bluuebunny/crossref_metadata_2025 huggingface dataset:
Cone Beam CT Assessment of Bone Width of Upper and Lower Jaws for Dental Implant Placement: An Iraqi Study
Authors: Khazaal Al-Jaboori Aseel S. , Hassan Nuhad A.
Published: April 2023

Background. Implantology focuses on the measurement of bone thickness in both the lower and upper jaws. This study aimed to measure and compare alveolar bone thickness of the upper and lower jaws at single edentate sites and cortical bone thickness of their mesial and distal dentate sites. Methods. Thickness of alveolar bone thickness was measured in 80 upper and 80 lower implant edentate sites and that of buccal and lingual cortical plates of their mesial and distal dentate sites using Cone beam CT. The bone thickness of the edentulous sites was recorded at 3 points (crestal bone, five mm from the crest, and ten mm from the crest), while the bone thickness of the dentate sites was determined at four points (crestal bone, midroot bone, mid of the alveolar bone housing, and apical portion). Results. An increased amount of bone was measured from the crest to the apical portion of the dentate sites on the buccal and lingual sides of both jaws with a highly significant difference detected among all the tested points (

P
<
 
0.0001

). No statistical difference was detected between the means of buccal bone width at the first 3 points, except at point 4 (the apical portion), where the mean of the lower jaw (3.35 ± 0.54) was significantly larger than that of the upper jaw (3.17 ± 0.55) (

P
=
0.04

). Bone width measured in the edentulous sites showed a gradual increase from the crest to the apical portions in both jaws. Conclusion. Bone thickness at the coronal levels is low and susceptible to resorption compared to the apical portions regardless of the dentate state.
Comparison of a New 5% Minoxidil Foam and Rogaine® in the Treatment of Androgenetic Alopecia in Chinese Men: A Randomized, Double‐Blind, Phase III, Equivalence Trial
Authors: Zhou Cheng , Fan Weixin , Zou Jianfeng , Zhang Jianglin , Fang Hong , Lv Zhongfa , Yang Dingquan , Lai Wei , Gao Xinghua , Yang Qinping , Chen Aijun , Lou Jing , Zheng Lili , Zhang Jianzhong
Published: April 2023

Androgenetic alopecia (AGA) is a common cause of hair loss in adults. We aimed to compare the efficacy and safety of topical generic 5% new minoxidil foam (NMF) versus 5% minoxidil Rogaine® foam in male patients with AGA. A randomized, double‐blind, controlled, phase III, equivalence trial in 10 centers in China between December 25, 2019, and June 28, 2021, was performed. In total, 417 men patients (≥18 years) with AGA were randomized to receive 5% NMF (211 patients) or 5% Rogaine® foam (206 patients) 1 g two times daily for 24 weeks. The primary outcome was the changes in nonvellus target area hair counts (TAHC) from baseline to week 24. Equivalence was concluded if the 95% confidence interval (CI) for the treatment difference between the 5% NMF and Rogaine® groups was within (−8.00, 8.00). After 24 weeks of treatment, the mean difference in the change of nonvellus TAHC between the 5% NMF group and the Rogaine® group was −3.85 ± 1.62 hair/cm2 in full‐analysis set (FAS) and −3.96 ± 1.68 hair/cm2 in per‐protocol set (PPS), and the 95% CI of mean difference was (−7.03, −0.67) in FAS and (−7.26, −0.66) in PPS. No significant differences were found between the two groups in hair diameter, the ratio of terminal hair to vellus hair, the global photographic assessment by investigators, and adverse events (all P > 0.05). 5% NMF is as effective as Rogaine® in increasing hair density and hair diameter in AGA patients and was found to be safe. This trial is registered with CTR20191708.
Validity of Machine Learning in Detecting Complicated Appendicitis in a Resource‐Limited Setting: Findings from Vietnam
Authors: Phan-Mai Tuong-Anh , Thai Truc Thanh , Mai Thanh Quoc , Vu Kiet Anh , Mai Cong Chi , Nguyen Dung Anh
Published: April 2023

Background. Complicated appendicitis, a potentially life‐threatening condition, is common. However, the diagnosis of this condition is mainly based on physician’s experiences and advanced diagnostic equipment. This study built and validated machine learning models to facilitate the detection of complicated appendicitis. Methods. A retrospective cohort study was conducted based on medical charts of all patients undergoing a laparoscopic appendectomy at a city hospital during 2016‐2020. The synthetic minority over‐sampling technique (SMOTE) was used to adjust for the imbalance. Multiple classification approaches were used to train and validate models including support vector machine (SVM), decision tree (DT), K‐nearest neighbor (KNN), logistic regression (LR), artificial neural network (ANN), and gradient boosting (GB). Results. Among 1,950 patients included in the data analysis, there were 483 patients identified as having complicated appendicitis (24.8%). Based on data without SMOTE adjustment for imbalance, the accuracy levels and AUCs were high in all models using different parameters, ranging from 0.687 to 0.815. After adjusting for imbalance data using SMOTE, AUC and accuracy levels in the models using imbalance adjusted data were higher. Of these, the GB had all AUC and accuracy values of approximately 0.8 or more in both adjusted and unadjusted data. Conclusions. Machine learning approaches including SVM, DT, logistic, KNN, ANN, and GB have a high level of validity in classifying patients with complicated appendicitis and patients without complicated appendicitis. Among these, GB had the highest level of validity and should be used or further validated. Our study indicates the beneficial potentials of machine learning techniques in a clinical setting in general and in the diagnosis of complicated appendicitis in particular.
An Approximation Method for Variational Inequality with Uncertain Variables
Authors: Li Cunlin , Zhang Hongyu , Yuan Rui , Min Yee Hooi , Yin Tzu-Chien
Published: April 2023

