bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-Target Smooth Universal Adversarial Perturbations for CNNs in Electroencephalogram-Based Brain–Computer Interface Systems
Authors: Zhang Jie , Zhong Xiaowen
Published: October 2024

EEG-based brain–computer interface systems have demonstrated impressive capability in the context of the broad use of deep learning. However, serious security flaws have been shown by their vulnerability to adversarial sample attacks. It is not possible to directly apply traditional attack strategies from the image domain to EEG signals because of their unique visualization and dynamic features. A unique multi-target smooth universal adversarial perturbation (MS-UAP) approach designed specifically for EEG data is presented in this paper to address this difficulty. We define a loss function and optimize parameters based on UAP for both target and nontarget class samples, respectively, to address the temporal nature of the EEG signal and the attack’s flexibility. Additionally, this research generates a smoothed adversarial sample by convolution operations, yielding a more disorienting effect, to avoid the introduction of physiologically untrustworthy square wave distortions caused by typical visual attack approaches. Three public EEG datasets were used for extensive testing and assessments, and the results show that MS-UAP successfully targets convolutional neural network (CNN) classifiers and launches simultaneous attacks on several classes, exhibiting strong model transferability. To ensure accurate attacks that go undetected, MS-UAP creates a single disturbance that is targeted at target classes and has the least negative effect on other classes. In order to facilitate effective real-time attacks, MS-UAP, an offline-generated universal perturbation template, can be smoothly incorporated into EEG data. The study is significant since it emphasizes how important it is to improve BCI system security and promote the creation of stronger defenses.
The algebraic classification of low-dimensional nilpotent n-Lie algebras
Authors: Darabi Hamid , Eshrati Mehdi , Saeedi Farshid
Published: October 2024

In this paper, we study the low-dimensional nilpotent [Formula: see text]-Lie algebras and classify nilpotent [Formula: see text]-Lie algebras of dimension [Formula: see text] and nilpotent [Formula: see text]-Lie algebras of class two with dimension [Formula: see text].
Subsampling Suffices for Adaptive Data Analysis
Authors: Blanc Guy
Published: October 2024

Ensuring that analyses performed on a dataset are representative of the entire population is one of the central problems in statistics. Most classical techniques assume that the dataset is independent of the analyst’s query and break down in the common setting where a dataset is reused for multiple, adaptively chosen, queries. This problem of
adaptive data analysis
was formalized in the seminal works of Dwork et al. (STOC 2015) and Hardt and Ullman (FOCS 2014).

We identify a remarkably simple set of assumptions under which the queries will continue to be representative even when chosen adaptively: the only requirements are that each query takes as input a random subsample and outputs few bits. This result shows that the noise inherent in subsampling is sufficient to guarantee that query responses generalize. The simplicity of this subsampling-based framework allows it to model a variety of real-world scenarios not covered by prior work.

In addition to its simplicity, we demonstrate the utility of this framework by designing mechanisms for two foundational tasks: statistical queries and median finding. In particular, our mechanism for answering the broadly applicable class of statistical queries is both extremely simple and state of the art in many parameter regimes.
Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics
Authors: Meier Rudolf , Lawniczak Mara K.N. , Srivathsan Amrita
Published: October 2024

Most insects encountered in the field are initially entomological dark matter in that they cannot be identified to species while alive. This explains the enduring quest for efficient ways to identify collected specimens. Morphological tools came first but are now routinely replaced or complemented with DNA barcodes. Initially too expensive for widespread use, these barcodes have since evolved into powerful tools for specimen identification and sorting, given that the evolution of sequencing approaches has dramatically reduced the cost of barcodes, thus enabling decentralized deployment across the planet. In this article, we review how DNA barcodes have become a key tool for accelerating biodiversity discovery and analyzing insect communities through both megabarcoding and metabarcoding in an era of insect decline. We predict that DNA barcodes will be particularly important for assembling image training sets for deep learning algorithms, global biodiversity genomics, and functional analysis of insect communities.
Positive Identity Construction in Diverse Organizations
Authors: Roberts Laura Morgan , Caza Brianna Barker
Published: October 2024

Our desire to cultivate and sustain positive identities has a powerful influence on workplace diversity, equity, and inclusion (DEI) dynamics. While sometimes the quest for positive identities promotes celebration of diversity and uniqueness, in many other circumstances our inherent motivation to strive toward building more positive identities can have unintended consequences for DEI in organizations. In this review, we organize research on positive identities at work to better understand the experiences of the diverse set of individuals that compose our work organizations today. We invite a critical examination of how individuals with underrepresented and dominant identities deal with identity demands in diverse workplaces in both helpful and harmful ways. We conclude with directions for future research on interventions that mitigate identity threat and promote inclusion.
Hawkes Models and Their Applications
Authors: Laub Patrick J. , Lee Young , Pollett Philip K. , Taimre Thomas
Published: October 2024

The Hawkes process is a model for counting the number of arrivals to a system that exhibits the self-exciting property—that one arrival creates a heightened chance of further arrivals in the near future. The model and its generalizations have been applied in a plethora of disparate domains, though two particularly developed applications are in seismology and in finance. As the original model is elegantly simple, generalizations have been proposed that track marks for each arrival, are multivariate, have a spatial component, are driven by renewal processes, treat time as discrete, and so on. This article creates a cohesive review of the traditional Hawkes model and the modern generalizations, providing details on their construction and simulation algorithms, and giving key references to the appropriate literature for a detailed treatment.
Quantifying the Temperature Dependence of the Multi-Species, Multi-Reaction Model. Part 1: Parameterization for a Meso-Carbon Micro-Bead Graphite
Authors: Paul Abigail , Wolfe Kody , Verbrugge Mark W. , Koch Brian J. , Lowe Jeffrey S. , Trembly Jason , Staser John A. , Garrick Taylor R.
Published: October 2024

