bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethnic inequalities in positive SARS-CoV-2 tests, infection prognosis, COVID-19 hospitalisations and deaths: analysis of 2 years of a record linked national cohort study in Scotland
Authors: Amele Sarah , Kibuchi Eliud , McCabe Ronan , Pearce Anna , Henery Paul , Hainey Kirsten , Fagbamigbe Adeniyi Francis , Kurdi Amanj , McCowan Colin , Simpson Colin R , Dibben Chris , Buchanan Duncan , Demou Evangelia , Almaghrabi Fatima , Anghelescu Gina , Taylor Harry , Tibble Holly , Rudan Igor , Nazroo James , Bécares Laia , Daines Luke , Irizar Patricia , Jayacodi Sandra , Pattaro Serena , Sheikh Aziz , Katikireddi Srinivasa Vittal
Published: August 2023

Background

This study aims to estimate ethnic inequalities in risk for positive SARS-CoV-2 tests, COVID-19 hospitalisations and deaths over time in Scotland.

Methods

We conducted a population-based cohort study where the 2011 Scottish Census was linked to health records. We included all individuals ≥ 16 years living in Scotland on 1 March 2020. The study period was from 1 March 2020 to 17 April 2022. Self-reported ethnic group was taken from the census and Cox proportional hazard models estimated HRs for positive SARS-CoV-2 tests, hospitalisations and deaths, adjusted for age, sex and health board. We also conducted separate analyses for each of the four waves of COVID-19 to assess changes in risk over time.

Findings

Of the 4 358 339 individuals analysed, 1 093 234 positive SARS-CoV-2 tests, 37 437 hospitalisations and 14 158 deaths occurred. The risk of COVID-19 hospitalisation or death among ethnic minority groups was often higher for White Gypsy/Traveller (HR 2.21, 95% CI (1.61 to 3.06)) and Pakistani 2.09 (1.90 to 2.29) groups compared with the white Scottish group. The risk of COVID-19 hospitalisation or death following confirmed positive SARS-CoV-2 test was particularly higher for White Gypsy/Traveller 2.55 (1.81–3.58), Pakistani 1.75 (1.59–1.73) and African 1.61 (1.28–2.03) individuals relative to white Scottish individuals. However, the risk of COVID-19-related death following hospitalisation did not differ. The risk of COVID-19 outcomes for ethnic minority groups was higher in the first three waves compared with the fourth wave.

Interpretation

Most ethnic minority groups were at increased risk of adverse COVID-19 outcomes in Scotland, especially White Gypsy/Traveller and Pakistani groups. Ethnic inequalities persisted following community infection but not following hospitalisation, suggesting differences in hospital treatment did not substantially contribute to ethnic inequalities.
Treatment with intravenous alteplase in ischaemic stroke patients with onset time between 4.5 and 24 hours (HOPE): protocol for a randomised, controlled, multicentre study
Authors: Luo Zhongyu , Zhou Ying , He Yaode , Yan Shenqiang , Chen Zhicai , Zhang Xuting , Chen Yi , Tong Lu-Sha , Zhong Wansi , Hu Haitao , Zhang Kemeng , Yang Jiansheng , Campbell Bruce C V , Lou Min
Published: August 2023

Background

While intravenous thrombolysis is recommended for patients who had an acute ischaemic stroke (AIS) within 4.5 hours of symptom onset, there are few randomised trials investigating the benefits of thrombolysis beyond this therapeutic window.

Aim

To determine whether patients who had an AIS selected with the presence of potentially salvageable tissue on CT perfusion at 4.5–24 hours after stroke onset (for stroke with unknown onset time, the midpoint of the time last known to be well and symptom recognition time; for wake-up stroke, the midpoint of the time last known to be well or sleep onset and wake up time) will benefit from intravenous thrombolysis.

Design

HOPE is a prospective, multicentre, randomised, open-label blinded endpoint trial with the stage of phase III. The treatment allocation employs 1:1 randomisation. The treatment arm under investigation is alteplase with standard therapy, the control arm is standard therapy. Eligibility imaging criteria include ischaemic core volume ≤70 mL, penumbra ≥10 mL and mismatch ≥20%.

Study outcomes

The primary outcome is non-disabled functional outcome (assessed as modified Rankin Scale score of 0–1 at 90 days).

Discussion

HOPE is the first trial to investigate whether intravenous thrombolysis with alteplase offers benefits in patients who had an AIS presenting within 4.5–24 hours, which has the potential to extend time window and expand eligible population for thrombolysis therapy.
A Jiangshanian (Cambrian; Furongian) trilobite fauna from the Cow Head Group, western Newfoundland
Authors: Westrop Stephen R. , Eoff Jennifer D.
Published: August 2023

Three shelf-derived boulders in debris flow conglomerates of the Downes Point Member of the Shallow Bay Formation of western Newfoundland yielded the first record of an Upper Cambrian shelf-margin trilobite fauna from the Elvinia Zone (Steptoean; Jiangshanian) in eastern North America. The fauna is dominated by the “catillicephalid” Buttsia Wilson, 1951, and resembles trilobite biofacies from microbial buildups in the Gatesburg Formation of Pennsylvania. It is correlative with the Cliffia latagenae Subzone, which is the youngest Steptoean biostratigraphic unit in the Gatesburg. New taxa are Triorygma burkhalteri gen. et sp. nov. and Buttsia trema sp. nov.
Navigating the skies: examining the FAA’s remote identification rule for unmanned aircraft systems
Authors: Phadke Abhishek , Boyd Josh , Medrano F. Antonio , Starek Michael
Published: August 2023