In this paper, a Stieltjes integral approximation method for uncertain variational inequality problem (UVIP) is studied. Firstly, uncertain variables are introduced on the basis of variational inequality. Since the uncertain variables are based on nonadditive measures, there is usually no density function. Secondly, the expected value model of UVIP is established after the expected value is discretized by the Stieltjes integral. Furthermore, a gap function is constructed to transform UVIP into an uncertain constraint optimization problem, and the optimal value of the constraint problem is proved to be the solution of UVIP. Finally, the convergence of solutions of the Stieltjes integral discretization approximation problem is proved.
NT-proBNP Levels and Collateral Circulation Status in Patients with Acute Ischemic Stroke
Authors: Shen Xiaozhu , Zhang Xianxian , Liu Mengqian , Dong Nan , Liao Juan , Zhou Guoqing , Cao Zhiyong , Yu Liqiang , Xu Yiwen , Jiang Yi , Wan Yue , Fang Qi
Published: April 2023

Background and Objectives. Strokes resulting from atrial fibrillation (AF) increase with age. The relationship between N-terminal- (NT-) prohormone brain natriuretic peptide (NT-proBNP) level and National Institutes of Health Stroke Scale (NIHSS) score is not well established. Also, the collateral circulation plays an important role in NHISS scores. In this study, the effects of NT-proBNP on collateralization were assessed in patients with and without AF. Methods. In this study, 326 hospitalized patients with acute anterior circulation ischemic stroke (AACIS) were included. A comparison of the clinical characteristics of those with and without AF was conducted. The Spearman rank correlation was used for the correlation analysis of plasma NT-proBNP level, regional leptomeningeal collateral (rLMC) score, and computed tomography perfusion (CTP) status in the AF and non-AF groups. An analysis of multivariate linear regression was used to determine how plasma NT-proBNP level, rLMC score, and CTP status influenced the score on the NIHSS. Results. There was a greater plasma NT-proBNP level in the AF group compared with the non-AF group, an increased CTP volume (including CTP ischemic volume, CTP infarct core volume, and CTP ischemic penumbra volume (

P
=
0.002

)), higher NIHSS score on admission, and lower rLMC score (

P
<
0.001

for the remaining parameters). A negative correlation exists between plasma NT-proBNP level and rLMC score (

r
=
−
0.156

,

P
=
0.022

), but a positive correlation exists between plasma NT-proBNP level and both CTP ischemic volume and CTP infarct core volume (

r
=
0.148

,

P
=
0.003

) in the AF group, but not in the non-AF group. Multivariate linear regression analysis demonstrated that NT-proBNP, CTP ischemic penumbra volume, and rLMC score were associated with NIHSS score, and NT-proBNP was positively associated with NIHSS scores (95% confidence interval (CI), 0.000-0.002;

P
=
0.004

) in the AF group, whatever in the unadjusted model or adjusted models, but not in the nonlarge artery atherosclerosis (LAA) group. Conclusion. In AACIS patients with AF, NT-proBNP level negatively correlated with collateral status, positively with CTP ischemic volume, and positively with NIHSS score.
The Identification and Clinical Value Evaluation of CYCS Related to Asthma through Bioinformatics Analysis and Functional Experiments
Authors: Li Yan , Li Li , Zhao Hua , Gao Xiwen , Li Shanqun
Published: April 2023

Background. Asthma is one of the most common respiratory diseases and one of the largest burdens of health care resources across the world. This study is aimed at using bioinformatics methods to find effective clinical indicators for asthma and conducting experimental validation. Methods. We downloaded GSE64913 data and performed differentially expressed gene (DEG) screening. Weighted gene coexpression network analysis (WGCNA) on DEGs was applied to identify key module most associated with asthma for protein-protein interaction (PPI) analysis. According to the degree value, ten genes were obtained and subjected to expression analysis and receiver operating characteristic (ROC) analysis. Next, key genes were screened for expression analysis and immunological analysis. Finally, cell counting kit-8 (CCK-8) and qRT-PCR were also conducted to observe the influence of hub gene on cell proliferation and inflammatory cytokines. Results. From the GSE64913 dataset, 711 upregulated and 684 downregulated DEGs were found. In WGCNA, the top 10 genes in the key module were examined by expression analysis in asthma, and CYCS was determined as an asthma-related oncogene with a good predictive ability for the prognosis of asthmatic patients. CYCS is significantly associated with immune cells, such as HHLA2, IDO1, TGFBR1, and CCL18 and promoted the proliferation of asthmatic cells in vitro. Conclusion. CYCS plays an oncogenic role in the pathophysiology of asthma, indicating that this gene may become a novel diagnostic biomarker and promising target of asthma treatment.
Photobiomodulation Therapy for the Symptoms Related to Temporomandibular Joint Disk Displacement
Authors: Regulski Piotr A. , Szopinski Kazimierz T. , Levičnik-Höfferle Špela
Published: April 2023