In this work, the temperature impact on the Multi-Species, Multi-Reaction (MSMR) model is studied. This is accomplished by acquiring data from slow rate lithiation and delithiation of a meso-carbon micro-bead (MCMB) graphite. The MSMR model is used to simulate linear-sweep voltammetry data of a porous electrode composed of graphite, and because the electrode is close to a state of dynamic equilibrium, the peaks in the differential voltage spectroscopy plot can be analyzed. Through this analysis, the temperature impact on the total fraction of available host sites in a particular MSMR gallery (Xj), the impact on the reference potential (U°j), and the impact on the parameter detailing the deviation from Nernstian behavior (ω
j) can be found. This is the first time the temperature dependence of the MSMR parameters have been experimentally analyzed. In Part 2, the impact of the temperature dependence of the MSMR parameters on the entropy coefficient of an intercalation material will be studied.
Identification of FGFR4 as a regulator of myofibroblast differentiation in pulmonary fibrosis
Authors: Ghanem Mada , Justet Aurélien , Jaillet Madeleine , Vasarmidi Eirini , Boghanim Tiara , Hachem Mouna , Vadel Aurélie , Joannes Audrey , Mordant Pierre , Balayev Agshin , Adams Taylor , Mal Hervé , Cazes Aurélie , Poté Nicolas , Mailleux Arnaud , Crestani Bruno
Published: October 2024

FGFR4 has been reported to have antifibrotic effects in the liver. We aimed to determine the involvement of FGFR4 during IPF. Our data suggest that FGFR4 exerts profibrotic properties by enhancing TGF-β signaling in vitro. However, the inhibition of FGFR4 is not sufficient to prevent the development of pulmonary fibrosis in vivo. To our knowledge, this is the first study to assess the profibrotic action of FGFR4 during pulmonary fibrosis.
Postepidemic Epidemiology of Porcine Epidemic Diarrhea Virus in the United States
Authors: Makau Dennis N. , Pamornchainavakul Nakarin , VanderWaal Kimberly , Kikuti Mariana , Picasso-Risso Catalina , Geary Emily , Corzo Cesar A.
Published: October 2024

Porcine epidemic diarrhea virus (PEDV) emerged in the United States (U.S.) swine population in 2013, initiating an initial significant epidemic followed by a state of endemicity in the U.S. Despite continued monitoring, the epidemiology of PEDV during its endemic phase remains inadequately researched. Our study aimed to characterize the spatial–temporal distribution of postepidemic PEDV cases in the U.S. breeding herd and identify associated risk factors. Data from 1089 breeding farms in 27 states, reported to the Morrison Swine Health Monitoring Project from July 2014 to June 2021, were analyzed. We stratified the data into six U.S. regions and employed SaTScan for spatiotemporal permutation and cluster analysis. Survival analysis was used to assess risk factors. A notable seasonal clustering of PEDV cases was observed in winter (January–March; p = 0.001, relative risk = 2.2) with regional variation. Ten high‐rate spatial–temporal clusters (p  < 0.05) were identified ranging from 2.5 to 833.7 km2 and lasting 1–5 months, occurring in four regions between 2015 and 2021. For the study period, a total of 625 cases of PEDV were recorded on 372 farms. The total number of PEDV cases decreased from 95 breeding farms in 32 counties (2014–2015) to 53 farms in 28 counties (2020–2021), indicating an overall reduction in occurrence and spatial extent. Feed mitigants demonstrated a protective effect, significantly reducing the risk of PEDV occurrence (hazard ratio = 0.3, p = 0.003), while air filtration systems exhibited marginal benefits (hazard ratio = 0.3, p = 0.06). Other important risk factors included county farm density with farms in high‐density regions (>31 farms/100 km2) being 1.3 times more likely to experience outbreaks than in medium‐density regions (13–31 farms/1000 km2; p  < 0.001). Additionally, farms in region E had higher odds of outbreaks compared to region B. The overall decline in PEDV cases and reduced spatial extent reflect industry efforts in postepidemic control and elimination. The protective effects of feed mitigants warrant further investigation. Our findings underscore the opportunity for coordinated efforts to eliminate PEDV in the U.S. and emphasize the need for comprehensive risk profiling associated with industry practices.
Optimal Resiliency‐Oriented Scheduling Framework for Integrated Power‐Gas‐Transportation Networks Based on Model Predictive Control Approach to Increase Electric Load Supply
Authors: Akbari-Dibavar Alireza , Mohammadi-Ivatloo Behnam , Zare Kazem , Najafi Ravadanegh Sajad , Vahidinasab Vahid
Published: October 2024

Today’s societies need a sustainable supply of energy more than ever, whereas unseen events challenge the electric power supply. The coordinated operation of a power‐gas‐transportation system can decrease the effects of such faults in the distribution level. This paper proposes a model predictive control approach for dynamic load restoration in an integrated energy system. The coordination of electric and gas networks besides the mobile energy storage (MES) units provides a novel resilient alternative to serve active and reactive loads. First, the location and time of drastic events are identified as the initialization phase in this paper using a vulnerability analysis by a master–slave problem to find the weak points of the electric grid. Then, a rolling horizon model predictive control‐based approach is proposed to make corrective decisions to serve loads. Meanwhile, a new linearization approach for the Weymouth equation has been proposed based on the binary expansion method. The proposed linear resiliency‐oriented scheduling problem is tested on IEEE 33‐bus and IEEE 69‐bus integrated with a seven‐node gas distribution grid and a six‐station transportation railway. The analysis revealed that the coordination between electric and gas resources minimizes the not‐supplied load; MES units act as certain emergency tools to serve the critical loads.
Effects of Acute Ammonia Exposure on the Antioxidant System and Anti‐Inflammatory Factors in Opsariichthys bidens
Authors: Tong Wanqing , Chen Huixian , Cai Zhuo , Li Ming , Guo Shuirong , Zheng Shanjian
Published: October 2024