As technology and innovations in unmanned aerial vehicles progress, so does the need for regulations in place to create safe and controlled flying scenarios. The Federal Aviation Administration (FAA) is a governing body under the United States Department of Transportation that is responsible for a wide range of regulatory activities related to the United States airspace. In a recently published final rule, the FAA addresses several concerns such as the need for a system to identify all aircrafts flying in national airspace, as well as the implementation of a separate system from the prevalent Automatic Dependent Surveillance–Broadcast system to prevent interference with manned aircrafts. Their solution to these concerns is the deployment of remote identification (RID) on all unmanned aircraft systems (UAS) flying under its implied jurisdiction. While US governing agencies retain the use of the word UAS for now, the International Civil Aviation Organization terminology is remotely piloted aircraft systems. The FAA describes the RID implementation as a “ Digital license plate” for all UAS flying in the United States airspace. They outline additional policies including several options for compliance, operating rules, and design and production guidelines for manufacturers. As the September 2023 deadline for compliance draws near, this article highlights possible deployment applications and challenges.
Text Document Clustering Using Modified Particle Swarm Optimization with k-means Model
Authors: Dodda Ratnam , Babu A. Suresh
Published: August 2023

In the present digital era, vast amounts of data are generated by millions of Internet users in the form of unstructured text documents. The clustering and organizing of text documents play a crucial role in the applications of data analysis and market research. In this research manuscript, a new modified version of metaheuristic-based optimization technique is proposed with k-means for clustering the text documents. In the initial phase, the input data are acquired from the three-benchmark databases such as Reuters-21578, 20-Newsgroup and British Broadcasting Corporation (BBC)-sport. Further, the data denoising is accomplished by using the common techniques: stemming, lemmatization, tokenization, and stop word removal. In addition to this, the denoised data are transformed into feature vectors by utilizing Term Frequency (TF)-Inverse Document Frequency (IDF) technique. The computed feature vectors are given to the Modified Particle Swarm Optimization (MPSO) with k-means to group the closely related text documents by minimizing the similarity in different clusters. The experimental examination showed that the proposed MPSO with k-means model achieved accuracy of 0.85, 0.85 and 0.86 on the Reuters-21578, 20-Newsgroup and BBC-sport databases, which are superior to the comparative models.
ACM Conference on Recommender Systems September 18--22, 2023 at Singapore
Authors: Zheng Yong , Hauptmann Hanna , Guo Guibing
Published: August 2023

ACM Conference on Recommender Systems (RecSys) is the premier international forum for the presentation of new research results, systems and techniques in the broad field of recommender systems. RecSys 2023 will be held in Singapore and will bring together the major international research groups working on recommender systems, along with many of the world's leading companies active in e-commerce and other adjacent domains. It is a SIGCHI-sponsored conference, that will attract also several leading industry sponsors. The proceedings will be published by ACM as part of the ACM Digital Library.
Semi-supervised Video Object Segmentation Via an Edge Attention Gated Graph Convolutional Network
Authors: Zhang Yuqing , Zhang Yong , Wang Shaofan , Liang Yun , Yin Baocai
Published: August 2023

Video object segmentation (VOS) exhibits heavy occlusions, large deformation, and severe motion blur. While many remarkable convolutional neural networks are devoted to the VOS task, they often mis-identify background noise as the target or output coarse object boundaries, due to the failure of mining detail information and high-order correlations of pixels within the whole video. In this work, we propose an edge attention gated graph convolutional network (GCN) for VOS. The seed point initialization and graph construction stages construct a spatio-temporal graph of the video by exploring the spatial intra-frame correlation and the temporal inter-frame correlation of superpixels. The node classification stage identifies foreground superpixels by using an edge attention gated GCN which mines higher-order correlations between superpixels and propagates features among different nodes. The segmentation optimization stage optimizes the classification of foreground superpixels and reduces segmentation errors by using a global appearance model which captures the long-term stable feature of objects. In summary, the key contribution of our framework is twofold: (a) the spatio-temporal graph representation can propagate the seed points of the first frame to subsequent frames and facilitate our framework for the semi-supervised VOS task; and (b) the edge attention gated GCN can learn the importance of each node with respect to both the neighboring nodes and the whole task with a small number of layers. Experiments on Davis 2016 and Davis 2017 datasets show that our framework achieves the excellent performance with only small training samples (45 video sequences).
Sea Surface Temperature Affects the Reproductive Biology of Female Pearl Perch (Glaucosoma scapulare Macleay, 1881) in Queensland, Australia
Authors: Campbell Matthew J. , Joiner Jaimee E. , McLennan Mark F. , Tibbetts Ian R.
Published: August 2023

Pearl perch (Glaucosoma scapulare) are endemic to the east coast of Australia and have a long history of exploitation. Recent stock assessments indicate that the current rate of fishing mortality is unsustainable in the long term. To better inform the management of the pearl perch stock and to address gaps in our understanding of their reproductive biology, we investigated patterns in gonad development and estimated length- and age-at-maturity and batch fecundity from females collected from southern and central Queensland waters between 2018 and 2022. The mean gonadosomatic index (GSI) varied both temporally and spatially, with maxima in the austral autumn in southern Queensland and in summer in central Queensland, coinciding with sea surface temperatures between 25.26 and 26.32°C. The length- and age-at-maturity of females were 353 mm (fork length, FL) and 4.42 years, respectively, and batch fecundity (B) was correlated to FL such that Ln(B) = 2.45 × Ln(FL) + 3.90. Our results will inform a management strategy to recover the stock to acceptable levels of exploitation.
Epidemiological Characteristics of Generalized COVID-19 Deterministic Disease Model
Authors: Li Shuo , Hussain Nasir , Khan Ihsan Ullah , Hussain Amjid , Teklu Shewafera Wondimagegnhu
Published: August 2023

