bluuebunny/crossref_metadata_2025 huggingface dataset:
Release from same-talker speech-in-speech masking: Effects of masker intelligibility and other contributing factors
Authors: Huo Mingyue , Sun Yinglun , Fogerty Daniel , Tang Yan
Published: November 2024

Human speech perception declines in the presence of masking speech, particularly when the masker is intelligible and acoustically similar to the target. A prior investigation demonstrated a substantial reduction in masking when the intelligibility of competing speech was reduced by corrupting voiced segments with noise [Huo, Sun, Fogerty, and Tang (2023), “Quantifying informational masking due to masker intelligibility in same-talker speech-in-speech perception,” in Interspeech 2023, pp. 1783–1787]. As this processing also reduced the prominence of voiced segments, it was unclear whether the unmasking was due to reduced linguistic content, acoustic similarity, or both. The current study compared the masking of original competing speech (high intelligibility) to competing speech with time reversal of voiced segments (VS-reversed, low intelligibility) at various target-to-masker ratios. Modeling results demonstrated similar energetic masking between the two maskers. However, intelligibility of the target speech was considerably better with the VS-reversed masker compared to the original masker, likely due to the reduced linguistic content. Further corrupting the masker's voiced segments resulted in additional release from masking. Acoustic analyses showed that the portion of target voiced segments overlapping with masker voiced segments and the similarity between target and masker overlapped voiced segments impacted listeners' speech recognition. Evidence also suggested modulation masking in the spectro-temporal domain interferes with listeners' ability to glimpse the target.
Sparsity-based direction-of-arrival estimation in the presence of near-field and far-field interferences for small-scale platform sonar arrays
Authors: Du Zhiyao , Hao Yu , Qiu Longhao , Li Chenmu , Liang Guolong
Published: November 2024

For the sonar arrays mounted on an unmanned underwater vehicle (UUV), the direction-of-arrival (DOA) estimation of the far-field (FF) weak sources is influenced by the near-field (NF) interferences generated from the radiated self-noise of the UUV and the FF interferences simultaneously. To address the problem, a sparsity-based DOA estimation method resistant to the NF and FF interferences is proposed in this paper. This method isolates the FF signals from the NF signals by sparse reconstruction. Additionally, subspace projection is applied to address the masking problem of the weak target signal by the strong interferences in the spatial domain, effectively enhancing the capacity of estimating the DOA of the weak target signal in the presence of strong interferences. Numerical simulations and experimental results demonstrate the effectiveness of the proposed method. Compared to other advanced DOA estimation methods, the proposed method exhibits better DOA estimation performance in the presence of strong NF and FF interferences.
Potential climate predictability of renewable energy supply and demand for Texas given the ENSO hidden state
Authors: Zhang Mengjie , Yan Lei , Amonkar Yash , Nayak Adam , Lall Upmanu
Published: November 2024

Climate variability influences renewable electricity supply and demand and hence system reliability. Using the hidden states of the sea surface temperature of tropical Pacific Ocean that reflect El Niño–Southern Oscillation (ENSO) dynamics that is objectively identified by a nonhomogeneous hidden Markov model, we provide a first example of the potential predictability of monthly wind and solar energy and heating and cooling energy demand for 1 to 6 months ahead for Texas, United States, a region that has a high penetration of renewable electricity and is susceptible to disruption by climate-driven supply-demand imbalances. We find a statistically significant potential for oversupply or undersupply of energy and anomalous heating/cooling demand depending on the ENSO state and the calendar month. Implications for financial securitization and the potential application of forecasts are discussed.
Proteomimetic polymer blocks mitochondrial damage, rescues Huntington’s neurons, and slows onset of neuropathology in vivo
Authors: Choi Wonmin , Fattah Mara , Shang Yutong , Thompson Matthew P. , Carrow Kendal P. , Hu Di , Liu Zunren , Avram Michael J. , Bailey Keith , Berger Or , Qi Xin , Gianneschi Nathan C.
Published: November 2024

Recently, it has been shown that blocking the binding of valosin-containing protein (VCP) to mutant huntingtin (mtHtt) can prevent neuronal mitochondrial autophagy in Huntington’s disease (HD) models. Herein, we describe the development and efficacy of a protein-like polymer (PLP) for inhibiting this interaction in cellular and in vivo models of HD. PLPs exhibit bioactivity in HD mouse striatal cells by successfully inhibiting mitochondrial destruction. PLP is notably resilient to in vitro enzyme, serum, and liver microsome stability assays, which render analogous control oligopeptides ineffective. PLP demonstrates a 2000-fold increase in circulation half-life compared to peptides, exhibiting an elimination half-life of 152 hours. In vivo efficacy studies in HD transgenic mice (R6/2) confirm the superior bioactivity of PLP compared to free peptide through behavioral and neuropathological analyses. PLP functions by preventing pathologic VCP/mtHtt binding in HD animal models; exhibits enhanced efficacy over the parent, free peptide; and implicates the PLP as a platform with potential for translational central nervous system therapeutics.
Reprogramming cellular senescence in the tumor microenvironment augments cancer immunotherapy through multifunctional nanocrystals
Authors: Wang Zheng , Chen Yinglu , Fang Hui , Xiao Kai , Wu Ziping , Xie Xiaochun , Liu Jie , Chen Fangman , He Yi , Wang Liang , Yang Chao , Pei Renjun , Shao Dan
Published: November 2024

