bluuebunny/crossref_metadata_2025 huggingface dataset:
A 3D Offline Packing Algorithm considering Cargo Orientation and Stability
Authors: Wang Xianpei , Gong Li , Zhao Haocheng , Li Bowen , Tian Meng
Published: March 2023

The box packing problem can be generalized as placing a batch of cargos with a specified number of different physical characteristics into a specified box. Suppose that a batch of cuboid cargos of different sizes are to be loaded into a batch of boxes of the same type, the cargos have constraints such as orientation and stability. Taking the mean value of the reciprocal of space utilization as the objective function, this paper designs a hybrid genetic algorithm that combines genetic algorithm and tabu search algorithm. Aiming at the information of the packing sequence and the rotating state of the box in the packing scheme, a two-stage real number encoding method and decoding method based on random keys are designed, and a crossover operation based on partial random keys and uniform crossover is designed. In order to convert the solution searched by the optimization algorithm into the actual packing scheme, a heuristic loading algorithm is designed while using the positioning rule of the lower left corner, the space selection rule of the minimum space, and the division and merging rules of the remaining space. In the early stage, the roulette method was used to strengthen the global search ability, and in the later stage, the optimal preservation strategy was used to speed up the algorithm convergence. To make up for the shortcomings of the genetic algorithm’s weak local search ability and slow convergence speed, the tabu search algorithm was used as a mutation operation in the genetic algorithm. The solution in the generation is used as the initial solution of the tabu search algorithm, and the search process is carried out. Finally, this paper tests the proposed hybrid algorithm on 6 groups of weakly heterogeneous and strongly heterogeneous data in the BR dataset. The results prove that the proposed algorithm can reduce the usage of boxes.
Inhibition of miR‐182‐5p Targets FGF9 to Alleviate Osteoarthritis
Authors: Sun Yang , Su Sanmao , Li Mengjun , Deng Ang
Published: March 2023

Background. The pathogenesis of osteoarthritis (OA) is complex and there is no specific drug for treatment. The aim of this study was to identify the molecular targets of OA therapy, focusing on the expression and biological functions of miR‐182‐5p and its target genes in OA. Methods. miR‐182‐5p and fibroblast growth factor 9 (FGF9) were overexpressed or knocked down in IL‐1β‐induced chondrocytes. An OA knee model was performed by surgically destroying the medial meniscus. The gene expression of miR‐182‐5p and FGF9 was calculated. The protein FGF9 was tested by western blotting. Cell counting kit‐8 (CCK8), plate cloning assay, and flow cytometry were conducted to evaluate cell proliferation and apoptosis. The expression of inflammatory factors, tumor necrosis factor‐alpha (TNF‐α), interleukin (IL)‐6, and interleukin (IL)‐8, was evaluated using enzyme‐linked immunosorbent assay (ELISA). Dual‐luciferase reporter assays validated the targeting relationship between miR‐182‐5p and FGF9. Hematoxylin–eosin (HE) and safranin O‐fast Green (S–O) staining were utilized to access cartilage damage. Ki67 expression in cartilage was detected using immunohistochemistry (IHC). TdT‐mediated dUTP nick‐end labeling (TUNEL) assays were used to calculate the apoptosis rate of cartilage. Results. The expression of miR‐182‐5p was upregulated, and FGF9 was downregulated in the IL‐1β‐induced chondrocytes. OA chondrocytes proliferation ability in the miR‐182‐5p mimics group was decreased, and the apoptosis rate and inflammatory factor were increased. Transfection with miR‐182‐5p inhibitor increased the proliferative ability and decreased the apoptosis rate in the IL‐1β‐induced chondrocytes. Transfection with miR‐182‐5p inhibitor reversed IL‐1β‐induced inflammatory factor release in chondrocytes. Targeted binding sites existed between miR‐182‐5p and FGF9. After overexpression of FGF9, the miR‐182‐5p effect on OA chondrocytes was reversed. The hyaline cartilage thickness and proteoglycan content decreased in OA rats, and this was reversed by miR‐182‐5p inhibitor treatment. Conclusions. miR‐182‐5p expression levels were increased in OA chondrocytes and regulated chondrocyte proliferation, apoptosis, and inflammation by targeting FGF9. miR‐182‐5p is a potential gene for OA treatment.
Abundance of Exact Solutions of a Nonlinear Forced (2 + 1)-Dimensional Zakharov–Kuznetsov Equation for Rossby Waves
Authors: renmandula Na , Yin Xiaojun
Published: March 2023

In this paper, an improved tan (φ/2) expansion method is used to solve the exact solution of the nonlinear forced (2 + 1)-dimensional Zakharov–Kuznetsov equation. Firstly, we analyse the research status of the improved tan (φ/2) expansion method. Then, exact solutions of the nonlinear forced (2 + 1)-dimensional Zakharov–Kuznetsov equation are obtained by the perturbation expansion method and the multi-spatiotemporal scale method. It is shown that the improved tan (φ/2) expansion method can obtain more exact solutions, including exact periodic travelling wave solutions, exact solitary wave solutions, and singular kink travelling wave solutions. Finally, the three-dimensional figure and the corresponding plane figure of the corresponding solution are given by using MATLAB to illustrate the influence of external source, dimension variable y, and dispersion coefficient on the propagation of the Rossby wave.
Alterations in Human Hippocampus Subregions across the Lifespan: Reflections on White Matter Structure and Functional Connectivity
Authors: Tan Jianling , Wang Zhongyan , Tang Yi , Tian Yin
Published: March 2023