Coronavirus disease 2019 (COVID-19) is an infection that can result in lung issues such as pneumonia and, in extreme situations, the most severe acute respiratory syndrome. COVID-19 is widely investigated by researchers through mathematical models from different aspects. Inspired from the literature, in the present paper, the generalized deterministic COVID-19 model is considered and examined. The basic reproduction number is obtained which is a key factor in defining the nonlinear dynamics of biological and physical obstacles in the study of mathematical models of COVID-19 disease. To better comprehend the dynamical behavior of the continuous model, two unconditionally stable schemes, i.e., mixed Euler and nonstandard finite difference (NSFD) schemes are developed for the continuous model. For the discrete NSFD scheme, the boundedness and positivity of solutions are discussed in detail. The local stability of disease-free and endemic equilibria is demonstrated by constructing Jacobian matrices for NSFD scheme; nevertheless, the global stability of aforementioned equilibria is verified by using Lyapunov functions. Numerical simulations are also presented that demonstrate how both the schemes are effective and suitable for solving the continuous model. Consequently, the outcomes obtained through these schemes are completely according to the solutions of the continuous model.
Application of the Finite Difference Parabolic Equation Model in Forestry Remote Telemetry
Authors: Guo Qi , Lan Yubin , Deng Xiaoling , Diao Yinliang
Published: August 2023

In this article, the finite difference parabolic equation (FDPE) method is presented to calculate the propagation loss (PL) for electromagnetic waves (EWs) in the forest environment. The FDPE method is more efficient and convenient than the empirical models and has more advantages on compatibility and accuracy for long-range EWs prediction. The Debye–Cole dual dispersion model is used to simulate the effective permittivity of vegetation. The results of the FDPE model are compared with those of the advanced refractive effects prediction system and measurement results, and a good agreement is observed. Research found that PL for EWs varies with the effective permittivity. Also, the effective permittivity is a function of radio frequency, weight moisture content, and volume content of vegetation. Thus, it is necessary to establish a statistical model to determine some relations between the PL and plant biophysical parameters. The polynomial fitting method is adopted to process a large amount of PL data for obtaining a linear function. Then, the volume content and moisture content of vegetation can be determined according to the polynomial fitting function. It provides a novel and efficient method for forestry remote telemetry, which is specifically suitable for large-scale inaccessible region with serious environment.
The Role of Potent Thiols in “Empyreumatic” Flint/Struck-Match/Mineral Odours in Chardonnay Wine
Authors: Espinase Nandorfy Damian , Siebert Tracey , Bilogrevic Eleanor , Likos Desireé , Watson Flynn , Barter Sheridan , Pisaniello Lisa , Kulcsar Allie , Shellie Robert A. , Keast Russell , Francis Leigh , Bekker Marlize
Published: August 2023

Background and Aims. A wide range of Chardonnay styles exist on the market, from fruit-forward examples to wines displaying “empyreumatic” aromas such as flint, smoky, mineral, and struck-match. The thiols 2-furylmethanethiol and phenylmethanethiol have been linked to these aromas, and this study aimed to determine the contribution of these compounds to specific sensory properties in Chardonnay wines, as well as the consumer acceptance of wine displaying “empyreumatic” aromas. Methods and Results. Twenty-four Australian and New Zealand Chardonnay wines were selected for volatile analysis and quantitative sensory descriptive analysis. Consumer liking of a subset of six wines was also determined, and a further sensory study involving additions of the thiols to a base wine was conducted. Partial least squares regression showed that flint/struck-match/mineral aromas were related to 2-furylmethanethiol concentration with phenylmethanethiol less well associated. The odorant addition study confirmed that 2-furylmethanethiol directed flint/struck-match/mineral aromas and exerted strong suppression of other aromas while phenylmethanethiol played a lesser role. Consumer acceptance (n = 92) was overall lower for wines displaying high flint/struck-match/mineral aromas, although cluster analysis of the liking scores identified a sizeable consumer group (33%) who preferred wines with this attribute. Conclusions. The potent thiol 2-furylmethanethiol was indicated to be the primary contributor to flint/struck-match/mineral aromas in Chardonnay wines, with phenylmethanethiol playing a subordinate role. Significance of the Study. Increased concentration of 2-furylmethanethiol and the conferred “empyreumatic” odours should be carefully considered when producing wine styles to appeal to consumers.
Table S1 from Oxidative Phosphorylation Fueled by Fatty Acid Oxidation Sensitizes Leukemic Stem Cells to Cold
Authors: Griessinger Emmanuel , Pereira-Martins Diego , Nebout Marielle , Bosc Claudie , Saland Estelle , Boet Emiline , Sahal Ambrine , Chiche Johanna , Debayle Delphine , Fleuriot Lucile , Pruis Maurien , De Mas Véronique , Vergez François , Récher Christian , Huls Gerwin , Sarry Jean-Emmanuel , Schuringa Jan Jacob , Peyron Jean-François
Published: August 2023

AML_Patient_Clinical features
Table S3 from Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci
Authors: Kanholm Tomas , Rentia Uzma , Hadley Melissa , Karlow Jennifer A. , Cox Olivia L. , Diab Noor , Bendall Matthew L. , Dawson Tyson , McDonald James I. , Xie Wenbing , Crandall Keith A. , Burns Kathleen H. , Baylin Stephen B. , Easwaran Hari , Chiappinelli Katherine B.
Published: August 2023

Table S3
Table S1 from Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci
Authors: Kanholm Tomas , Rentia Uzma , Hadley Melissa , Karlow Jennifer A. , Cox Olivia L. , Diab Noor , Bendall Matthew L. , Dawson Tyson , McDonald James I. , Xie Wenbing , Crandall Keith A. , Burns Kathleen H. , Baylin Stephen B. , Easwaran Hari , Chiappinelli Katherine B.
Published: August 2023

Table S1
Figure S8 from Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci
Authors: Kanholm Tomas , Rentia Uzma , Hadley Melissa , Karlow Jennifer A. , Cox Olivia L. , Diab Noor , Bendall Matthew L. , Dawson Tyson , McDonald James I. , Xie Wenbing , Crandall Keith A. , Burns Kathleen H. , Baylin Stephen B. , Easwaran Hari , Chiappinelli Katherine B.
Published: August 2023

Supplemental Figure 8
Supplementary File 5 from Proteasome Inhibition Sensitizes Liposarcoma to MDM2 Inhibition with Nutlin-3 by Activating the ATF4/CHOP Stress Response Pathway
Authors: Ludwig Michael P. , Galbraith Matthew D. , Eduthan Neetha Paul , Hill Amanda A. , Clay Michael R. , Tellez Cristiam Moreno , Wilky Breelyn A. , Elias Anthony , Espinosa Joaquin M. , Sullivan Kelly D.
Published: August 2023

