correlation (DIC). DIC is a contactless approach applicable for obtaining the full field of strains and deformations of full‐scale real structures. Although the DIC approach has been widely used in world engineering practice for monitoring bridges and has proved to be a reliable and accurate method, there is a lack of systematic integral review on previous practical applications, revealing limitations and perspectives. This is the main motivation and novelty of this study, which will describe selected case studies in which DIC was used on real full‐scale bridge structures and propose improvements for the method.
Return to Sport, Reinjury Rate, and Tissue Changes after Muscle Strain Injury: A Narrative Review
Authors: Wulff Mette W. , Mackey Abigail L. , Kjær Michael , Bayer Monika L.
Published: September 2024

A major challenge in sports medicine is to facilitate the fastest possible recovery from injury without increasing the risk of subsequent reruptures, and thus effective rehabilitation programs should balance between these two factors. The present review focuses on examining the role of different resistance training interventions in rehabilitation of acute muscle strain in the time frame from injury until return to sport (RTS), the rate of reinjuries, and tissue changes after injury. Randomized, controlled trials dealing with a component of resistance training in their rehabilitation protocols, as well as observational studies on tissue morphology and tissue changes as a result to muscle strain injuries, were included. The mean time for RTS varied from 15 to 86 days between studies (n = 8), and the mean rate of reinjury spanned from 0 to 70%. Eccentric resistance training at long muscle length and rapid introduction to rehabilitation postinjury led to significant improvement regarding RTS, and core‐stabilizing exercises as well as implementing an individualized algorithm for rehabilitation seem to reduce the risk of reinjury in studies with a high rerupture rate. Independent of the rehabilitation program, structural changes appear to persist for a long time, if not permanently, after a strain injury.
Rare Pathology Case Report: Low‐Grade Endometrial Stromal Sarcoma Forming Sex Cord– and Endometrioid Gland–Like Differentiation in Metastatic Foci
Authors: Al-Maghrabi Haneen , Mokhtar Ghadeer , Al-Maghrabi Jaudah
Published: September 2024

Low‐grade endometrial stromal sarcomas (LGESSs) are indolent tumors with a slow progression rate that tend to recur locally. They represent up to 10% of all primary sarcomas of the uterus and endometrium and only 0.2% of all genital tract tumors. They are commonly present in a younger demographic compared to other uterine tumors, with patients’ ages typically between 42 and 58 years old. Although the overall 5‐year survival rate is excellent, it has a natural history of delayed metastases which may manifest even decades after the disease was first diagnosed. They typically present as poorly defined lesions infiltrating the myometrium, along with extensive engagement of surrounding vascular structures. LGESS may display variants of different morphologies such as smooth muscle, fibromyxoid, sex cord‐like, and endometrioid‐type gland differentiation. These variations can pose a diagnostic challenge. The occurrence of this differentiation in a metastatic focus rather than in the primary tumor is seldom recorded in the literature. We present a case of a 51‐year‐old lady with a history of LGESS who was treated with surgery and radiotherapy and then presented after 12 years with an inferior vena cava (IVC) mass, which was confirmed histologically to be metastatic LGESS. Immunohistochemistry studies reveal strong positivity for CD10, WT1, and PR. These markers were negative in the sex cord and endometrioid gland–like differentiation counterparts. The patient had her initial follow‐up appointment after the IVC mass resection, and she was in good health with no complications. To the best of our knowledge, this case represents a unique instance of metastatic LGESS exhibiting both sex cord and endometrioid gland–like differentiation that has not been observed in the primary tumor.
Supplementary Figure Legends 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

Legends for Supplementary Figures S1-S6
Supplementary Data from Obesity Induces Temporally Regulated Alterations in the Extracellular Matrix That Drive Breast Tumor Invasion and Metastasis
Authors: Conner Sydney J. , Borges Hannah B. , Guarin Justinne R. , Gerton Thomas J. , Yui Anna , Salhany Kenneth J. , Mensah Diamond N. , Hamilton Grace A. , Le Giang H. , Lew Katherine C. , Zhang Crystal , Oudin Madeleine J.
Published: September 2024

