bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein and transcriptional biomarker profiling may inform treatment strategies in lower respiratory tract infections by indicating bacterial–viral differentiation
Authors: Sivakumaran Dhanasekaran , Jenum Synne , Markussen Dagfinn Lunde , Serigstad Sondre , Srivastava Aashish , Saghaug Christina Skår , Ulvestad Elling , Knoop Siri Tandberg , Grewal Harleen M. S.
Published: September 2024

Lower respiratory tract infections (LRTIs) remain a significant global cause of infectious disease-related mortality. Accurate discrimination between acute bacterial and viral LRTIs is crucial for optimal patient care, prevention of unnecessary antibiotic prescriptions, and resource allocation. Plasma samples from LRTI patients with bacterial (
n
= 36), viral (
n
= 27; excluding SARS-CoV-2), SARS-CoV-2 (
n
= 22), and mixed bacterial–viral (
n
= 38) etiology were analyzed for protein profiling. Whole-blood RNA samples from a subset of patients (bacterial,
n
= 8; viral,
n
= 8; and SARS-CoV-2,
n
= 8) were analyzed for transcriptional profiling. Lasso regression modeling identified a seven-protein signature (CRP, IL4, IL9, IP10, MIP1α, MIP1β, and TNFα) that discriminated between patients with bacterial (
n
= 36) vs viral (
n
= 27) infections with an area under the curve (AUC) of 0.98. When comparing patients with bacterial and mixed bacterial–viral infections (antibiotics clinically justified;
n
= 74) vs patients with viral and SARS-CoV-2 infections (antibiotics clinically not justified;
n
= 49), a 10-protein signature (CRP, bFGF, eotaxin, IFNγ, IL1β, IL7, IP10, MIP1α, MIP1β, and TNFα) with an AUC of 0.94 was identified. The transcriptional profiling analysis identified 232 differentially expressed genes distinguishing bacterial (
n
= 8) from viral and SARS-CoV-2 (
n
= 16) etiology. Protein–protein interaction enrichment analysis identified 20 genes that could be useful in the differentiation between bacterial and viral infections. Finally, we examined the performance of selected published gene signatures for bacterial–viral differentiation in our gene set, yielding promising results. Further validation of both protein and gene signatures in diverse clinical settings is warranted to establish their potential to guide the treatment of acute LRTIs.

IMPORTANCE

Accurate differentiation between bacterial and viral lower respiratory tract infections (LRTIs) is vital for effective patient care and resource allocation. This study investigated specific protein signatures and gene expression patterns in plasma and blood samples from LRTI patients that distinguished bacterial and viral infections. The identified signatures can inform the design of point-of-care tests that can aid healthcare providers in making informed decisions about antibiotic prescriptions in order to reduce unnecessary use, thereby contributing to reduced side effects and antibiotic resistance. Furthermore, the potential for faster and more accurate diagnoses for improved patient management in acute LRTIs is compelling.
Supplemental Material: Miocene ice sheet dynamics and sediment deposition in the central Ross Sea, Antarctica
Authors: McKay Robert , al. et
Published: September 2024

Grain size data for IODP Site U1521. 
Estimating size-at-harvest from Indigenous archaeological clamshell assemblages in Coastal British Columbia
Authors: Hillis Dylan , Barclay Kristina M. , Foster Erin , Kobluk Hannah M. , Vollman Taylor , Salomon Anne K. , Darimont Chris T. , McKechnie Iain
Published: September 2024

Shellfish have supported Indigenous lifeways on the Pacific Coast of North America for millennia. Despite the ubiquity of clamshells in archaeological sites, shell size measurements are rarely reported due to a lack of applicable basis for generating size estimates from fragmentary remains. We present a linear regression-based method for determining shell length from hinge and umbo measurements of littleneck ( Leukoma staminea; n = 239), butter ( Saxidomus gigantea; n = 274), and horse ( Tresus nuttallii; n = 92) clams using both contemporary and archaeological shells collected from three regions in coastal British Columbia, Canada. We examine the accuracy of these size estimations, which indicate that 83%–97% of the variability in dorsal shell length is predicted by umbo thickness and hinge length. Hinge length generated higher R2 values yet exhibited greater intra- and inter-observer error. While the predicted dorsal length for each species differed by region, this size difference was smaller than intra- and inter-observer error, suggesting broad applicability for these simple measurements. We applied these formulae to a Tseshaht First Nation archaeological clamshell assemblage ( n = 488) on western Vancouver Island spanning 3000 years and observed profiles that resemble contemporary legal size limits, which suggests the sustained use and maintenance of local shellfisheries. The accuracy of these regression models for determining shell length from fragments highlights the utility of this approach as a basis for assessing past shellfish management practices.
Nodal solutions for a weighted (N,p)-Kirchhoff-type problem with double exponential growth non-linearity
Authors: Baraket Sami , Chetouane Rima , Dridi Brahim , Jaidane Rached , Mahmoudi Fethi
Published: September 2024

This paper investigates the existence of sign-changing solutions for a logarithmic weighted Kirchhoff [Formula: see text]-Laplacian problem in the unit ball [Formula: see text] of [Formula: see text] where [Formula: see text]. The non-linearity of the equation is assumed to have double exponential growth, which is motivated by Trudinger–Moser-type inequalities. To prove the existence of these solutions, we employ techniques such as constrained minimization within the Nehari set, a quantitative deformation lemma and results from degree theory.
Analytical estimation of the C-rate and numerical and experimental investigation of the EV battery pack
Authors: Bele Rohit , Patil Naveen , Kolhe Shailesh , Rane Sandeep
Published: September 2024