Nutlin-3-proteasome inhibitor drug interaction SRB data.
Supplementary File 4 from Proteasome Inhibition Sensitizes Liposarcoma to MDM2 Inhibition with Nutlin-3 by Activating the ATF4/CHOP Stress Response Pathway
Authors: Ludwig Michael P. , Galbraith Matthew D. , Eduthan Neetha Paul , Hill Amanda A. , Clay Michael R. , Tellez Cristiam Moreno , Wilky Breelyn A. , Elias Anthony , Espinosa Joaquin M. , Sullivan Kelly D.
Published: August 2023

Genome-wide CRISPR Nutlin-3 Sensitizing Gene screen data.
Supplementary File 1 from Proteasome Inhibition Sensitizes Liposarcoma to MDM2 Inhibition with Nutlin-3 by Activating the ATF4/CHOP Stress Response Pathway
Authors: Ludwig Michael P. , Galbraith Matthew D. , Eduthan Neetha Paul , Hill Amanda A. , Clay Michael R. , Tellez Cristiam Moreno , Wilky Breelyn A. , Elias Anthony , Espinosa Joaquin M. , Sullivan Kelly D.
Published: August 2023

Reagents used in this study.
Supplementary Data from A Genetic Locus within the FMN1/GREM1 Gene Region Interacts with Body Mass Index in Colorectal Cancer Risk
Authors: Aglago Elom K. , Kim Andre , Lin Yi , Qu Conghui , Evangelou Marina , Ren Yu , Morrison John , Albanes Demetrius , Arndt Volker , Barry Elizabeth L. , Baurley James W. , Berndt Sonja I. , Bien Stephanie A. , Bishop D. Timothy , Bouras Emmanouil , Brenner Hermann , Buchanan Daniel D. , Budiarto Arif , Carreras-Torres Robert , Casey Graham , Cenggoro Tjeng Wawan , Chan Andrew T. , Chang-Claude Jenny , Chen Xuechen , Conti David V. , Devall Matthew , Diez-Obrero Virginia , Dimou Niki , Drew David , Figueiredo Jane C. , Gallinger Steven , Giles Graham G. , Gruber Stephen B. , Gsur Andrea , Gunter Marc J. , Hampel Heather , Harlid Sophia , Hidaka Akihisa , Harrison Tabitha A. , Hoffmeister Michael , Huyghe Jeroen R. , Jenkins Mark A. , Jordahl Kristina , Joshi Amit D. , Kawaguchi Eric S. , Keku Temitope O. , Kundaje Anshul , Larsson Susanna C. , Marchand Loic Le , Lewinger Juan Pablo , Li Li , Lynch Brigid M. , Mahesworo Bharuno , Mandic Marko , Obón-Santacana Mireia , Moreno Victor , Murphy Neil , Nan Hongmei , Nassir Rami , Newcomb Polly A. , Ogino Shuji , Ose Jennifer , Pai Rish K. , Palmer Julie R. , Papadimitriou Nikos , Pardamean Bens , Peoples Anita R. , Platz Elizabeth A. , Potter John D. , Prentice Ross L. , Rennert Gad , Ruiz-Narvaez Edward , Sakoda Lori C. , Scacheri Peter C. , Schmit Stephanie L. , Schoen Robert E. , Shcherbina Anna , Slattery Martha L. , Stern Mariana C. , Su Yu-Ru , Tangen Catherine M. , Thibodeau Stephen N. , Thomas Duncan C. , Tian Yu , Ulrich Cornelia M. , van Duijnhoven Franzel JB , Van Guelpen Bethany , Visvanathan Kala , Vodicka Pavel , Wang Jun , White Emily , Wolk Alicja , Woods Michael O. , Wu Anna H. , Zemlianskaia Natalia , Hsu Li , Gauderman W. James , Peters Ulrike , Tsilidis Konstantinos K. , Campbell Peter T.
Published: August 2023

supplementary materials
Supplementary Table S6 from Deficiency of the Polycomb Protein RYBP and TET Methylcytosine Oxidases Promotes Extensive CpG Island Hypermethylation and Malignant Transformation
Authors: Cui Wei , Huang Zhijun , Jin Seung-Gi , Johnson Jennifer , Lau Kin H. , Hostetter Galen , Pfeifer Gerd P.
Published: August 2023

Hypermethylated DMR regions of R/TET123 QKO that intersect with CGIs and associated genes
Supplementary Table S1 from Deficiency of the Polycomb Protein RYBP and TET Methylcytosine Oxidases Promotes Extensive CpG Island Hypermethylation and Malignant Transformation
Authors: Cui Wei , Huang Zhijun , Jin Seung-Gi , Johnson Jennifer , Lau Kin H. , Hostetter Galen , Pfeifer Gerd P.
Published: August 2023

List of DNA oligonucleotides and antibodies
Supplementary tables from Hypoxia-Responsive lncRNA AC115619 Encodes a Micropeptide That Suppresses m6A Modifications and Hepatocellular Carcinoma Progression
Authors: Zhang Qiangnu , Wei Teng , Yan Lesen , Zhu Siqi , Jin Wen , Bai Yu , Zeng Yuandi , Zhang XiaoFei , Yin Zexin , Yang Jilin , Zhang Wenjian , Wu Meilong , Zhang Yusen , Liu Liping
Published: August 2023

Information on the details of the materials involved in this study
Supplementary figures from Hypoxia-Responsive lncRNA AC115619 Encodes a Micropeptide That Suppresses m6A Modifications and Hepatocellular Carcinoma Progression
Authors: Zhang Qiangnu , Wei Teng , Yan Lesen , Zhu Siqi , Jin Wen , Bai Yu , Zeng Yuandi , Zhang XiaoFei , Yin Zexin , Yang Jilin , Zhang Wenjian , Wu Meilong , Zhang Yusen , Liu Liping
Published: August 2023