Harnessing the immunogenic potential of senescent tumor cells provides an opportunity to remodel tumor microenvironment (TME) and boost antitumor immunity. However, this potential needs to be sophisticatedly wielded to avoid additional immunosuppressive capacity of senescent cells. Our study shows that blocking the JAK2/STAT3 pathway enhances immunogenic efficacy of Aurora kinase inhibitor alisertib (Ali)–induced senescence by reducing immunosuppressive senescence-associated secretory phenotype (SASP) while preserving immunogenic SASP. Hypothesizing that SASP reprogramming with Ali and JAK2 inhibitor ruxolitinib (Rux) will benefit cancer immunotherapy, we create nanoparticulate crystals (Ali-Rux) composed of Ali and Rux with a fully active pharmaceutical ingredient. Immunization with Ali-Rux–orchestrated senescent cells promotes stronger activation of antigen-presenting cells, enhancing antitumor immune surveillance. This approach remodels the TME by increasing CD8
+
T cell and NK recruitment and activation while decreasing MDSCs. Combined with PD-L1 blockade, Ali-Rux elicits a durable antitumor immune response, suggesting the TME reshaping approach as a potential cancer immunotherapy.
Purcell-enhanced x-ray scintillation
Authors: Kurman Yaniv , Lahav Neta , Schuetz Roman , Shultzman Avner , Roques-Carmes Charles , Lifshits Alon , Zaken Segev , Lenkiewicz Tom , Strassberg Rotem , Be’er Orr , Bekenstein Yehonadav , Kaminer Ido
Published: November 2024

Scintillation materials convert high-energy radiation to optical light through a complex multistage process. The last stage of the process is spontaneous light emission, which usually governs and limits the scintillator emission rate and light yield. For decades, scintillator research focused on developing faster-emitting materials or external photonic coatings for improving light yields. Here, we experimentally demonstrate a fundamentally different approach: enhancing the scintillation rate and yield via the Purcell effect, utilizing optical environment engineering to boost spontaneous emission. This enhancement is universally applicable to any scintillating material and dopant when the material’s nanoscale geometry is engineered. We design a thin multilayer nanophotonic scintillator, demonstrating Purcell-enhanced scintillation with 50% enhancement in emission rate and 80% enhancement in light yield. The emission is robust to fabrication disorder, further highlighting its potential for x-ray applications. Our results show prospects for bridging nanophotonics and scintillator science toward reduced radiation dosage and increased resolution for high-energy particle detection.
Deep-ultraviolet transparent conducting SrSnO
3
via heterostructure design
Authors: Liu Fengdeng , Yang Zhifei , Abramovitch David , Guo Silu , Mkhoyan K. Andre , Bernardi Marco , Jalan Bharat
Published: November 2024

Exploration and advancements in ultrawide bandgap (UWBG) semiconductors are pivotal for next-generation high-power electronics and deep-ultraviolet (DUV) optoelectronics. Here, we used a thin heterostructure design to facilitate high conductivity due to the low electron mass and relatively weak electron-phonon coupling, while the atomically thin films ensured high transparency. We used a heterostructure comprising SrSnO
3
/La:SrSnO
3
/GdScO
3
(110), and applied electrostatic gating, which allow us to effectively separate charge carriers in SrSnO
3
from dopants and achieve phonon-limited transport behavior in strain-stabilized tetragonal SrSnO
3
. This led to a modulation of carrier density from 10
18
to 10
20
cm
−3
, with room temperature mobilities ranging from 40 to 140 cm
2
V
−1
s
−1
. The phonon-limited mobility, calculated from first principles, closely matched experimental results, suggesting that room temperature mobility could be further increased with higher electron density. In addition, the sample exhibited 85% optical transparency at a 300-nm wavelength. These findings highlight the potential of heterostructure design for transparent UWBG semiconductor applications, especially in DUV regime.
Kupffer cell reverse migration into the liver sinusoids mitigates neonatal sepsis and meningitis
Authors: Araujo David Bruna , Atif Jawairia , Vargas e Silva Castanheira Fernanda , Yasmin Tamanna , Guillot Adrien , Ait Ahmed Yeni , Peiseler Moritz , Hommes Josefien W. , Salm Lilian , Brundler Marie-Anne , Surewaard Bas G. J. , Elhenawy Wael , MacParland Sonya , Ginhoux Florent , McCoy Kathy , Kubes Paul
Published: November 2024

In adults, liver-resident macrophages, or Kupffer cells (KCs), reside in the sinusoids and sterilize circulating blood by capturing rapidly flowing microbes. We developed quantitative intravital imaging of 1-day-old mice combined with transcriptomics, genetic manipulation, and in vivo infection assays to interrogate increased susceptibility of newborns to bloodstream infections. Whereas 1-day-old KCs were better at catching
Escherichia coli
in vitro, we uncovered a critical 1-week window postpartum when KCs have limited access to blood and must translocate from liver parenchyma into the sinusoids. KC migration was independent of the microbiome but depended on macrophage migration inhibitory factor, its receptor CD74, and the adhesion molecule CD44. On the basis of our findings, we propose a model of progenitor macrophage seeding of the liver sinusoids via a reverse transmigration process from liver parenchyma. These results also illustrate the importance of developing newborn mouse models to understand newborn immunity and disease.
Giant aggressive angiomyxoma of the vulva in two women
Authors: Haider Aleena , Kumar Vandana , Agrawal Smriti
Published: November 2024