Supplementary figures
Supplementary Table S1 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 S1
Supplementary Figure Legends and Tables list 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 Figure Legends and Tables list
Resource table 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

Resource table
Supplementary Figure 9 from Comprehensive Proteogenomic Profiling Reveals the Molecular Characteristics of Colorectal Cancer at Distinct Stages of Progression
Authors: Li Lingling , Jiang Dongxian , Liu Hui , Guo Chunmei , Zhang Qiao , Li Xuedong , Chen Xiaojian , Chen Zheqi , Feng Jinwen , Tan Subei , Huang Wen , Huang Jie , Xu Chen , Liu Chen-Ying , Yu Wei , Hou Yingyong , Ding Chen
Published: September 2024

Supplementary Figure 9 and related legend of the revised manuscript.
Supplementary Figure 8 from Comprehensive Proteogenomic Profiling Reveals the Molecular Characteristics of Colorectal Cancer at Distinct Stages of Progression
Authors: Li Lingling , Jiang Dongxian , Liu Hui , Guo Chunmei , Zhang Qiao , Li Xuedong , Chen Xiaojian , Chen Zheqi , Feng Jinwen , Tan Subei , Huang Wen , Huang Jie , Xu Chen , Liu Chen-Ying , Yu Wei , Hou Yingyong , Ding Chen
Published: September 2024

Supplementary Figure 8 and related legend of the revised manuscript.
Supplementary Figure 6 from Comprehensive Proteogenomic Profiling Reveals the Molecular Characteristics of Colorectal Cancer at Distinct Stages of Progression
Authors: Li Lingling , Jiang Dongxian , Liu Hui , Guo Chunmei , Zhang Qiao , Li Xuedong , Chen Xiaojian , Chen Zheqi , Feng Jinwen , Tan Subei , Huang Wen , Huang Jie , Xu Chen , Liu Chen-Ying , Yu Wei , Hou Yingyong , Ding Chen
Published: September 2024

Supplementary Figure 6 and related legend of the revised manuscript.
Supplementary Figure 2 from Comprehensive Proteogenomic Profiling Reveals the Molecular Characteristics of Colorectal Cancer at Distinct Stages of Progression
Authors: Li Lingling , Jiang Dongxian , Liu Hui , Guo Chunmei , Zhang Qiao , Li Xuedong , Chen Xiaojian , Chen Zheqi , Feng Jinwen , Tan Subei , Huang Wen , Huang Jie , Xu Chen , Liu Chen-Ying , Yu Wei , Hou Yingyong , Ding Chen
Published: September 2024

Supplementary Figure 2 and related legend of the revised manuscript.
Supplementary Data from Comprehensive Proteogenomic Profiling Reveals the Molecular Characteristics of Colorectal Cancer at Distinct Stages of Progression
Authors: Li Lingling , Jiang Dongxian , Liu Hui , Guo Chunmei , Zhang Qiao , Li Xuedong , Chen Xiaojian , Chen Zheqi , Feng Jinwen , Tan Subei , Huang Wen , Huang Jie , Xu Chen , Liu Chen-Ying , Yu Wei , Hou Yingyong , Ding Chen
Published: September 2024

Supplementary material
Data 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

Abstract
Intratumoral hypoxia stimulates enrichment of breast cancer stem cells (BCSC), which are critical for metastasis and patient mortality. Here we report a metabolic adaptation that is required for hypoxia-induced BCSC enrichment and metastasis. Hypoxia-inducible factors coordinately regulate expression of genes encoding phosphoglycerate dehydrogenase (PHGDH) and five downstream enzymes in the serine synthesis pathway and mitochondrial one-carbon (folate) cycle. RNAi-mediated silencing of PHGDH expression in both estrogen receptor–positive and negative breast cancer cells led to decreased NADPH levels, disturbed mitochondrial redox homeostasis, and increased apoptosis, which abrogated BCSC enrichment under hypoxic conditions. PHGDH-deficient cells exhibited increased oxidant levels and apoptosis, as well as loss of BCSC enrichment, in response to treatment with carboplatin or doxorubicin. PHGDH-deficient cells were relatively weakly tumorigenic and tumors that did form were deficient in BCSCs, abolishing metastatic capacity. Our findings highlight a role for PHGDH in the formation of secondary (recurrent or metastatic) tumors, with potential implications for therapeutic targeting of advanced cancers. Cancer Res; 76(15); 4430–42. ©2016 AACR.
Data 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