The present experiment was performed to reveal the mechanisms of toxic effects of ammonia nitrogen on Chinese hook snout carp (Opsariichthys bidens) based on the levels of antioxidant enzyme activities and the expression of 70‐kDa heat shock protein gene (HSP70) and tumor necrosis factor‐α (TNF‐α) after 96 h of acute toxic ammonia exposure to investigate its adaptability. The result showed that activities of antioxidant enzymes and lipid peroxidation in the intestine, liver, brain, and gills showed a general trend of increasing and then decreasing when exposed to ammonia nitrogen. The intestinal tissue structure was damaged to varying degrees, the expression of the HSP70 in the brain and gills increased at 0–12 h, and the expression of the TNF‐α in brain tissues decreased at 0–12 h. The expression of TNF‐α in the liver was continuously upregulated in the late stages of stress, and it did not decrease until the stress was released. The above results indicate that high concentrations of ammonia nitrogen caused varying degrees of damage to the neurological, respiratory, and metabolic‐related organs of the O. bidens.
Antibiotic Resistance and Virulence Factors in Clinical Isolates of Stenotrophomonas maltophilia from Hospitalized Patients in Tehran, Iran
Authors: Bahrami Mahrokh , Bostanghadiri Narjess , Goudarzi Mehdi , Khodaei Niloufar , Hashemi Ali
Published: October 2024

Stenotrophomonas maltophilia causes challenging infections in immunocompromised patients, exhibiting increasing resistance to multiple antimicrobials and possessing various virulence genes, including emerging resistance to trimethoprim‐sulfamethoxazole. A total of 80 clinical isolates of S. maltophilia were collected from multiple hospitals in Tehran, Iran. This study conducted an analysis of antibiotic susceptibility by disc diffusion method and E‐test assay, resistance and virulence gene frequencies were examined by PCR‐sequencing, and multilocus sequencing typing (MLST) was performed for strain typing. Across the tested isolates, we observed notably high resistance rates for imipenem 80 (100%), meropenem 78(97.5%), and ceftazidime 72 (90%), while trimethoprim‐sulfamethoxazole (SXT) showed a lower resistance rate of 2 (2.5%). Minocycline and levofloxacin demonstrated the highest susceptibility rates, with 70 (87.5%) and 80 (100%), respectively. The prevalence of antibiotic resistance genes blaL1, and blaL2 was 71 (88.75%) and 76 (95%), respectively. Additionally, the PCR analysis revealed that the frequency of virulence genes (fliC, virB, papD, pilU, hlyIII, stmPr1, and stmPr2) was 78 (97.5%), 77 (96.25%), 58 (72.5%), 77 (96.2%), 76 (95%), 31 (38.75%), and 80 (100%), respectively. Resistance to SXT isolate belong to the sequence type (ST15) and exhibits allelic profiles of (10, 29, 21, 21, 32, 32, and 10). The data obtained from our investigation have indicated that SXT remains an efficacious antibiotic and also highlighted the importance of effective management, identification of resistant isolates, and typing methods to address the global prevalence of antibiotic resistance in S. maltophilia.
In Silico Assessment for Risk of Possible Human Transmission of FCoV‐23
Authors: Ozketen Ahmet Caglar , Kazan Hasan Huseyin , Özverel Cenk Serhan , Şanlıdağ Tamer
Published: October 2024

Since the pandemic in 2019, coronaviruses (CoVs) have been a great concern for public health burden. The fact that CoVs can infect all animals including domestic ones and livestock points to a future pandemic even though interaction between human and wildlife animals is restricted. Moreover, interspecies transmission abilities of CoVs by mutations make them drastically risky not only for humans but also for animal health. Recently, a new CoV outbreak in cats in Cyprus, the so‐called FCoV‐23, has been realized. In addition to worries over animal health, any possible transmission to humans is now controversial. However, there have been limited characterization studies on FCoV‐23. Thus, we aimed to assess the possible transmission of FCoV‐23 to humans using in silico prediction tools. Accordingly, we first checked the binding affinities of receptor binding domain (RBD) of FCoV‐23 against feline target protein and its human homolog. Next, we randomly and rationally created mutations on the RBD sequence and evaluated the binding affinities using protein docking tools. Our results underlined that multiple mutations at the same time were needed for increased binding affinity towards human target protein, demonstrating that the probability of transmission to humans was extremely low when mutation rates were regarded. Still, further molecular studies are required to comprehensively conclude the possible transmission risk.
Development of Synchronous Transportation Model for Trackless Vehicle Dispatching During the Construction of Long‐Distance Single‐Headed Shield Tunnel
Authors: Wu Jian , Tang Shao-Hui , Zhou Chui-Yi , Huang Yong , Huang Lei , Lu Hong-Bo , Miao Ning
Published: October 2024