The electrification of transportation has led to an increased emphasis on the thermal management of battery packs to ensure their safety, efficiency, and longevity. This study presents a comprehensive estimation of the C-rate through analytical and the thermal behavior of an electric two-wheeler battery pack (3.2[Formula: see text]kWh) under varying operational conditions through a combination of simulation and experimental testing. Numerical analysis was conducted using Celsius EC Solver (version 2023.2) software, with a specific focus on parameters such as C-rate and temperature distribution. Experimental validation was performed under controlled conditions, and key metrics such as ambient temperature, maximum temperature reached at various locations, heat generation rates, voltage, and current were measured. The findings of this study demonstrate that there is less than 4% error which is well agreed between simulation and experimental results. This indicates a significant congruence between the simulated and experimental data, underscoring the reliability of the proposed simulation model. This analysis provides valuable insights for optimizing thermal management strategies in battery packs.
Theoretical comparison of transition rate B(E2) and deformation parameter with experimental data for calcium (20Ca) isotopes using shell model theory
Authors: Ali Ahmed H. , Akkoyun Serkan , Abbasi Akbar , Hossain I. , Korna A. H. , Deressu Tilahun T. , Alshammari H. , Al Ali Ahmet S.
Published: September 2024

A theoretical comparison has been made for some calcium isotopes ([Formula: see text]Ca) which are even–even nuclei and have the atomic mass (Z = 20) with its previous experimental data. Theoretical calculations of some [Formula: see text]Ca isotopes (A = 42, 44, 46, 48, 50, 52) adopted by the shell model theory were performed to calculate the transition rate B(E2), theoretical intrinsic quadruple moments ([Formula: see text] and theoretical deformation parameters ([Formula: see text], [Formula: see text] were calculated by two methods by using different effective interactions for each isotope such as, su3fp, fpbm, fprkb, fpd6, kb3. Through code NuShellX@MSU, the single-body density matrix was calculated. The effects of the core polarization were neglected by adopting various effective charges that were employed, effective charges of conventional (Con-E), effective charges of standard (St-E) and effective charges of Bohr and Mottelson (B-M-E) which were calculated. The theoretical values of the B(E2)Th, the [Formula: see text] and the ([Formula: see text], [Formula: see text] were then compared with the previous experimental data where values of the transition rate B(E2)Th, theoretical intrinsic quadrupole moments [Formula: see text] and theoretical deformation parameter ([Formula: see text], [Formula: see text], using the fpbm, the fpd6 and the kb3 interactions were the best.
Unraveling the Potential: A Systematic Review and Performance Evaluation of Data-Driven Network Anomaly Detection Techniques
Authors: Sharma Niharika , Arora Bhavna
Published: September 2024

Network anomalies significantly impact the efficiency and stability of network systems, making effective anomaly detection crucial for optimal performance and prevention of network breakdowns. However, conventional methods must be improved for handling anomalies’ complexities and evolving nature. Despite extensive research in network anomaly detection (NAD) techniques, there is a need for more systematic literature reviews incorporating recent advances, particularly in dynamic and heterogeneous network settings. Moreover, most review papers focus on individual detection methods, needing a unified framework for comprehensive anomaly detection. To bridge these gaps, this paper conducts a comprehensive analysis by conducting a systematic literature review and formulating five research questions to outline the objectives of this study. A holistic framework is proposed, integrating techniques based on preprocessing and Feature Selection into prediction models to develop more accurate, efficient, and reliable anomaly detection systems. The empirical evaluation assesses the effectiveness, accuracy, efficiency, and reliability of the data-driven NAD techniques. Finally, the study identifies research gaps and potential future directions to guide further advancements in developing accurate and efficient anomaly detection models. By synthesizing and analyzing 116 top-cited papers, this study contributes to the existing body of knowledge by highlighting the potential of emerging anomaly detection techniques in complex and dynamic network environments.
New Approach in Booth Decoder/Encoder and 5-2 Compressor for Multipliers
Authors: Ebrahimzadeh Ebrahim , Fathi Amir , Mashoufi Behbood
Published: September 2024

This paper proposes two novel approaches: a signed–unsigned modified Booth decoder/encoder that is used for the production of partial products and a 5-2 compressor for the addition stage of partial products. The improvement of a circuit can be done at the transistor level and the gate level. To improve the circuits at the gate level for the modified Booth decoder/encoder, a new table was designed and also the 5-2 compressor was obtained by changing the truth table. Speed, power consumption and area were improved in the proposed structures. In this paper, at the transistor level, the gate diffusion input (GDI) technique was used to implement logical gates and the gate-level delay of the GDI structures was also calculated. The results indicated that the proposed 5-2 compressor had a delay of 119 ps with a power consumption of 65[Formula: see text][Formula: see text]W, which shows a 23.5% improvement in power delay product (PDP) compared to the best structure in the comparison table, whereas the proposed Booth decoder/encoder had a delay of 257 ps with a power consumption of 61.74[Formula: see text][Formula: see text]W and shows a 63.7% improvement in PDP compared to previous studies. By using the proposed structures in the multiplier, a 22% improvement in PDP was observed. To simulate the obtained structures, the TSMC 0.18 and 0.09[Formula: see text][Formula: see text]m technologies and the HSPICE software were used. Cadence software was used to implement the layouts of the proposed structures.
Steering Mechanism and Capability of Forced Steering Device for Low-Floor Light Rail Train
Authors: Zhang Yanyan , Yang Xinwen , Xiang Kaiwen , Zuo Anguo
Published: September 2024

For 70% low-floor trains on the light rail lines in Changchun, a multi-linkage forced steering device (FSD) is developed aiming at relieving the independently rotating wheelset (IRW) excessive flange wear and improving IRW bogie system running safety on curve line. This FSD employs guiding mode of steering four independently rotating wheels separately in a two-axle bogie, that is, four FSDs are employed to work together to realize the steering of a two-axle bogie. One side of an FSD is connected to the axle of an independently rotating wheel while the other side is attached to the front or rear vehicle body. When train passes through curve, the yaw angle between the IRW bogie and the front or rear carbody drives the linkage system to rotate to guide the independently rotating wheel towards its radial position. The coupled vehicle-track dynamics model for a 6-module single-type low-floor light rail train is developed and simulations of the train passing through tangent and curved tracks with and without FSD proposed are carried out. The results indicate that the FSD can improve the IRW restoring capability on tangent track and curve negotiation performance on whether sharp, medium, or large curved track. For example, passing through a curve with a radius of 200[Formula: see text]m, the IRW friction work has the biggest drop by 62.07% and the wheelset attack angle is second with a reduction rate of 55.02%. Adopting of larger steering stiffness, smaller steering clearance, and lever ratio greater than the ideal value can guarantee the higher steering ability of FSD. Besides, lower longitudinal stiffness of the trailer primary suspension is recommended because it can also enhance the steering ability of the FSD.
Ac-slant curves in Euclidean 3-space
Authors: Mak Mahmut , Altınbaş Hasan , Kula Levent
Published: September 2024