Aggressive angiomyxoma (AA) of the vulva is a rare, benign, slow-growing tumour that arises from the myxoid cells of the connective tissue. It has a low tendency to metastasise, but a high chance of multiple local recurrences. Here, we report two cases of AA of the vulva. In both these cases, women in the reproductive age group presented with the condition of a large, fleshy, pedunculated mass on the labia majora. The mass was surgically resected and sent for histopathology, which confirmed the diagnosis. AA should be kept as one of the differential diagnoses for a vulvovaginal mass. Its correct diagnosis, optimal treatment and long-term follow-up are necessary for appropriate management of such patients.
Optimization Analysis of Tennis Player Training Mode Based on 3D Simulation Model
Authors: Miao Guolin , Xie Yanan
Published: November 2024

This paper is based on 3D simulation technology and deeply analyzes the optimization strategy of tennis player training mode. The research focuses on two core systems: one is a remote motion monitoring system based on architecture, which captures and analyzes athletes’ motion data in real time, providing coaches with accurate motion feedback and training effectiveness evaluation; The second is a 3D-based safety monitoring system, which uses 3D simulation technology to simulate the training environment, monitor and warn potential safety risks in real time, and ensure the safety of athletes during training. These two systems are designed for different demand scenarios in tennis training, with complementary functions, and together constitute an intelligent solution for optimizing the training mode of tennis players. By continuously improving algorithms, optimizing data storage and computation methods, and improving the accuracy of data analysis and mapping, this study aims to enhance the scientific, efficient, and safe training of tennis players, providing strong support for the comprehensive improvement of their skills and physical fitness.
Research on the Reform and Innovation of College Music Teaching Based on Collaborative Filtering Algorithm
Authors: Cao Hongxing , Xiaoyong Tao
Published: November 2024

With the rapid development of artificial intelligence technology, collaborative filtering (CF) algorithms are becoming increasingly widely used in the field of education. This paper aims to explore the application of CF algorithms in the reform and innovation of music teaching in universities, in order to improve teaching effectiveness and students’ learning experience. First, this paper analyzes the problems existing in current music teaching in universities, such as single teaching methods and low student participation. In order to complete the research on the extension of online music systems in music teaching, this paper reused the post filtering paradigm of contextual information and redesigned the two-stage process of the hybrid algorithm. After the initial screening of CF, the algorithm extracts recommendation results with contextual bias based on tag information. Then, based on the improved algorithm, an online music teaching system was implemented. Applying hybrid algorithm intelligent algorithms to university music teaching can not only improve the personalization and interactivity of teaching, but also promote the cultivation of students’ creativity and critical thinking abilities. The experimental results show that the music teaching system using hybrid intelligent algorithms significantly improves students’ learning participation, with an average participation rate increased by 30% compared to traditional teaching methods. At the same time, students’ learning outcomes have also significantly improved, with an average score increase of 15% in music theory exams. And in the assessment of creativity and critical thinking ability, students show stronger thinking activity and innovation ability. In addition, system feedback indicates that over 90% of students are satisfied with the teaching system, believing that it enhances the fun and interactivity of learning.
Crop Leaf Type Classification and Multi-Class Leaf Disease Identification with Tangent Hunter Prey Optimization-Based LeNet
Authors: Karthi S , Bhavani R , Arunmozhi B , Saranya K , Karthika K
Published: November 2024

The early detection and accurate rate of classification of plant leaf disease are more important for reliable and good agriculture, which prevents unwanted financial loss and resources. In this study, Tangent Hunter Prey Optimization-based LeNet (THPO-LeNet) is utilized for crop leaf classification and multi-class plant leaf disease identification. In this case, the input image that goes through the image pre-processing step is obtained from the plant village dataset. An adaptive Wiener filter is applied at the pre-processing stage to reduce needless mistakes and improve image quality. The pre-processed image is then sent to the leaf segmentation step, where a Mask Region-based Convolution Neural Network (Mask R-CNN) performs the segmentation. Consequently, image augmentation is performed using techniques such as scaling, rotation, translation, flipping, contrast, saturation, and hue. Afterwards, first-level classification plant leaf classification is processed by LeNet, which is optimized by Tangent Hunter Prey Optimization (THPO). The THPO is the incorporation of a Tangent Search Algorithm (TSA) and Hunter–Prey Optimizer (HPO). At last, the second-level classification of plant leaf disease is conducted by THPO-LeNet. Furthermore, the efficiency of THPO-LeNet is examined based on measures, like accuracy, Negative Predictive Value (NPV), True Positive Rate (TPR), True Negative Rate (TNR), Positive Predictive Value (PPV), loss value, and False Positive Rate (FPR), and the value attained is 95.68%, 92.50%, 91.48%, 92.25%, 92.54%, 8.321%, and 7.754%, respectively.
Detecting and Classifying Problematic Behavior: A Method Based on Multi-Dimensional Software Modeling Behavioral Characteristics
Authors: Wang Yiting , Li Tong , You Jiahui , Zhang Xinran , Geng Congkai , Liu Yu
Published: November 2024