With the increasing demands for long‐distance single‐headed tunnels, trackless vehicles have been widely accepted for transporting construction materials from storage yard to working face. During the trackless transportation of construction materials, the synchronization of material supply and shield tunneling is critical to ensure tunneling efficiency. However, there is still a lack of a reliable synchronous transportation model for trackless vehicle dispatching. In the present study, the material transportation processes and vehicle transportation parameters have been investigated based on the Sutong GIL Yangtze River Crossing Cable Tunnel. The synchronous transportation model has been established to improve transportation efficiency during the construction stage. An optimized scheme of vehicle schedule has been proposed to minimize trackless vehicle and retention time. Comparative analysis has been carried out to evaluate the trackless vehicle and retention time between the optimized scheme and the original scheme. The results indicate that the number of dual‐headed trucks required for material transportation decreases from nine to six, and the maximum retention time decreases from 166 to 35 min. Compared with the original scheme, the optimized scheme is available for reducing the number of trackless vehicles and improving the efficiency of material transportation. The present study contributes to optimizing material transport scheduling and synchronizing material supply with tunnel excavation in long‐distance single‐headed shield tunnels.
Genetic Characterization of Canine morbillivirus (Canine Distemper Virus) Field Strains in Dogs, Chile, 2022–2023
Authors: Ariyama Naomi , Agüero Belén , Bennett Benjamín , Urzúa Constanza , Berrios Felipe , Verdugo Claudio , Neira Víctor
Published: October 2024

Canine distemper virus (CDV) poses a significant threat to dogs and wildlife worldwide, and this study sought to provide an updated genetic characterization of CDV field strains in Chile during 2022–2023. We collected samples from 52 suspected CDV cases in domestic dogs and detected viral RNA through real‐time RT‐PCR in 28 dogs (54%). Factors like age and vaccination status were determinants of CDV positivity, with young adult and unvaccinated dogs facing a higher infection risk. We isolated CDV from positive samples in VeroDogSLAM cells. From these isolates and direct samples, we obtained sequences and estimated the phylogeny based on gene H. CDV isolates from nasal and conjunctival swabs exhibited cytopathic effects, and sequence analysis unveiled a substantial genetic diversity among the strains. Chilean CDV strains demonstrated a genetic distance to vaccine strains of approximately 10%, antigenic‐change‐related amino acid substitutions, and novel putative glycosylation sites. In the phylogeny, Chilean CDV field strains clustered into two lineages, Europe/South America‐1 and North/South America‐4, indicating the emergence of the North/South America‐4 lineage in Chile and underscoring the genetic complexity of CDV in the country. Interestingly, certain Chilean viruses shared a close common ancestor with Brazilian and Peruvian viruses, suggesting viral spreading patterns. Further investigations are warranted to comprehend the potential antigenic implications of these genetically diverse CDV strains.
Supplementary Figure 3 from A Prime-Boost Vaccination Approach Induces Lung Resident Memory CD8+ T Cells Derived from Central Memory T Cells That Prevent Tumor Lung Metastasis
Authors: Xu Haoran , Yue Ming , Zhou Runhong , Wang Pui , Wong Michael Yik-Chun , Wang Jinlin , Huang Huarong , Chen Bohao , Mo Yufei , Tam Rachel Chun-Yee , Zhou Biao , Du Zhenglong , Huang Haode , Liu Li , Tan Zhiwu , Yuen Kwok-Yung , Song Youqiang , Chen Honglin , Chen Zhiwei
Published: October 2024

Enhanced memory T cell response by systematic prime-nasal booster immunization in the spleen
Table S3 from Proteomic Profiling of Serum Extracellular Vesicles Identifies Diagnostic Signatures and Therapeutic Targets in Breast Cancer
Authors: Xu Ganfei , Huang Rui , Wumaier Reziya , Lyu Jiacheng , Huang Minjing , Zhang Yaya , Chen Qingjian , Liu Wenting , Tao Mengyu , Li Junjian , Tao Zhonghua , Yu Bo , Xu Erxiang , Wang Lingfeng , Yu Guoying , Gires Olivier , Zhou Lei , Zhu Wei , Ding Chen , Wang Hongxia
Published: October 2024

Differentially expressed proteins in luminal A, luminal B, Her2-enriched, and TNBC samples (Student t-test, p < 0.05). Related to Figure 3.
Figure S2 from Hypoxic Memory Mediates Prolonged Tumor-Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression
Authors: Iriondo Oihana , Mecenas Desirea , Li Yilin , Chin Christopher R. , Thomas Amal , Moriarty Aidan , Marker Rebecca , Wang Yiru J. , Hendrick Haley , Amzaleg Yonatan , Ortiz Veronica , MacKay Matthew , Dickerson Amber , Lee Grace , Harotoonian Sevana , Benayoun Bérénice A. , Smith Andrew , Mason Christopher E. , Roussos Torres Evanthia T. , Klotz Remi , Yu Min
Published: October 2024

In vivo breast tumors show inverse correlation between hypoxia and IFN/AP gene signatures
Figure S1 from Hypoxic Memory Mediates Prolonged Tumor-Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression
Authors: Iriondo Oihana , Mecenas Desirea , Li Yilin , Chin Christopher R. , Thomas Amal , Moriarty Aidan , Marker Rebecca , Wang Yiru J. , Hendrick Haley , Amzaleg Yonatan , Ortiz Veronica , MacKay Matthew , Dickerson Amber , Lee Grace , Harotoonian Sevana , Benayoun Bérénice A. , Smith Andrew , Mason Christopher E. , Roussos Torres Evanthia T. , Klotz Remi , Yu Min
Published: October 2024

In vitro and in vivo growth of CTC lines influenced by different oxygen culture conditions
The Next Frontier for Colorectal Cancer Screening: Blood-Based Tests
Authors: Rolfo Christian , Russo Alessandro
Published: October 2024

Colorectal cancer is associated with substantial morbidity and mortality worldwide. Detection of early colorectal cancer is possible through approved screening tests but overall adherence is quite low. Implementation of effective noninvasive options could increase screening uptake and prevent a significant number of deaths. Noninvasive early cancer detection can potentially be achieved using a liquid biopsy. In this issue of Cancer Research, Cao and colleagues report on a novel multidimensional fragmentomics assay, named FRAGTECT, for colorectal cancer detection in circulating cell-free DNA with promising results.