During growth and aging, the role of the hippocampus in memory depends on its interactions with related brain regions. Particularly, two subregions, anterior hippocampus (aHipp) and posterior hippocampus (pHipp), play different and critical roles in memory processing. However, age-related changes of hippocampus subregions on structure and function are still unclear. Here, we investigated age-related structural and functional characteristics of 106 participants (7-85 years old) in resting state based on fractional anisotropy (FA) and functional connectivity (FC) in aHipp and pHipp in the lifespan. The correlation between FA and FC was also explored to identify the coupling. Furthermore, the Wechsler Abbreviated Scale of Intelligence (WASI) was used to explore the relationship between cognitive ability and hippocampal changes. Results showed that there was functional separation and integration in aHipp and pHipp, and the number of functional connections in pHipp was more than that in aHipp across the lifespan. The age-related FC changes showed four different trends (U-shaped/inverted U-shaped/linear upward/linear downward). And around the age of 40 was a critical period for transformation. Then, FA analyses indicated that all effects of age on the hippocampal structures were nonlinear, and the white matter integrity of pHipp was higher than that of aHipp. In the functional-structural coupling, we found that the age-related FA of the right aHipp (aHipp.R) was negatively related to the FC. Finally, through the WASI, we found that the age-related FA of the left aHipp (aHipp.L) was positively correlated with verbal IQ (VERB) and vocabulary comprehension (VOCAB.T), the FA of aHipp.R was only positively correlated with VERB, and the FA of the left pHipp (pHipp.L) was only positively correlated with VOCAB.T. These FC and FA results supported that age-related normal memory changes were closely related to the hippocampus subregions. We also provided empirical evidence that memory ability was altered with the hippocampus, and its efficiency tended to decline after age 40.
T Cell Subsets and the Expression of Related MicroRNAs in Patients with Recurrent Early Pregnancy Loss
Authors: Yan Ya-ni , Zhang Jian , Yang Na , Chen Chaochao , Li Weiwei
Published: March 2023

This study explored the role of T cell subsets and the expression of related microRNAs in patients with recurrent early pregnancy loss (EPL). Fifty patients with EPL loss between May 2018 and May 2021 were randomly selected as the EPL group, and 50 pregnant women with normal pregnancies or normal delivery outcomes were randomly selected as the control group. The expression levels of T cell subset-related markers and T cell subset-related miRNAs, in addition to the frequencies of T cell subsets, in peripheral blood of the two groups were analyzed. In terms of T cell-related markers, the results showed that the expression levels of the transcriptional regulator TBX-21 (T-bet) and interferon regulatory factor 4 (IRF4) were significantly upregulated in peripheral blood of the patients in the EPL group (

P
<
0.05

), whereas the expression levels of GATA binding protein 3 (GATA3) and glucocorticoid-induced tumor necrosis factor receptor (GITR) were significantly downregulated (

P
<
0.05

). In the EPL group, the expression of mir-106b, mir-93, and mir-25 was upregulated (

1.51
±
0.129

,

1.43
±
0.132

, and

1.73
±
0.156

, respectively) in regulatory T (Treg) cell-related T cell subsets, whereas the expression of miR-146a and miR-155 was downregulated (

P
<
0.05

). The frequencies of Treg and exhausted T cells in the EPL group were significantly lower than those in the control group (

P
<
0.05

). The cell frequencies of T helper 17 (Th17) cells and exhausted Treg cells in the EPL group were significantly higher than those in the control group (

P
<
0.05

). In conclusion, immune cells and associated miRNA profiles can be used as prognostic biomarkers for the treatment of human reproductive disorders, such as EPL.
UAV Mission Path Planning Based on Reinforcement Learning in Dynamic Environment
Authors: Fu Gui , Gao Yang , Liu Liwen , Yang Mingye , Zhu Xinyu
Published: March 2023

With the rapid development of information technology, various products used in information technology are also constantly optimized. Among them, the task and path planning of UAV in the high-end robot industry has always been the focus of relevant researchers. In the high-end robot industry, in addition to the research and development of UAVs, they also continue to learn and strengthen the task and path planning of UAVs. Nowadays, using unmanned aerial vehicles for real-time shooting has become the trend of this era. Drones have brought great convenience to people’s lives, and more and more people are willing to use drones. Based on the above situation, this paper studies the task and path planning of UAV based on reinforcement learning in dynamic environment. In the case of unpredictable scene parameters, reinforcement learning method can be established by value function. Thus, a more reasonable path can be given to realize the reconnaissance and detection of points of interest. MATLAB simulation experiments show that the algorithm can effectively detect targets in complex terrain composed of terrain restricted areas, and return to the designated end point to complete communication. Firstly, the development of unmanned aerial vehicles in various countries and the social status of unmanned aerial vehicles are discussed. By making UAV build threat model and task allocation in dynamic environment. The path planning and optimization of UAV in dynamic environment is studied, and the path planning algorithm and Hungarian algorithm are added. The optimized UAV has the fastest data transmission and calculation speed, while the other two types of UAVs have slower data transmission and calculation speed. In particular, ordinary UAVs also have data transmission failures, resulting in incomplete experimental results. The results show that the optimized UAV system is better in data calculation and transmission, which also shows that the UAV can quickly plan and process flight paths, which is suitable for practical applications.
Prognosis of Biomarker of Alzheimer’s Disease in the Function of the Retina and Secondary Molecular Structure Variation of the Retina and Brain
Authors: Gaber Heba Ahmed , Aly Eman Mohamed , Mohamed Eman Saad , Elfouly Marwa , Talaat Mona Salah , El-Sayed El-Sayed Mahmoud
Published: March 2023