Understanding software modelers’ difficulties and evaluating their performance is crucial to Model-Driven Engineering (MDE) education. The software modeling process contains fine-grained information about the modelers’ analysis and thought processes. However, existing research primarily focuses on identifying obvious issues in the software modeling process, such as incorrect connections or misunderstandings, but neglects the behavioral patterns that can reveal underlying, unaddressed modeling problems. This oversight fails to identify deeper problems that do not manifest as obvious issues but still represent significant potential problems in the software modeling process. Our research concentrates on detecting and classifying problematic modeling behaviors from software modeling process data, revealing the potential problems hidden in the process for MDE education. Specifically, we first construct problematic modeling behavior patterns from three dimensions, including anomalous time intervals, repetitions, and frequencies, to further identify characteristics and priorities relevant to problematic modeling behaviors. Then, we design rules with characteristics and priorities to detect and classify problematic modeling behaviors from problematic patterns. To evaluate the effectiveness of our proposal, we apply it to a data-flow diagram modeling platform. This platform can record modelers’ processes and has been practically used in software engineering courses for five years. We have conducted a case study with 12 participants. The macro F1 of detection and classification problematic modeling behaviors is 82.3%, which shows the effectiveness of our approach. Then, to evaluate the usefulness of our proposal for assisting modeling instructors in MDE education, we conducted another case study with 5 modeling instructors. The results show that our approach can help instructors uncover problems hidden in the software modeling process. The results of two case studies demonstrate that our approach effectively detects and classifies problematic modeling behaviors, enabling instructors to better adjust their instructional plans and improve MDE education.
Seawater Electrolysis at Ultra-High Current Density: A Comparative Analysis of Cylindrical versus Conical Electrodes
Authors: Tornøe Søren , Koster John , Surin Andy V. , Sands Jacob H. , Kobayashi Nobuhiko Paul
Published: November 2024

Seawater electrolysis preferentially leans towards Chlorine Evolution Reaction (CER) over Oxygen Evolution Reactions (OER) under conventional conditions, but OER becomes more dominant at sufficiently higher current densities. In this study, we evaluated the effector of cylindrical and conical electrode geometries on CER and hydrogen production at high current density (i.e., >1 A/cm2). We found the point of lowest CER within a voltage range of 40 V to 90 V. Conical electrodes, optimized to reduce CER, produced a magnitude less chloride (502 ppb) than cylindrical electrodes (1485 ppb) at nearly double the current density (~12 and ~6 A/cm2 respectively). However, this reduction in CER with conical electrodes was accompanied by a 25% decrease in hydrogen production. In addition, both cylindrical and conical electrodes were able to heat 500 ml of seawater by approximately 6-7 degrees Celsius over a two-minute period with cylindrical electrodes heating slightly less than conical electrodes.
Unbalanced Feature Identification of Rotor System Based on Fused Cross‐Correlation Fast Fourier Transform
Authors: Sheng Yiheng , Wang Zinan , Zhou Peng , Wang Zhan , Wang Qian , Niu Siqi
Published: November 2024

Rotor system unbalance is one of the most important factors that affects the operating accuracy and stability in aerospace engineering. The extraction and identification of unbalanced features is the premise for the dynamic balance of rotor system. In order to accurately identify the unbalanced vibration feature, based on the fused cross‐correlation fast Fourier transform (FC‐CFFT) method, an unbalanced feature extraction method of the rotor system is proposed. The convolution window weighs the data of the vibration sequence and carries out delay processing. Through spectrum calculation, the phase information of the vibration signal is obtained. And the amplitude information of the vibration feature can be acquired through cross‐correlation calculation. The unbalanced features of the rotor system vibration signals are identified under different working conditions through simulation and experiment. The results show that this method is more accurate than FFT, the cross‐power method, and the sine‐approximation method in extracting different unbalanced vibration features of the rotor system. The extraction accuracy of unbalanced feature phase and amplitude reaches 98.61% and 97.27%, respectively. After the unbalanced feature is extracted, the dynamic balance experiment can be carried out. The unbalanced feature is used for dynamic balance compensation. In this way, the average amplitude decreased by 76.35%. The high accuracy of the FC‐CFFT method for extracting the unbalanced feature has been verified. This research provides a theoretical foundation for the vibration signal processing and dynamic balance control of the rotor system.
Antibiotic Concentrations Affect the Virulence of Klebsiella quasipneumoniae subsp. similipneumoniae Isolates
Authors: Eroğlu Berfin , Delik Eda , Tefon-Öztürk Burcu Emine
Published: November 2024

Klebsiella species are becoming a major global public health concern. In particular, the increase in multidrug‐resistant strains is a cause for concern. This study was aimed at determining the antibiotic susceptibility of two different isolates of Klebsiella quasipneumoniae subsp. similipneumoniae and determining the virulence characteristics and bacterial morphology under subminimum inhibitory concentrations (sub‐MICs) of antibiotics. In this study, two multidrug‐resistant K. quasipneumoniae subsp. similipneumoniae isolates were identified, one of which was clinical, and the other was isolated from freshwater. The MICs of the antibiotics meropenem, chloramphenicol, ciprofloxacin, and kanamycin were determined for these isolates. The effects of the sub‐MICs on the virulence and morphological characteristics of the bacteria were investigated in comparison with K. pneumoniae (ATCC 13883). The MICs of meropenem, chloramphenicol, ciprofloxacin, and kanamycin were 0.04, 20, 2, and 8 μg/mL in the clinical isolate; 0.2, 15, 5, and 2 μg/mL in the freshwater isolate; and 0.03, 3, 0.1, and 0.3 μg/mL for K. pneumoniae. The biofilm‐forming ability of K. quasipneumoniae subsp. similipneumoniae isolates decreased with antibiotic sub‐MICs. Siderophore activity increased only with MIC/4 of kanamycin and MIC/2 of chloramphenicol in the clinical isolate (p > 0.05). Furthermore, bacterial morphology and expression of virulence genes were affected differently by the sub‐MICs. This study showed that biofilm formation decreased and that the changes in bacterial morphology and expression of virulence genes were very different in the presence of 1/2 and 1/4 sub‐MIC antibiotics.
Pan‐Cancer Analysis Reveals PRIM2 as a Potential Biomarker for Diagnosis, Prognosis, and Immunomodulatory
Authors: Zhang Xi , Zhang Yuanyu , Liu Leheng , Gong Zheng , Zhou Kecheng
Published: November 2024

Purpose: DNA primase subunit 2 (PRIM2) is a component of the DNA polymerase α‐primase complex involved in DNA replication. Previous studies have implicated PRIM2 in cancer progression, but a comprehensive pan‐cancer analysis is lacking. Here, we systematically analyzed PRIM2 across various cancer types to elucidate its potential role in cancer biology.