See related article by Cao et al., p. 3286
Remembering Hypoxia: Uncovering the Long-Term Effects of Transient Oxygen Deprivation on IFN Signaling and Progression of Breast Cancer
Authors: Purdy Stephen Connor , Ford Heide L.
Published: October 2024

Hypoxia occurs in 50-60% of solid tumors and is strongly associated with an increased propensity for metastasis. Hypoxia induces tumor progression largely through inducing HIF-mediated transcription, resulting in alterations to tumor cell metabolism, as well as increases in migration and invasion. Hypoxia also results in a myriad of changes to the tumor microenvironment (TME). While many studies have examined the immediate effects of hypoxia on tumor cells and the associated TME, far fewer have focused on the long-term consequences of transient reductions in oxygen. In this issue of Cancer Research, Iriondo and colleagues examined whether short-term exposure to hypoxia leads to a “hypoxic memory” in the context of breast cancer. The authors used established cell lines and circulating tumor cell lines to demonstrate that these cells harbor a hypoxic memory that sustains downregulation of IFN signaling and antigen presentation (AP) pathways that contribute to tumor progression via alterations to tumor cells and the TME. The authors further showed that cells that have experienced hypoxia maintain the reduction in IFN signaling in vivo and are more aggressive. They determined that the hypoxic memory and reduction of IFN signaling can be reversed with a histone deacetylase inhibitor, entinostat, providing a potential means to reverse hypoxia-induced suppression of IFN signaling. As suppression of IFN signaling has the potential to influence both tumor cells and the TME, the identification of a strategy to inhibit long-term suppression of IFN signaling downstream of hypoxia could prove to be an effective means to target tumor progression.

See related article by Iriondo et al., p. 3141
Supplementary Figure S19 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 19. KEAPness and pathway-level signatures (PROGENy) in the pooled SU2C/OAK/POPLAR cohort
Supplementary Figure S13 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 13. Sensitivity analyses in the SU2C cohort upon exclusion of patients who received prior targeted agents.
Supplementary Figure S11 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 11. Immune-related processes and the KEAPness-dominant phenotype in the SU2C and OAK/POPLAR cohorts
Supplementary Figure S5 from Targeting the Dendritic Cell-Secreted Immunoregulatory Cytokine CCL22 Alleviates Radioresistance
Authors: Bugno Jason , Wang Liangliang , Yu Xianbin , Cao Xuezhi , Wang Jiaai , Huang Xiaona , Yang Kaiting , Piffko Andras , Chen Katherine , Luo Stephen Y. , Naccasha Emile , Hou Yuzhu , Fu Sherry , He Chuan , Fu Yang-xin , Liang Hua L. , Weichselbaum Ralph R.
Published: October 2024

Supplementary Figure S5. Correlation of a Human DC_Ccl22 Homolog Score and CCL22 expression among multiple TCGA cohorts
Supplemental Figure S1 from Genomic Profiling to Contextualize the Results of Intervention for Smoldering Multiple Myeloma
Authors: Kazandjian Dickran , Diamond Benjamin , Papadimitriou Marios , Hill Elizabeth , Sklavenitis-Pistofidis Romanos , Ziccheddu Bachisio , Blaney Patrick , Chojnacka Monika , Durante Michael , Maclachlan Kylee , Young Ryan , Usmani Saad , Davies Faith , Getz Gad , Ghobrial Irene , Korde Neha , Morgan Gareth , Maura Francesco , Landgren Ola
Published: October 2024

Supplemental Figure S1: Sample Overview.
Supplementary Data 1 from Decoding Patient Heterogeneity Influencing Radiation-Induced Brain Necrosis
Authors: Chamseddine Ibrahim , Shah Keyur , Lee Hoyeon , Ehret Felix , Schuemann Jan , Bertolet Alejandro , Shih Helen A. , Paganetti Harald
Published: October 2024

Data processing details, statistical rules details and subgroup analysis details.
Supplementary Data 1 from Cervical Cancer Evades the Host Immune System through the Inhibition of Type I Interferon and CXCL9 by LIF
Authors: Bonfill-Teixidor Ester , Neva-Alejo Almudena , Arias Alexandra , Cuartas Isabel , Iurlaro Raffaella , Planas-Rigol Ester , Solé Laura , Pecharromán Irene , Cabrera Silvia , García Ángel , Garcia-Illescas David , Espinosa Lluís , Gil-Moreno Antonio , Oaknin Ana , Seoane Joan
Published: October 2024

Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Table S1, Supplementary methods
Supplementary Figure S6 from Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim
Authors: Andersson Axel , Escriva Conde Maria , Surova Olga , Vermeulen Peter , Wählby Carolina , Nilsson Mats , Nyström Hanna
Published: October 2024

Supplementary Figure S6. Distance-based analysis. Gene concentration as a function of distance to different regions in the tissue.
Supplementary Figure S3 from Early Detection of Malignant and Premalignant Peripheral Nerve Tumors Using Cell-Free DNA Fragmentomics
Authors: Sundby R. Taylor , Szymanski Jeffrey J. , Pan Alexander C. , Jones Paul A. , Mahmood Sana Z. , Reid Olivia H. , Srihari Divya , Armstrong Amy E. , Chamberlain Stacey , Burgic Sanita , Weekley Kara , Murray Béga , Patel Sneh , Qaium Faridi , Lucas Andrea N. , Fagan Margaret , Dufek Anne , Meyer Christian F. , Collins Natalie B. , Pratilas Christine A. , Dombi Eva , Gross Andrea M. , Kim AeRang , Chrisinger John S.A. , Dehner Carina A. , Widemann Brigitte C. , Hirbe Angela C. , Chaudhuri Aadel A. , Shern Jack F.
Published: October 2024