Alzheimer’s disease (AD) is one of the most serious neurodegenerative diseases in the globe. As a result, there is an acute need to discover indications that allow for early disease detection. There is growing scientific data showing the similarities between the eye and other central nervous system components, suggesting that information obtained in ophthalmic research might be valuable in the study and diagnosis of AD. Fifty male albino Wistar rats were separated into five groups: the first group served as control, and the other four groups of animals were administrated aluminium chloride (AlCl3) in a dose of 100 mg/kg body weight (b.w.) for 2, 4, 6, and 8 weeks, respectively. Insights into the function of the retina by electroretinogram (ERG) and the changes thought to have occurred in the molecular structure of the retina and brain using Fourier transform infrared spectroscopy (FTIR) as a result of AD progression induced by AlCl3 in rats were done. Moreover, the measurement of acetylcholinesterase (AchE) was done. After 6 and 8 weeks of AlCl3 injection, there was a substantial reduction (

p
≤
0.05

) in a- and b-wave amplitudes and a significant rise (

p
≤
0.05

) in implicit time compared to controls. A significant elevation (

p
≤
0.05

) of AchE content was observed after 4, 6, and 8 weeks. FTIR revealed a significant increase (

p
≤
0.05

) of β-turn and β-sheet content associated with significant decrease (

p
≤
0.05

) of α-helix content for all groups administrated with AlCl3. Our findings suggest that retinal biomarkers such as ERG of the retina may be used as a screening tool for detection of AD. Secondary structural changes in the proteins of the retina and the brain were similar in AD rats’ model and precede retinal dysfunction.
Downstream Distribution and Postdepositional Mobilization of Cadmium in Alluvial Soils
Authors: Cappuyns Valérie
Published: March 2023

The geochemical signature in alluvial soils is a witness of human activities that took place in a river catchment. Sampling of alluvial soils at depth, in combination with information on sedimentological history and age of samples, may even allow to reconstruct the pollution history of the river basin. In the present study, data on alluvial soils contaminated by a major pollution source were analyzed, with special attention for these soils as an archive for information on the pollution history of a river/river catchment, and on the postdepositional downward migration of metal(loid)s in the alluvial soils. Besides the lateral variation of soil properties and metal(loid) concentrations in the alluvial soils, the vertical distribution of metal(loid)s in soil profiles, as well as the evolution of soil composition in relation to the distance from the river, was addressed. The postdepositional mobilization of Cd was evaluated in a fine-scale sampled alluvial soil core, by comparing data from 137Cs dating with data about the Cd emissions through time and by using leaching tests to calculate the downward migration of Cd. A substantial amount of Cd could leach from superficial to deeper soil layers. Therefore, the low-resolution (cm-scale) sampling of the alluvial soil was not reliable to reconstruct the pollution history of the river catchment, because the elevated chloride-concentrations in the river water increased the downward leaching of Cd through the formation of chloro-complexes. Moreover, the variability in flooding and sedimentation regimes along the river resulted in a heterogeneous composition of the alluvial soils, allowing very large differences in metal(loid) concentrations in places only a few meters apart.
Real-Time SLAM Mobile Robot and Navigation Based on Cloud-Based Implementation
Authors: Ahmed Abdulsaheb Jaafar , Jasim Kadhim Dheyaa
Published: March 2023

This study investigates the feasibility of a mobile robot navigating and discovering its location in unknown environments, followed by the creation of maps of these navigated environments for future use. First, a real mobile robot named TurtleBot3 Burger was used to achieve the simultaneous localization and mapping (SLAM) technique for a complex environment with 12 obstacles of different sizes based on the Rviz library, which is built on the robot operating system (ROS) booted in Linux. It is possible to control the robot and perform this process remotely by using an Amazon Elastic Compute Cloud (Amazon EC2) instance service. Then, the map to the Amazon Simple Storage Service (Amazon S3) cloud was uploaded. This provides a database to display maps and use them at any time for navigation without the need to redraw the map. This map can be accessed by using an authentication process (username and password) supervised by the cloud server administrator. After that, using the serverless image handler (SIH), with the aid of this solution, you can change the size of images, change the color of the background, format them, or add watermarks. Experiment results demonstrated the ability to build a map of an unknown location in a complex environment and use it for navigation tasks on a real mobile robot via remote control. It also showed the success of the process of storing the map for future use and the process of modifying the map using SIH.
Supplemental video 4 from NCI Imaging Data Commons
Authors: Fedorov Andrey , Longabaugh William J.R. , Pot David , Clunie David A. , Pieper Steve , Aerts Hugo J.W.L. , Homeyer André , Lewis Rob , Akbarzadeh Afshin , Bontempi Dennis , Clifford William , Herrmann Markus D. , Höfener Henning , Octaviano Igor , Osborne Chad , Paquette Suzanne , Petts James , Punzo Davide , Reyes Madelyn , Schacherer Daniela P. , Tian Mi , White George , Ziegler Erik , Shmulevich Ilya , Pihl Todd , Wagner Ulrike , Farahani Keyvan , Kikinis Ron
Published: March 2023

Supplemental video 4 from NCI Imaging Data Commons
Data from Development of a Novel Mouse Model of Spontaneous High-Risk HPVE6/E7–Expressing Carcinoma in the Cervicovaginal Tract
Authors: Henkle Talia R. , Lam Brandon , Kung Yu Jui , Lin John , Tseng Ssu-Hsueh , Ferrall Louise , Xing Deyin , Hung Chien-Fu , Wu T.-C.
Published: March 2023

