bluuebunny/crossref_metadata_2025 huggingface dataset:
Utility of peripheral blood macrophage factor Apo10 and TKTL1 as markers in distinguishing malignant from benign lung nodules: a protocol for a prospective cohort study in Southern China
Authors: Xie Chuanbo , Huang Qiyu , Liu Yuying
Published: November 2023

Introduction

Lung nodules are one of the most prevalent diseases. Medical imaging methods have a high false positive rate for distinguishing malignant nodules from benign nodules. Therefore, developing new technologies with high accuracy for screening malignant nodules is of great importance for lung nodule surveillance. Use of flow cytometry to detect biomarkers in blood macrophages (epitop detect in macrophages/macrophages) has opened a new era for early and noninvasive diagnosis of cancer. This planned study aims to examine whether the peripheral blood macrophage factors Apo10 and TKTL1 accurately distinguish malignant nodules from benign nodules.

Methods and analyses

We plan to enrol in this study 3825 participants with lung nodules who will attend their annual physical examination at Sun Yat-sen University Cancer Center. Apo10 and TKTL1 levels in all patients will be tested at 60 min after their last meal every 6 months during their 3-year follow-up. Biopsy or surgical pathology results will be collected as the gold standard to assess the accuracy of Apo10 and TKTL1 in distinguishing malignant nodules from benign nodules. The sensitivity, specificity, positive predictive value, negative predictive value and area under the receiving operating characteristic curve will also be evaluated.

Ethics and dissemination

The study is approved by the medical ethics committee of Sun Yat-sen University (SL-G2022-005-02). The results of this study will be disseminated in peer-reviewed publications and presentations at international scientific meetings and will also be disseminated to the participants.

Trial registration number

ChiCTR2300073823; Pre-results.
Association between antibiotics and asthma risk among adults aged over 40 years: a nationally representative retrospective cohort study
Authors: Choi Jiwon , Park Sun Jae , Park Young Jun , Hong Jaeyi , Jeong Seogsong , Chang Jooyoung , Kim Sung Min , Song Jihun , Cho Yoosun , Park Sang Min
Published: November 2023

Introduction

Several studies have reported that exposure to antibiotics can lead to asthma during early childhood. However, the association between antibiotic use and risk of asthma in the adult population remains unclear. This study aimed to investigate the association between antibiotic use and asthma in adults.

Methods

We used data from the National Health Insurance Service (NHIS)-Health Screening Cohort, which included participants aged ≥40 years who had health screening examination data in 2005–2006. A total of 248 961 participants with a mean age of 55.43 years were enrolled in this retrospective cohort study. To evaluate antibiotic exposure from the NHIS database for 5 years (2002–2006), cumulative usage and multiclass prescriptions were identified, respectively. During the follow-up period (2007–2019), 42 452 patients were diagnosed with asthma. A multivariate Cox proportional hazard regression model was used to assess the association between antibiotic use and newly diagnosed asthma.

Results

Participants with antibiotic use for ≥91 days showed a higher risk of asthma (adjusted HR (aHR) 1.84, 95% CI 1.72 to 1.96) compared with participants who did not use antibiotics (n=38 450), with a duration-dependent association (ptrend<0.001). Furthermore, ≥4 antibiotic class user group had an increased risk of asthma (aHR 1.44, 95% CI 1.39 to 1.49) compared with one class of antibiotic use (n=64 698). Also, one class of antibiotic use had a higher risk of asthma (aHR 1.21, 95% CI 1.17 to 1.26) compared with non-users, and it also showed a duration-dependent relationship in all classes, including 1, 2, 3 and ≥4 class group (ptrend<0.001). The duration-response relationship between antibiotic use and increased risk of asthma remained in our sensitivity analyses with the washout and shifting of the index date.

Conclusions

The duration-response pattern observed in antibiotic use and asthma may suggest the implication of proper antibiotic use and management in adults.
PER2 binding to HSP90 enhances immune response against oral squamous cell carcinoma by inhibiting IKK/NF-κB pathway and PD-L1 expression
Authors: Zhang Zhiwei , Sun Deping , Tang Hong , Ren Jie , Yin Shilin , Yang Kai
Published: November 2023

Background

Programmed death-ligand 1 (PD-L1) contributes to the immune escape of tumor cells and is a critical target for antitumor immunotherapy. However, the molecular mechanisms regulating PD-L1 expression remain unclear, hindering the development of effective therapies. Here we investigate the role and molecular mechanism of the core clock gene Period2 (PER2) in regulating PD-L1 expression and its role in the combination therapy of oral squamous cell carcinoma (OSCC).

Methods

Quantitative real-time PCR, western blotting or immunohistochemistry to detect expression of PER2 and PD-L1 in OSCC tissues and cells. Overexpression and knockdown of PER2 detects the function of PER2. Bioinformatics, immunoprecipitation, GST pull-down, CHX chase assay and western blot and strip to detect the mechanism of PER2 regulation for PD-L1. A humanized immune reconstitution subcutaneous xenograft mouse model was established to investigate the combination therapy efficacy.

Results

In OSCC tissues and cells, PER2 expression was reduced and PD-L1 expression was increased, the expression of PER2 was significantly negatively correlated with PD-L1. In vitro and in vivo experiments demonstrated that PER2 inhibited PD-L1 expression and enhanced T-cell-mediated OSCC cell killing by suppressing the IKK/NF-κB pathway. Mechanistically, PER2 binds to heat shock protein 90 (HSP90) through the PAS1 domain and reduces the interaction of HSP90 with inhibitors of kappa B kinase (IKKs), promoting the ubiquitination of IKKα/β and p65 nuclear translocation to inhibit IKK/NF-κB pathway, thereby suppressing PD-L1 expression. In humanized immune reconstitution subcutaneous xenograft mouse model, it was demonstrated that PER2 targeting combined with anti-PD-L1 treatment improved the inhibition of OSCC growth by promoting CD8+T-cell infiltration into the tumor.