Methods: The expression data of PRIM2 was obtained from The Cancer Genome Atlas (TCGA) and Genotype‐Tissue Expression Project (GTEx) databases. A range of bioinformatics tools were employed to analyze the expression of PRIM2 with the correlation of clinical data, diagnosis, prognosis, subtypes, immunomodulatory, and drug sensitivity. Further validation experiments were performed in HT‐29 and HepG2 cell lines.

Results: PRIM2 expression was elevated in most tumor tissues, indicating its potential diagnostic value. Elevated PRIM2 levels affected prognosis and survival and varied with clinical status. Mutations and methylation events drove the aberrant expression of PRIM2 in various cancers. Furthermore, PRIM2 was linked to key immunoregulatory genes such as PD‐L1 and infiltration of Th2 cells in tumor tissues. Our findings suggested that PRIM2 is correlated to immunotherapy and may be sensitive to specific small molecule PLK1 inhibitors. Knocking down PRIM2 in HT‐29 and HepG2 cell lines reduced their proliferation, migration, invasion, and epithelial‐mesenchymal transition.

Conclusion: This research highlights the potential of PRIM2 as a biomarker for cancer diagnosis and prognosis, and as a target for immunomodulatory therapy, offering valuable insights for clinical applications.
Exploring the Link Between the Gut Mycobiome and Neurological Disorders
Authors: Yetgin Ali
Published: November 2024

Long‐standing theories link genetics, environmental factors, and microbial dysbiosis as causes of neurological diseases. Even though the role of the human gut mycobiome in these disorders has drawn a lot of attention, recent research has begun to shed light on another microbial component, the gut mycobiome, and its potential involvement in neurological diseases. In an effort to comprehend the connection between the gut mycobiome and neurological illnesses, this exploratory investigation concentrates on the complex interactions between fungal populations and the central nervous system. This study investigates the mechanisms through which fungus species and their metabolites impact brain health and disease progression by evaluating the body of literature and recent discoveries. It also investigates how the gut mycobiome affects the blood–brain barrier’s integrity, the control of neurotransmitters, and immune system modulation. The outcomes provide new information on therapeutic approaches that target the fungal component of the gut microbiota and imply that changes in the composition and function of the gut mycobiome contribute to the onset and progression of neurological diseases. It is necessary to conduct more studies to clarify the precise mechanisms underpinning the gut mycobiome’s impact on neurological illnesses and to investigate the possibility of new diagnostic and therapeutic approaches based on fungus modulation.
Supplementary Table S2 from KHSRP Stabilizes m6A-Modified Transcripts to Activate FAK Signaling and Promote Pancreatic Ductal Adenocarcinoma Progression
Authors: Xu Zilan , Zhou Yifan , Liu Shaoqiu , Zhao Hongzhe , Chen Ziming , Li Rui , Li Mei , Huang Xudong , Deng Shuang , Zeng Lingxing , Zhao Sihan , Zhang Shaoping , He Xiaowei , Liu Ji , Xue Chunling , Bai Ruihong , Zhuang Lisha , Zhou Quanbo , Chen Rufu , Lin Dongxin , Zheng Jian , Zhang Jialiang
Published: November 2024

Supplementary Table S2
Supplementary Table S10 from KHSRP Stabilizes m6A-Modified Transcripts to Activate FAK Signaling and Promote Pancreatic Ductal Adenocarcinoma Progression
Authors: Xu Zilan , Zhou Yifan , Liu Shaoqiu , Zhao Hongzhe , Chen Ziming , Li Rui , Li Mei , Huang Xudong , Deng Shuang , Zeng Lingxing , Zhao Sihan , Zhang Shaoping , He Xiaowei , Liu Ji , Xue Chunling , Bai Ruihong , Zhuang Lisha , Zhou Quanbo , Chen Rufu , Lin Dongxin , Zheng Jian , Zhang Jialiang
Published: November 2024

Supplementary Table S10
Figure S3 from KHSRP Stabilizes m6A-Modified Transcripts to Activate FAK Signaling and Promote Pancreatic Ductal Adenocarcinoma Progression
Authors: Xu Zilan , Zhou Yifan , Liu Shaoqiu , Zhao Hongzhe , Chen Ziming , Li Rui , Li Mei , Huang Xudong , Deng Shuang , Zeng Lingxing , Zhao Sihan , Zhang Shaoping , He Xiaowei , Liu Ji , Xue Chunling , Bai Ruihong , Zhuang Lisha , Zhou Quanbo , Chen Rufu , Lin Dongxin , Zheng Jian , Zhang Jialiang
Published: November 2024

Figure S3 and it's legend
Table S3 from Molecular Characterization and Classification of HER2-Positive Breast Cancer Inform Tailored Therapeutic Strategies
Authors: Li Yu-Wei , Dai Lei-Jie , Wu Xiang-Rong , Zhao Shen , Xu Yu-Zheng , Jin Xi , Xiao Yi , Wang Ying , Lin Cai-Jin , Zhou Yi-Fan , Fu Tong , Yang Wen-Tao , Li Ming , Lv Hong , Chen Siyuan , Grigoriadis Anita , Jiang Yi-Zhou , Ma Ding , Shao Zhi-Ming
Published: November 2024