Abstract
Current preclinical models for cervical cancer lack important clinical and pathologic features. To improve upon these models, we aimed to develop a novel, spontaneous HPV16-expressing carcinoma model that captures major aspects of HPV-associated cancer in the female genital tract. This novel preclinical model features (i) expression of HPV oncogenes E6 and E7 in the tumors in female reproductive tract of mice, (ii) spontaneous progression through high-grade squamous intraepithelial lesion (HSIL) to carcinoma, and (iii) flexibility to model cancers from different high-risk HPV genotypes. This was accomplished by injecting plasmids expressing HPV16 E6/E7-luciferase, AKT, c-myc, and Sleeping Beauty transposase into the cervicovaginal tract of C57BL/6 mice followed by electroporation. Cell lines derived from these tumors expressed HPV16 E6/E7 oncogenes, formed tumors in immunocompetent mice, and displayed carcinoma morphology. In all, this novel HPV-associated cervicogenital carcinoma model and HPV16E6/E7–expressing tumor cell line improves upon current HPV16-E6/E7–expressing tumor models. These tumor models may serve as important preclinical models for the development of therapeutic HPV vaccines or novel therapeutic interventions against HPV E6/E7–expressing tumors.
Significance:
This study describes the development of a clinically relevant mouse model of cervicovaginal carcinoma that progresses from high-grade lesions and recapitulates key features of human HPV+ cervical cancer.
Comprehensive DNA Methylation Analysis Indicates That Pancreatic Intraepithelial Neoplasia Lesions Are Acinar-Derived and Epigenetically Primed for Carcinogenesis
Authors: Lo Emily K.W. , Mears Brian M. , Maurer H. Carlo , Idrizi Adrian , Hansen Kasper D. , Thompson Elizabeth D. , Hruban Ralph H. , Olive Kenneth P. , Feinberg Andrew P.
Published: March 2023

Pancreatic ductal adenocarcinoma (PDAC) is believed to arise from the accumulation of a series of somatic mutations and is also frequently associated with pancreatic intraepithelial neoplasia (PanIN) lesions. However, there is still debate as to whether the cell type-of-origin of PanINs and PDACs in humans is acinar or ductal. As cell type identity is maintained epigenetically, DNA methylation changes during pancreatic neoplasia can provide a compelling perspective to examine this question. Here, we performed laser-capture microdissection on surgically resected specimens from 18 patients to isolate, with high purity, DNA for whole-genome bisulfite sequencing from four relevant cell types: acini, nonneoplastic ducts, PanIN lesions, and PDAC lesions. Differentially methylated regions (DMR) were identified using two complementary analytical approaches: bsseq, which identifies any DMRs but is particularly useful for large block-like DMRs, and informME, which profiles the potential energy landscape across the genome and is particularly useful for identifying differential methylation entropy. Both global methylation profiles and block DMRs clearly implicated an acinar origin for PanINs. At the gene level, PanIN lesions exhibited an intermediate acinar-ductal phenotype resembling acinar-to-ductal metaplasia. In 97.6% of PanIN-specific DMRs, PanIN lesions had an intermediate methylation level between normal and PDAC, which suggests from an information theory perspective that PanIN lesions are epigenetically primed to progress to PDAC. Thus, epigenomic analysis complements histopathology to define molecular progression toward PDAC. The shared epigenetic lineage between PanIN and PDAC lesions could provide an opportunity for prevention by targeting aberrantly methylated progression-related genes.

Significance:

Analysis of DNA methylation landscapes provides insights into the cell-of-origin of PanIN lesions, clarifies the role of PanIN lesions as metaplastic precursors to human PDAC, and suggests potential targets for chemoprevention.
Table S2 from Deep Transcriptome Profiling of Multiple Myeloma Using Quantitative Phenotypes
Authors: Griffin Rosalie , Hanson Heidi A. , Avery Brian J. , Madsen Michael J. , Sborov Douglas W. , Camp Nicola J.
Published: March 2023

Hazard ratios of high vs low risk of progression free survival.
Table S1 from Linking Physical Activity to Breast Cancer via Inflammation, Part 2: The Effect of Inflammation on Breast Cancer Risk
Authors: Lou Makayla W.C. , Drummond Ann E. , Swain Christopher T.V. , Milne Roger L. , English Dallas R. , Brown Kristy A. , van Roekel Eline H. , Skinner Tina L. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Table 1 presents the search terminology for the systematic review
Table S1 from Deep Transcriptome Profiling of Multiple Myeloma Using Quantitative Phenotypes
Authors: Griffin Rosalie , Hanson Heidi A. , Avery Brian J. , Madsen Michael J. , Sborov Douglas W. , Camp Nicola J.
Published: March 2023

Cox regression beta coefficients for overall survival (OS), progression free survival (PFS), and time to treatment failure (TTF). Beta coefficients are by per spectra standard deviation. The quantitative spectra risk score for an outcome is the weighted sum of the spectra retained in its model based on their beta coefficients.
Supplemental Figure S2 from Deep Transcriptome Profiling of Multiple Myeloma Using Quantitative Phenotypes
Authors: Griffin Rosalie , Hanson Heidi A. , Avery Brian J. , Madsen Michael J. , Sborov Douglas W. , Camp Nicola J.
Published: March 2023

Diagram of predictive modeling.
Figure S3B from Linking Physical Activity to Breast Cancer via Inflammation, Part 2: The Effect of Inflammation on Breast Cancer Risk
Authors: Lou Makayla W.C. , Drummond Ann E. , Swain Christopher T.V. , Milne Roger L. , English Dallas R. , Brown Kristy A. , van Roekel Eline H. , Skinner Tina L. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Figure 3B presents the funnel plot from the meta-analysis of IL-6 and breast cancer risk
Figure S2B from Linking Physical Activity to Breast Cancer via Inflammation, Part 2: The Effect of Inflammation on Breast Cancer Risk
Authors: Lou Makayla W.C. , Drummond Ann E. , Swain Christopher T.V. , Milne Roger L. , English Dallas R. , Brown Kristy A. , van Roekel Eline H. , Skinner Tina L. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Figure 2B presents forest plots for TNF-alpha and breast cancer risk, excluding studies where exogenous hormone use status was unknown
Figure S6 from High-Throughput Peptide Arrays Identify Potential Diagnostic Autoantibody Signatures in Early-Stage Lung Adenocarcinoma
Authors: Luo Rongrong , Zhong Pei , Li Xiying , Cai Juan , Tao Yimin , Xiong Bangzhu , Zheng Hancheng , Zhang Zhishang , Tang Le , Yao Jiarui , Li Yingrui , Shi Yuankai , Han Xiaohong
Published: March 2023