Conclusions

Our findings reveal the role and mechanism of PD-L1 regulation by PER2 and support the potential clinical application of PER2 targeting in combination with anti-PD-L1 in OSCC immunotherapy.
Improved lung cancer clinical outcomes in patients with autoimmune rheumatic diseases
Authors: Ghanem Paola , Murray Joseph C , Marrone Kristen A , Scott Susan C , Feliciano Josephine L , Lam Vincent K , Hann Christine L , Ettinger David S , Levy Benjamin P , Forde Patrick M , Shah Ami A , Mecoli Christopher , Brahmer Julie , Cappelli Laura C
Published: November 2023

Purpose

Concomitant autoimmune rheumatic diseases (ARD) can add morbidity and complicate treatment decisions for patients with lung cancer. We evaluated the tumour characteristics at diagnosis and clinical outcomes in lung cancer patients with or without ARD.

Methods

This retrospective cohort study included 10 963 patients with lung cancer, treated at Johns Hopkins. Clinical data including tumour characteristics and outcomes were extracted from the cancer registry. Data on patients’ history of 20 ARD were extracted from the electronic medical record. Logistic regression was used to compare tumour characteristics between those with and without ARD; Kaplan-Meier curves and Cox proportional hazards models were performed to compare survival outcomes.

Results

ARD was present in 3.6% of patients (n=454). The mean age at diagnosis was 69 (SD 10) and 68 (SD 12) in patients with and without ARD (p=0.02). Female sex and smoking history were significantly associated with a history of ARD (OR: 1.75, OR: 1.46, p<0.05). Patients with ARD were more likely to be diagnosed with stage 1 lung cancer (36.8% vs 26.9%, p<0.001) and with smaller tumour size (OR: 0.76, p=0.01), controlling for sex, race and histology. Notably, lung cancer patients with ARD had a significantly prolonged median overall survival (OS) (7.11 years vs 1.7 years, p<0.001), independent of stage.

Conclusion

Patients with ARD and lung cancer had better OS compared with their counterparts, independent of cancer stage and treatments and were less likely to have advanced stage lung cancer at diagnosis. Additional studies are needed to investigate the differential immunological anti-tumour immune activity and genomic variations in patients with and without ARD.
Notes on the type classification of von Neumann algebras
Authors: Sorce Jonathan
Published: November 2023

This paper provides an explanation of the type classification of von Neumann algebras, which has made many appearances in the recent work on entanglement in quantum field theory and quantum gravity. The goal is to bridge a gap in the literature between resources that are too technical for the non-expert reader, and resources that seek to explain the broad intuition of the theory without giving precise definitions. Reading this paper will provide you with: (i) an argument for why “factors” are the fundamental von Neumann algebras that one needs to study; (ii) an intuitive explanation of the type classification of factors in terms of renormalization schemes that turn unnormalizable positive operators into “effective density matrices”; (iii) a mathematical explanation of the different types of renormalization schemes in terms of the allowed traces on a factor; (iv) an intuitive characterization of type I and type II factors in terms of their “standard forms”; and (v) a list of some interesting connections between type classification and modular theory, including the argument for why type III1 factors are believed to be the relevant ones in quantum field theory. None of the material is new, but the pedagogy is different from other sources the author has read; it is most similar in spirit to the recent work on gravity and the crossed product by Chandrasekaran, Longo, Penington, and Witten.
Numerical Study of Shape and Density Effect on Semi-Infinite Metallic Target Under Hypervelocity Impact
Authors: Kumar Kailash , Iqbal M. A. , Gupta P. K.
Published: November 2023

Numerical investigations are conducted to examine the penetration depth of ellipsoid-shaped projectiles into semi-infinite aluminum targets under conditions of hypervelocity impact. These results are then compared against empirical equations developed by various researchers for spherical projectiles. The semi-infinite aluminum target, sized at [Formula: see text][Formula: see text]mm, is composed of Al7075-T651. The projectiles are fashioned from Al-7075-T651, steel, and boron carbide. The projectile’s shape factor was determined using the L/d ratio, specifically for the symmetrical ellipsoidal shape. Employing Ansys Autodyn, a 3-dimensional finite element model (FEM) is created and calibrated using existing experimental findings from the literature. The validation utilized the Johnson–Cook (JC) and Johnson–Holmquist (JH-2) material models for both the targets and projectiles. These validated models are subsequently employed to analyze how the ellipsoid projectile’s shape and density influenced their interaction with the semi-infinite targets. Furthermore, the investigation also encompassed an analysis of the resulting crater shapes generated by the hypervelocity impact of both metallic and nonmetallic projectiles. It is observed that for a definite SF, max[Formula: see text] depth of penetration is observed due to steel project as compared to boron carbide and aluminum projectile. Both the diameter of the crater and the height of the bulge ([Formula: see text] are directly proportional to the impact velocity and density of projectiles, and inversely proportional to SF. However, for a particular material and impact velocity of the projectile, in the case of [Formula: see text], there are no clear-cut observations displayed it seems like a mixed variation.
Attitude Decay, Event Salience, and Emotional Reversal: Chinese Cyber-Nationalism after Pelosi’s Visit to Taiwan
Authors: ZHA YI-RU , JIN JIA-WEI
Published: November 2023

This paper examines the associations between timing, events, and nationalist sentiments among the mainland Chinese Weibo users toward Taiwan following the visit of Speaker Nancy Pelosi of the US House of Representatives on August 2, 2022. Utilizing a dataset of 4,353 Weibo comments and employing a combination of regression and interview analysis, our study has revealed several key findings: (1) Nationalist sentiments have diminished over time, and this can be attributed to an increasing immunity to Taiwan-related topics among netizens, habitual mood control, and the processing of new information. (2) Military action against Taiwanese separatists has the potential to intensify nationalist sentiments among the Chinese public, possibly due to its perceived efficacy in countering threats to the country’s sovereignty. (3) Military action’s positive association with nationalism tends to be amplified if this person is a male user. (4) Nationalist sentiments in response to political actions are more likely to diminish over time. (5) Nationalist sentiments in response to military actions tend to rise more slowly or diminish more quickly among those in the China’s Southeast (i.e., the provinces of Guangdong, Fujian, and Zhejiang). (6) The events after PLA’s military drills around Taiwan have a tendency to dampen nationalism whether people’s expectations for government action are fulfilled or not. This research supports the theories of inoculation, telic hedonism, and information utility in explaining the diminishing of nationalist sentiments among different groups. Furthermore, it validates and extends the EPPM in assessing how events interact with gender and regional factors to incite nationalist sentiments. Finally, this study highlights the potential for integrating reversal theory with Maslow’s theory of need to better understand reversals in nationalist sentiments.
USING SERIAL TRICHOTOMIZATION WITH MULTIPLE RADIOGRAPHIC PARAMETERS TO DIAGNOSE ATLANTOAXIAL INSTABILITY IN PREDISPOSED TOY-BREED DOGS
Authors: Chang Ya-Pei , Chiu Po-Yu , Huang Wei-Hsiang , Hammond Gawain , Chen Hsiang-Ju , Liu I-Hsuan , Liu Chen-Hsuan
Published: November 2023