In this study, we introduce a new type of space curve which is called ac-slant curve whose inner product of its acceleration vector and a fixed direction is a constant. Then, we give a characterization according to the curvatures of ac-slant curve. Later on, we obtain relationship between an ac-slant curve and some special curves (spherical curve, helix, slant helix, Salkowski curve, rectifying curve). Similarly to concept of ac-slant curves, we consider normalized ac-slant curve which has a unit acceleration vector and give a characterization with respect to its curvatures. Especially, we give some results for ac-slant or normalized ac-slant curves with respect to the magnitude of its velocity and acceleration vector.
A Comprehensive Journey of a Vanillic Aldehyde-Chloroaniline Schiff Base from Solvent-Free Synthesis to Electronic Structure, In Silico and In Vitro Biological Analysis
Authors: Rajimon K. J. , El-Serehy Hamed A. , Rajendran Nair Deepthi S. , Kannan Neha , Jayashree A. , Thomas Renjith
Published: September 2024

Schiff bases possess a range of unique physical, chemical and medicinal properties, which contribute to their potency as biological agents. A Schiff base was synthesized, which consisted of 4-chloro aniline and vanillin. The successful formation of the compound was confirmed by their comparable FTIR, UV–Vis, 1HNMR and [Formula: see text]CNMR spectra. The compound was analyzed using X-ray crystallography, which revealed that it crystallizes in the monoclinic system with the space group P21/c. The Hirshfeld surface analysis revealed valuable information about the intermolecular interactions present in the crystal lattice. The most common contacts observed were between hydrogen and hydrogen, as well as carbon and hydrogen. The obtained fluorescence values of 375 nm and 412 nm at excitation wavelength 322 nm strongly indicated the luminescent nature of the compound. The thermal stability of the compound was assessed through thermogravimetric analysis (TGA). DFT was used to optimize the geometry using the B3LYP/cc-pVDZ basis set. The compound exhibited an energy gap of 2.35 electron volts (eV). According to the analysis of molecular electrostatic potential, C and O atoms were found to be electrophilic. According to Mulliken charge analysis, C atoms possess both positive and negative charges, hydrogen atoms exclusively carry positive charges, and Cl, O and N atoms exclusively carry negative charges. Upon analysis of the molecule, the electron localization function discovered that the atoms of carbon, nitrogen and chlorine exhibited delocalized electron density. Also, the localized orbital locator identified the localized orbital positions in the hydrogen atoms. The reduced density gradient (RDG) maps exhibit a wide range of noncovalent interactions. In comparison to the standard amoxicillin, the synthesized compound demonstrated moderate antimicrobial efficacy against the gram-positive bacteria Klebsiella pneumoniae and the fungi Candida albicans. The compound’s concentration-dependent antioxidant and anti-inflammatory properties were demonstrated through in vitro biological evaluation using 2,2-diphenyl-1-picrylhydrazyl and human red blood cell (HRBC) methods. The compound was docked using the proteins 7BYE and 4LEB were chosen from both organisms. The lowest binding attractions obtained were −3.40 kcal/mol for 7BYE and −4.51 kcal/mol for 4LEB. To investigate the stability of the protein–ligand complex, molecular dynamic simulation was employed. The ligands in silico toxicity potentialities were analyzed using seven toxicity models and the results indicated that the ligand is biocompatible.
Unveiling Transformative Insights via Cross-Modal Learning and Natural Language Processing for Enhanced Supply Chain Intelligence
Authors: Wu Xiaobing
Published: September 2024

This day's quickly developing business landscape, supply chains have become more globalized, intricate, and multi-covering, making them crucial for companies to navigate through disruptions and unpredictability. The major which are addressed in the supply chain process are lack of transparency and visibility of the supply chain network and that's leads to delay and inefficiency in the process. In order to overcome those drawbacks in the supply chain process, in this article an enhanced supply chain intelligence is developed which performs Unveiling Transformative Insights using the learning process like Cross-Modal Learning (CML) and Natural Language Processing (NLP). The implementation of these techniques is carried out in the software Python. This analysis consists of certain calculation called enhanced supply chain analysis, sales revenue Vs SKU analysis, various modes cost analysis, Lead time vs different supplier and location. The comparative analysis is performed among the technique like RF regression, SARIMA-LSTM-BP and BiLSTM model. The parameters which are involved in this performance analysis are MAE, MSE, RMSE and R^2.
A Stable Idle Time Detection Platform for Real I/O Workloads
Authors: Lu Yen-Yu , Wu Chin-Hsien , Li Shih-Jen , Lee Cheng-Tze , Wu Cheng-Yen
Published: September 2024

It is important to utilize the idle time of a workload to improve the system performance. In the article, we will explore multiple idle time detection methods to predict the idle time of the real I/O workloads. The objective is to build a stable idle time detection platform by investigating the impact of multiple representative methods to pursue a more stable prediction accuracy. The experimental results show that the prediction accuracy of the proposed platform can be stable between 60% and 80%.
SuccinctKV: a CPU-efficient LSM-tree Based KV Store with Scan-based Compaction
Authors: Zhang Yinan , Yang Shun , Hu Huiqi , Yang Chengcheng , Cai Peng , Zhou Xuan
Published: September 2024