Abstract
Adaptive metabolic switches are proposed to underlie conversions between cellular states during normal development as well as in cancer evolution. Metabolic adaptations represent important therapeutic targets in tumors, highlighting the need to characterize the full spectrum, characteristics, and regulation of the metabolic switches. To investigate the hypothesis that metabolic switches associated with specific metabolic states can be recognized by locating large alternating gene expression patterns, we developed a method to identify interspersed gene sets by massive correlated biclustering and to predict their metabolic wiring. Testing the method on breast cancer transcriptome datasets revealed a series of gene sets with switch-like behavior that could be used to predict mitochondrial content, metabolic activity, and central carbon flux in tumors. The predictions were experimentally validated by bioenergetic profiling and metabolic flux analysis of 13C-labeled substrates. The metabolic switch positions also distinguished between cellular states, correlating with tumor pathology, prognosis, and chemosensitivity. The method is applicable to any large and heterogeneous transcriptome dataset to discover metabolic and associated pathophysiological states.

Significance: A method for identifying the transcriptomic signatures of metabolic switches underlying divergent routes of cellular transformation stratifies breast cancer into metabolic subtypes, predicting their biology, architecture, and clinical outcome.
Supplementary Figure S1 from MYTX-011: A pH-Dependent Anti–c-MET Antibody–Drug Conjugate Designed for Enhanced Payload Delivery to c-MET–Expressing Tumor Cells
Authors: Gera Nimish , Fitzgerald Kyle M. , Ramesh Vijay , Patel Purvi , Kanojia Deepak , Colombo Federico , Kien Lena , Aoyama Simon , Xu Lihui , Jean Jussekia , Deshpande Amit M. , Comb William C. , Chittenden Thomas , Fiske Brian P.
Published: September 2024

Displays mAb uptake in three cMET+ cell lines.
Supplementary Data Figure 3 from Radiation and Chemo-Sensitizing Effects of DNA-PK Inhibitors Are Proportional in Tumors and Normal Tissues
Authors: Baker Jennifer H.E. , Kyle Alastair H. , Liu Nannan A. , Wang Taixiang , Liu Xinhe , Teymori Sevin , Banáth Judit P. , Minchinton Andrew I.
Published: September 2024

DNA-PK activity reported by gH2AX in ATMKO FaDu xenograft tissues
Table S8 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

Pharmacokinetic parameters for HPN328 dosed IV in cynomolgus monkeys.
Table S5 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

EC50 Values for HPN328 mediated induction of CD25.
Table S3 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

EC50 Values from TDCC assays with anti-DLL3 TriTAC in the C:A:T Configuration (HPN328).
Figure S13 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

Validation of the hCD3ε Mouse Syngeneic Cell line.
Supplementary Figure 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 Figure 3. Flow cytometry analysis of cell death rates in HSC4.P and HSC4.RR Cell lines after exposure 8 Gy IR.
Figure S5 from Pretargeted Radioimmunotherapy with the Novel Anti-oxMIF/HSG Bispecific Antibody ON105 Results in Significant Tumor Regression in Murine Models of Cancer
Authors: Puchol Tarazona Alejandro A. , Schinagl Alexander , Mirkina Irina , Rossmueller Gregor , Kerschbaumer Randolf J. , Bachmann Friedmund , Thiele Michael
Published: September 2024