Objective radiographic measurements for determining atlantoaxial instability (AAI) in dogs have been reported. However, choosing a single optimal parameter among different studies is challenging. This study aimed to identify optimal parameters for AAI in small-breed dogs by simultaneously evaluating the flexed and nonflexed lateral radiographs. Moreover, the potential of using serial trichotomization with multiple parameters was investigated. Radiographs of 10 dogs diagnosed with AAI on magnetic resonance imaging (MRI) were compared with 26 control dogs to select parameters with the area under the curve ≥0.9 or ≤0.1. Parameters with outstanding discrimination included cranial border distance and C1–C2 angle on nonflexed radiographs and dens length on ventrodorsal radiographs. Using cutoff values reflecting 100% sensitivity and 100% specificity, the subject was determined into AAI diagnosed, ruled-out or indeterminate. The accuracy rate was 100% for each of the parameters. However, 31–47% of dogs were classified as indeterminate. Serial trichotomization in the order of dens length, cranial border distance, and C1–C2 angle significantly reduced the proportion of dogs in the uncertainty zone while maintaining accuracy. The established method was tested on 19 new subjects. A similar trend of high accuracy (100%) and small uncertainty zone (5%) was observed in the validation cohort. For certain breeds, serial trichotomization with dens length on the ventrodorsal radiograph and cranial border distance and C1–C2 angle on the nonflexed lateral radiograph showed good potential for determining AAI and identifying dogs in which advanced imaging is indicated for diagnosis.
Investigation of Ductile Point-Contact Yield Strength and Bilinear Reinforced Elastic–Plastic Mechanical Behavior Model
Authors: He Zhifeng , Zhu Haibin , Ma Shaopeng
Published: November 2023

Ductile point-contact structures are widely used in engineering applications, with their yield strength and mechanical behavior directly related to the application safety of relevant engineering structures. The Hertz elastic contact theory can effectively express the mechanical behavior of a point-contact structure at the initial stage of load bearing. However, it cannot be applied when the structure has a characteristic yield. In this study, by analyzing the stress distribution characteristics of a point-contact structure prior to characteristic yield, the maximum contact stress on the contact surface was numerically calculated and summarized. Based on the assumption of simplified bilinear constitutive relation of materials, an elastic–plastic analytical model was derived to characterise the mechanical behavior of ductile point-contact structures before and after yield, with its validity verified using the finite element numerical calculations and experimental method.
Preparation of Mo6+, Gd3+-doped TiO2 nanotube arrays and study of their organization and photocatalytic properties
Authors: Qin Chaoqian , Du Jinghong , Chen Jiaxing , Yang Jiarui , He Shengyang
Published: November 2023

Titanium dioxide nanotube arrays doped with [Formula: see text], [Formula: see text], and [Formula: see text]-[Formula: see text] were prepared by anodic oxidation combined with a two-step electrochemical method. The crystalline structure, surface morphology, light absorption properties, and crystalline transformation process were characterized using XRD, SEM, UV–Vis, DSC, and FT-IR. The results show that [Formula: see text] and [Formula: see text] single doping of TiO2 can promote the transformation of amorphous TiO2 to anatase and inhibit the transformation of anatase phase to rutile, but [Formula: see text]–[Formula: see text] co-doping promotes both phase transformations, and the anatase compositions of the TiO2 heat-treated at 450∘C were all over 91%; The tube diameters of TiO2 nanotubes were all around 60–70 nm; the [Formula: see text] - and [Formula: see text] -doped TiO2 light absorption peaks were all significantly red-shifted, with the most obvious change in the [Formula: see text]–[Formula: see text] co-doping, where the forbidden bandwidth was reduced to 3.01 eV; The degradation rate of pure TiO2 photocatalytic degradation of methylene blue for 8 h was only 41.9%, while the degradation rate of [Formula: see text]–[Formula: see text]co-doped TiO2 was as high as 91.51%; [Formula: see text], [Formula: see text], single doping and co-doping could increase the amount of •OH, •OOH adsorbed on the surface of TiO2, which led to the improvement of catalytic performance.
Tail bounds on the spectral norm of sub-exponential random matrices
Authors: Dai Guozheng , Su Zhonggen , Wang Hanchao
Published: November 2023

Let [Formula: see text] be an [Formula: see text] symmetric random matrix with independent but non-identically distributed entries. The deviation inequalities of the spectral norm of [Formula: see text] with Gaussian entries have been obtained by using the standard concentration of Gaussian measure results. This paper establishes an upper tail bound of the spectral norm of [Formula: see text] with sub-exponential entries. Our method relies upon a crucial ingredient of a novel chaining argument that essentially involves both the particular structure of the sets used for the chaining and the distribution of coordinates of a point on the unit sphere.
The Changing Face of Chapter 11 Bankruptcy: Insights from Recent Trends and Research
Authors: Hotchkiss Edith , Thorburn Karin S. , Wang Wei
Published: November 2023

Several recent trends have reshaped the nature of bargaining in Chapter 11. These include increasingly complex prebankruptcy capital structures, decreasing time in Chapter 11 due to prepacks and prenegotiated plans, growing use of restructuring support agreements (RSAs) and sales of substantially all assets, an increased number of defaulting private equity–owned firms, and an increase in activity of specialized distressed debt investors. These trends have changed the balance of power in favor of senior secured lenders, who further shape the course of out-of-court negotiations. We examine evidence of the impact of these changes on important stakeholders, including creditors and workers.
Impact of Heating Exposure on the Micro-Push-Out Bond Strength of Bioceramic Sealers
Authors: Rodrigues Cândido Lopes Guilherme , Paz Dotto Maria Eduarda , Hideo Nomura Lincon , Peressoni Vieira Schuldt Daniela , Garcia Lucas da Fonseca Roberti , da Silveira Teixeira Cleonice
Published: November 2023