Pain related to temporomandibular disorders (TMD) is a common problem that can significantly influence a patient’s quality of life. Laser photobiomodulation (PBM) has been reported as a promising method in medicine for wound and bone healing, pain relief, and treatment of the temporomandibular joint (TMJ). Our clinical case aimed to demonstrate the effectivity of PBM using 1064 nm Nd:YAG laser for the treatment of pain and restricted mandible movement in a patient with anterior disk displacement of the left TMJ, using subjective (pain on visual analogue scale - VAS) and objective outcome measures [dynamic magnetic resonance imaging (MRI)]. PBM was performed on the left condyle in four sessions using a 1064 nm Nd:YAG laser with a flat-top handpiece. Results after 10 weeks showed an increase in mouth opening and a painless joint on palpation, with no reported adverse effects. An MRI of the TMJ confirmed the left disk displacement, however, with no signs of inflammation or effusion and with less pronounced disk deformity as compared with the first MRI examination. Use of PBM with Nd:YAG laser may be an efficient method for the management of orofacial pain in patients with acute and chronic TMJ disk displacements and may reduce the recovery time.
Wideband Dual-Polarized Differential-Fed Filtering Microstrip Patch Antenna with High Suppression and Wide Stopband
Authors: Wu Quanwei , Shi Yan , Li Long
Published: April 2023

This paper presents a wideband dual-polarized filtering antenna with high suppression level and wide stopband. In the proposed antenna, the driven patch operates in a TM10 mode with an inherent radiation null caused by a higher mode TM12. Four dual-strip structures connected with the feeding probes are placed below the driven patch to achieve the capacitive coupling, thus resulting in a low-frequency radiation null with a sharp roll-off rate. The introduction of the parasitic patch and strips generates an in-band resonance and two high-frequency radiation nulls, which widens the upper stopband. Four slots are etched on the driven patch to excite the third resonance, thus achieving the wide operation band. The prototype of the proposed antenna is fabricated. With four controllable radiation nulls, the out-of-band suppression levels are above 29 dB in low-frequency band greater than 1 GHz and above 21 dB in high-frequency band up to 7 GHz, respectively. Due to the three in-band resonances, a wide impedance bandwidth of 2.93-3.96 GHz with a fractional band of 30% is obtained. With the rotational symmetry structure driven by differential probes, the proposed dual-polarized antenna has a cross-polarization ratio better than 28 dB, a high polarization isolation above 43 dB, and a good peak gain about 9.9 dBi.
Risky Sexual Behaviour among HIV‐Infected Adults in Sub‐Saharan Africa: A Systematic Review and Meta‐Analysis
Authors: Wondmeneh Temesgen Gebeyehu , Wondmeneh Ruhama Gebeyehu
Published: April 2023

Background. Risky sexual behaviour raises serious public health concerns. The pooled prevalence of risky sexual behaviours among adults living with HIV/AIDS in sub‐Saharan Africa was unknown. This systematic review determined the pooled prevalence of risky sexual behaviours and associated factors among HIV‐infected adults in sub‐Saharan Africa. Methods. International databases such as PubMed, CINAHL, Google Scholar, and African Journals OnLine were systematically searched to identify articles. The Preferred Reporting Items for Systematic Reviews and Meta‐Analysis (PRISMA) guideline was used to conduct the review. All necessary data were extracted independently. Heterogeneity and publication bias were assessed by I‐squared statistics and Egger’s test, respectively. The random‐effects meta‐analysis model was used to estimate the pooled prevalence. The association between predictors and dependent variable was determined by a pooled odds ratio (OR) with a 95% confidence interval (CI). Result. In this study, 3713 articles were retrieved from various databases, and 22 of them were included. The pooled prevalence of risky sexual behaviour in sub‐Saharan Africa was 36.16% (95% CI: 28.36‐44.34) with significant heterogeneity among studies (I2 = 98.86%, p < 0.001). Risky sexual behaviour was significantly associated with the nondisclosure of HIV status (AOR = 1.97, 95% CI: 1.18, 2.76) and alcohol consumption (AOR = 2.29, 95% CI: 1.21, 3.36). Conclusion. A significant percentage of participants engaged in risky sexual behaviour. Risky sexual behaviour was associated with failure to disclose HIV status and alcohol consumption. Healthcare professionals should advise HIV‐positive patients on risk reduction measures like disclosing their HIV status to their sexual partners and avoiding alcohol use in order to promote consistent condom use. PROSPERO Protocol Registration. The protocol for this systematic review and meta‐analysis has been registered (record ID: CRD42020170967, 09/06/2022).
Time and Distance Gaps of Primary-Secondary Crashes Prediction and Analysis Using Random Forests and SHAP Model
Authors: Liu Xinyuan , Tang Jinjun , Gao Fan , Ding Xizhi
Published: April 2023

Secondary crashes (SCs) are typically defined as the crash that occurs within the spatiotemporal boundaries of the impact area of the primary crashes (PCs), which will intensify traffic congestion and induce a series of road safety issues. Predicting and analyzing the time and distance gaps between the SCs and PCs will help to prevent the occurrence of SCs. In this paper, a combined data-driven method of static and dynamic approaches is applied to identify SCs. Then, the random forests (RF) method is implemented to predict the two gaps using temporal, primary crash, roadway, and real-time traffic characteristics data collected from 2016 to 2019 at California interstate freeways. Subsequently, the SHapley Additive explanation (SHAP) approach is employed to interpret the RF outputs. The results show that the traffic volume, speed, lighting, and population are considered the most significant factors in both gaps. Furthermore, the main and interaction effects of factors are also quantified. High volume possibly promotes the time and distance gaps, while low volume inhibits them. And volume affects the distance gap inconsiderably when it falls between 300 and 400 veh/5 min. Traffic conditions with high speed and low volume are strongly associated with short-time and short-distance gaps. Darker surroundings probably accelerate the occurrence of SCs. Moreover, crashes involving the violation categories of improper turns or unsafe lane changes likely result in long time and distance gaps. These results have important implications for proposing traffic management and improving road safety.
Experimental Studies on Mechanical Behavior of TIG and Friction Stir Welded AA5083 -AA7075 Dissimilar Aluminum Alloys
Authors: Goriparthi Veeraiah , Nallu Ramanaiah , Chebolu Rohinikumar , Indupuri Sudhakar , Rudrapati Ramesh
Published: April 2023