Table S3
Figure S9 from Targeting BCL2 with Venetoclax Enhances the Efficacy of the KRASG12D Inhibitor MRTX1133 in Pancreatic Cancer
Authors: Becker Jeffrey H. , Metropulos Anastasia E. , Spaulding Christina , Marinelarena Alejandra M. , Shields Mario A. , Principe Daniel R. , Pham Thao D. , Munshi Hidayatullah G.
Published: November 2024

Venetoclax enhances the efficacy of MRTX1133 in 2138-K and 1245-K tumors in vivo.
Supplemental Materials and Methods from Molecular Characterization and Classification of HER2-Positive Breast Cancer Inform Tailored Therapeutic Strategies
Authors: Li Yu-Wei , Dai Lei-Jie , Wu Xiang-Rong , Zhao Shen , Xu Yu-Zheng , Jin Xi , Xiao Yi , Wang Ying , Lin Cai-Jin , Zhou Yi-Fan , Fu Tong , Yang Wen-Tao , Li Ming , Lv Hong , Chen Siyuan , Grigoriadis Anita , Jiang Yi-Zhou , Ma Ding , Shao Zhi-Ming
Published: November 2024

Supplemental Materials and Methods
Figure S8 from Targeting BCL2 with Venetoclax Enhances the Efficacy of the KRASG12D Inhibitor MRTX1133 in Pancreatic Cancer
Authors: Becker Jeffrey H. , Metropulos Anastasia E. , Spaulding Christina , Marinelarena Alejandra M. , Shields Mario A. , Principe Daniel R. , Pham Thao D. , Munshi Hidayatullah G.
Published: November 2024

Effect of the combination of MRTX1133 and Venetoclax on the weights of KPC-K tumor-bearing mice.
Figure S6 from Targeting BCL2 with Venetoclax Enhances the Efficacy of the KRASG12D Inhibitor MRTX1133 in Pancreatic Cancer
Authors: Becker Jeffrey H. , Metropulos Anastasia E. , Spaulding Christina , Marinelarena Alejandra M. , Shields Mario A. , Principe Daniel R. , Pham Thao D. , Munshi Hidayatullah G.
Published: November 2024

2138-K and 3213-K cells grow rapidly in vivo.
Figure S5 from Targeting BCL2 with Venetoclax Enhances the Efficacy of the KRASG12D Inhibitor MRTX1133 in Pancreatic Cancer
Authors: Becker Jeffrey H. , Metropulos Anastasia E. , Spaulding Christina , Marinelarena Alejandra M. , Shields Mario A. , Principe Daniel R. , Pham Thao D. , Munshi Hidayatullah G.
Published: November 2024

Venetoclax enhances the efficacy of MRTX1133 in 2138 and 1245 tumors in vivo.
Figure S2 from Molecular Characterization and Classification of HER2-Positive Breast Cancer Inform Tailored Therapeutic Strategies
Authors: Li Yu-Wei , Dai Lei-Jie , Wu Xiang-Rong , Zhao Shen , Xu Yu-Zheng , Jin Xi , Xiao Yi , Wang Ying , Lin Cai-Jin , Zhou Yi-Fan , Fu Tong , Yang Wen-Tao , Li Ming , Lv Hong , Chen Siyuan , Grigoriadis Anita , Jiang Yi-Zhou , Ma Ding , Shao Zhi-Ming
Published: November 2024

Figure S2
Supplementary Table 5 from CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression
Authors: Lewis Michael W. , King Caitlin M. , Wisniewska Kamila , Regner Matthew J. , Coffey Alisha , Kelly Michael R. , Mendez-Giraldez Raul , Davis Eric S. , Phanstiel Douglas H. , Franco Hector L.
Published: November 2024

List of direct and indirect target genes for each super-enhancer based on HiC determined connections
Figure S8 from FOXP4 Is a Direct YAP1 Target That Promotes Gastric Cancer Stemness and Drives Metastasis
Authors: Liu Xiaoli , Chen Bonan , Xie Fuda , Wong Kit Yee , Cheung Alvin H.K. , Zhang Jinglin , Wu Qian , Fang Canbin , Hu Jintao , Wang Shouyu , Xu Dazhi , Chen Jianwu , Wang Yuzhi , Wong Chi Chun , Chen Huarong , Wu William K.K. , Yu Jun , Chan Michael W.Y. , Tsang Chi Man , Lo Kwok Wai , Tse Gary M.K. , To Ka-Fai , Kang Wei
Published: November 2024

Supplementary Figure S8
Supplementary Table 1 from CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression
Authors: Lewis Michael W. , King Caitlin M. , Wisniewska Kamila , Regner Matthew J. , Coffey Alisha , Kelly Michael R. , Mendez-Giraldez Raul , Davis Eric S. , Phanstiel Douglas H. , Franco Hector L.
Published: November 2024

List of oligos and plasmids
Figure S7 from FOXP4 Is a Direct YAP1 Target That Promotes Gastric Cancer Stemness and Drives Metastasis
Authors: Liu Xiaoli , Chen Bonan , Xie Fuda , Wong Kit Yee , Cheung Alvin H.K. , Zhang Jinglin , Wu Qian , Fang Canbin , Hu Jintao , Wang Shouyu , Xu Dazhi , Chen Jianwu , Wang Yuzhi , Wong Chi Chun , Chen Huarong , Wu William K.K. , Yu Jun , Chan Michael W.Y. , Tsang Chi Man , Lo Kwok Wai , Tse Gary M.K. , To Ka-Fai , Kang Wei
Published: November 2024