Introduction. The aim of this study was to evaluate the effect of heating of bioceramic and epoxy resin-based sealers on their micro-push-out bond strength (BS) to root canal dentin. Methods. After criterial selection, 30 human teeth were decoronated and 1-mm thick slices (n = 60) were obtained perpendicularly along tooth axis, from cervical and middle root thirds, with a diamond disc attached to a cutting machine. In each slice, three 1.0-mm diameter orifices were made. After rinsing with 17% EDTA and 2.5% NaOCl, each orifice was filled with Bio-C Sealer or BioRoot RCS or AH Plus, according to the manufacturers’ instructions. After filling, half of the slices (n = 30) were heated at 100°C for 1 min, and the other half were kept at room temperature. After 7 days-controlled storage, micro-push-out test was performed in a Universal Testing Machine. Failures were analyzed using a stereomicroscope. Statistical analysis was performed with One-Way ANOVA and post hoc Tukey (α = 5%) tests. Results. AH Plus demonstrated higher BS values after heating (

p
=
0.001

) when compared to nonheated. The other sealers did not show a statistically significant difference (

p
>
0.05

). When heated, the average BS values for AH Plus were higher than for BioRoot RCS and Bio-C Sealer (

p
<
0.001

). Cohesive failure mode was the most frequent, followed by adhesive and mixed ones. Conclusion. Heating provided a higher push-out BS to root dentin for AH Plus and did not influence BioRoot RCS or Bio-C sealer.
Supplementary Table 1 - Gene Expression from Parkin Deficiency Suppresses Antigen Presentation to Promote Tumor Immune Evasion and Immunotherapy Resistance
Authors: Perales-Linares Renzo , Leli Nektaria Maria , Mohei Hesham , Beghi Silvia , Rivera Osvaldo D. , Kostopoulos Nektarios , Giglio Andrea , George Subin S. , Uribe-Herranz Mireia , Costabile Francesca , Pierini Stefano , Pustylnikov Sergei , Skoufos Giorgos , Barash Yoseph , Hatzigeorgiou Artemis G. , Koumenis Constantinos , Maity Amit , Lotze Michael T. , Facciabene Andrea
Published: November 2023

Gene Expression-RNAseq. Summary gene expression data of the individual tumors included in Fig. 5a-c.
Supp. Figure 5 from Parkin Deficiency Suppresses Antigen Presentation to Promote Tumor Immune Evasion and Immunotherapy Resistance
Authors: Perales-Linares Renzo , Leli Nektaria Maria , Mohei Hesham , Beghi Silvia , Rivera Osvaldo D. , Kostopoulos Nektarios , Giglio Andrea , George Subin S. , Uribe-Herranz Mireia , Costabile Francesca , Pierini Stefano , Pustylnikov Sergei , Skoufos Giorgos , Barash Yoseph , Hatzigeorgiou Artemis G. , Koumenis Constantinos , Maity Amit , Lotze Michael T. , Facciabene Andrea
Published: November 2023

Figure S5
Supp. Figure 1 from Parkin Deficiency Suppresses Antigen Presentation to Promote Tumor Immune Evasion and Immunotherapy Resistance
Authors: Perales-Linares Renzo , Leli Nektaria Maria , Mohei Hesham , Beghi Silvia , Rivera Osvaldo D. , Kostopoulos Nektarios , Giglio Andrea , George Subin S. , Uribe-Herranz Mireia , Costabile Francesca , Pierini Stefano , Pustylnikov Sergei , Skoufos Giorgos , Barash Yoseph , Hatzigeorgiou Artemis G. , Koumenis Constantinos , Maity Amit , Lotze Michael T. , Facciabene Andrea
Published: November 2023

Figure S1
Supplementary Tables from Targeting BCL6 in Gastrointestinal Stromal Tumor Promotes p53-Mediated Apoptosis to Enhance the Antitumor Activity of Imatinib
Authors: Zeng Xiangyu , Zhao Fei , Jia Jie , Ma Xianxiong , Jiang Qi , Zhang Ruizhi , Li Chengguo , Wang Tao , Liu Weizhen , Hao Yalan , Tao Kaixiong , Lou Zhenkun , Zhang Peng
Published: November 2023

Supplementary Tables
Supplementary Tables from The IGF2BP3–COPS7B Axis Facilitates mRNA Translation to Drive Colorectal Cancer Progression
Authors: Tang Jing , Wang Shuoshuo , Weng Mingjiao , Guo Qingyu , Ren Lili , He Yan , Cui Zihan , Cong Mingqi , Qin Minglu , Yu Jia , Su Rui , Li Xiaobo
Published: November 2023

Supplementary Tables
Supplementary Figures from Biallelic Dicer1 Mutations in the Gynecologic Tract of Mice Drive Lineage-Specific Development of DICER1 Syndrome–Associated Cancer
Authors: Wang Yemin , Chen Shary Yuting , Ta Monica , Senz Janine , Tao Lan Valerie , Thornton Shelby , Tamvada Nirupama , Yang Winnie , Moscovitz Yana , Li Eunice , Guo Jingjie , Shen Cindy , Douglas J. Maxwell , EI-Naggar Amal M. , Kommoss Felix K.F. , Underhill T. Michael , Singh Naveena , Gilks C. Blake , Morin Gregg B. , Huntsman David G.
Published: November 2023

Supplementary Fig. S1-S11
Supplemental Tables 1 - 12 from Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance
Authors: Cotton Jennifer L. , Estrada Diez Javier , Sagar Vivek , Chen Julie , Piquet Michelle , Alford John , Song Youngchul , Li Xiaoyan , Riester Markus , DiMare Matthew T. , Schumacher Katja , Boulay Gaylor , Sprouffske Kathleen , Fan Lin , Burks Tyler , Mansur Leandra , Wagner Joel , Bhang Hyo-eun C. , Iartchouk Oleg , Reece-Hoyes John , Morris Erick J. , Hammerman Peter S. , Ruddy David A. , Korn Joshua M. , Engelman Jeffrey A. , Niederst Matthew J.
Published: November 2023