Figure S5
Supplementary Legends from Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation
Authors: Nguyen Lily L. , Watson Zachary L. , Ortega Raquel , Woodruff Elizabeth R. , Jordan Kimberly R. , Iwanaga Ritsuko , Yamamoto Tomomi M. , Bailey Courtney A. , To Francis , Jeong Abigail D. , Guntupalli Saketh R. , Behbakht Kian , Gibaja Veronica , Arnoult Nausica , Cocozaki Alexis , Chuong Edward B. , Bitler Benjamin G.
Published: September 2024

Supplementary Figure Legends
Supplementary Figure S6 from Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation
Authors: Nguyen Lily L. , Watson Zachary L. , Ortega Raquel , Woodruff Elizabeth R. , Jordan Kimberly R. , Iwanaga Ritsuko , Yamamoto Tomomi M. , Bailey Courtney A. , To Francis , Jeong Abigail D. , Guntupalli Saketh R. , Behbakht Kian , Gibaja Veronica , Arnoult Nausica , Cocozaki Alexis , Chuong Edward B. , Bitler Benjamin G.
Published: September 2024

Supplementary Figure S6 shows single-cell RNA sequencing data from 5 HGSC tumors, with cell-specific markers and EHMT1 and EHMT2.
Supplementary Figure S3 from Combining EHMT and PARP Inhibition: A Strategy to Diminish Therapy-Resistant Ovarian Cancer Tumor Growth while Stimulating Immune Activation
Authors: Nguyen Lily L. , Watson Zachary L. , Ortega Raquel , Woodruff Elizabeth R. , Jordan Kimberly R. , Iwanaga Ritsuko , Yamamoto Tomomi M. , Bailey Courtney A. , To Francis , Jeong Abigail D. , Guntupalli Saketh R. , Behbakht Kian , Gibaja Veronica , Arnoult Nausica , Cocozaki Alexis , Chuong Edward B. , Bitler Benjamin G.
Published: September 2024

Supplementary Figure S3 shows the knockdown of RIG-I and MDA5 in olaparib-resistant cells. It also shows cell viability of knockdown cells with or without treatment.
Supplementary Figure 1 from Enhancing Neutrophil Cytotoxicity of a Panel of Clinical EGFR Antibodies by Fc Engineering to IgA3.0
Authors: Chan Chilam , Jansen J.H. Marco , Hendriks Ilona S.T. , van der Peet Ida C. , Verdonschot Meggy E.L. , Passchier Elsemieke M. , Tsioumpekou Maria , Nederend Maaike , Klomp Sharon A. , Valerius Thomas , Peipp Matthias , Leusen Jeanette H.W. , Olofsen Patricia A.
Published: September 2024

Supplementary Figure 1: Purification of IgA3.0 EGFR mAbs.
Data from MYTX-011: A pH-Dependent Anti–c-MET Antibody–Drug Conjugate Designed for Enhanced Payload Delivery to c-MET–Expressing Tumor Cells
Authors: Gera Nimish , Fitzgerald Kyle M. , Ramesh Vijay , Patel Purvi , Kanojia Deepak , Colombo Federico , Kien Lena , Aoyama Simon , Xu Lihui , Jean Jussekia , Deshpande Amit M. , Comb William C. , Chittenden Thomas , Fiske Brian P.
Published: September 2024