Welding is a suitable and better process to manufacture complex objects for aerospace, naval, and automotive structures. Service conditions and complexity in load acting force the manufactures to make joints between dissimilar materials. Thus, there is a need for efficient welding techniques to form sound joints and an understanding of imperfections and their effects. In this study an attempt has been made to study the joining feasibility of dissimilar aluminum alloys by two different welding techniques, namely, tungsten inert gas welding (TIG) and friction stir welding (FSW). Dissimilar AA5083-O and AA7075-T651 aluminum alloys successfully joined by considered welding techniques. Metallurgical and mechanical characteristics of fabricated weld joints are studied at different weld currents (80–120 amp) for TIG and various rotational speeds (800, 1000, 1100, 1200, and 1400 rpm) with constant traverse speed for FSW. Weld joints made by FSW exhibit superior tensile strength, whereas the joint line microhardness of TIG samples is higher than the FSW ones.
ScoringNet: A Neural Network Based Pruning Criteria for Structured Pruning
Authors: Wang Shuang , Zhang Zhaogong
Published: April 2023

Convolutional neural networks (CNNs) have shown their great power in multiple computer vision tasks. However, many recent works improve their performance by adding more layers and parameters, which lead to computational redundancy in many application scenarios, making it harder to implement on low-end devices. To solve this problem, model pruning methods are proposed, which aim to lower the computational and memory requirements of CNNs. In this paper, we propose ScoringNet, a neural network (NN) based pruning criteria for structured pruning procedure. ScoringNet generates a set of scores for each output channel in a model, which is used to reconstruct a pruned model later in a structured pruning way. ScoringNet can also use the gradient information to generate better scores, making the pruned model perform better. By using NNs, there are fewer hyperparameters, making it easier to implement. Experiment results demonstrate that the proposed ScoringNet can outperform or achieve competitive results compared to many state-of-the-art methods in both postpruning and pruning-at-initialization setups.
The Driving Path of China’s Urban Resilience Enhancement in the Digital Economy Era
Authors: Tang Liang , Jiang Haifeng , Zhang Zhenling , Hou Shanshan , Liu Bo
Published: April 2023

Promoting the development of China’s digital economy and the level of urban disaster reduction and governance is of great significance for accelerating the improvement of China’s urban resilience and promoting the coordinated development of regional cities. This paper analyzed the spatial and temporal distribution characteristics and driving paths of urban resilience in 31 Chinese provinces, autonomous regions, and municipalities directly under the central government and proposed relevant measures to promote urban resilience. First, the urban resilience evaluation system was constructed and the entropy value method was applied to calculate the urban resilience index of each region. Second, the spatial distribution of urban resilience was explored based on the urban resilience index of each region. Finally, a qualitative comparative analysis method was used to explore the driving paths of urban resilience enhancement. The study showed that there were large regional differences in the urban resilience index, with an overall spatial pattern of “good in the east, middle in the center, and low in the west” and an overall trend of gradual increase. There are five configuration paths to generate a high urban resilience index, which can be specifically digital industry-driven path, technology factor-driven path, government input- and talent pool-driven path under market factors, technology factor- and government factor-driven path, and government investment- and infrastructure-driven path under market factors, and it is found that the digital industry-driven path is a more common path of digital economy-driven urban resilience improvement in China. The finding of this study reveals the nature of complex interactions among drivers in the process of urban resilience enhancement in China, which breaks through the limitations of traditional statistical analysis methods and provides a new perspective for the study of urban resilience issues.
Supplementary File 4 from Bayesian Machine Learning Enables Identification of Transcriptional Network Disruptions Associated with Drug-Resistant Prostate Cancer
Authors: Blatti Charles , de la Fuente Jesús , Gao Huanyao , Marín-Goñi Irene , Chen Zikun , Zhao Sihai D. , Tan Winston , Weinshilboum Richard , Kalari Krishna R. , Wang Liewei , Hernaez Mikel
Published: April 2023

Excel file with regulon edges and ChIP-seq enrichment scores for TraRe, GRNboost2 and ARACNE-AP
Supplementary File 3 from Bayesian Machine Learning Enables Identification of Transcriptional Network Disruptions Associated with Drug-Resistant Prostate Cancer
Authors: Blatti Charles , de la Fuente Jesús , Gao Huanyao , Marín-Goñi Irene , Chen Zikun , Zhao Sihai D. , Tan Winston , Weinshilboum Richard , Kalari Krishna R. , Wang Liewei , Hernaez Mikel
Published: April 2023