Supplementary Figure S7
Supplementary Figures from CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression
Authors: Lewis Michael W. , King Caitlin M. , Wisniewska Kamila , Regner Matthew J. , Coffey Alisha , Kelly Michael R. , Mendez-Giraldez Raul , Davis Eric S. , Phanstiel Douglas H. , Franco Hector L.
Published: November 2024

Single PDF containing all supplementary figures
Figure S3 from FOXP4 Is a Direct YAP1 Target That Promotes Gastric Cancer Stemness and Drives Metastasis
Authors: Liu Xiaoli , Chen Bonan , Xie Fuda , Wong Kit Yee , Cheung Alvin H.K. , Zhang Jinglin , Wu Qian , Fang Canbin , Hu Jintao , Wang Shouyu , Xu Dazhi , Chen Jianwu , Wang Yuzhi , Wong Chi Chun , Chen Huarong , Wu William K.K. , Yu Jun , Chan Michael W.Y. , Tsang Chi Man , Lo Kwok Wai , Tse Gary M.K. , To Ka-Fai , Kang Wei
Published: November 2024

Supplementary Figure S3
Supplementary Data from Targeting Catechol-O-Methyltransferase Induces Mitochondrial Dysfunction and Enhances the Efficacy of Radiotherapy in Glioma
Authors: Jiao Meng , Pirozzi Christopher J. , Yu Chen , Bao Xuhui , Hu Mengjie , Pan Dong , Littleton Sejiro , Reynolds Nathan , Saban Daniel R. , Li Fang , Li Chuan-Yuan
Published: November 2024

Supplementary figures and tables
Figure S11 from FOXP4 Is a Direct YAP1 Target That Promotes Gastric Cancer Stemness and Drives Metastasis
Authors: Liu Xiaoli , Chen Bonan , Xie Fuda , Wong Kit Yee , Cheung Alvin H.K. , Zhang Jinglin , Wu Qian , Fang Canbin , Hu Jintao , Wang Shouyu , Xu Dazhi , Chen Jianwu , Wang Yuzhi , Wong Chi Chun , Chen Huarong , Wu William K.K. , Yu Jun , Chan Michael W.Y. , Tsang Chi Man , Lo Kwok Wai , Tse Gary M.K. , To Ka-Fai , Kang Wei
Published: November 2024

Supplementary Figure S11
Figure S1-S12 from H3K18 Lactylation Potentiates Immune Escape of Non–Small Cell Lung Cancer
Authors: Zhang Cai , Zhou Lijie , Zhang Mingyuan , Du Yue , Li Cai , Ren Huijun , Zheng Lu
Published: November 2024

Supplementary Figures
Data from The Genomic Landscape of Benign and Malignant Thyroid Tumors from Individuals Carrying Germline PTEN Variants Is Distinct from Sporadic Thyroid Cancers
Authors: Plitt Gilman , Brewer Takae , Yehia Lamis , Rabinowitz Laura , Griffith Christopher C. , Eng Charis
Published: November 2024

Abstract
Patients with PTEN hamartoma tumor syndrome (PHTS), a molecular diagnosis for those carrying germline PTEN pathogenic variants, have a high prevalence of benign and malignant thyroid disease. Characterizing the genomic landscape in PHTS thyroid tumors could provide insights into malignant potential and tumor progression to help optimize diagnosis, surveillance, and treatment in this population. To reveal the somatic alterations in PHTS-associated thyroid tumors, we conducted exome sequencing on 58 thyroid tumors (28 cancers, 30 benign nodules) from 19 patients with PHTS. A control cohort of 447 sporadic papillary thyroid cancers (PTC) from The Cancer Genome Atlas was used for comparison. PHTS-associated thyroid tumors had a unique genomic landscape in the setting of a pathogenic germline PTEN mutation, when compared with the general population. PHTS-associated thyroid tumors demonstrated a high frequency of second-hit somatic PTEN alterations, including variants and loss-of-heterozygosity events. Second-hit somatic PTEN alterations were more prevalent in PHTS-associated PTC than sporadic PTC (65.2% vs. 0.067%), occurring frequently in PHTS-associated follicular thyroid cancer (100%) and benign follicular nodules (90%). PHTS-associated PTC additionally harbored somatic alterations in BRAF, RAS family members, and genes associated with DNA double-stranded break repair, as well as somatic arm-level copy-number variations. Together, these findings suggest that biallelic PTEN alterations may function as foundational mutations in PHTS thyroid tissue, promoting benign growth and increasing potential for malignant transformation through impaired DNA double-stranded break repair and increased genomic instability. The unique genomic landscape of PHTS-associated thyroid tumors carries implications for molecular-targeted therapies for patients.