Abstract
Advances in linker payload technology and target selection have been at the forefront of recent improvements in antibody–drug conjugate (ADC) design, leading to several approvals over the last decade. In contrast, the potential of novel ADC technologies to enhance payload delivery to tumors is relatively underexplored. We demonstrate that incorporation of pH-dependent binding in the antibody component of a c-mesenchymal–epithelial transition (MET)–targeting ADC (MYTX-011) can overcome the requirement for high c-MET expression on tumors, an innovation that has the potential to benefit a broader population of patients with lower c-MET levels. MYTX-011 drove fourfold higher net internalization than a non–pH-engineered parent ADC in non–small cell lung cancer (NSCLC) cells and showed increased cytotoxicity against a panel of cell lines from various solid tumors. A single dose of MYTX-011 showed at least threefold higher efficacy than a benchmark ADC in mouse xenograft models of NSCLC ranging from low to high c-MET expression. Moreover, MYTX-011 showed improved pharmacokinetics over parent and benchmark ADCs. In a repeat dose toxicology study, MYTX-011 exhibited a toxicity profile similar to other monomethyl auristatin E–based ADCs. These results highlight the potential of MYTX-011 for treating a broader range of patients with NSCLC with c-MET expression than other c-MET–targeting ADCs. A first-in-human study is ongoing to determine the safety, tolerability, and preliminary efficacy of MYTX-011 in patients with NSCLC (NCT05652868).
Supplementary Figure S6 from Crizotinib Enhances PARP Inhibitor Efficacy in Ovarian Cancer Cells and Xenograft Models by Inducing Autophagy
Authors: Santiago-O’Farrill Janice M. , Blessing Bollu Alicia , Yang Hailing , Orellana Vivian , Pina Marc , Zhang Xudong , Liu Jinsong , Bast Robert C. , Lu Zhen
Published: September 2024

Supplementary Figure S6 shows the effect of the combination of Olaparib and crizotinib in tumor growth
Supplementary Figure 7 from Hepatitis B Virus X Protein Represses Expression of Tumor Suppressor PTPN18 in Hepatocellular Carcinoma
Authors: Zhou Zhenyu , Yu Wei , Li Huoming , Shi Juanyi , Meng Shiyu , Yan Yongcong , Chen Ruibin , Liu Haohan , Wang Jie , Sun Jian , Xiao Zhiyu , Zhang Jianlong
Published: September 2024

The other two biological replicates related to the figure 7G.
Supplementary Figure 4 from Hepatitis B Virus X Protein Represses Expression of Tumor Suppressor PTPN18 in Hepatocellular Carcinoma
Authors: Zhou Zhenyu , Yu Wei , Li Huoming , Shi Juanyi , Meng Shiyu , Yan Yongcong , Chen Ruibin , Liu Haohan , Wang Jie , Sun Jian , Xiao Zhiyu , Zhang Jianlong
Published: September 2024

PTPN18 overexpression affects cell cycle of HCC cells.
Supplementary data from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Supplementary Methods, Legends to Supplementary Figures and Videos
Supplementary Video 7 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

3D video of a U87 cell during mitosis.
Figure S9 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Glioma cells experience changes in volume due to Cl- currents and associated water movements.
Supplementary Figure S9 from USP44 Overexpression Drives a MYC-Like Gene Expression Program in Neuroblastoma through Epigenetic Reprogramming
Authors: Ekstrom Thomas L. , Hussain Sajjad , Bedekovics Tibor , Ali Asma , Paolini Lucia , Mahmood Hina , Rosok Raya M. , Koster Jan , Johnsen Steven A. , Galardy Paul J.
Published: September 2024

The expression of USP44 is not correlated with its copy number in neuroblastoma.
Supplementary Figure S8 from USP44 Overexpression Drives a MYC-Like Gene Expression Program in Neuroblastoma through Epigenetic Reprogramming
Authors: Ekstrom Thomas L. , Hussain Sajjad , Bedekovics Tibor , Ali Asma , Paolini Lucia , Mahmood Hina , Rosok Raya M. , Koster Jan , Johnsen Steven A. , Galardy Paul J.
Published: September 2024

USP44 is not induced by MYCN.
Supplementary Figure S7 from USP44 Overexpression Drives a MYC-Like Gene Expression Program in Neuroblastoma through Epigenetic Reprogramming
Authors: Ekstrom Thomas L. , Hussain Sajjad , Bedekovics Tibor , Ali Asma , Paolini Lucia , Mahmood Hina , Rosok Raya M. , Koster Jan , Johnsen Steven A. , Galardy Paul J.
Published: September 2024