Random forest model and GO enrichment. a, Schematic plot of random forest; b, GO terms enriched by the matched proteins of differential peptide probes.
Figure S2 from High-Throughput Peptide Arrays Identify Potential Diagnostic Autoantibody Signatures in Early-Stage Lung Adenocarcinoma
Authors: Luo Rongrong , Zhong Pei , Li Xiying , Cai Juan , Tao Yimin , Xiong Bangzhu , Zheng Hancheng , Zhang Zhishang , Tang Le , Yao Jiarui , Li Yingrui , Shi Yuankai , Han Xiaohong
Published: March 2023

Corresponding signal of previous reported autoantibodies for early lung cancer detection were evaluated in our study cohort with both HuProtTM protein microarray (detail data not shown) and peptide array. All peptides were aligned to 10 proteins using blastp method, 246 peptides were mapped under the set of e-value of 1 and identity of 90. Accumulated peptide signal was set as autoantibody signal of corresponding antigen protein. Nine autoantibodies had effective testing value in HuprotTM. a.t test P value of autoantibodies signals for Early-LUAD versus NHC from peptide array and HuProtTM detection respectively. Two autoantibodies from peptide array and 2 autoantibodies from HuProtTM showed higher signal in Early-LUAD group under P <0.05. Five autoantibodies from peptide array and 2 autoantibodies from HuProtTM showed higher signal in Early-LUAD group under P < 0.1.b.Volcano plot of peptides signals corresponding to 10 autoantigens. X-axis represents the log10 of the fold change, y-axis represents -log10 (P adjust) for Early-LUAD versus NHC. Significantly up-regulated and down-regulated peptides in Early-LUAD group are shown in light red and blue. Two hundred and forty-six peptides mapped to the 10 autoantibodies were shown in green, and 8 significantly upregulated peptides in Early-LUAD shown in green cross. No intersection between the green mapped signals and the peptides used for classifier model (dark red).
Supplementary Figure S3 from Neighborhood Socioeconomic Status and Racial and Ethnic Survival Disparities in Oral Cavity and Laryngeal Cancer
Authors: Liu Yupeng , Zhong Lydia , Puram Sidharth V. , Mazul Angela L.
Published: March 2023

Four KM curves depicting 5-year overall survival of oral cavity cancer patients in Asian subgroups.
Supplementary Figure S2 from Neighborhood Socioeconomic Status and Racial and Ethnic Survival Disparities in Oral Cavity and Laryngeal Cancer
Authors: Liu Yupeng , Zhong Lydia , Puram Sidharth V. , Mazul Angela L.
Published: March 2023

KM curve depicting the 5-year overall survival of larynx cavity cancer patients.
Supplementary Figure S1 from Neighborhood Socioeconomic Status and Racial and Ethnic Survival Disparities in Oral Cavity and Laryngeal Cancer
Authors: Liu Yupeng , Zhong Lydia , Puram Sidharth V. , Mazul Angela L.
Published: March 2023

KM curve depicting 5-year overall survival of oral cavity cancer patients.
Table S6 from Diet Quality and All-Cause Mortality in Women with Breast Cancer from the Breast Cancer Family Registry
Authors: Haslam Danielle E. , John Esther M. , Knight Julia A. , Li Zhongyu , Buys Saundra S. , Andrulis Irene L. , Daly Mary B. , Genkinger Jeanine M. , Terry Mary Beth , Zhang Fang Fang
Published: March 2023

Table S6 Shows Hazard Ratios and 95% Confidence Intervals for All-Cause Mortality in Women Diagnosed with Breast Cancer According to AHEI and aMED, Stratified by Patient and Treatment Characteristics
Table S5 from Diet Quality and All-Cause Mortality in Women with Breast Cancer from the Breast Cancer Family Registry
Authors: Haslam Danielle E. , John Esther M. , Knight Julia A. , Li Zhongyu , Buys Saundra S. , Andrulis Irene L. , Daly Mary B. , Genkinger Jeanine M. , Terry Mary Beth , Zhang Fang Fang
Published: March 2023

Table S5 Shows Hazard Ratios and 95% Confidence Intervals for All-Cause Mortality in Women Diagnosed with Breast Cancer According to DASH and HEI-2015, Stratified by Patient and Treatment Characteristics
Table S6A from Linking Physical Activity to Breast Cancer Risk via Inflammation, Part 1: The Effect of Physical Activity on Inflammation
Authors: Swain Christopher T.V. , Drummond Ann E. , Milne Roger L. , English Dallas R. , Brown Kristy A. , Lou Makayla W.C. , Boing Leonessa , Bageley Amy , Skinner Tina L. , van Roekel Eline H. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Table 6A presents findings of individual parallel group RCTs
Table S4 from Diet Quality and All-Cause Mortality in Women with Breast Cancer from the Breast Cancer Family Registry
Authors: Haslam Danielle E. , John Esther M. , Knight Julia A. , Li Zhongyu , Buys Saundra S. , Andrulis Irene L. , Daly Mary B. , Genkinger Jeanine M. , Terry Mary Beth , Zhang Fang Fang
Published: March 2023