Supplementary figures with legends
Figure S2 from BRCA1 Insufficiency Induces a Hypersialylated Acidic Tumor Microenvironment That Promotes Metastasis and Immunotherapy Resistance
Authors: Shu Xiaodong , Li Jianjie , Chan Un In , Su Sek Man , Shi Changxiang , Zhang Xin , An Tingting , Xu Jun , Mo Lihua , Liu Jianlin , Wang Yuqing , Li Xiaoling , Deng Min , Lei Josh Haipeng , Wang Chunfei , Tian Hao , Heng Sun , Shim Joong Sup , Zhang Xuanjun , Dai Yunlu , Yao Zhicheng , Kuang Xiaying , Lin Ying , Deng Chu-Xia , Xu Xiaoling
Published: August 2023

Original picture
Figure S1 from BRCA1 Insufficiency Induces a Hypersialylated Acidic Tumor Microenvironment That Promotes Metastasis and Immunotherapy Resistance
Authors: Shu Xiaodong , Li Jianjie , Chan Un In , Su Sek Man , Shi Changxiang , Zhang Xin , An Tingting , Xu Jun , Mo Lihua , Liu Jianlin , Wang Yuqing , Li Xiaoling , Deng Min , Lei Josh Haipeng , Wang Chunfei , Tian Hao , Heng Sun , Shim Joong Sup , Zhang Xuanjun , Dai Yunlu , Yao Zhicheng , Kuang Xiaying , Lin Ying , Deng Chu-Xia , Xu Xiaoling
Published: August 2023

Original picture
Supplementary Data from Plasma Membrane Channel TRPM4 Mediates Immunogenic Therapy–Induced Necrosis
Authors: Ghosh Santanu , Yang Rachel , Duraki Darjan , Zhu Junyao , Kim Ji Eun , Jabeen Musarrat , Mao Chengjian , Dai Xinyi , Livezey Mara R. , Boudreau Matthew W. , Park Ben H. , Nelson Erik R. , Hergenrother Paul J. , Shapiro David J.
Published: August 2023

Supplementary Movie 3
Data from Characterizing evolutionary dynamics reveals strategies to exhaust the spectrum of subclonal resistance in EGFR-mutant lung cancer
Authors: Müller Nina , Lorenz Carina , Ostendorp Jenny , Heisel Felix S. , Friese Ulrich P. , Cartolano Maria , Plenker Dennis , Tumbrink Hannah L. , Heimsoeth Alena , Baedeker Philipp , Ortiz-Cuaran Sandra , Weiss Jonathan , Büttner Reinhard , Peifer Martin , Thomas Roman K. , Sos Martin L. , Berg Johannes , Brägelmann Johannes
Published: August 2023

Abstract
The emergence of resistance to targeted therapies restrains their efficacy. The development of rational-ly guided drug combinations could overcome this currently insurmountable clinical challenge. However, our limited understanding of the trajectories that drive the outgrowth of resistant clones in cancer cell populations precludes design of drug combinations to forestall resistance. Here, we propose an iterative treatment strategy coupled with genomic profiling and genome-wide CRISPR activation screening to systematically extract and define pre-existing resistant subpopulations in an EGFR-driven lung cancer cell line. Integrating these modalities identifies several resistance mechanisms, including activation of YAP/TAZ signaling by WWTR1 amplification, and estimated the associated cellular fitness for mathematical population modeling. These observations led to the development of a combina-tion therapy that eradicated resistant clones in large cancer cell line populations by exhausting the spectrum of genomic resistance mechanisms. However, a small fraction of cancer cells was able to enter a reversible non-proliferative state of drug tolerance. This sub-population exhibited mesenchy-mal properties, NRF2 target gene expression and sensitivity to ferroptotic cell death. Exploiting this induced collateral sensitivity by GPX4 inhibition clears drug tolerant populations and led to tumor cell eradication. Overall, this experimental in vitro data and theoretical modeling demonstrate why targeted mono- and dual therapies will likely fail in sufficiently large cancer cell populations to limit long-term efficacy. Our approach is not tied to a particular driver mechanism and can be used to systematically assess and ideally exhaust the resistance landscape for different cancer types to rationally design com-bination therapies.
Data from Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation of Transposable Element Loci
Authors: Kanholm Tomas , Rentia Uzma , Hadley Melissa , Karlow Jennifer A. , Cox Olivia L. , Diab Noor , Bendall Matthew L. , Dawson Tyson , McDonald James I. , Xie Wenbing , Crandall Keith A. , Burns Kathleen H. , Baylin Stephen B. , Easwaran Hariharan , Chiappinelli Katherine B.
Published: August 2023

Abstract
Transposable elements (TEs) are typically silenced by DNA methylation and repressive histone modifications in differentiated healthy human tissues. However, TE expression increases in a wide range of cancers and is correlated with global hypomethylation of cancer genomes. We assessed expression and DNA methylation of TEs in fibroblast cells that were serially transduced with hTERT, SV40, and HRASR24C to immortalize and then transform them, which models the different steps of the tumorigenesis process. RNA-sequencing and whole-genome bisulfite sequencing were performed at each stage of transformation. TE expression significantly increased as cells progressed through transformation, with the largest increase in expression after the final stage of transformation, consistent with data from human tumors. The upregulated TEs were dominated by endogenous retroviruses (LTRs). Most differentially methylated regions (DMRs) in all stages were hypomethylated, with the greatest hypomethylation in the final stage of transformation. A majority of the DMRs overlapped TEs from the RepeatMasker database, indicating that TEs are preferentially demethylated. Many hypomethylated TEs displayed a concordant increase in expression. Demethylation began during immortalization and continued into transformation, while upregulation of TE transcription occurred in transformation. Numerous LTR elements upregulated in the model were also identified in TCGA datasets of breast, colon, and prostate cancer. Overall, these findings indicate that transposable elements, specifically endogenous retroviruses, are demethylated and transcribed during transformation.
Data from Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C
Authors: Hu Chunling , Nagaraj Anil Belur , Shimelis Hermela , Montalban Gemma , Lee Kun Y. , Huang Huaizhi , Lumby Carolyn A. , Na Jie , Susswein Lisa R. , Roberts Maegan E. , Marshall Megan L. , Hiraki Susan , LaDuca Holly , Chao Elizabeth , Yussuf Amal , Pesaran Tina , Neuhausen Susan L. , Haiman Christopher A. , Kraft Peter , Lindstrom Sara , Palmer Julie R. , Teras Lauren R. , Vachon Celine M. , Yao Song , Ong Irene , Nathanson Katherine L. , Weitzel Jeffrey N. , Boddicker Nicholas , Gnanaolivu Rohan , Polley Eric C. , Mer Georges , Cui Gaofeng , Karam Rachid , Richardson Marcy E. , Domchek Susan M. , Yadav Siddhartha , Hruska Kathleen S. , Dolinsky Jill , Weroha S. John , Hart Steven N. , Simard Jacques , Masson Jean Yves , Pang Yuan-Ping , Couch Fergus J.
Published: August 2023