The CPU overhead of the LSM-tree becomes increasingly significant when high-speed storage devices are utilized. In this article, we propose
SuccinctKV
, a key-value store based on LSM-tree that is optimized to improve CPU efficiency in mixed workload scenarios. To achieve this,
SuccinctKV
reduces the CPU overhead of compaction by writing scan-sorted data directly to the storage device.
SuccinctKV
also redesigns the merge-sort operation of the LSM-tree, enhancing CPU locality and reducing the unnecessary CPU overhead of cache accesses and I/O system calls. Additionally,
SuccinctKV
introduces a scheduler to resolve potential bursty I/O contention by autonomously initiating I/O requests at appropriate times and quickly relieving I/O pressure by terminating background I/O requests. We implement
SuccinctKV
on RocksDB and conduct extensive experiments to evaluate our proposed methods. The experimental results demonstrate that, compared with RocksDB,
SuccinctKV
achieves a maximum improvement of 2.6x in scan performance and reduces CPU overhead of compaction by up to 89% under mixed workloads.
Identifying the Failure-Revealing Test Cases in Metamorphic Testing: A Statistical Approach
Authors: Zheng Zheng , Ren Daixu , Liu Huai , Chen Tsong Yueh , Li Tiancheng
Published: September 2024

Metamorphic testing, thanks to its high failure-detection effectiveness especially in the absence of test oracle, has been widely applied in both the traditional context of software testing and other relevant fields such as fault localization and program repair. Its core element is a set of metamorphic relations, which are the necessary properties of the target algorithm in the form of the relationships among multiple inputs and corresponding expected outputs. When a relation is violated by the outputs of a group of test cases, namely metamorphic group of test cases, that are constructed based on the relation, a failure is said to be revealed. Traditionally, the primary task of software testing is to reveal failures. Therefore, from the perspective of software testing, it may not need to know which test case(s) in the metamorphic group cause the violation and thus the failure. However, such information is definitely helpful for other software engineering activities, such as software debugging. The current literature of metamorphic testing lacks a systematic mechanism of identifying the actual failure-revealing test cases, which hinders its applicability and effectiveness in other relevant fields. In this article, we propose a new technique for the FAILure-revealing Test case Identification in Metamorphic testing, namely FAILTIM. The approach is based on a novel application of statistical methods. More specifically, we leverage and adapt the basic ideas of spectrum-based techniques, which are originally used in fault localization, and propose the utilization of a set of risk formulas to estimate the suspiciousness of each individual test case in metamorphic groups. Failure-revealing test cases are then suggested according to their suspiciousness. A series of experiments have been conducted to evaluate the effectiveness and efficiency of FAILTIM using 9 subject programs and 30 risk formulas. The experimental results showed that the new approach can achieve a high accuracy in identifying the actual failure-revealing test cases in metamorphic testing. Consequently, our study will help boost the applicability and performance of metamorphic testing beyond testing to other software engineering areas. The present work also unfolds a number of research directions for further advancing the theory of metamorphic testing and more broadly, software testing.
Why "Artificial Intelligence" Should Not Be Regulated
Authors: Braun Daniel
Published: September 2024

Lawmakers all over the world have started to draft new regulations for Artificial Intelligence (AI). While the European Union is currently leading the way with its AI Act, many other legislators will follow and already positioned themselves with white papers and other publications. This commentary argues that “Artificial Intelligence”, including Generative AI, should not be used as a regulatory category. Not because there is no potential for harm from AI systems and not because AI systems should not be regulated, but because “Artificial Intelligence” is a vaguely defined label that is neither suitable nor necessary for comprehensive regulation of technological risks. Instead of regulating a particular set of approaches and algorithms, lawmakers should focus and double down on regulating high-risk applications of software, independent of whether it is labelled as AI or not.
A Lane Change Strategy to Enhance Traffic Safety in the Coexistence of Autonomous Vehicles and Manual Vehicles
Authors: Jo Young , Oh Cheol
Published: September 2024

Vehicle interactions with different driving behaviors in mixed traffic conditions, in which autonomous vehicles (AVs) and manual vehicles (MVs) coexist, would result in unstable traffic flow leading to a potential crash risk. A proactive traffic management strategy is required to enhance both safety and mobility by preventing hazardous events in connected environments. The purpose of this study is to develop a Proactive Lane‐changE Assistant Strategy for Automated iNnovative Transportation (PLEASANT) to enhance traffic safety. PLEASANT is a strategy for providing lane change assistance information to vehicles approaching risky situations such as crashes, broken vehicles, and upcoming hazardous obstacles. In addition, this study proposed a comprehensive simulation framework that incorporates driving simulation and traffic simulation to evaluate the performance of PLEASANT when dealing with mixed traffic. To characterize vehicle interactions between AVs and MVs, this study analyzes driving behavior in mixed car‐following situations based on multiagent driving simulation (MADS), which is able to synchronize the space and time domains on the road by connecting two driving simulators. The characteristics of vehicle interactions between AVs and MVs were incorporated into microscopic traffic simulations. The effectiveness of PLEASANT was evaluated based on the crash potential index from the perspective of safety. The results showed that PLEASANT was capable of enhancing traffic safety by approximately 21%. PLEASANT is expected to be useful as a novel management strategy for enhancing traffic safety in mixed‐traffic environments.
Geospatial and Temporal Analysis of Avian Influenza Risk in Thailand: A GIS‐Based Multi‐Criteria Decision Analysis Approach for Enhanced Surveillance and Control
Authors: Sangrat Waratida , Thanapongtharm Weerapong , Kasemsuwan Suwicha , Boonyawiwat Visanu , Sajapitak Somchai , Poolkhet Chaithep
Published: September 2024

Avian influenza (AI) is a viral infection that profoundly affects global poultry production. This study aimed to identify the spatial and temporal factors associated with AI in Thailand, using a geographic information system (GIS)–based multi‐criteria decision analysis (MCDA) approach. We discovered that high‐risk areas for AI were primarily concentrated in the central and lower northern regions of the country, with fewer occurrences in the northeastern and southern regions. Model validation using historical outbreak data showed moderate agreement (AUC = 0.60, 95% CI = 0.58–0.61). This study provides valuable insights for planning national AI surveillance programs and aiding in disease prevention and control efforts. The efficiency and effectiveness of disease surveillance at the national level can be improved using this GIS‐based MCDA, in conjunction with temporal risk factor analysis.
Associations of Prostate Tumor Immune Landscape with Vigorous Physical Activity and Prostate Cancer Progression
Authors: Huang Lanshan , Winter Sarah J. , Olsson Linnea T. , Hamilton Alina M. , Halliday Sophia R. , Kirk Erin L. , Farnan Laura , Gerstel Adrian , Craig Stephanie G. , Finn Stephen P. , LaBonte Wilson Melissa , Jain Suneil , Troester Melissa A. , Butler Eboneé N. , Bensen Jeannette T. , Wobker Sara E. , Allott Emma H.
Published: September 2024

Background:

Vigorous physical activity has been associated with lower risk of fatal prostate cancer. However, mechanisms contributing to this relationship are not understood.