USP44 impairs retinoic acid-induced neuritic development in neuroblastoma cell lines.
Figure S4 from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Cl- signals and large Ca2+ flares in round cells.
Supplementary Figure S1 from USP44 Overexpression Drives a MYC-Like Gene Expression Program in Neuroblastoma through Epigenetic Reprogramming
Authors: Ekstrom Thomas L. , Hussain Sajjad , Bedekovics Tibor , Ali Asma , Paolini Lucia , Mahmood Hina , Rosok Raya M. , Koster Jan , Johnsen Steven A. , Galardy Paul J.
Published: September 2024

USP44 expression identifies patients with aggressive neuroblastoma.
Supplementary Table S5 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

miR-497 family predicted target genes significantly downregulated with miR-497 mimic.
Supplementary Table S2 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

SYBR and miRCURY primers used for qRT-PCR.
Supplementary Table 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

STR Validation of cell lines.
Supplementary Figure 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

Validation of miR-497 target genes.
Figure 4 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 additional clinically relevant organs in huNOG-EXL mice. A, Bioluminescent images taken of femurs. B, Quantified bioluminescence of femur metastasis. C, Bioluminescent images taken of mouse brain. D, Quantified bioluminescence of brain metastasis. E, Bioluminescent images taken of mouse liver. F, Quantified bioluminescence of liver metastasis. G, Kidney (adrenal gland) bioluminescent images. H, Quantified bioluminescence of kidney (tumor mostly in adrenal gland).
Table S2 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

The sequence of primers used for qRT-PCR
Figure S6 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

Supplementary Figure S6, referred to Figure 6.
Data from Intrinsic Epigenetic State of Primary Osteosarcoma Drives Metastasis
Authors: Singh Irtisha , Rainusso Nino , Kurenbekova Lyazat , Nirala Bikesh K. , Dou Juan , Muruganandham Abhinaya , Yustein Jason T.
Published: September 2024

Abstract
Osteosarcoma is the most common primary malignant bone tumor affecting the pediatric population with a high potential to metastasize. However, insights into the molecular features enabling its metastatic potential are limited. We mapped the active chromatin landscapes of osteosarcoma tumors by integrating histone H3 lysine–acetylated chromatin state (n = 13), chromatin accessibility profiles (n = 11), and gene expression (n = 13) to understand the differences in their active chromatin profiles and their impact on molecular mechanisms driving the malignant phenotypes. Primary osteosarcoma tumors from patients with metastasis (primary met) have a distinct active chromatin landscape compared with those without metastasis (localized). This difference shapes the transcriptional profile of osteosarcoma. We identified novel candidate genes, including PPP1R1B, PREX1, and IGF2BP1, that exhibit increased chromatin activity in primary met. Loss of PREX1 in primary met osteosarcoma cells significantly diminishes osteosarcoma proliferation, invasion, migration, and colony formation capacity. Differential chromatin activity in primary met is associated with genes regulating cytoskeleton organization, cellular adhesion, and extracellular matrix, suggesting their role in facilitating osteosarcoma metastasis. Chromatin profiling of tumors from metastatic lung lesions shows increased chromatin activity in genes involved in cell migration and Wnt pathway. These data demonstrate that metastatic potential is intrinsically present in primary met tumors, with cellular chromatin profiles further adapting for successful dissemination, migration, and colonization at the distal site.

Implications: Our study demonstrates that metastatic potential is intrinsic to primary metastatic osteosarcoma tumors, with chromatin profiles further adapting for successful dissemination, migration, and colonization at the distal metastatic site.
Data from Mechanisms of Glioblastoma Replication: Ca2+ Flares and Cl− Currents
Authors: Li Yunzhen , Sanchez Triviño Cesar Adolfo , Hernandez Andres , Mortal Simone , Spada Federica , Krivosheia Ilona , Franco Nicoletta , Spelat Renza , Cesselli Daniela , Manini Ivana , Skrap Miran , Menini Anna , Cesca Fabrizia , Torre Vincent
Published: September 2024