Supplemental Tables 1 - 12
Supplemental Figure S7 from Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance
Authors: Cotton Jennifer L. , Estrada Diez Javier , Sagar Vivek , Chen Julie , Piquet Michelle , Alford John , Song Youngchul , Li Xiaoyan , Riester Markus , DiMare Matthew T. , Schumacher Katja , Boulay Gaylor , Sprouffske Kathleen , Fan Lin , Burks Tyler , Mansur Leandra , Wagner Joel , Bhang Hyo-eun C. , Iartchouk Oleg , Reece-Hoyes John , Morris Erick J. , Hammerman Peter S. , Ruddy David A. , Korn Joshua M. , Engelman Jeffrey A. , Niederst Matthew J.
Published: November 2023

Supplemental Figure S7 shows clone family gene signature set expression at drug tolerance.
Table S3 from Matrix Stiffness Triggers Lipid Metabolic Cross-talk between Tumor and Stromal Cells to Mediate Bevacizumab Resistance in Colorectal Cancer Liver Metastases
Authors: Zheng Yannan , Zhou Rui , Cai Jianan , Yang Nanyan , Wen Zhaowei , Zhang Zhihua , Sun Huiying , Huang Genjie , Guan Yijin , Huang Na , Shi Min , Liao Yulin , Bin Jianping , Liao Wangjun
Published: November 2023

Supplementary Table S3. Reagents or Resources
Table S1 from Matrix Stiffness Triggers Lipid Metabolic Cross-talk between Tumor and Stromal Cells to Mediate Bevacizumab Resistance in Colorectal Cancer Liver Metastases
Authors: Zheng Yannan , Zhou Rui , Cai Jianan , Yang Nanyan , Wen Zhaowei , Zhang Zhihua , Sun Huiying , Huang Genjie , Guan Yijin , Huang Na , Shi Min , Liao Yulin , Bin Jianping , Liao Wangjun
Published: November 2023

Supplementary Table S1. Patient Information
Figure S5 from Matrix Stiffness Triggers Lipid Metabolic Cross-talk between Tumor and Stromal Cells to Mediate Bevacizumab Resistance in Colorectal Cancer Liver Metastases
Authors: Zheng Yannan , Zhou Rui , Cai Jianan , Yang Nanyan , Wen Zhaowei , Zhang Zhihua , Sun Huiying , Huang Genjie , Guan Yijin , Huang Na , Shi Min , Liao Yulin , Bin Jianping , Liao Wangjun
Published: November 2023

Figure. S5 Matrix stiffness activates lipolysis in HSCs.
Table S2 from Cross-talk between Myeloid and B Cells Shapes the Distinct Microenvironments of Primary and Secondary Liver Cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: November 2023

Table S2
Figure S8 from Cross-talk between Myeloid and B Cells Shapes the Distinct Microenvironments of Primary and Secondary Liver Cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: November 2023

Figure S8
Figure S7 from Cross-talk between Myeloid and B Cells Shapes the Distinct Microenvironments of Primary and Secondary Liver Cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: November 2023

Figure S7
Figure S11 from Cross-talk between Myeloid and B Cells Shapes the Distinct Microenvironments of Primary and Secondary Liver Cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: November 2023

Figure S11
Figure S10 from Cross-talk between Myeloid and B Cells Shapes the Distinct Microenvironments of Primary and Secondary Liver Cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: November 2023

Figure S10
Data from Genetic Variants That Impact Alternative Polyadenylation in Cancer Represent Candidate Causal Risk Loci
Authors: Li Bin , Cai Yimin , Chen Can , Li Gaoyuan , Zhang Ming , Lu Zequn , Zhang Fuwei , Huang Jinyu , Fan Linyun , Ning Caibo , Li Yanmin , Wang Wenzhuo , Geng Hui , Liu Yizhuo , Chen Shuoni , Li Hanting , Yang Shuhui , Zhang Heng , Tian Wen , Zhu Zhongchao , Xu Bin , Li Heng , Li Haijie , Jin Meng , Wang Xiaoyang , Zhang Shaokai , Liu Jiuyang , Huang Chaoqun , Yang Xiaojun , Wei Yongchang , Zhu Ying , Tian Jianbo , Miao Xiaoping
Published: November 2023

Abstract
Alternative polyadenylation (APA) is emerging as a major mechanism of posttranscriptional regulation. APA can impact the development and progression of cancer, suggesting that the genetic determinants of APA might play an important role in regulating cancer risk. Here, we depicted a pan-cancer atlas of human APA quantitative trait loci (apaQTL), containing approximately 0.7 million apaQTLs across 32 cancer types. Systematic multiomics analyses indicated that cancer apaQTLs could contribute to APA regulation by altering poly(A) motifs, RNA-binding proteins (RBP), and chromatin regulatory elements and were preferentially enriched in genome-wide association studies (GWAS)–identified cancer susceptibility loci. Moreover, apaQTL-related genes (aGene) were broadly related to cancer signaling pathways, high mutational burden, immune infiltration, and drug response, implicating their potential as therapeutic targets. Furthermore, apaQTLs were mapped in Chinese colorectal cancer tumor tissues and then screened for functional apaQTLs associated with colorectal cancer risk in 17,789 cases and 19,951 controls using GWAS-ChIP data, with independent validation in a large-scale population consisting of 6,024 cases and 10,022 controls. A multi-ancestry–associated apaQTL variant rs1020670 with a C>G change in DNM1L was identified, and the G allele contributed to an increased risk of colorectal cancer. Mechanistically, the risk variant promoted aberrant APA and facilitated higher usage of DNM1L proximal poly(A) sites mediated by the RBP CSTF2T, which led to higher expression of DNM1L with a short 3′UTR. This stabilized DNM1L to upregulate its expression, provoking colorectal cancer cell proliferation. Collectively, these findings generate a resource for understanding APA regulation and the genetic basis of human cancers, providing insights into cancer etiology.
Significance:
Cancer risk is mediated by alternative polyadenylation quantitative trait loci, including the rs1020670-G variant that promotes alternative polyadenylation of DNM1L and increases colorectal cancer risk.
Table S3 from Effectiveness and Cost of an Enhanced Mailed Fecal Test Outreach Colorectal Cancer Screening Program: Findings from the PROMPT Stepped-Wedge Trial
Authors: Coronado Gloria D. , Nyongesa Denis B. , Escaron Anne L. , Petrik Amanda F. , Thompson Jamie H. , Smith Dave , Davis Melinda M. , Schneider Jennifer L. , Rivelli Jennifer S. , Laguna Tanya , Leo Michael C.
Published: November 2023