Abstract
Pathogenic protein-truncating variants of RAD51C, which plays an integral role in promoting DNA damage repair, increase the risk of breast and ovarian cancer. A large number of RAD51C missense variants of uncertain significance (VUS) have been identified, but the effects of the majority of these variants on RAD51C function and cancer predisposition have not been established. Here, analysis of 173 missense variants by a homology-directed repair (HDR) assay in reconstituted RAD51C−/− cells identified 30 nonfunctional (deleterious) variants, including 18 in a hotspot within the ATP-binding region. The deleterious variants conferred sensitivity to cisplatin and olaparib and disrupted formation of RAD51C/XRCC3 and RAD51B/RAD51C/RAD51D/XRCC2 complexes. Computational analysis indicated the deleterious variant effects were consistent with structural effects on ATP-binding to RAD51C. A subset of the variants displayed similar effects on RAD51C activity in reconstituted human RAD51C-depleted cancer cells. Case–control association studies of deleterious variants in women with breast and ovarian cancer and noncancer controls showed associations with moderate breast cancer risk [OR, 3.92; 95% confidence interval (95% CI), 2.18–7.59] and high ovarian cancer risk (OR, 14.8; 95% CI, 7.71–30.36), similar to protein-truncating variants. This functional data supports the clinical classification of inactivating RAD51C missense variants as pathogenic or likely pathogenic, which may improve the clinical management of variant carriers.
Significance:
Functional analysis of the impact of a large number of missense variants on RAD51C function provides insight into RAD51C activity and information for classification of the cancer relevance of RAD51C variants.
Data from Hypoxia-responsive lncRNA AC115619 encodes a micropeptide that suppresses m6A modifications and hepatocellular carcinoma progression
Authors: Zhang Qiangnu , Wei Teng , Yan Lesen , Zhu Siqi , Jin Wen , Bai Yu , Zeng Yuandi , Zhang Xiaofei , Yin Zexin , Yang Jilin , Zhang Wenjian , Wu Meilong , Zhang Yusen , Liu Liping
Published: August 2023

Abstract
Long non-coding RNAs (lncRNAs) regulate a number of aspects of cancer biology. Recent research has shown that lncRNAs can encode micropeptides that mediate their functions in tumors. Here, we revealed that the liver-specific putative lncRNA, AC115619, is expressed at low levels in hepatocellular carcinoma (HCC) and encodes a micropeptide, designated as AC115619-22aa. AC115619 played a crucial role in the regulation of tumor progression and was a prognostic indicator in HCC. The encoded micropeptide AC115619-22aa inhibited the progression of HCC by binding to WTAP and impeding the assembly of the N6-methyladenosine (m6A) methyltransferase complex, which regulates the expression of tumor-associated genes, such as SOCS2 and ATG14. AC115619 was co-transcribed with the adjacent upstream coding gene APOB, and hypoxia induced transcriptional repression of both APOB and AC115619 by controlling HIF1A/HDAC3 and HNF4A signaling. In animal and patient-derived models, AC115619-22aa reduced global m6A levels and suppressed tumor growth. In conclusion, this study establishes AC115619 and its encoded micropeptide as potential prognostic markers and therapeutic targets for patients with HCC
Data from The mTOR Signaling Pathway Interacts with the ER Stress Response and the Unfolded Protein Response in Cancer
Authors: Mafi Sahar , Ahmadi Elham , Meehan Eileen , Chiari Conner , Mansoori Behzad , Sadeghi Hossein , Milani Sahar , Jafarinia Morteza , Taeb Shahram , Mafakheri Bashmagh Bayan , Mansoorian Seyed Mohammad Ali. , Soltani-Zangbar Mohammad Sadegh , Wang Kepeng , Rostamzadeh Davoud
Published: August 2023

Abstract
The mTOR complex 1 (mTORC1) coordinates several important environmental and intracellular cues to control a variety of biological processes, such as cell growth, survival, autophagy, and metabolism in response to energy levels, growth signals, and nutrients. The endoplasmic reticulum (ER) is a crucial intracellular organelle that is essential for numerous cellular functions, including the synthesis, folding and modification of newly synthesized proteins, stress responsiveness, and maintainence of cellular homeostasis. mTOR-mediated upregulation of protein synthesis induces the accumulation of misfolded or unfolded proteins in the ER lumen which induces ER stress, leading to activation of the unfolded protein response (UPR) pathway. Reciprocally, ER stress regulates the PI3K/AKT/mTOR signaling pathway. Therefore, under pathological conditions, the crosstalk between the mTOR and UPR signaling pathways during cellular stress can critically affect cancer cell fate and may be involved in the pathogenesis and therapeutic outcome of cancer. Here, we discuss accumulating evidence showing the mechanism of action, interconnections, and molecular links between mTOR signaling and ER stress in tumorigenesis and highlight potential therapeutic implications for numerous cancers.
Data from PP2Ac Deficiency Enhances Tumor Immunogenicity by Activating STING-Type I Interferon Signaling in Glioblastoma
Authors: Mondal Isha , Das Oishika , Sun Raymond , Gao Jian , Yu Bohyeon , Diaz Aaron , Behnan Jinan , Dubey Abhishek , Meng Zhipeng , Eskandar Emad , Xu Beisi , Lu Rongze Olivia. , Ho Winson S.
Published: August 2023