Methods:

We studied 117 men with prostate cancer in the University of North Carolina Cancer Survivorship Cohort (UNC CSC) who underwent radical prostatectomy and 101 radiation-treated patients with prostate cancer in FASTMAN. Structured questionnaires administered in UNC CSC assessed physical activity. In both studies, digital image analysis of hematoxylin and eosin–stained tissues was applied to quantify tumor-infiltrating lymphocytes in segmented regions. NanoString gene expression profiling in UNC CSC and microarray in FASTMAN were performed on tumor tissue, and a 50-gene signature utilized to predict immune cell types.

Results:

Vigorous recreational activity, reported by 34 (29.1%) UNC CSC men, was inversely associated with tumor-infiltrating lymphocyte abundance. Tumors of men reporting any vigorous activity versus none showed lower gene expression–predicted abundance of Th, exhausted CD4 T cells, and macrophages. T-cell subsets, including regulatory T cells, Th, Tfh, exhausted CD4 T cells, and macrophages, were associated with an increased risk of biochemical recurrence, only among men with ERG-positive tumors.

Conclusions:

Vigorous activity was associated with lower prostate tumor inflammation and immune microenvironment differences. Macrophages and T-cell subsets, including those with immunosuppressive roles and those with lower abundance in men reporting vigorous exercise, were associated with worse outcomes in ERG-positive prostate cancer.

Impact:

Our novel findings contribute to our understanding of the role of the tumor immune microenvironment in prostate cancer progression and may provide insights into how vigorous exercise could affect prostate tumor biology.
Supplementary Table S7 from A Phase II Placebo-Controlled Study of the Effect and Safety of Nanvuranlat in Patients with Advanced Biliary Tract Cancers Previously Treated by Systemic Chemotherapy
Authors: Furuse Junji , Ikeda Masafumi , Ueno Makoto , Furukawa Masayuki , Morizane Chigusa , Takehara Tetsuo , Nishina Tomohiro , Todaka Akiko , Okano Naohiro , Hara Kazuo , Nakai Yousuke , Ohkawa Kazuyoshi , Sasaki Takashi , Sugimori Kazuya , Yokoyama Naoyuki , Yamamoto Kouji
Published: September 2024

Supplementary Table S7. Heterogenous response by nanvuranlat by BTC-subtypes and LAT1 expression.
Supplementary Video S2 from Low-Dose Ionizing γ-Radiation Elicits the Extrusion of Neutrophil Extracellular Traps
Authors: Teijeira Alvaro , Garasa Saray , Ochoa Maria C. , Sanchez-Gregorio Sandra , Gomis Gabriel , Luri-Rey Carlos , Martinez-Monge Rafael , Pinci Beatrice , Valencia Karmele , Palencia Belen , Barbés Benigno , Bolaños Elixabet , Azpilikueta Arantza , García-Cardosa Marina , Burguete Javier , Eguren-Santamaría Iñaki , Garate-Soraluze Eneko , Berraondo Pedro , Perez-Gracia Jose L. , de Andrea Carlos E. , Rodriguez-Ruiz Maria E. , Melero Ignacio
Published: September 2024

Supplementary Video S2. Time-lapse confocal microscopy of co-cultures of tumor spheroids covered by radiation-induced NETs and cytotoxic lymphocytes. HT29 tumor cell-spheroids stained with CMRA (red) were cocultured or not with 2 Gy-irradiated neutrophils in the presence/absence of DNAse I to allow the presence of NETs (Sytox Green, green) around the spheroids. Cytotoxic immune cells (T or NK lymphocytes, blue) were pre-stained and cocultured with tumor spheroids for 4 hours before confocal microscopy acquisition. Time-lapse videos show a representative z-slice of the co-cultures over time (8 hours, 2,400× accelerated). As quantified in Figures 2 A, B and D, E, kinetically monitoring the tracks of the lymphocytes, data show evidence for the avoidance of the NETs in the migration paths.
Supplementary Figure S3 from Low-Dose Ionizing γ-Radiation Elicits the Extrusion of Neutrophil Extracellular Traps
Authors: Teijeira Alvaro , Garasa Saray , Ochoa Maria C. , Sanchez-Gregorio Sandra , Gomis Gabriel , Luri-Rey Carlos , Martinez-Monge Rafael , Pinci Beatrice , Valencia Karmele , Palencia Belen , Barbés Benigno , Bolaños Elixabet , Azpilikueta Arantza , García-Cardosa Marina , Burguete Javier , Eguren-Santamaría Iñaki , Garate-Soraluze Eneko , Berraondo Pedro , Perez-Gracia Jose L. , de Andrea Carlos E. , Rodriguez-Ruiz Maria E. , Melero Ignacio
Published: September 2024

Supplementary Figure S3. The serum protein thioredoxin blocks low-dose g-irradiation induced NETosis.
Supplemental Table S2 from Tumor-Localized Interleukin-2 and Interleukin-12 Combine with Radiation Therapy to Safely Potentiate Regression of Advanced Malignant Melanoma in Pet Dogs
Authors: Stinson Jordan A. , Barbosa Matheus Moreno P. , Sheen Allison , Momin Noor , Fink Elizabeth , Hampel Jordan , Selting Kim A. , Kamerer Rebecca L. , Bailey Keith L. , Wittrup Karl D. , Fan Timothy M.
Published: September 2024

Supplemental Table S2. Allometric scaling of IL2 and IL12 doses for canine dosing.
Supplementary Figure S2 from Associations of Immune Checkpoint Predictive Biomarkers (MHC-I and MHC-II) with Clinical and Molecular Features in a Diverse Breast Cancer Cohort
Authors: Sun Xiaopeng , Kennedy Laura C. , Gonzalez-Ericsson Paula I. , Sanchez Violeta , Sanders Melinda , Perou Charles M. , Troester Melissa A. , Balko Justin M. , Reid Sonya A.
Published: September 2024