Supplementary File 3: Excel file with Supplementary tables S6 - S9
Table S4 from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Authors: Yao Lijun , Wang Julia T. , Jayasinghe Reyka G. , O'Neal Julie , Tsai Chia-Feng , Rettig Michael P. , Song Yizhe , Liu Ruiyang , Zhao Yanyan , Ibrahim Omar M. , Fiala Mark A. , Fortier Julie M. , Chen Siqi , Gehrs Leah , Rodrigues Fernanda Martins , Wendl Michael C. , Kohnen Daniel , Shinkle Andrew , Cao Song , Foltz Steven M. , Zhou Daniel Cui , Storrs Erik , Wyczalkowski Matthew A. , Mani Smrithi , Goldsmith Scott R. , Zhu Ying , Hamilton Mark , Liu Tao , Chen Feng , Vij Ravi , Ding Li , DiPersio John F.
Published: April 2023

NetMHC analysis output for tissue-specific intracellular genes. Only peptides identified as strong binders (% rank <0.5) are shown. Detailed explanation of each column can be found here: http://www.cbs.dtu.dk/services/NetMHC/output.php.
Suppl video 1 from Neutrophil Conversion to a Tumor-Killing Phenotype Underpins Effective Microbial Therapy
Authors: Yam Andrew O. , Bailey Jacqueline , Lin Francis , Jakovija Arnolda , Youlten Scott E. , Counoupas Claudio , Gunzer Matthias , Bald Tobias , Woodruff Trent M. , Triccas James A. , Goldstein Leonard D. , Gallego-Ortega David , Grey Shane T. , Chtanova Tatyana
Published: April 2023

Neutrophil migration before and after microbial bioparticle treatment.
Supplementary Table S1-19 from Germline Cancer Gene Expression Quantitative Trait Loci Are Associated with Local and Global Tumor Mutations
Authors: Liu Yuxi , Gusev Alexander , Kraft Peter
Published: April 2023

Supplementary Table S1-19
Table S9 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S9: Results of ATAC-seq of primary and TONSL-immortalized cells.
Table S3 from Dysregulation of Mitochondrial Translation Caused by CBFB Deficiency Cooperates with Mutant PIK3CA and Is a Vulnerability in Breast Cancer
Authors: Malik Navdeep , Kim Young-Im , Yan Hualong , Tseng Yu-Chou , du Bois Wendy , Ayaz Gamze , Tran Andy D. , Vera-Ramirez Laura , Yang Howard , Michalowski Aleksandra M. , Kruhlak Michael , Lee Maxwell , Hunter Kent W. , Huang Jing
Published: April 2023

This is supplementary Table 3.
Table S2 from Dysregulation of Mitochondrial Translation Caused by CBFB Deficiency Cooperates with Mutant PIK3CA and Is a Vulnerability in Breast Cancer
Authors: Malik Navdeep , Kim Young-Im , Yan Hualong , Tseng Yu-Chou , du Bois Wendy , Ayaz Gamze , Tran Andy D. , Vera-Ramirez Laura , Yang Howard , Michalowski Aleksandra M. , Kruhlak Michael , Lee Maxwell , Hunter Kent W. , Huang Jing
Published: April 2023

This is supplementary Table 2.
Table S2 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S2: Gene expression differences between mature luminal and luminal progenitor cells of the breast. Data are from 15 samples, five each from women of European, African and Latina ancestry.
Table S15 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S15: List of genes differentially expressed upon TONSL overexpression in primary cells with genes differentially expressed in TMD-436 upon TONSL knockdown. Fold changes in gene expression are indicated.
Supplementary Data from Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases
Authors: Wood Colin S. , Pennel Kathryn A.F. , Leslie Holly , Legrini Assya , Cameron Andrew J. , Melissourgou-Syka Lydia , Quinn Jean A. , van Wyk Hester C. , Hay Jennifer , Roseweir Antonia K. , Nixon Colin , Roxburgh Campbell S.D. , McMillan Donald C. , Biankin Andrew V. , Sansom Owen J. , Horgan Paul G. , Edwards Joanne , Steele Colin W. , Jamieson Nigel B.
Published: April 2023

All supplementary figures and supplementary tables 1 and 2 from the manuscript
Table S10 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S10: Results of RNA-seq analysis of primary and TONSL-immortalized cells. Fold differences in expression are shown.
Table S1 from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Table S1: Gene expression differences between primary and hTERT-immortalized breast epithelial cell lines.
Data from TONSL Is an Immortalizing Oncogene and a Therapeutic Target in Breast Cancer
Authors: Khatpe Aditi S. , Dirks Rebecca , Bhat-Nakshatri Poornima , Mang Henry , Batic Katie , Swiezy Sarah , Olson Jacob , Rao Xi , Wang Yue , Tanaka Hiromi , Liu Sheng , Wan Jun , Chen Duojiao , Liu Yunlong , Fang Fang , Althouse Sandra , Hulsey Emily , Granatir Maggie M. , Addison Rebekah , Temm Constance J. , Sandusky George , Lee-Gosselin Audrey , Nephew Kenneth , Miller Kathy D. , Nakshatri Harikrishna
Published: April 2023