Significance: Exome sequencing reveals the distinct mutational landscape of PTEN hamartoma tumor syndrome–associated thyroid cancers from sporadic counterparts, providing insights into tumor progression and behavior that could help improve diagnosis, surveillance, and treatment.
Supplementary Figure S6 from Durvalumab ± Tremelimumab + Platinum-Etoposide in Extensive-Stage Small Cell Lung Cancer (CASPIAN): Outcomes by PD-L1 Expression and Tissue Tumor Mutational Burden
Authors: Paz-Ares Luis , Garassino Marina Chiara , Chen Yuanbin , Reinmuth Niels , Hotta Katsuyuki , Poltoratskiy Artem , Trukhin Dmytro , Hochmair Maximilian J. , Özgüroğlu Mustafa , Ji Jun Ho , Statsenko Galina , Conev Nikolay , Bondarenko Igor , Havel Libor , Losonczy György , Xie Mingchao , Lai Zhongwu , Godin-Heymann Nadia , Mann Helen , Jiang Haiyi , Shrestha Yashaswi , Goldman Jonathan W.
Published: November 2024

Subgroup analysis of PFS by tTMB for (A) durvalumab plus tremelimumab plus EP versus EP and (B) durvalumab plus EP versus EP. In each panel, the shaded band shows the confidence interval for the ITT population; circle sizes are proportional to the number of events.
Table 1 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Summary information for main patient cohort used within this study (n = 40).
Supplementary Data from TOP2B Enzymatic Activity on Promoters and Introns Modulates Multiple Oncogenes in Human Gliomas
Authors: Gonzalez-Buendia Edgar , Zhao Junfei , Wang Lu , Mukherjee Subhas , Zhang Daniel , Arrieta Víctor A. , Feldstein Eric , Kane J. Robert , Kang Seong Jae , Lee-Chang Catalina , Mahajan Aayushi , Chen Li , Realubit Ronald , Karan Charles , Magnuson Lisa , Horbinski Craig , Marshall Stacy A. , Sarkaria Jann N. , Mohyeldin Ahmed , Nakano Ichiro , Bansal Mukesh , James Charles D. , Brat Daniel J. , Ahmed Atique , Canoll Peter , Rabadan Raul , Shilatifard Ali , Sonabend Adam M.
Published: November 2024

Figure S1-S11
Supplementary Table 1 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Characteristic data for primary CLL cells from to main 40 patient cohort.
Supplementary Legend from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Supplementary Legend
Supplementary Figure 4 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Supplementary Figure 4: A; Relative changes to surface IgM (sIgM) (GeoMFI) expression for 4 IcICLLe clinical trial patients between baseline and 1-month after initial receipt of ibrutinib treatment. B; Representative immunoblotting confirming presence of BTK within the input lysate of the baseline (BL) and 1-month (1M) treatment samples from a patient recruited to the IcICLLe clinical trial. C; Immunoblotting to illustrate loss of BTK binding to kinobeads through in vivo action of ibrutinib. Kinobead isolation was performed on matched samples for 2 representative patients, comparing the baseline sample to that taken 1-month following commencement of ibrutinib treatment. Kinobead elutions were mixed with loading buffer and separated by SDS-PAGE prior to blotting and probing.
Supplementary Dataset 2 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Intensities for kinases detected from Nanostring experiments involving primary CLL cells.
Figure 3 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Kinobead-MS can detect reprogramming of sIgM signaling induced through exposure to IL4. A, Schematic cartoon illustrating cell conditions/treatments prior to protein lysis and incorporation into the kinobead assay. B, Representative immunoblotting (n = 2) verifying the action of IL4 pretreatment and anti-IgM stimulation in primary CLL cells. Activation of STAT6, SYK, BTK, and ERK1/2 was measured in cells treated for 5 minutes with 20 μg/mL of either control F(ab')2 or anti-IgM F(ab')2 (±24 hours pretreatment at 37°C with 10 ng/mL IL4). IL4 treatment alone was used as comparative control. C, Heatmaps showing relative changes to kinome signature in a group of 5 patients with CLL stimulated with anti-IgM (±overnight pretreatment with IL4). D, Comparison of changes to KEGG pathways (log2 scale) within these 5 patients in response to anti-IgM alone or a combination of IL4 and anti-IgM.
Figure 2 from Kinobead Profiling Reveals Reprogramming of BCR Signaling in Response to Therapy within Primary CLL Cells
Authors: Linley Adam J. , Karydis Laura I. , Mondru Anil K. , D'Avola Annalisa , Al Shmrany Humood , Cicconi Silvia , Griffin Rebecca , Forconi Francesco , Pettitt Andrew R. , Kalakonda Nagesh , Rawstron Andrew C. , Hillmen Peter , Steele Andrew J. , MacEwan David J. , Packham Graham , Prior Ian A. , Slupsky Joseph R.
Published: November 2024

Kinobead profiling of primary CLL cells. A, Schematic of the kinobead approach involving primary CLL cells. Protein lysates were prepared from primary cells from patients with CLL (n = 40) incubated with control F(ab')2 antibody (no stimulation) or anti-IgM. Kinase binding was assessed using Ki-NET beads and MS. B, Heatmap showing responses for signature of 104 kinases illustrating relative changes in kinase binding (log2 fold change vs. control cells) in response to sIgM stimulation for each patient. C, Heatmaps showing signature of 32 kinases for signaler patients. Each patient (columns) was stratified on the basis of either sIgM expression or the proportion of malignant cells capable of iCa2+ flux. D, Graph derived from STRING analysis of the 32-kinase fingerprint, illustrating the KEGG pathways identified by STRING analysis and the number of kinases from the fingerprint that are involved in each pathway. Pathways are ordered on the basis of FDR. E, Graph to show changes in identified KEGG pathways in signaler patients compared with non-signaler patients in response to anti-IgM stimulation. y-axis shows on average change in abundance for detected kinases within each KEGG pathway (Student t test; *, P < 0.05; **, P < 0.01; ***, P < 0.001).