Supplementary Table S3 shows a description (demographic and healthcare use characteristics) of eligible adults in intention-to-treat analysis sample, by study timepoint.
Table S2 from Effectiveness and Cost of an Enhanced Mailed Fecal Test Outreach Colorectal Cancer Screening Program: Findings from the PROMPT Stepped-Wedge Trial
Authors: Coronado Gloria D. , Nyongesa Denis B. , Escaron Anne L. , Petrik Amanda F. , Thompson Jamie H. , Smith Dave , Davis Melinda M. , Schneider Jennifer L. , Rivelli Jennifer S. , Laguna Tanya , Leo Michael C.
Published: November 2023

Supplementary Table S2 shows when each intervention component was delivered, by study year.
Table S1 from Effectiveness and Cost of an Enhanced Mailed Fecal Test Outreach Colorectal Cancer Screening Program: Findings from the PROMPT Stepped-Wedge Trial
Authors: Coronado Gloria D. , Nyongesa Denis B. , Escaron Anne L. , Petrik Amanda F. , Thompson Jamie H. , Smith Dave , Davis Melinda M. , Schneider Jennifer L. , Rivelli Jennifer S. , Laguna Tanya , Leo Michael C.
Published: November 2023

Supplementary Table S1 shows the text used for advance notifications (text messages and live phone calls) and reminders (automated phone calls), in English and Spanish.
Supplementary Figure S1 from Impact of BMI on Prevalence of Dense Breasts by Race and Ethnicity
Authors: Kerlikowske Karla , Bissell Michael C. S. , Sprague Brian L. , Tice Jeffrey A. , Tossas Katherine Y. , Bowles Erin J. A. , Ho Thao-Quyen H. , Keegan Theresa H. M. , Miglioretti Diana L.
Published: November 2023

Supplementary Figure S1. Distribution of breast density within BMI categories by race and ethnicity
Figure S1 from Impact on the Volume of Pathology Reports Before and During the COVID-19 Pandemic in SEER Cancer Registries
Authors: Chtourou Amina , Sanchez Pamela V. , Golden Todd , Chen Huann-Sheng , Schwartz Stephen M. , Wu Xiao-Cheng , Hernandez Brenda Y. , Harrison Jovanka N. , Penberthy Lynne , Negoita Serban
Published: November 2023

Figure S1. Pathology report volume in 2020 compared to the volume of COVID-19 cases by geographic region and month.
1Centers for Disease Control and Prevention. COVID Data Tracker. Atlanta, GA: US Department of Health and Human Services, CDC; 2023, March 27.
Supplemental Table 2 from Cigarette and Alternative Tobacco Product Use among Adult Cancer Survivors Enrolled in 9 ECOG-ACRIN Clinical Trials
Authors: Streck Joanna M. , Lee Ju-Whei , Walter Angela Wangari , Rosen Rachel L. , Gareen Ilana F. , Kircher Sheetal Mehta , Herman Benjamin A. , Carlos Ruth C. , Kumar Shaji , Mayer Ingrid A. , Saba Nabil F. , Fenske Timothy S. , Neal Joel W. , Atkins Michael B. , Hodi F. Stephen , Kyriakopoulos Christos E. , Tempany Clare , Shanafelt Tait D. , Wagner Lynne I. , Land Stephanie R. , Park Elyse R. , Ostroff Jamie S.
Published: November 2023

Supplemental Table 2 shows associations of baseline continuous participant characteristics with past 30-day tobacco product use
Table S1 from Gene–Environment Analyses in a UK Biobank Skin Cancer Cohort Identifies Important SNPs in DNA Repair Genes That May Help Prognosticate Disease Risk
Authors: Jeremian Richie , Xie Pingxing , Fotovati Misha , Lefrançois Philippe , Litvinov Ivan V.
Published: November 2023

Table S1. Selected genes that are involved in DNA repair mechanisms.
Figure S3 from Gene–Environment Analyses in a UK Biobank Skin Cancer Cohort Identifies Important SNPs in DNA Repair Genes That May Help Prognosticate Disease Risk
Authors: Jeremian Richie , Xie Pingxing , Fotovati Misha , Lefrançois Philippe , Litvinov Ivan V.
Published: November 2023

Figure S3. Waterfall plot highlighting SNP-environment interactions in in situ melanoma (M-is).
Relationships were computed using a robust joint interaction test and assessed for significance using the False Discovery Rate (FDR) method. These findings highlight sunlamp use and history of childhood sunburns as major and moderate (respectively) interacting factors with DNA repair genes to mediate the risk of M-is. This figure also highlights POLK and MNAT as critical genes which interact with nearly every demographic, environmental and behavioral variable.
Figure S2 from Gene–Environment Analyses in a UK Biobank Skin Cancer Cohort Identifies Important SNPs in DNA Repair Genes That May Help Prognosticate Disease Risk
Authors: Jeremian Richie , Xie Pingxing , Fotovati Misha , Lefrançois Philippe , Litvinov Ivan V.
Published: November 2023

Figure S2. Waterfall plot highlighting SNP-environment interactions in cutaneous squamous cell carcinoma (cSCC).
Relationships were computed using a robust joint interaction test and assessed for significance using the False Discovery Rate (FDR) method. These findings highlight sunlamp use as a major interacting factor with DNA repair genes to mediate the risk of cSCC. This figure also highlights CHEK2 as a critical gene which interact with sex, ease of tanning, history of childhood sunburns, subjective aging appearance and sunlamp use.
Supplementary Table 3 from Long-term Cancer Survival Trends by Updated Summary Stage
Authors: Forjaz Gonçalo , Ries Lynn , Devasia Theresa P. , Flynn Gretchen , Ruhl Jennifer , Mariotto Angela B.
Published: November 2023