Abstract
Study of genomic aberrations leading to immortalization of epithelial cells has been technically challenging due to the lack of isogenic models. To address this, we used healthy primary breast luminal epithelial cells of different genetic ancestry and their hTERT-immortalized counterparts to identify transcriptomic changes associated with immortalization. Elevated expression of TONSL (Tonsoku-like, DNA repair protein) was identified as one of the earliest events during immortalization. TONSL, which is located on chromosome 8q24.3, was found to be amplified in approximately 20% of breast cancers. TONSL alone immortalized primary breast epithelial cells and increased telomerase activity, but overexpression was insufficient for neoplastic transformation. However, TONSL-immortalized primary cells overexpressing defined oncogenes generated estrogen receptor–positive adenocarcinomas in mice. Analysis of a breast tumor microarray with approximately 600 tumors revealed poor overall and progression-free survival of patients with TONSL-overexpressing tumors. TONSL increased chromatin accessibility to pro-oncogenic transcription factors, including NF-κB and limited access to the tumor-suppressor p53. TONSL overexpression resulted in significant changes in the expression of genes associated with DNA repair hubs, including upregulation of several genes in the homologous recombination (HR) and Fanconi anemia pathways. Consistent with these results, TONSL-overexpressing primary cells exhibited upregulated DNA repair via HR. Moreover, TONSL was essential for growth of TONSL-amplified breast cancer cell lines in vivo, and these cells were sensitive to TONSL–FACT complex inhibitor CBL0137. Together, these findings identify TONSL as a regulator of epithelial cell immortalization to facilitate cancer initiation and as a target for breast cancer therapy.
Significance:
The chr.8q24.3 amplicon-resident gene TONSL is upregulated during the initial steps of tumorigenesis to support neoplastic transformation by increasing DNA repair and represents a potential therapeutic target for treating breast cancer.
Data from Active remodeling of capillary endothelium via cancer cell-derived MMP9 promotes metastatic brain colonization
Authors: Karreman Matthia A. , Bauer Alexander T. , Solecki Gergely , Berghoff Anna S. , Mayer Chanté D. , Frey Katharina , Hebach Nils , Feinauer Manuel J. , Schieber Nicole L. , Tehranian Cedric , Mercier Luc , Singhal Mahak , Venkataramani Varun , Schubert Marc C. , Hinze Daniel , Hölzel Michael , Helfrich Iris , Schadendorf Dirk , Schneider Stefan W. , Westphal Dana , Augustin Hellmut G. , Goetz Jacky G. , Schwab Yannick , Wick Wolfgang , Winkler Frank
Published: April 2023

Abstract
Crossing the blood-brain barrier is a crucial, rate-limiting step of brain metastasis. Understanding of the mechanisms of cancer cell extravasation from brain microcapillaries is limited as the underlying cellular and molecular processes cannot be adequately investigated using in vitro models and end-point in vivo experiments. Using ultrastructural and functional imaging, we demonstrate that dynamic changes of activated brain microcapillaries promote the mandatory first steps of brain colonization. Successful extravasation of arrested cancer cells occurred when adjacent capillary endothelial cells (ECs) entered into a distinct remodeling process. After extravasation, capillary loops were formed, which was characteristic of aggressive metastatic growth. Upon cancer cell arrest in brain microcapillaries, matrix-metalloprotease 9 (MMP9) was expressed. Inhibition of MMP2/9 and genetic perturbation of MMP9 in cancer cells, but not the host, reduced EC projections, extravasation, and brain metastasis outgrowth. These findings establish an active role of ECs in the process of cancer cell extravasation, facilitated by crosstalk between the two cell types. This extends our understanding of how host cells can contribute to brain metastasis formation and how to prevent it.
Supplementary Table from Systemic Levels of Estrogens and PGE2 Synthesis in Relation to Postmenopausal Breast Cancer Risk
Authors: Kim Sangmi , Campbell Jeff , Yoo Wonsuk , Taylor Jack A. , Sandler Dale P.
Published: April 2023

Supplementary Table from Systemic Levels of Estrogens and PGE2 Synthesis in Relation to Postmenopausal Breast Cancer Risk
Supplementary Table S3 from Phase I Study of the Liposomal Formulation of Eribulin (E7389-LF): Results from the Advanced Gastric Cancer Expansion Cohort
Authors: Shitara Kohei , Hirao Motohiro , Iwasa Satoru , Oshima Takashi , Komatsu Yoshito , Kawazoe Akihito , Sato Yasuyoshi , Hamakawa Takuya , Yonemori Kan , Machida Nozomu , Yuki Satoshi , Suzuki Takuya , Okumura Shiori , Takase Takao , Semba Taro , Zimmermann Bob , Teng Angela , Yamaguchi Kensei
Published: April 2023

Supplementary Table S3 provides a summary of infusion-related reactions during cycle 1, per premedication.
Table S2 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplementary Table S2
Supplementary Figure S4 from Phase I Study of the Liposomal Formulation of Eribulin (E7389-LF): Results from the Advanced Gastric Cancer Expansion Cohort
Authors: Shitara Kohei , Hirao Motohiro , Iwasa Satoru , Oshima Takashi , Komatsu Yoshito , Kawazoe Akihito , Sato Yasuyoshi , Hamakawa Takuya , Yonemori Kan , Machida Nozomu , Yuki Satoshi , Suzuki Takuya , Okumura Shiori , Takase Takao , Semba Taro , Zimmermann Bob , Teng Angela , Yamaguchi Kensei
Published: April 2023