Supplemental Figure 3. Number of NMF components versus AUC. Performance (AUC) of NMF models in OVO comparisons is plotted against the number n components (Methods) used. The number of components approaches the AUC’s asymptote in each OVO at or before 20 components. Optimal number of components for each OVO was defined as the number of components yielding the highest AUC. AUC, area under the curve; OVO, one-versus-one comparison; NMF, non-negative matrix factorization.
Supplementary Data 1 from First-Line Anlotinib Treatment for Soft-Tissue Sarcoma in Chemotherapy-Ineligible Patients: An Open-Label, Single-Arm, Phase 2 Clinical Trial
Authors: Li Tao , Dong Ying , Wei Yongzhong , Wang Shoufeng , Liu Yunxia , Chen Jia , Xiong Wenhua , Lin Nong , Huang Xin , Liu Meng , Yan Xiaobo , Ye Zhaoming , Li Binghao
Published: October 2024

Supplementary File 1. Inclusion and exclusion criteria.Supplementary Table S1. Representativeness of trial patients.Supplementary Table S2. Summary of adverse events.
Supplemental Table 6 from Abiraterone, Olaparib, or Abiraterone + Olaparib in First-Line Metastatic Castration-Resistant Prostate Cancer with DNA Repair Defects (BRCAAway)
Authors: Hussain Maha , Kocherginsky Masha , Agarwal Neeraj , Adra Nabil , Zhang Jingsong , Paller Channing J. , Picus Joel , Reichert Zachery R. , Szmulewitz Russell Z. , Tagawa Scott T. , Kuzel Timothy M. , Bazzi Latifa A. , Daignault-Newton Stephanie , Whang Young E. , Dreicer Robert , Stephenson Ryan D. , Rettig Matthew B. , Shevrin Daniel , Gerke Travis , Chinnaiyan Arul M. , Antonarakis Emmanuel S.
Published: October 2024

Supplemental Table 6. Representativeness of Study Patients.
Supplemental Table 3 from Abiraterone, Olaparib, or Abiraterone + Olaparib in First-Line Metastatic Castration-Resistant Prostate Cancer with DNA Repair Defects (BRCAAway)
Authors: Hussain Maha , Kocherginsky Masha , Agarwal Neeraj , Adra Nabil , Zhang Jingsong , Paller Channing J. , Picus Joel , Reichert Zachery R. , Szmulewitz Russell Z. , Tagawa Scott T. , Kuzel Timothy M. , Bazzi Latifa A. , Daignault-Newton Stephanie , Whang Young E. , Dreicer Robert , Stephenson Ryan D. , Rettig Matthew B. , Shevrin Daniel , Gerke Travis , Chinnaiyan Arul M. , Antonarakis Emmanuel S.
Published: October 2024

Supplemental Table 3. Reasons for not crossing over per arm.
Supplementary Figure S5 from Pharmacologic Inhibition of EIF4A Blocks NRF2 Synthesis to Prevent Osteosarcoma Metastasis
Authors: Lizardo Michael M. , Hughes Christopher , Huang Yue Z. , Shyp Taras , Delaidelli Alberto , Zhang Hai-Feng , Shaool Sol Snir , Renner Annalena F. , Burwag Farez , Sayles Leanne C. , Lee Alex G. , Sweet-Cordero Alejandro , Sorensen Poul H.
Published: October 2024

Fig. S5. GSEA of pathways affected by CR-1-31B single-agent treatment.
Supplementary Figure S4 from Pharmacologic Inhibition of EIF4A Blocks NRF2 Synthesis to Prevent Osteosarcoma Metastasis
Authors: Lizardo Michael M. , Hughes Christopher , Huang Yue Z. , Shyp Taras , Delaidelli Alberto , Zhang Hai-Feng , Shaool Sol Snir , Renner Annalena F. , Burwag Farez , Sayles Leanne C. , Lee Alex G. , Sweet-Cordero Alejandro , Sorensen Poul H.
Published: October 2024

Fig. S4. CR-1-31B down-regulates known targets of rocaglate-based inhibitors
Supplementary Figure S12 from Pharmacologic Inhibition of EIF4A Blocks NRF2 Synthesis to Prevent Osteosarcoma Metastasis
Authors: Lizardo Michael M. , Hughes Christopher , Huang Yue Z. , Shyp Taras , Delaidelli Alberto , Zhang Hai-Feng , Shaool Sol Snir , Renner Annalena F. , Burwag Farez , Sayles Leanne C. , Lee Alex G. , Sweet-Cordero Alejandro , Sorensen Poul H.
Published: October 2024

Fig. S12. eFT226 inhibits proliferation of a metastatic PDX OS cell line model under oxidative stress.
Supplementary Table S7 from Tyrosine Protein Kinase SYK-Related Gene Signature in Baseline Immune Cells Associated with Adjuvant Immunotherapy–Induced Immune-Related Adverse Events in Melanoma
Authors: Monson Kelsey R. , Ferguson Robert , Handzlik Joanna E. , Xiong Jiahan , Dagayev Sasha , Morales Leah , Chat Vylyny , Bunis Anabelle , Sreenivasaiah Chaitra , Dolfi Sonia , Tenney Daniel J. , Shao Yongzhao , Osman Iman , Weber Jeffrey S. , Kirchhoff Tomas
Published: October 2024

Supplementary Table S7. Assessing model stability and reproducibility for LASSO regularized cross-validation logistic regression model over 300 iterations.
Supplementary Figure S4 from Tyrosine Protein Kinase SYK-Related Gene Signature in Baseline Immune Cells Associated with Adjuvant Immunotherapy–Induced Immune-Related Adverse Events in Melanoma
Authors: Monson Kelsey R. , Ferguson Robert , Handzlik Joanna E. , Xiong Jiahan , Dagayev Sasha , Morales Leah , Chat Vylyny , Bunis Anabelle , Sreenivasaiah Chaitra , Dolfi Sonia , Tenney Daniel J. , Shao Yongzhao , Osman Iman , Weber Jeffrey S. , Kirchhoff Tomas
Published: October 2024