Trends in mortality rates for selected cancers, United States, 1975-2019
Supplementary Table 1 from Long-term Cancer Survival Trends by Updated Summary Stage
Authors: Forjaz Gonçalo , Ries Lynn , Devasia Theresa P. , Flynn Gretchen , Ruhl Jennifer , Mariotto Angela B.
Published: November 2023

Trends in five-year relative survival for selected cancers by long-term summary stage, SEER-8, 1975-2018
Supplementary Table 6 from Lifetime Body Weight Trajectories and Risk of Renal Cell Cancer: A Large U.S. Prospective Cohort Study
Authors: Deng Zhengyi , Hajihosseini Morteza , Moore Justin X. , Khan Saira , Graff Rebecca E. , Bondy Melissa L. , Chung Benjamin I. , Langston Marvin E.
Published: November 2023

Association between weight change and renal cell cancer incidence among participants > 62 years (mean age) at baseline.
Supplementary Table 3 from Lifetime Body Weight Trajectories and Risk of Renal Cell Cancer: A Large U.S. Prospective Cohort Study
Authors: Deng Zhengyi , Hajihosseini Morteza , Moore Justin X. , Khan Saira , Graff Rebecca E. , Bondy Melissa L. , Chung Benjamin I. , Langston Marvin E.
Published: November 2023

Association between weighted years living overweight or obese (WYO) and renal cell cancer incidence stratified by quartile of baseline age.
Supplementary Table 2 from Sources of Disparities in Surveillance Mammography Performance and Risk-Guided Recommendations for Supplemental Breast Imaging: A Simulation Study
Authors: Hubbard Rebecca A. , Pujol Toyya A. , Alhajjar Elie , Edoh Kossi , Martin Melissa L.
Published: November 2023

Supplementary Table 2. Additional descriptive statistics for the Breast Cancer Surveillance Consortium cohort of surveillance mammograms
Supplementary Table S2 from Reproductive Factors in the Risk of Bladder Cancer and Upper Urinary Tract Cancer: The Japan Public Health Center-Based Prospective Study
Authors: Minami Tetsuji , Inoue Manami , Yamaji Taiki , Iwasaki Motoki , Tsugane Shoichiro , Sawada Norie
Published: November 2023

Supplementary Table S2: HRs and 95% CI of UC according to reproductive factors by complete case analyses.
Data from Long-term Cancer Survival Trends by Updated Summary Stage
Authors: Forjaz Gonçalo , Ries Lynn , Devasia Theresa P. , Flynn Gretchen , Ruhl Jennifer , Mariotto Angela B.
Published: November 2023

AbstractBackground:
Stage is the most important prognostic factor for understanding cancer survival trends. Summary stage (SS) classifies cancer based on the extent of spread: In situ, Localized, Regional, or Distant. Continual updating of staging systems poses challenges to stage comparisons over time. We use a consistent summary stage classification and present survival trends for 25 cancer sites using the joinpoint survival (JPSurv) model.
Methods:
We developed a modified summary stage variable, Long-Term Site-Specific Summary Stage, based on as consistent a definition as possible and applied it to a maximum number of diagnosis years, 1975–2019. We estimated trends by stage by applying JPSurv to relative survival data for 25 cancer sites in SEER-8, 1975–2018, followed through December 31, 2019. To help interpret survival trends, we report incidence and mortality trends using the joinpoint model.
Results:
Five-year relative survival improved for nearly all sites and stages. Large improvements were observed for localized pancreatic cancer [4.25 percentage points annually, 2007–2012 (95% confidence interval, 3.40–5.10)], distant skin melanoma [2.15 percentage points annually, 2008–2018 (1.73–2.57)], and localized esophagus cancer [1.18 percentage points annually, 1975–2018 (1.11–1.26)].
Conclusions:
This is the first analysis of survival trends by summary stage for multiple cancer sites. The largest survival increases were seen for cancers with a traditionally poor prognosis and no organized screening, which likely reflects clinical management advances.
Impact:
Our study will be particularly useful for understanding the population-level impact of new treatments and identifying emerging trends in health disparities research.
Supplemental Table S2 from Inhibition of NAD+-Dependent Metabolic Processes Induces Cellular Necrosis and Tumor Regression in Rhabdomyosarcoma Models
Authors: McKay-Corkum Grace B. , Collins Victor J. , Yeung Choh , Ito Takeshi , Issaq Sameer H. , Holland David , Vulikh Ksenia , Zhang Yiping , Lee Unsun , Lei Haiyan , Mendoza Arnulfo , Shern Jack F. , Yohe Marielle E. , Yamamoto Kazutoshi , Wilson Kelli , Ji Jiuping , Karim Baktiar O. , Thomas Craig J. , Krishna Murali C. , Neckers Leonard M. , Heske Christine M.
Published: November 2023

Supplemental Table S2: Dose range testing and IC50 parameters for OT-82 in RMS cell lines
Supplementary Table S7 from Atezolizumab plus Magrolimab, Niraparib, or Tocilizumab versus Atezolizumab Monotherapy in Platinum-Refractory Metastatic Urothelial Carcinoma: A Phase Ib/II Open-Label, Multicenter, Randomized Umbrella Study (MORPHEUS Urothelial Carcinoma)
Authors: Drakaki Alexandra , Powles Thomas , Bamias Aristotelis , Martin-Liberal Juan , Shin Sang Joon , Friedlander Terence , Tosi Diego , Park Chandler , Gomez-Roca Carlos , Joly Lobbedez Florence , Castellano Daniel , Morales-Barrera Rafael , Moreno-Candilejo Irene , Fléchon Aude , Yuen Kobe , Rishipathak Deepali , DuPree Kelly , Young Fiona , Michielin Francesca , Shemesh Colby S. , Steinberg Elizabeth E. , Williams Patrick , Lee Jae Lyun
Published: November 2023