Supplementary Figure S4 shows the median change in biomarker expression from baseline to cycle 2 day 1 in the gastric cancer cohort (A) and all study 114 cohorts (B).
Figure S8 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplemental Fig.S8. Inhibitors of TYK2 (deucravacitinib) and MEK (mirdametinib) act synergistically to reduce proliferation and increase apoptosis in JH-2-002 MPNST cells.
Figure S5 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplemental Fig.S5. Validation of select gene expression changes with TYK2 inhibitor treatment that were identified by qPCR array. JH-2-002 cells were incubated with 40 µMWU-12 or control for 48 hours, and gene expression was analyzed by qPCR for select(A)up-regulated or(B)down-regulated genes.
Supplementary Figure S1 from Phase I Study of the Liposomal Formulation of Eribulin (E7389-LF): Results from the Advanced Gastric Cancer Expansion Cohort
Authors: Shitara Kohei , Hirao Motohiro , Iwasa Satoru , Oshima Takashi , Komatsu Yoshito , Kawazoe Akihito , Sato Yasuyoshi , Hamakawa Takuya , Yonemori Kan , Machida Nozomu , Yuki Satoshi , Suzuki Takuya , Okumura Shiori , Takase Takao , Semba Taro , Zimmermann Bob , Teng Angela , Yamaguchi Kensei
Published: April 2023

Supplementary Figure S1 shows the Kaplan–Meier plots of progression-free survival (A) and overall survival (B) by duration of time from prior anti-PD-1 treatment to start of study drug.
Figure S2 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplemental Fig.S2. TYK2 inhibitors reduce proliferation and induce apoptosis in MPNST-724 cells.
Figure S10 from MEK Inhibition Synergizes with TYK2 Inhibitors in NF1-Associated Malignant Peripheral Nerve Sheath Tumors
Authors: Borcherding Dana C. , Amin Neha V. , He Kevin , Zhang Xiaochun , Lyu Yang , Dehner Carina , Bhatia Himanshi , Gothra Angad , Daud Layla , Ruminski Peter , Pratilas Christine A. , Pollard Kai , Sundby Taylor , Widemann Brigitte C. , Hirbe Angela C.
Published: April 2023

Supplemental Fig.S10. Treatment with deucravacitinib and/or mirdametinib did not decrease mouse body weight over time.
Supplementary fig 3 from Impact of Genomic and Clinical Factors on Outcome of Children ≥18 Months of Age with Stage 3 Neuroblastoma with Unfavorable Histology and without MYCN Amplification: A Children's Oncology Group (COG) Report
Authors: Pinto Navin , Naranjo Arlene , Ding Xiangming , Zhang Fan F. , Hibbitts Emily , Kennedy Rebekah , Tibbetts Rachelle , Wong-Michalak Shannon , Craig David W. , Manojlovic Zarko , Hogarty Michael D. , Kreissman Susan , Bagatell Rochelle , Irwin Meredith S. , Park Julie R. , Asgharzadeh Shahab
Published: April 2023

Supplemental Figure S3 Non-negative Matrix Factorization (NMF) Clustering of Tumor Specimens. (A) Clustering similarity matrix and (B) Silhouette plot of samples by cluster id. (C) Enrichment score for adrenergic (ADRN), mesenchymal (MES), and Schwann cell profile (SCP) gene signatures.
Supplementary fig 2 from Impact of Genomic and Clinical Factors on Outcome of Children ≥18 Months of Age with Stage 3 Neuroblastoma with Unfavorable Histology and without MYCN Amplification: A Children's Oncology Group (COG) Report
Authors: Pinto Navin , Naranjo Arlene , Ding Xiangming , Zhang Fan F. , Hibbitts Emily , Kennedy Rebekah , Tibbetts Rachelle , Wong-Michalak Shannon , Craig David W. , Manojlovic Zarko , Hogarty Michael D. , Kreissman Susan , Bagatell Rochelle , Irwin Meredith S. , Park Julie R. , Asgharzadeh Shahab
Published: April 2023

Supplemental Figure S2 Outcome by Chromosome 9 Status. (A) EFS and (B) OS by Chromosome 9 status
Table S5 from Genomic and Transcriptomic Characteristics of Metastatic Thyroid Cancers with Exceptional Responses to Radioactive Iodine Therapy
Authors: Boucai Laura , Saqcena Mahesh , Kuo Fengshen , Grewal Ravinder K. , Socci Nicholas , Knauf Jeffrey A. , Krishnamoorthy Gnana P. , Ryder Mabel , Ho Alan L. , Ghossein Ronald A. , Morris Luc G.T. , Seshan Venkatraman , Fagin James A.
Published: April 2023

Expression of chr1q genes in BRAFV600E with chr1q gain and copy number quiet tumors in the TCGA RNAseq dataset.
Supplemental Figure 3 from Brief Report: Combination of Osimertinib and Dacomitinib to Mitigate Primary and Acquired Resistance in EGFR-Mutant Lung Adenocarcinomas
Authors: Elkrief Arielle , Makhnin Alex , Moses Khadeja A. , Ahn Linda S. , Preeshagul Isabel R. , Iqbal Afsheen N. , Hayes Sara A. , Plodkowski Andrew J. , Paik Paul K. , Ladanyi Marc , Kris Mark G. , Riely Gregory J. , Michor Franziska , Yu Helena A.
Published: April 2023

Supplemental Figure 3. A. Median progression-free survival and B. Overall survival for patients enrolled in the initial therapy study
Supplemental Figure 2 from Brief Report: Combination of Osimertinib and Dacomitinib to Mitigate Primary and Acquired Resistance in EGFR-Mutant Lung Adenocarcinomas
Authors: Elkrief Arielle , Makhnin Alex , Moses Khadeja A. , Ahn Linda S. , Preeshagul Isabel R. , Iqbal Afsheen N. , Hayes Sara A. , Plodkowski Andrew J. , Paik Paul K. , Ladanyi Marc , Kris Mark G. , Riely Gregory J. , Michor Franziska , Yu Helena A.
Published: April 2023