Table S4 Shows Hazard Ratios and 95% Confidence Intervals for Risk of Breast Cancer- and CVD-Specific Mortality in Women Diagnosed with Breast Cancer According to Dietary Quality Indices in the Northern California Breast Cancer Family Registry Site
Table S3 from Diet Quality and All-Cause Mortality in Women with Breast Cancer from the Breast Cancer Family Registry
Authors: Haslam Danielle E. , John Esther M. , Knight Julia A. , Li Zhongyu , Buys Saundra S. , Andrulis Irene L. , Daly Mary B. , Genkinger Jeanine M. , Terry Mary Beth , Zhang Fang Fang
Published: March 2023

Table S3 Shows Hazard Ratios and 95% Confidence Intervals for All-Cause Mortality in Women Diagnosed with Breast Cancer (unrelated women)
Table S4 from Linking Physical Activity to Breast Cancer Risk via Inflammation, Part 1: The Effect of Physical Activity on Inflammation
Authors: Swain Christopher T.V. , Drummond Ann E. , Milne Roger L. , English Dallas R. , Brown Kristy A. , Lou Makayla W.C. , Boing Leonessa , Bageley Amy , Skinner Tina L. , van Roekel Eline H. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Table 4 presents the outcomes of the meta-regression analysis conducted for CRP
Table S2 from Diet Quality and All-Cause Mortality in Women with Breast Cancer from the Breast Cancer Family Registry
Authors: Haslam Danielle E. , John Esther M. , Knight Julia A. , Li Zhongyu , Buys Saundra S. , Andrulis Irene L. , Daly Mary B. , Genkinger Jeanine M. , Terry Mary Beth , Zhang Fang Fang
Published: March 2023

Table S2 Shows Pearson's Correlation Coefficients (r) for Diet Quality Index Scores
Table S1 from Diet Quality and All-Cause Mortality in Women with Breast Cancer from the Breast Cancer Family Registry
Authors: Haslam Danielle E. , John Esther M. , Knight Julia A. , Li Zhongyu , Buys Saundra S. , Andrulis Irene L. , Daly Mary B. , Genkinger Jeanine M. , Terry Mary Beth , Zhang Fang Fang
Published: March 2023

Table S1 Shows Criteria for Maximum Scoring for 4 Diet Quality Indices Using Standardized Cup and Ounce Equivalents from the MyPyramid Equivalents Database
Table S3A from Linking Physical Activity to Breast Cancer Risk via Inflammation, Part 1: The Effect of Physical Activity on Inflammation
Authors: Swain Christopher T.V. , Drummond Ann E. , Milne Roger L. , English Dallas R. , Brown Kristy A. , Lou Makayla W.C. , Boing Leonessa , Bageley Amy , Skinner Tina L. , van Roekel Eline H. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Table 3A presents the risk of bias for randomised controlled and randomised cross-over trials, using the Cochrane Collaboration Tool
Table S2C from Linking Physical Activity to Breast Cancer Risk via Inflammation, Part 1: The Effect of Physical Activity on Inflammation
Authors: Swain Christopher T.V. , Drummond Ann E. , Milne Roger L. , English Dallas R. , Brown Kristy A. , Lou Makayla W.C. , Boing Leonessa , Bageley Amy , Skinner Tina L. , van Roekel Eline H. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Table 2C presents the study characteristics for non-randomised interventions
Figure S4 from Linking Physical Activity to Breast Cancer Risk via Inflammation, Part 1: The Effect of Physical Activity on Inflammation
Authors: Swain Christopher T.V. , Drummond Ann E. , Milne Roger L. , English Dallas R. , Brown Kristy A. , Lou Makayla W.C. , Boing Leonessa , Bageley Amy , Skinner Tina L. , van Roekel Eline H. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Figure 4 presents funnel plots for physical activity to inflammatory biomarkers meta-analyses
Figure S3B from Linking Physical Activity to Breast Cancer Risk via Inflammation, Part 1: The Effect of Physical Activity on Inflammation
Authors: Swain Christopher T.V. , Drummond Ann E. , Milne Roger L. , English Dallas R. , Brown Kristy A. , Lou Makayla W.C. , Boing Leonessa , Bageley Amy , Skinner Tina L. , van Roekel Eline H. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: March 2023

Supplementary Figure 3B presents forest plots for physical activity and IL-6, by exercise type
Data from Neighborhood Socioeconomic Status and Racial and Ethnic Survival Disparities in Oral Cavity and Laryngeal Cancer
Authors: Liu Yupeng , Zhong Lydia , Puram Sidharth V. , Mazul Angela L.
Published: March 2023

AbstractBackground:
Oral cavity cancer (OCC) and laryngeal cancer are among the most common cancers worldwide. This study investigated survival in non-Hispanic (NH) Black, NH White, Asian, and Hispanic patients with OCC and laryngeal cancer of low, intermediate, and high neighborhood socioeconomic status (nSES).
Methods:
We used data from the SEER 18 Census Tract-level SES and Rurality Database of the National Cancer Institute to create cohorts of OCC and laryngeal cancer patients from 2013 to 2018. Univariate survival analysis was performed with Kaplan–Meier curves and log-rank P values by nSES and then the cross-classification of race, ethnicity, and nSES. We used Cox proportional hazards regression model for multivariable analysis.
Results:
Higher nSES was associated with better OCC survival for NH White, NH Black, and Asian patients, and better laryngeal cancer survival for NH White, NH Black, Hispanic, and Asian patients. In the multivariable analyses of both OCC and laryngeal cancer survival, NH Black patients had worse survival than NH White patients in the high nSES tertile. NH Black patients with OCC were at higher risk of death than NH White patients at all nSES levels. Conversely, Asian patients with laryngeal cancer demonstrated better survival than other races within the high nSES.
Conclusions:
Overall survival differs between racial and ethnic groups of similar nSESs. These health disparities in patients with OCC and laryngeal cancer reflect broader inequities in the cancer control continuum.
Impact:
The cross-classification of race, ethnicity, and nSES revealed disparities in the 5-year overall survival of patients with OCC and laryngeal cancer and highlights the importance of intersectionality in the discussion of health equity.
Data from Diet Quality and All-Cause Mortality in Women with Breast Cancer from the Breast Cancer Family Registry
Authors: Haslam Danielle E. , John Esther M. , Knight Julia A. , Li Zhongyu , Buys Saundra S. , Andrulis Irene L. , Daly Mary B. , Genkinger Jeanine M. , Terry Mary Beth , Zhang Fang Fang
Published: March 2023