Abstract
Glioblastoma (GBM) is an immunologically “cold” tumor that does not respond to current immunotherapy. Here, we demonstrate a fundamental role for the α-isoform of the catalytic subunit of protein phosphatase-2A (PP2Ac) in regulating glioma immunogenicity. Genetic ablation of PP2Ac in glioma cells enhanced double stranded DNA (dsDNA) production and cGAS-type I interferon (IFN) signaling, MHC-I expression, and tumor mutational burden. In co-culture experiments, PP2Ac deficiency in glioma cells promoted dendritic cell (DC) cross presentation and clonal expansion of CD8+ T cells. In vivo, PP2Ac depletion sensitized tumors to immune checkpoint blockade and radiotherapy treatment. Single cell analysis demonstrated that PP2Ac deficiency increased CD8+ T cell, NK cell, and DC accumulation and reduced immunosuppressive tumor associated macrophages. Furthermore, loss of PP2Ac increased IFN signaling in myeloid and tumor cells and reduced expression of a tumor gene signature associated with worse patient survival in TCGA. Collectively, this study establishes a novel role for PP2Ac in inhibiting dsDNA-cGAS-STING signaling to suppress anti-tumor immunity in glioma.
Data from PP2Ac Deficiency Enhances Tumor Immunogenicity by Activating STING–Type I Interferon Signaling in Glioblastoma
Authors: Mondal Isha , Das Oishika , Sun Raymond , Gao Jian , Yu Bohyeon , Diaz Aaron , Behnan Jinan , Dubey Abhishek , Meng Zhipeng , Eskandar Emad , Xu Beisi , Lu Rongze Olivia , Ho Winson S.
Published: August 2023

Abstract
Glioblastoma (GBM) is an immunologically “cold” tumor that does not respond to current immunotherapy. Here, we demonstrate a fundamental role for the α-isoform of the catalytic subunit of protein phosphatase-2A (PP2Ac) in regulating glioma immunogenicity. Genetic ablation of PP2Ac in glioma cells enhanced double-stranded DNA (dsDNA) production and cGAS–type I IFN signaling, MHC-I expression, and tumor mutational burden. In coculture experiments, PP2Ac deficiency in glioma cells promoted dendritic cell (DC) cross-presentation and clonal expansion of CD8+ T cells. In vivo, PP2Ac depletion sensitized tumors to immune-checkpoint blockade and radiotherapy treatment. Single-cell analysis demonstrated that PP2Ac deficiency increased CD8+ T-cell, natural killer cell, and DC accumulation and reduced immunosuppressive tumor-associated macrophages. Furthermore, loss of PP2Ac increased IFN signaling in myeloid and tumor cells and reduced expression of a tumor gene signature associated with worse patient survival in The Cancer Genome Atlas. Collectively, this study establishes a novel role for PP2Ac in inhibiting dsDNA–cGAS–STING signaling to suppress antitumor immunity in glioma.
Significance:
PP2Ac deficiency promotes cGAS–STING signaling in glioma to induce a tumor-suppressive immune microenvironment, highlighting PP2Ac as a potential therapeutic target to enhance tumor immunogenicity and improve response to immunotherapy.
Figure S2: The total follow-up period (time from diagnosis to end of the study) of articles included in this review, sorted by end of the study period. from A Review of the Application of Spatial Survival Methods in Cancer Research: Trends, Modeling, and Visualization Techniques
Authors: Bizuayehu Habtamu Mellie , Cameron Jessica K. , Dasgupta Paramita , Baade Peter D.
Published: August 2023

Supplementary Figure S2 shows article's study period in years
Figure S1 Summary of the keywords provided by authors of the original articles included in the review. from A Review of the Application of Spatial Survival Methods in Cancer Research: Trends, Modeling, and Visualization Techniques
Authors: Bizuayehu Habtamu Mellie , Cameron Jessica K. , Dasgupta Paramita , Baade Peter D.
Published: August 2023

Supplementary Figure S1 shows summary of keywords extracted from articles
Supplementary Table 2 from Medical Financial Hardship and Food Security among Cancer Survivors in the United States
Authors: Hallgren Emily , Narcisse Marie-Rachelle , Andersen Jennifer A. , Willis Don E. , Thompson Tess , Bryant-Smith Gwendolyn , McElfish Pearl A.
Published: August 2023

Supplementary Table 2 shows the results of the analysis exploring the moderating effect of a cancer history on the relationship between medical financial hardship and food security among cancer survivors and individuals without a cancer history.
Supplementary Table 2 from Folate Intake and Ovarian Cancer Risk among Women with Endometriosis: A Case–Control Study from the Ovarian Cancer Association Consortium
Authors: Gersekowski Kate , Ibiebele Torukiri I , Doherty Jennifer A. , Harris Holly R. , Goodman Marc T. , Terry Kathryn L. , Wu Anna H. , Bandera Elisa V. , Qin Bo , Ong Jue-Sheng , Tyrer Jonathan P. , Dixon-Suen Suzanne C. , Modugno Francesmary , Risch Harvey A , Webb Penelope M.
Published: August 2023