Supplementary Figure 2: MHC-I and MHC-II expression is higher in Stage I/II, premenopausal patients. The relative frequency difference of tumors having (A) high MHC-I expression and (B) ≥ 5% tumor cells expressing MHC-II are compared between stage and menopausal status . Relative frequency difference calculated using Stage I/II and premenopausal as control condition, with negative RFD representing frequency higher in Stage I/II or premenopausal patients. Bootstrap method used to generate standard errors.
Supplemental Table S1 from Tumor-Localized Interleukin-2 and Interleukin-12 Combine with Radiation Therapy to Safely Potentiate Regression of Advanced Malignant Melanoma in Pet Dogs
Authors: Stinson Jordan A. , Barbosa Matheus Moreno P. , Sheen Allison , Momin Noor , Fink Elizabeth , Hampel Jordan , Selting Kim A. , Kamerer Rebecca L. , Bailey Keith L. , Wittrup Karl D. , Fan Timothy M.
Published: September 2024

Supplemental Table S1. Additional patient characteristics and CT response data.
Supplemental Figure S9 from Tumor-Localized Interleukin-2 and Interleukin-12 Combine with Radiation Therapy to Safely Potentiate Regression of Advanced Malignant Melanoma in Pet Dogs
Authors: Stinson Jordan A. , Barbosa Matheus Moreno P. , Sheen Allison , Momin Noor , Fink Elizabeth , Hampel Jordan , Selting Kim A. , Kamerer Rebecca L. , Bailey Keith L. , Wittrup Karl D. , Fan Timothy M.
Published: September 2024

Supplemental Figure S9. Combined tumor and metastatic LN treatment response.
Supplemental Figure S8 from Tumor-Localized Interleukin-2 and Interleukin-12 Combine with Radiation Therapy to Safely Potentiate Regression of Advanced Malignant Melanoma in Pet Dogs
Authors: Stinson Jordan A. , Barbosa Matheus Moreno P. , Sheen Allison , Momin Noor , Fink Elizabeth , Hampel Jordan , Selting Kim A. , Kamerer Rebecca L. , Bailey Keith L. , Wittrup Karl D. , Fan Timothy M.
Published: September 2024

Supplemental Figure S8. IHC analysis of CD3 infiltration in progressor dogs.
Supplemental Figure S6 from Tumor-Localized Interleukin-2 and Interleukin-12 Combine with Radiation Therapy to Safely Potentiate Regression of Advanced Malignant Melanoma in Pet Dogs
Authors: Stinson Jordan A. , Barbosa Matheus Moreno P. , Sheen Allison , Momin Noor , Fink Elizabeth , Hampel Jordan , Selting Kim A. , Kamerer Rebecca L. , Bailey Keith L. , Wittrup Karl D. , Fan Timothy M.
Published: September 2024

Supplemental Figure S6. Characterization of antidrug antibody responses in treated dogs.
Supplementary Figure S9 from Spatial Heterogeneity of Immune Regulators Drives Dynamic Changes in Local Immune Responses, Affecting Disease Outcomes in Pancreatic Cancer
Authors: Karamitopoulou Eva , Wenning Anna S. , Acharjee Animesh , Aeschbacher Pauline , Marinoni Ilaria , Zlobec Inti , Gloor Beat , Perren Aurel
Published: September 2024

Suppl.Figure S9: PD-1 / PD-L1 staining across immune subgroups. Multiplex immuno-fluorescence (mIF) x200
Supplemental Figure S1 from Tumor-Localized Interleukin-2 and Interleukin-12 Combine with Radiation Therapy to Safely Potentiate Regression of Advanced Malignant Melanoma in Pet Dogs
Authors: Stinson Jordan A. , Barbosa Matheus Moreno P. , Sheen Allison , Momin Noor , Fink Elizabeth , Hampel Jordan , Selting Kim A. , Kamerer Rebecca L. , Bailey Keith L. , Wittrup Karl D. , Fan Timothy M.
Published: September 2024

Supplemental Figure S1. Local RT causes transient lymphodepletion in murine melanomas.
Supplementary Figure S4 from Spatial Heterogeneity of Immune Regulators Drives Dynamic Changes in Local Immune Responses, Affecting Disease Outcomes in Pancreatic Cancer
Authors: Karamitopoulou Eva , Wenning Anna S. , Acharjee Animesh , Aeschbacher Pauline , Marinoni Ilaria , Zlobec Inti , Gloor Beat , Perren Aurel
Published: September 2024

Suppl. Figure S4: mRNA expression across the tumor center and invasive tumor front of the LIPDACs.
Supplementary Figure S1 from Spatial Heterogeneity of Immune Regulators Drives Dynamic Changes in Local Immune Responses, Affecting Disease Outcomes in Pancreatic Cancer
Authors: Karamitopoulou Eva , Wenning Anna S. , Acharjee Animesh , Aeschbacher Pauline , Marinoni Ilaria , Zlobec Inti , Gloor Beat , Perren Aurel
Published: September 2024

Suppl. Figure S1: Study Design
Supplementary Data 1 from Novel ERBB2 Variant Potentially Associated with Resistance against Anti-HER2 Monoclonal Antibody–Based Therapy in ERBB2-Amplified Metastatic Colorectal Cancer
Authors: Iida Naoko , Imai Mitsuho , Okamoto Wataru , Kato Takeshi , Esaki Taito , Kato Ken , Komatsu Yoshito , Yuki Satoshi , Masuishi Toshiki , Nishina Tomohiro , Ebi Hiromichi , Taniguchi Hiroya , Nonomura Norio , Sunakawa Yu , Shiozawa Manabu , Yamazaki Kentaro , Boku Shogen , Bando Hideaki , Shiraishi Yuichi , Kobayashi Maki , Goto Hiroki , Sato Akihiro , Fujii Satoshi , Yoshino Takayuki , Nakamura Yoshiaki
Published: September 2024