Abstract
Glioblastoma (GBM) is amongst the deadliest types of cancers, with no resolutive cure currently available. GBM cell proliferation in the patient’s brain is a complex phenomenon controlled by multiple mechanisms. The aim of this study was to determine whether the ionic fluxes controlling cell duplication could represent a target for GBM therapy. In this work, we combined multi-channel Ca2+ and Cl− imaging, optical tweezers, electrophysiology, and immunohistochemistry to describe the role of ion fluxes in mediating the cell volume changes that accompany mitosis of U87 GBM cells. We identified three main steps: (i) in round GBM cells undergoing mitosis, during the transition from anaphase to telophase and cytokinesis, large Ca2+ flares occur, reaching values of 0.5 to 1 μmol/L; (ii) these Ca2+ flares activate Ca2+-dependent Cl− channels, allowing the entry of Cl− ions; and (iii) to maintain osmotic balance, GBM cells swell to complete mitosis. This sequence of steps was validated by electrophysiological experiments showing that Cl− channels are activated either directly or indirectly by Ca2+, and by additional live-cell imaging experiments. Cl− channel blockers with different molecular structures, such as niflumic acid and carbenoxolone, blocked GBM replication by arresting GBM cells in a round configuration. These results describe the central role of Ca2+ flares and Cl− fluxes during mitosis and show that inhibition of Ca2+-activated Cl− channels blocks GBM replication, opening the way to new approaches for the clinical treatment of GBM.

Implications: Our work identifies ionic fluxes occurring during cell division as targets for devising novel therapies for glioblastoma treatment.
Data 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

Abstract
Angiosarcoma is a vascular sarcoma that is highly aggressive and metastatic. Because of its rarity, treatment options for patients are limited. Therefore, more research is needed to identify possible therapeutic vulnerabilities. We previously found that conditional deletion of Dicer1 drives angiosarcoma development in mice. Given the role of DICER1 in canonical miRNA biogenesis, this suggests that miRNA loss is important in angiosarcoma development. After testing miRNAs previously suggested to have a tumor-suppressive role in angiosarcoma, miRNA-497-5p (miR-497) suppressed cell viability most significantly. We also found that miR-497 overexpression led to significantly reduced cell migration and tumor formation. To understand the mechanism of miR-497 in tumor suppression, we identified clinically relevant target genes using a combination of RNA-sequencing data in an angiosarcoma cell line, expression data from patients with angiosarcoma, and target prediction algorithms. We validated miR-497 direct regulation of cyclin-D2, cyclin-dependent kinase 6, and vesicle amine transport protein 1 (VAT1). One of these genes, VAT1, is an understudied protein that has been suggested to promote cell migration and metastasis in other cancers. Indeed, we find that pharmacologic inhibition of VAT1 with the natural product neocarzilin A reduces angiosarcoma migration.

Implications: This work supports the potent tumor-suppressive abilities of miR-497 in angiosarcoma, providing evidence for its potential as a therapeutic agent, and provides insight into the mechanisms of tumor suppression through analysis of the target gene regulatory network of miR-497.
Supplementary Table S1 from Effect of Clonal Hematopoiesis Mutations and Canakinumab Treatment on Incidence of Solid Tumors in the CANTOS Randomized Clinical Trial
Authors: Woo Janghee , Zhai Tingting , Yang Fang , Xu Huilei , Healey Margaret L. , Yates Denise P. , Beste Michael T. , Steensma David P.
Published: September 2024

Supplementary Table S1 shows the incidence of malignancy by treatment in CANTOS.
Supplemental Figure 1 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 1: Diet regulates fecal microbiota populations. A. Summarized OTU abundances into Bray–Curtis dissimilarities and performed a non-metric multidimensional scaling (NMDS) ordination. There is a strong overall effect of diet on community-level differences between diet types (permutational multivariate analysis of variance: P < 0.001, R-squared = 0.44, n = 5). B. Microbial diversity, measured by the Shannon index, was not significantly affected by diet type. C. OTUs were aggregated into family-level taxa, and the relative abundance of the most abundant microbes was plotted. General linear models were used to test for differences in OTU abundances by examining the overall community alone. After adjusting for P-values (α value threshold = 0.01), we found 106 differentially abundant OTUs.