Supplementary Table 7. Summary of serum concentrations and incidence of treatment-emergent antidrug antibodies.
Supplementary Data S13 from Genomic Profiling of Metastatic Castration-Resistant Prostate Cancer Samples Resistant to Androgen Receptor Pathway Inhibitors
Authors: Menssouri Naoual , Poiraudeau Loïc , Helissey Carole , Bigot Ludovic , Sabio Jonathan , Ibrahim Tony , Pobel Cédric , Nicotra Claudio , Ngo-Camus Maud , Lacroix Ludovic , Rouleau Etienne , Tselikas Lambros , Chauchereau Anne , Blanc-Durand Félix , Bernard-Tessier Alice , Patrikidou Anna , Naoun Natacha , Flippot Ronan , Colomba Emeline , Fuerea Alina , Albiges Laurence , Lavaud Pernelle , van de Wiel Paul , den Biezen Eveline , Wesseling-Rozendaal Yvonne , Ponce Santiago , Michiels Stefan , Massard Christophe , Gautheret Daniel , Barlesi Fabrice , André Fabrice , Besse Benjamin , Scoazec Jean-Yves , Friboulet Luc , Fizazi Karim , Loriot Yohann
Published: November 2023

Supplementary data 13 describes the GSEA analysis of resistant samples vs baseline samples from patients with acquired resistance and neuroendocrine features
Supplementary Data S11 from Genomic Profiling of Metastatic Castration-Resistant Prostate Cancer Samples Resistant to Androgen Receptor Pathway Inhibitors
Authors: Menssouri Naoual , Poiraudeau Loïc , Helissey Carole , Bigot Ludovic , Sabio Jonathan , Ibrahim Tony , Pobel Cédric , Nicotra Claudio , Ngo-Camus Maud , Lacroix Ludovic , Rouleau Etienne , Tselikas Lambros , Chauchereau Anne , Blanc-Durand Félix , Bernard-Tessier Alice , Patrikidou Anna , Naoun Natacha , Flippot Ronan , Colomba Emeline , Fuerea Alina , Albiges Laurence , Lavaud Pernelle , van de Wiel Paul , den Biezen Eveline , Wesseling-Rozendaal Yvonne , Ponce Santiago , Michiels Stefan , Massard Christophe , Gautheret Daniel , Barlesi Fabrice , André Fabrice , Besse Benjamin , Scoazec Jean-Yves , Friboulet Luc , Fizazi Karim , Loriot Yohann
Published: November 2023

Supplementary data 11 describes the GSEA analysis of paired biopsies
Supplementary Table S2 from Atezolizumab plus Magrolimab, Niraparib, or Tocilizumab versus Atezolizumab Monotherapy in Platinum-Refractory Metastatic Urothelial Carcinoma: A Phase Ib/II Open-Label, Multicenter, Randomized Umbrella Study (MORPHEUS Urothelial Carcinoma)
Authors: Drakaki Alexandra , Powles Thomas , Bamias Aristotelis , Martin-Liberal Juan , Shin Sang Joon , Friedlander Terence , Tosi Diego , Park Chandler , Gomez-Roca Carlos , Joly Lobbedez Florence , Castellano Daniel , Morales-Barrera Rafael , Moreno-Candilejo Irene , Fléchon Aude , Yuen Kobe , Rishipathak Deepali , DuPree Kelly , Young Fiona , Michielin Francesca , Shemesh Colby S. , Steinberg Elizabeth E. , Williams Patrick , Lee Jae Lyun
Published: November 2023

Supplementary Table 2. Representativeness of Study Participants.
Supplementary Table S4 from Dissecting the Mechanisms Underlying the Cytokine Release Syndrome (CRS) Mediated by T-Cell Bispecific Antibodies
Authors: Leclercq-Cohen Gabrielle , Steinhoff Nathalie , Albertí Servera Llucia , Nassiri Sina , Danilin Sabrina , Piccione Emily , Yángüez Emilio , Hüsser Tamara , Herter Sylvia , Schmeing Stephan , Gerber Petra , Schwalie Petra , Sam Johannes , Briner Stefanie , Jenni Sylvia , Bianchi Roberta , Biehl Marlene , Cremasco Floriana , Apostolopoulou Katerina , Haegel Hélène , Klein Christian , Umaña Pablo , Bacac Marina
Published: November 2023

Supplementary Table S4. Specification of reagents for flow cytometry (In vivo work)
Supplementary Figure S8 from Dissecting the Mechanisms Underlying the Cytokine Release Syndrome (CRS) Mediated by T-Cell Bispecific Antibodies
Authors: Leclercq-Cohen Gabrielle , Steinhoff Nathalie , Albertí Servera Llucia , Nassiri Sina , Danilin Sabrina , Piccione Emily , Yángüez Emilio , Hüsser Tamara , Herter Sylvia , Schmeing Stephan , Gerber Petra , Schwalie Petra , Sam Johannes , Briner Stefanie , Jenni Sylvia , Bianchi Roberta , Biehl Marlene , Cremasco Floriana , Apostolopoulou Katerina , Haegel Hélène , Klein Christian , Umaña Pablo , Bacac Marina
Published: November 2023

Supplementary Figure S8. Single cell RNA-sequencing of whole blood treated with 0.2 μg/mL CD20-TCB was performed using the BD Rhapsody platform.
Supplementary Table S8 from Exercise Training Reduces the Inflammatory Response and Promotes Intestinal Mucosa-Associated Immunity in Lynch Syndrome
Authors: Deng Nan , Reyes-Uribe Laura , Fahrmann Johannes F. , Thoman Whittney S. , Munsell Mark F. , Dennison Jennifer B. , Murage Eunice , Wu Ranran , Hawk Ernest T. , Thirumurthi Selvi , Lynch Patrick M. , Dieli-Conwright Christina M. , Lazar Alexander J. , Jindal Sonali , Chu Khoi , Chelvanambi Manoj , Basen-Engquist Karen , Li Yisheng , Wargo Jennifer A. , McAllister Florencia , Allison James P. , Sharma Padmanee , Sinha Krishna M. , Hanash Samir , Gilchrist Susan C. , Vilar Eduardo
Published: November 2023

Supplementary Table 8. Representativeness of Study Participants