Supplementary Data
Figure S3 from Novel ERBB2 Variant Potentially Associated with Resistance against Anti-HER2 Monoclonal Antibody–Based Therapy in ERBB2-Amplified Metastatic Colorectal Cancer
Authors: Iida Naoko , Imai Mitsuho , Okamoto Wataru , Kato Takeshi , Esaki Taito , Kato Ken , Komatsu Yoshito , Yuki Satoshi , Masuishi Toshiki , Nishina Tomohiro , Ebi Hiromichi , Taniguchi Hiroya , Nonomura Norio , Sunakawa Yu , Shiozawa Manabu , Yamazaki Kentaro , Boku Shogen , Bando Hideaki , Shiraishi Yuichi , Kobayashi Maki , Goto Hiroki , Sato Akihiro , Fujii Satoshi , Yoshino Takayuki , Nakamura Yoshiaki
Published: September 2024

Figure S3
Supplementary Table S2 from Interim Phase II Results Using Panitumumab-IRDye800CW during Transoral Robotic Surgery in Patients with Oropharyngeal Cancer
Authors: Stone Logan D. , Kasten Benjamin B. , Rao Shilpa , Gonzalez Manuel. L. , Stevens Todd M. , Lin Diana , Carroll William , Greene Benjamin , Moore Lindsay S. , Fuson Andrew , James Sherin , Hartman Yolanda E. , McCammon Susan , Panuganti Bharat , Nabell Lisle M. , Li Yufeng , Li Mei , Bailey Luke , Rosenthal Eben L. , Jeyarajan Harishanker , Thomas Carissa M. , Warram Jason M.
Published: September 2024

Supplementary Table S2: Surgeon survey assessing the value of fluorescence imaging during the procedure.
Supplementary Data1 from HER2DX Genomic Assay in HER2-Positive Early Breast Cancer Treated with Trastuzumab and Pertuzumab: A Correlative Analysis from the PHERGain Phase II Trial
Authors: Llombart-Cussac Antonio , Pérez-García Jose , Brasó-Maristany Fara , Paré Laia , Villacampa Guillermo , Gion Maria , Schmid Peter , Colleoni Marco , Borrego Manuel R. , Galván Patricia , Parker Joel S. , Buckingham Wesley , Perou Charles M. , Villagrasa Patricia , Guerrero Jose A. , Sampayo-Cordero Miguel , Mancino Mario , Prat Aleix , Cortés Javier
Published: September 2024

Supplementary Tables 1 and 2, and Supplementary Figures 1 and 2.
Figure S5 from Overcoming Osimertinib Resistance with AKT Inhibition in EGFRm-Driven Non–Small Cell Lung Cancer with PIK3CA/PTEN Alterations
Authors: Grazini Ursula , Markovets Aleksandra , Ireland Lucy , O’Neill Daniel , Phillips Benjamin , Xu Man , Pfeifer Matthias , Vaclova Tereza , Martin Matthew J. , Bigot Ludovic , Friboulet Luc , Hartmaier Ryan , Cuomo Maria E. , Barry Simon T. , Smith Paul D. , Floc’h Nicolas
Published: September 2024

Figure S5: Percentage change in mouse body weight across the in vivo studies.
Supplementary Table S4 from Circulating Tumor DNA Assessment for Treatment Monitoring Adds Value to PSA in Metastatic Castration-Resistant Prostate Cancer
Authors: Sweeney Christopher J. , Petry Russell , Xu Chang , Childress Merrida , He Jie , Fabrizio David , Gjoerup Ole , Morley Samantha , Catlett Timothy , Assaf Zoe J. , Yuen Kobe , Wongchenko Matthew , Shah Kalpit , Gupta Pratyush , Hegde Priti , Pasquina Lincoln W. , Mariathasan Sanjeev , Graf Ryon P. , Powles Thomas
Published: September 2024

Patient characteristics of the biomarker evaluable population (BEP) cohort by ctDNA TF detection change
Supplementary Figure S2 from Reconstitution of the Multiple Myeloma Microenvironment Following Lymphodepletion with BCMA CAR-T Therapy
Authors: Yang Yazi , Qin Sen , Yang Mengyu , Wang Ting , Feng Ru , Zhang Chunli , Zheng Enrun , Li Qinghua , Xiang Pengyu , Ning Shangyong , Xu Xiaodong , Zuo Xin , Zhang Shuai , Yun Xiaoya , Zhou Xuehong , Wang Yue , He Lin , Shang Yongfeng , Sun Luyang , Liu Hui
Published: September 2024

Supplementary Figure S2. Clustering of the Cells within the MM Microenvironment.
Supplementary Figure S6 from Circulating Tumor DNA Assessment for Treatment Monitoring Adds Value to PSA in Metastatic Castration-Resistant Prostate Cancer
Authors: Sweeney Christopher J. , Petry Russell , Xu Chang , Childress Merrida , He Jie , Fabrizio David , Gjoerup Ole , Morley Samantha , Catlett Timothy , Assaf Zoe J. , Yuen Kobe , Wongchenko Matthew , Shah Kalpit , Gupta Pratyush , Hegde Priti , Pasquina Lincoln W. , Mariathasan Sanjeev , Graf Ryon P. , Powles Thomas
Published: September 2024

Prognostic value of 50% PSA reduction
Supplementary Figure 2 from Cryoablation Does Not Significantly Contribute to Systemic Effector Immune Responses in a Poorly Immunogenic B16F10 Melanoma Model
Authors: Yakkala Chakradhar , Corria-Osorio Jesus , Kandalaft Lana , Denys Alban , Koppolu Bhanu , Duran Rafael
Published: September 2024