Supplementary Figure S4. Semi-supervised hierarchical clustering of the DEGs comparing TOXlow vs TOXhighin CD4+ cells from NIVO-treated patients (n = 124) identified from PPI analysis.
Supplementary Table 1 from Colorectal Cancer Recurrence Prediction Using a Tissue-Free Epigenomic Minimal Residual Disease Assay
Authors: Nakamura Yoshiaki , Tsukada Yuichiro , Matsuhashi Nobuhisa , Murano Tatsuro , Shiozawa Manabu , Takahashi Yusuke , Oki Eiji , Goto Masahiro , Kagawa Yoshinori , Kanazawa Akiyoshi , Ohta Takashi , Ouchi Akira , Bando Hideaki , Uchigata Hiroshi , Notake Chiemi , Ikematsu Hiroaki , Yoshino Takayuki
Published: October 2024

Supplementary Table 1. Clinicopathologic Characteristics of the 342 Enrolled Patients with Clinical Stage I-III CRC.
Supplementary Table S2 from The Innate Immune Landscape of dMMR/MSI Cancers Predicts the Outcome of Nivolumab Treatment: Results from the Drug Rediscovery Protocol
Authors: Zeverijn Laurien J. , Geurts Birgit S. , Battaglia Thomas W. , van Berge Henegouwen Jade M. , de Wit Gijs F. , Hoes Louisa R. , van der Wijngaart Hanneke , van der Noort Vincent , Roepman Paul , de Leng Wendy W.J. , Jansen Anne M.L. , Chalabi Myriam , van Herpen Carla M.L. , Devriese Lot A. , Erdkamp Frans L.G. , Labots Mariette , de Jonge Maja J.A. , Kerver Emile D. , Bins Adriaan D. , Leek Lindsay V.M. , Notohardjo Jessica C.L. , van den Eertwegh Alfonsus J.M. , Wessels Lodewyk F.A. , Verheul Henk M.W. , Gelderblom Hans , van de Haar Joris , Voest Emile E.
Published: October 2024

Supplementary Table S2. Inclusion and exclusion criteria.
Supplementary Figure 1 from Colorectal Cancer Recurrence Prediction Using a Tissue-Free Epigenomic Minimal Residual Disease Assay
Authors: Nakamura Yoshiaki , Tsukada Yuichiro , Matsuhashi Nobuhisa , Murano Tatsuro , Shiozawa Manabu , Takahashi Yusuke , Oki Eiji , Goto Masahiro , Kagawa Yoshinori , Kanazawa Akiyoshi , Ohta Takashi , Ouchi Akira , Bando Hideaki , Uchigata Hiroshi , Notake Chiemi , Ikematsu Hiroaki , Yoshino Takayuki
Published: October 2024

Supplementary Figure 1. Sample Collection and Imaging Schedule.
Supplementary Figure S9 from Clinical Value of Liquid Biopsy in Patients with FGFR2 Fusion–Positive Cholangiocarcinoma During Targeted Therapy
Authors: González-Medina Alberto , Vila-Casadesús Maria , Gomez-Rey Marina , Fabregat-Franco Carles , Sierra Alexandre , Tian Tian V. , Castet Florian , Castillo Gloria , Matito Judit , Martinez Paola , Miquel Josep M. , Nuciforo Paolo , Pérez-López Raquel , Macarulla Teresa , Vivancos Ana
Published: October 2024

Supplementary Figure S9. Follow-up in plasma samples collected periodically.
Supplementary Figure S6 from Clinical Value of Liquid Biopsy in Patients with FGFR2 Fusion–Positive Cholangiocarcinoma During Targeted Therapy
Authors: González-Medina Alberto , Vila-Casadesús Maria , Gomez-Rey Marina , Fabregat-Franco Carles , Sierra Alexandre , Tian Tian V. , Castet Florian , Castillo Gloria , Matito Judit , Martinez Paola , Miquel Josep M. , Nuciforo Paolo , Pérez-López Raquel , Macarulla Teresa , Vivancos Ana
Published: October 2024

Supplementary Figure S6. Coverage profiles for intron 17 and exon 18 of FGFR2 (patients 10–18).
Supplementary Data1 from Ipatasertib plus Paclitaxel for Patients with PIK3CA/AKT1/PTEN-Altered Locally Advanced Unresectable or Metastatic Triple-Negative Breast Cancer in the IPATunity130 Phase III Trial
Authors: Dent Rebecca A. , Kim Sung-Bae , Oliveira Mafalda , Barrios Carlos , O’Shaughnessy Joyce , Isakoff Steven J. , Saji Shigehira , Freitas-Junior Ruffo , Philco Manuel , Bondarenko Igor , Lian Qinshu , Bradley Denise , Hinton Heather , Wongchenko Matthew J. , Reilly Sarah-Jayne , Turner Nicholas
Published: October 2024

Additional details of methodology, representativeness of study participants, and additional results
Data from Decoding Patient Heterogeneity Influencing Radiation-Induced Brain Necrosis
Authors: Chamseddine Ibrahim , Shah Keyur , Lee Hoyeon , Ehret Felix , Schuemann Jan , Bertolet Alejandro , Shih Helen A. , Paganetti Harald
Published: October 2024