Supplemental Figure 2. Dose modifications of Dacomitinib +/- Osimertinib (acquired resistance study).
Supplemental Figure 1 from Brief Report: Combination of Osimertinib and Dacomitinib to Mitigate Primary and Acquired Resistance in EGFR-Mutant Lung Adenocarcinomas
Authors: Elkrief Arielle , Makhnin Alex , Moses Khadeja A. , Ahn Linda S. , Preeshagul Isabel R. , Iqbal Afsheen N. , Hayes Sara A. , Plodkowski Andrew J. , Paik Paul K. , Ladanyi Marc , Kris Mark G. , Riely Gregory J. , Michor Franziska , Yu Helena A.
Published: April 2023

Supplemental Figure 1. Dose modifications of Combination Osimertinib and Dacomitinib (initial therapy study).
Table S1 from Genomic and Transcriptomic Characteristics of Metastatic Thyroid Cancers with Exceptional Responses to Radioactive Iodine Therapy
Authors: Boucai Laura , Saqcena Mahesh , Kuo Fengshen , Grewal Ravinder K. , Socci Nicholas , Knauf Jeffrey A. , Krishnamoorthy Gnana P. , Ryder Mabel , Ho Alan L. , Ghossein Ronald A. , Morris Luc G.T. , Seshan Venkatraman , Fagin James A.
Published: April 2023

Clinical characteristics of exceptional responders to radioactive iodine.
Supplemental Table S2 from [18F]FluorThanatrace ([18F]FTT) PET Imaging of PARP-Inhibitor Drug-Target Engagement as a Biomarker of Response in Ovarian Cancer, a Pilot Study
Authors: Pantel Austin R. , Gitto Sarah B. , Makvandi Mehran , Kim Hyoung , Medvedv Sergey , Weeks Joanna K. , Torigian Drew A. , Hsieh Chia-Ju , Ferman Benjamin , Latif Nawar A. , Tanyi Janos L. , Martin Lainie P. , Lanzo Shannon M. , Liu Fang , Cao Quy , Mills Gordon B. , Doot Robert K. , Mankoff David A. , Mach Robert H. , Lin Lilie L. , Simpkins Fiona
Published: April 2023

PARPi treatment and response.
Figure S3 from Genomic and Transcriptomic Characteristics of Metastatic Thyroid Cancers with Exceptional Responses to Radioactive Iodine Therapy
Authors: Boucai Laura , Saqcena Mahesh , Kuo Fengshen , Grewal Ravinder K. , Socci Nicholas , Knauf Jeffrey A. , Krishnamoorthy Gnana P. , Ryder Mabel , Ho Alan L. , Ghossein Ronald A. , Morris Luc G.T. , Seshan Venkatraman , Fagin James A.
Published: April 2023

Supplementary Figure S3.
Supplemental Figure S5 from [18F]FluorThanatrace ([18F]FTT) PET Imaging of PARP-Inhibitor Drug-Target Engagement as a Biomarker of Response in Ovarian Cancer, a Pilot Study
Authors: Pantel Austin R. , Gitto Sarah B. , Makvandi Mehran , Kim Hyoung , Medvedv Sergey , Weeks Joanna K. , Torigian Drew A. , Hsieh Chia-Ju , Ferman Benjamin , Latif Nawar A. , Tanyi Janos L. , Martin Lainie P. , Lanzo Shannon M. , Liu Fang , Cao Quy , Mills Gordon B. , Doot Robert K. , Mankoff David A. , Mach Robert H. , Lin Lilie L. , Simpkins Fiona
Published: April 2023

Clinical response correlates.
Figure S4 from Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases
Authors: Jenkins Sarah , Zhang Wei , Steinberg Seth M. , Nousome Darryl , Houston Nicole , Wu Xiaolin , Armstrong Terri S. , Burton Eric , Smart Dee Dee , Shah Ritu , Peer Cody J. , Mozarsky Brett , Arisa Oluwatobi , Figg William D. , Mendoza Tito R. , Vera Elizabeth , Brastianos Priscilla , Carter Scott , Gilbert Mark R. , Anders Carey K. , Connolly Roisín M. , Tweed Carol , Smith Karen L. , Khan Imran , Lipkowitz Stanley , Steeg Patricia S. , Zimmer Alexandra S.
Published: April 2023

Supplemental Fig. 4. Histogram illustrating ERBB2 relative copy number in plasma and CSF cfDNA samples from 12 patients during their T samples from 12 patients during their Tsamples from 12 patients during their T samples from 12 patients during their T-DM1/TMZ combination therapy.
Supplementary Table S2 from Cell-Free Urine and Plasma DNA Mutational Analysis Predicts Neoadjuvant Chemotherapy Response and Outcome in Patients with Muscle-Invasive Bladder Cancer
Authors: Christensen Emil , Nordentoft Iver , Birkenkamp-Demtröder Karin , Elbæk Sara K. , Lindskrog Sia V. , Taber Ann , Andreasen Tine G. , Strandgaard Trine , Knudsen Michael , Lamy Philippe , Agerbæk Mads , Jensen Jørgen B. , Dyrskjøt Lars
Published: April 2023

Clinical data and follow-up data