Supplementary Figure 2: Tumor growth and survival of mice transplanted with CD8+ T-cell enriched splenocytes.
Supplementary Figure S5 from Circulating Tumor DNA Assessment for Treatment Monitoring Adds Value to PSA in Metastatic Castration-Resistant Prostate Cancer
Authors: Sweeney Christopher J. , Petry Russell , Xu Chang , Childress Merrida , He Jie , Fabrizio David , Gjoerup Ole , Morley Samantha , Catlett Timothy , Assaf Zoe J. , Yuen Kobe , Wongchenko Matthew , Shah Kalpit , Gupta Pratyush , Hegde Priti , Pasquina Lincoln W. , Mariathasan Sanjeev , Graf Ryon P. , Powles Thomas
Published: September 2024

ctDNA tumor fraction and standard clinical features and associated hazard ratios
Supplementary Figure 1 from Cryoablation Does Not Significantly Contribute to Systemic Effector Immune Responses in a Poorly Immunogenic B16F10 Melanoma Model
Authors: Yakkala Chakradhar , Corria-Osorio Jesus , Kandalaft Lana , Denys Alban , Koppolu Bhanu , Duran Rafael
Published: September 2024

Supplementary Figure 1: Proof of depletion of different immune cell types.
Supplementary Figure S3 from Circulating Tumor DNA Assessment for Treatment Monitoring Adds Value to PSA in Metastatic Castration-Resistant Prostate Cancer
Authors: Sweeney Christopher J. , Petry Russell , Xu Chang , Childress Merrida , He Jie , Fabrizio David , Gjoerup Ole , Morley Samantha , Catlett Timothy , Assaf Zoe J. , Yuen Kobe , Wongchenko Matthew , Shah Kalpit , Gupta Pratyush , Hegde Priti , Pasquina Lincoln W. , Mariathasan Sanjeev , Graf Ryon P. , Powles Thomas
Published: September 2024

ctDNA tumor fraction pre-enzalutamide to prognosticate overall survival and progression-free survival on enzalutamide post-abiraterone
Supplementary Figure S2 from CDK9 Inhibition by Dinaciclib Is a Therapeutic Vulnerability in Epithelioid Hemangioendothelioma
Authors: Pobbati Ajaybabu V. , Burtscher Ashley , Rajaram Siva Nandini , Hallett Andrea , Romigh Todd , Che Kepeng , Zhao Bin , Coker Jesse A. , Wang Nancy , Stauffer Shaun R. , Rubin Brian P.
Published: September 2024

Figure S2. Localization of TC following Dina + MG132 treatment
Supplementary Figure S11 from Circulating Tumor DNA Assessment for Treatment Monitoring Adds Value to PSA in Metastatic Castration-Resistant Prostate Cancer
Authors: Sweeney Christopher J. , Petry Russell , Xu Chang , Childress Merrida , He Jie , Fabrizio David , Gjoerup Ole , Morley Samantha , Catlett Timothy , Assaf Zoe J. , Yuen Kobe , Wongchenko Matthew , Shah Kalpit , Gupta Pratyush , Hegde Priti , Pasquina Lincoln W. , Mariathasan Sanjeev , Graf Ryon P. , Powles Thomas
Published: September 2024

ctDNA TF response is more closely correlated with survival than PSA50 response in discordant cases
Supplementary Data1 from CSF1R Inhibition in Patients with Advanced Solid Tumors or Tenosynovial Giant Cell Tumor: A Phase I Study of Vimseltinib
Authors: Gelderblom Hans , Razak Albiruni A. , Taylor Matthew H. , Bauer Todd M. , Wilky Breelyn , Martin-Broto Javier , Gonzalez Alejandro F. , Rutkowski Piotr , Szostakowski Bartlomiej , Alcindor Thierry , Saleh Ramy , Genta Sofia , Stacchiotti Silvia , van de Sande Michiel , Wagner Andrew J. , Bernthal Nicholas , Davis Lara E. , Vuky Jacqueline , Tait Christopher , Matin Bahar , Narasimhan Supraja , Sharma Maitreyi G. , Ruiz-Soto Rodrigo , Sherman Matthew L. , Tap William D.
Published: September 2024

Supplement to CSF1R Inhibition in Patients With Advanced Solid Tumors or Tenosynovial Giant Cell Tumor: A Phase 1 Study of Vimseltinib. Contains supplementary methods, tables, and figures.
Supplementary Data 1 from Novel Combinations of Immunotherapies or DNA Damage Repair Inhibitors in Platinum-Refractory Extensive-Stage Small Cell Lung Cancer: The Phase II BALTIC Study
Authors: Reinmuth Niels , Juan-Vidal Oscar , Kowalski Dariusz , Bryl Maciej , Kryzhanivska Anna , Vicente David , Horváth Zsolt , Gálffy Gabriella , Csánky Eszter , Pápai Székely Zsolt , Vynnychenko Ihor , Armstrong Jon , Dalvi Tapashi , Xie Mingchao , Iyer Sonia , Shrestha Yashaswi , Jiang Haiyi , Bondarenko Igor
Published: September 2024

Supplementary tables and figures
Supplementary Table S1 from Phase II Trial of HER-Vaxx, a B-cell Peptide-Based Vaccine, in HER2-Overexpressing Advanced Gastric Cancer Patients Under Platinum-Based Chemotherapy (HERIZON)
Authors: Tobias Joshua , Maglakelidze Marina , Andrić Zoran , Ryspayeva Dinara , Bulat Iurie , Nikolić Ivan , Petrović Zoran , Chawla Tanuj , Nagarkar Rajnish , Garner-Spitzer Erika , Zielinski Christoph C. , Chong Leslie Mi Ok , Nixon Bonnie , Ede Nicholas J. , Yavrom Sharon , Kundi Michael , Wiedermann Ursula
Published: September 2024

Supplementary Table S1. Inclusion and exclusion criteria.
Supplementary Figure S8 from Phase II Trial of HER-Vaxx, a B-cell Peptide-Based Vaccine, in HER2-Overexpressing Advanced Gastric Cancer Patients Under Platinum-Based Chemotherapy (HERIZON)
Authors: Tobias Joshua , Maglakelidze Marina , Andrić Zoran , Ryspayeva Dinara , Bulat Iurie , Nikolić Ivan , Petrović Zoran , Chawla Tanuj , Nagarkar Rajnish , Garner-Spitzer Erika , Zielinski Christoph C. , Chong Leslie Mi Ok , Nixon Bonnie , Ede Nicholas J. , Yavrom Sharon , Kundi Michael , Wiedermann Ursula
Published: September 2024

Supplementary Figure S8. Association between decreased FOXP + Tregs and induced HER2-specific IgG antibody levels.