AbstractBackground:
The impact of diet on breast cancer survival remains inconclusive. We assessed associations of all-cause mortality with adherence to the four diet quality indices: Healthy Eating Index-2015 (HEI-2015), Alternative Healthy Eating Index (AHEI), Alternative Mediterranean Diet (aMED), and Dietary Approaches to Stop Hypertension (DASH).
Methods:
Dietary intake data were evaluated for 6,157 North American women enrolled in the Breast Cancer Family Registry who had been diagnosed with invasive breast cancer from 1993 to 2011 and were followed through 2018. Pre-diagnosis (n = 4,557) or post-diagnosis (n = 1,600) dietary intake was estimated through a food frequency questionnaire. During a median follow-up time of 11.3 years, 1,265 deaths occurred. Cox proportional hazards models were used to estimate multivariable-adjusted HR and 95% confidence intervals (CI).
Results:
Women in the highest versus lowest quartile of adherence to the HEI-2015, AHEI, aMED, and DASH indices had a lower risk of all-cause mortality. HR (95% CI) were 0.88 (0.74–1.04; Ptrend = 0.12) for HEI-2015; 0.82 (0.69–0.97; Ptrend = 0.02) for AHEI; 0.73 (0.59–0.92; Ptrend = 0.02) for aMED; and 0.78 (0.65–0.94; Ptrend = 0.006) for DASH. In subgroup analyses, the associations with higher adherence to the four indices were similar for pre- or post-diagnosis dietary intake and were confined to women with a body mass index <25 kg/m2 and women with hormone receptor positive tumors.
Conclusions:
Higher adherence to the HEI-2015, AHEI, aMED, and DASH indices was associated with lower mortality among women with breast cancer.
Impact:
Adherence to a healthy diet may improve survival of women with breast cancer.
Figure S2 from Immunologic Predictors for Clinical Responses during Immune Checkpoint Blockade in Patients with Myelodysplastic Syndromes
Authors: Lee Sung-Eun , Wang Feng , Grefe Maison , Trujillo-Ocampo Abel , Ruiz-Vasquez Wilfredo , Takahashi Koichi , Abbas Hussein A. , Borges Pamella , Antunes Dinler Amaral , Al-Atrash Gheath , Daver Naval , Molldrem Jeffrey J. , Futreal Andrew , Garcia-Manero Guillermo , Im Jin S.
Published: March 2023

Figure S2. Schema for study design
Figure S1 from Immunologic Predictors for Clinical Responses during Immune Checkpoint Blockade in Patients with Myelodysplastic Syndromes
Authors: Lee Sung-Eun , Wang Feng , Grefe Maison , Trujillo-Ocampo Abel , Ruiz-Vasquez Wilfredo , Takahashi Koichi , Abbas Hussein A. , Borges Pamella , Antunes Dinler Amaral , Al-Atrash Gheath , Daver Naval , Molldrem Jeffrey J. , Futreal Andrew , Garcia-Manero Guillermo , Im Jin S.
Published: March 2023

Figure S1. Information on treatment and available testing results for analysis
Can Molecular Imaging Find a Path to Navigate Evolving Breast Cancer Treatments?
Authors: Linden Hannah M. , Mankoff David A.
Published: March 2023

[18F]fluoroestradiol (FES) PET is an FDA-approved imaging biomarker. Like IHC, FES positivity predicts clinical benefit of endocrine therapy. In addition, FES measures the target activity in endocrine agent drug development. A recent study found that whole body tumor heterogeneity of expression predicts clinical benefit, and serial FES monitors estrogen receptor blockade and posttreatment release.

See related article by Iqbal et al., p. 2075
Supplementary Data Table S2 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: March 2023

Significant enriched pathways in JMJD6-KO MCF7 and MDA-MB231 cells
Supplementary Data Table S1 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: March 2023

List of BC patients with ER-positive tumors included in the METABRIC dataset
Figure S4 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: March 2023

Jmjd6-mediated ANXA1 secretion promotes M2 macrophage differentiation in vitro and ex vivo. A) Mean fluorescence intensity (MFI) of M1 and M2 markers in BMDM differentiated into M0, M1 and M2.** p<0,001, *** means p<0,0001, **** p<0,00001 without conditioned medium. B) Real time PCR showing the expression M1 (CD40 and NOS2) and M2 (CD206 and ARG1) markers in BMDMs differentiated into M0, M1 and M2 macrophages without CM. Datapoints show technical replicates.** p<0,001, *** p<0,0001. C) Gating strategies for FACS analysis on ex vivo mouse samples of Figure 6D. CD45+ leukocytes were gated on live cells, excluding dead cells and debris. In CD45+ population, myeloid cells were analyzed by the expression of CD11b, Gr-1, Ly6C and F4/80 markers. Monocyte-like myleloid-derived immunosuppressive cells (M-MDSC) were identified as Ly6Chigh Gr-1int expression. Granulocyte-like myeloid-derived immunosuppressive cells (G-MDSC) were identified as Gr-1high Ly6Cint cells. M2 macrophages were identified as CD206+ cells in the F4/80 gate. G-MDSC were identified as Gr-1high Ly6Cint cells. M2 macrophages were identified as CD206+ cells in the F4/80 gate.
Figure S2 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: March 2023