AbstractPurpose:
In radiotherapy (RT) for brain tumors, patient heterogeneity masks treatment effects, complicating the prediction and mitigation of radiation-induced brain necrosis. Therefore, understanding this heterogeneity is essential for improving outcome assessments and reducing toxicity.
Experimental Design:
We developed a clinically practical pipeline to clarify the relationship between dosimetric features and outcomes by identifying key variables. We processed data from a cohort of 130 patients treated with proton therapy for brain and head and neck tumors, utilizing an expert-augmented Bayesian network to understand variable interdependencies and assess structural dependencies. Critical evaluation involved a three-level grading system for each network connection and a Markov blanket analysis to identify variables directly impacting necrosis risk. Statistical assessments included log-likelihood ratio, integrated discrimination index, net reclassification index, and receiver operating characteristic (ROC).
Results:
The analysis highlighted tumor location and proximity to critical structures such as white matter and ventricles as major determinants of necrosis risk. The majority of network connections were clinically supported, with quantitative measures confirming the significance of these variables in patient stratification (log-likelihood ratio = 12.17; P = 0.016; integrated discrimination index = 0.15; net reclassification index = 0.74). The ROC curve area was 0.66, emphasizing the discriminative value of nondosimetric variables.
Conclusions:
Key patient variables critical to understanding brain necrosis post-RT were identified, aiding the study of dosimetric impacts and providing treatment confounders and moderators. This pipeline aims to enhance outcome assessments by revealing at-risk patients, offering a versatile tool for broader applications in RT to improve treatment personalization in different disease sites.
Data from Single-Cell Profiling of Sarcomas from Archival Tissue Reveals Programs Associated with Resistance to Immune Checkpoint Blockade
Authors: Luthria Karan , Shah Parin , Caldwell Blake , Melms Johannes C. , Abuzaid Sinan , Jakubikova Viktoria , Brodtman D. Zack , Bose Sminu , Amin Amit Dipak , Ho Patricia , Biermann Jana , Tagore Somnath , Ingham Matthew , Schwartz Gary K. , Izar Benjamin
Published: October 2024

AbstractPurpose:
Sarcoma encompasses a diverse group of cancers that are typically resistant to current therapies, including immune checkpoint blockade (ICB), and underlying mechanisms are poorly understood. The contexture of sarcomas limits generation of high-quality data using cutting-edge molecular profiling methods, such as single-cell RNA-sequencing, thus hampering progress in understanding these understudied cancers.
Experimental Design:
Here, we demonstrate feasibility of producing multimodal single-cell genomics and whole-genome sequencing data from frozen tissues, profiling 75,716 cell transcriptomes of five undifferentiated pleomorphic sarcoma and three intimal sarcoma samples, including paired specimens from two patients treated with ICB.
Results:
We find that genomic diversity decreases in patients with response to ICB, and, in unbiased analyses, identify cancer cell programs associated with therapy resistance. Although interactions of tumor-infiltrating T lymphocytes within the tumor ecosystem increase in ICB responders, clonal expansion of CD8+ T cells alone was insufficient to predict drug responses.
Conclusions:
This study provides a framework for studying rare tumors and identifies salient and treatment-associated cancer cell intrinsic and tumor microenvironmental features in sarcomas.
Data from Elacestrant in ER+, HER2− Metastatic Breast Cancer with ESR1-Mutated Tumors: Subgroup Analyses from the Phase III EMERALD Trial by Prior Duration of Endocrine Therapy plus CDK4/6 Inhibitor and in Clinical Subgroups
Authors: Bardia Aditya , Cortés Javier , Bidard François-Clément , Neven Patrick , Garcia-Sáenz José , Aftimos Phillipe , O’Shaughnessy Joyce , Lu Janice , Tonini Giulia , Scartoni Simona , Paoli Alessandro , Binaschi Monica , Wasserman Tomer , Kaklamani Virginia
Published: October 2024

AbstractPurpose:
Elacestrant significantly prolonged progression-free survival (PFS) with manageable safety versus standard-of-care (SOC) endocrine therapy (ET) in patients with estrogen receptor–positive (ER+), HER2− metastatic breast cancer and tumors harboring estrogen receptor 1 (ESR1) mutation following ET plus a cyclin-dependent kinase 4/6 inhibitor (ET+CDK4/6i). In patients with ESR1-mutated tumors, we evaluated the efficacy and safety of elacestrant versus SOC based on prior ET+CDK4/6i duration and in clinical subgroups with prior ET+CDK4/6i ≥12 months.
Patients and Methods:
EMERALD, an open-label phase III trial, randomly assigned patients with ER+, HER2− metastatic breast cancer who had received 1–2 prior lines of ET, mandatory CDK4/6i, and ≤1 chemotherapy to elacestrant (345 mg daily) or SOC (aromatase inhibitor or fulvestrant). PFS was assessed across subgroups in post hoc exploratory analyses without adjustment for multiple testing.
Results:
In patients with ESR1-mutated tumors and prior ET+CDK4/6i ≥12 months, the median PFS for elacestrant versus SOC was 8.6 versus 1.9 months (HR, 0.41; 95% confidence interval, 0.26–0.63). In this population, the median PFS (in months) for elacestrant versus SOC was 9.1 versus 1.9 (bone metastases), 7.3 versus 1.9 (liver and/or lung metastases), 9.0 versus 1.9 (<3 metastatic sites), 10.8 versus 1.8 (≥3 metastatic sites), 5.5 versus 1.9 (PIK3 catalytic subunit α mutation), 8.6 versus 1.9 (tumor protein p53 gene mutation), 9.0 versus 1.9 (HER2-low), 9.0 versus 1.9 (ESR1D538G-mutated tumors), and 9.0 versus 1.9 (ESR1Y537S/N-mutated tumors). Subgroup safety was consistent with the overall population.
Conclusions:
The duration of prior ET+CDK4/6i ≥12 months in metastatic breast cancer was associated with a clinically meaningful improvement in PFS for elacestrant compared with SOC and was consistent across all subgroups evaluated in patients with ER+, HER2−, ESR1-mutated tumors.