JMJD6 regulates lipid metabolism in MCF7 cells. A) Immunohistochemistry staining for ANXA1 (brown) combined with Oil red-O staining (pink) for lipid droplets visualization in wild-type MCF7 cells B) Gene set enrichment plot for 'Hallmark of Adipogenesis' found to be significantly downregulated in JMJD6 KO MCF7 cells compared to scramble control. C) List of 'Reactome Pathways' found to be regulated by the genes included in the gene set enrichment pathway of 'Hallmark of Adipogenesis' and present in the DEGs list of JMJD6 KO versus scramble MCF7 cells.
Figure S1 from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: March 2023

Effect of JMJD6 KO in ER positive and negative cell lines. A) Western blot showing the expression of JMJD6 and ERα in wild-type, scramble or JMJD6 KO BT474 cells both in mass cultures (Left panel) and in single clones (right panel). Vinculin is shown as loading control. B) Volcano plot showing the most upregulated (red) and downregulated (green) genes between scramble and wild-type (parental) MCF7 (left) and MDA-MB231 (right) cells.
Supplementary Tables 1-9 from Targeting Unc51-like Autophagy Activating Kinase 1 (ULK1) Overcomes Adaptive Drug Resistance in Acute Myelogenous Leukemia
Authors: Bhattacharya Seemana , Piya Sujan , Ma Huaxian , Sharma Priyanka , Zhang Qi , Baran Natalia , Ruvolo Vivian R. , McQueen Teresa , Davis R. Eric , Pourebrahim Rasoul , Konopleva Marina , Kantarjian Hagop , Cosford Nicholas D. P. , Andreeff Michael , Borthakur Gautam
Published: March 2023

Supplementary Table S1. Abbreviations of cell populations analyzed using Bloodspot.
Supplementary Table S2. Comparative analysis of significance based on survival curves generated using GraphPad.
Supplementary Table S3. Mutational profiles of AML cell lines and their sensitivity to SBI-0206965.
Supplementary Table S4. Mutational profiles of AML patient derived primary samples.
Supplementary Table S5. IC50 values of drug resistant cells.
Supplementary Table S6. Combinatorial Index (CI-value) of combination treatments.
Supplementary Table S7. Comparative analysis of significance based on survival curves generated using GraphPad (Ex vivo model).
Supplementary Table S8. List of Antibodies.
Supplementary Table S9. List of Primers.
Data from JMJD6 Shapes a Pro-tumor Microenvironment via ANXA1-Dependent Macrophage Polarization in Breast Cancer
Authors: Cioni Bianca , Ratti Silvia , Piva Annamaria , Tripodi Irene , Milani Matteo , Menichetti Francesca , Langella Tiziana , Botti Laura , De Cecco Loris , Chiodoni Claudia , Lecis Daniele , Colombo Mario P.
Published: March 2023

Abstract
Breast cancer is the most common type of cancer in women worldwide, with the luminal subtype being the most widespread. Although characterized by better prognosis compared with other subtypes, luminal breast cancer is still considered a threatening disease due to therapy resistance, which occurs via both cell- and non–cell-autonomous mechanisms. Jumonji domain-containing 6, arginine demethylase and lysine hydroxylase (JMJD6) is endowed with a negative prognostic value in luminal breast cancer and, via its epigenetic activity, it is known to regulate many intrinsic cancer cell pathways. So far, the effect of JMJD6 in molding the surrounding microenvironment has not been explored.

Here, we describe a novel function of JMJD6 showing that its genetic inhibition in breast cancer cells suppresses lipid droplet formation and ANXA1 expression, via estrogen receptor alpha and PPARα modulation. Reduction of intracellular ANXA1 results in decreased release in the tumor microenvironment (TME), ultimately preventing M2-type macrophage polarization and tumor aggressiveness.
Implications:
Our findings identify JMJD6 as a determinant of breast cancer aggressiveness and provide the rationale for the development of inhibitory molecules to reduce disease progression also through the remodeling of TME composition.
Disease and Quality of Life Aspects of Cat Allergy in Non-Pet Owners with Allergic Rhinitis
Authors: Yüksel Aslıer Nesibe Gül , Saatçi Özlem , Aslier Mustafa
Published: March 2023

Introduction: The severity of cat allergy-related symptoms varies widely. The rising prevalence of cat owning makes it a significant human health problem. The aim of this study was to evaluate disease severity and quality of life (QoL) aspects of cat sensitization and allergy in non-pet owners with allergic rhinitis (AR). Methods: In this study, 231 out of 596 patients with AR were enrolled. The disease severity and QoL measures of the non-pet owner patients were evaluated according to their demographics and allergen sensitizations. The data were re-gathered after cat exposure for cat-sensitized patients (n = 53). Results: The median age of the patients (174 females, 57 males) was 33 (18–70). The overall frequency of cat sensitization was 12.6% (75/596). The frequency of cat allergy in this cohort was 13.9% (32/231). Family history of atopy and multi-allergen sensitization were more common in the cat-sensitized patients. Disease severity and QoL scores were higher in the cat allergy group after cat exposure. Cat allergy was the major independent risk factor for the severity of AR and QoL measures. Conclusion: Due to the fact that indirect exposure to cat dander allergens can occur anywhere, even where cats are not present, cat-sensitized people should be aware of cat allergy. Cat allergy appears to be an independent risk factor for disease severity and QoL effects for non-pet owner patients with AR.