Supplementary Table 2 shows the single nucleotide polymorphisms (SNPs) used as instruments for folate level in the Mendelian randomization analysis.
Table S6 from Field Synopsis of Environmental and Genetic Risk Factors of Sporadic Early-Onset Colorectal Cancer and Advanced Adenoma
Authors: Zhang Rongqi , Boakye Daniel , Yang Nan , Zhou Xuan , Zhou Yajing , Jiang Fangyuan , Yu Lili , Wang Lijuan , Sun Jing , Yuan Shuai , Chen Jie , Hamilton Ashleigh C. , Coleman Helen G. , Larsson Susanna C. , Little Julian , Dunlop Malcolm G. , Giovannucci Edward L. , Theodoratou Evropi , Li Xue
Published: August 2023

Supplementary Table 6 shows the basic characteristics of EOCRC, LOCRC and healthy controls in UK Biobank.
Table S5 from Field Synopsis of Environmental and Genetic Risk Factors of Sporadic Early-Onset Colorectal Cancer and Advanced Adenoma
Authors: Zhang Rongqi , Boakye Daniel , Yang Nan , Zhou Xuan , Zhou Yajing , Jiang Fangyuan , Yu Lili , Wang Lijuan , Sun Jing , Yuan Shuai , Chen Jie , Hamilton Ashleigh C. , Coleman Helen G. , Larsson Susanna C. , Little Julian , Dunlop Malcolm G. , Giovannucci Edward L. , Theodoratou Evropi , Li Xue
Published: August 2023

Supplementary Table 5 shows the list of genes and variants and their associations with early-onset colorectal cancer.
Supplement Table 2 from Cost-effectiveness of Human Papillomavirus Self-collection Intervention on Cervical Cancer Screening Uptake among Underscreened U.S. Persons with a Cervix
Authors: Spees Lisa P. , Biddell Caitlin B. , Smith Jennifer S. , Des Marais Andrea C. , Hudgens Michael G. , Sanusi Busola , Jackson Sarah , Brewer Noel T. , Wheeler Stephanie B.
Published: August 2023

Deterministic Sensitivity Analyses Results
Supplementary Table S6 from Associations of Race and Ethnicity with Hepatocellular Carcinoma, Decompensation, and Mortality in US Veterans with Cirrhosis
Authors: VoPham Trang , Cravero Anne , Feld Lauren D. , Green Pamela , Feng Ziding , Berry Kristin , Kim Nicole J. , Vutien Philip , Mendoza Jason A. , Ioannou George N.
Published: August 2023

Supplementary Table S6. Association between race/ethnicity and risk of all-cause mortality in patients with cirrhosis overall and by cirrhosis etiology: follow-up from cirrhosis diagnosis (2001-2014) to 2020
Supplementary Table S1 from Associations of Race and Ethnicity with Hepatocellular Carcinoma, Decompensation, and Mortality in US Veterans with Cirrhosis
Authors: VoPham Trang , Cravero Anne , Feld Lauren D. , Green Pamela , Feng Ziding , Berry Kristin , Kim Nicole J. , Vutien Philip , Mendoza Jason A. , Ioannou George N.
Published: August 2023

Supplementary Table S1. ICD-9 and ICD-10 codes for cirrhosis, decompensated cirrhosis, liver transplantation, and hepatocellular carcinoma
Data from A Review of the Application of Spatial Survival Methods in Cancer Research: Trends, Modeling, and Visualization Techniques
Authors: Bizuayehu Habtamu Mellie , Cameron Jessica K. , Dasgupta Paramita , Baade Peter D.
Published: August 2023

Abstract
Spatial modeling of cancer survival is an important tool for identifying geographic disparities and providing an evidence base for resource allocation. Many different approaches have attempted to understand how survival varies geographically. This is the first scoping review to describe different methods and visualization techniques and to assess temporal trends in publications. The review was carried out using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline using PubMed and Web of Science databases. Two authors independently screened articles. Articles were eligible for review if they measured cancer survival outcomes in small geographical areas by using spatial regression and/or mapping. Thirty-two articles were included, and the number increased over time. Most articles have been conducted in high-income countries using cancer registry databases. Eight different methods of modeling spatial survival were identified, and there were seven different ways of visualizing the results. Increasing the use of spatial modeling through enhanced data availability and knowledge sharing could help inform and motivate efforts to improve cancer outcomes and reduce excess deaths due to geographical inequalities. Efforts to improve the coverage and completeness of population-based cancer registries should continue to be a priority, in addition to encouraging the open sharing of relevant statistical programming syntax and international collaborations.
Data from Folate Intake and Ovarian Cancer Risk among Women with Endometriosis: A Case–Control Study from the Ovarian Cancer Association Consortium
Authors: Gersekowski Kate , Ibiebele Torukiri I , Doherty Jennifer A. , Harris Holly R. , Goodman Marc T. , Terry Kathryn L. , Wu Anna H. , Bandera Elisa V. , Qin Bo , Ong Jue-Sheng , Tyrer Jonathan P. , Dixon-Suen Suzanne C. , Modugno Francesmary , Risch Harvey A , Webb Penelope M.
Published: August 2023

AbstractBackground:
Although folate intake has not been associated with an increased risk of ovarian cancer overall, studies of other cancer types have suggested that high folate intake may promote carcinogenesis in precancerous lesions. Women with endometriosis (a potential precancerous lesion) have an increased risk of developing ovarian cancer; however, whether high folate intake increases risk in this group is unknown.
Methods:
We conducted a pooled analysis of six case–control studies from the Ovarian Cancer Association Consortium to investigate the association between folate intake and risk of ovarian cancer among women with and without self-reported endometriosis. We included 570 cases/558 controls with and 5,171/7,559 without endometriosis. We used logistic regression to estimate odds ratios (OR) and 95% confidence intervals for the association between folate intake (dietary, supplemental, and total) and ovarian cancer risk. Finally, we used Mendelian randomization (MR) to evaluate our results using genetic markers as a proxy for folate status.
Results:
Higher dietary folate intake was associated with an increased risk of ovarian cancer for women with endometriosis [OR, 1.37 (1.01–1.86)] but not for women without endometriosis. There was no association between supplemental folate intake and ovarian cancer risk for women with or without endometriosis. A similar pattern was seen using MR.
Conclusions:
High dietary folate intake may be associated with an increased risk of ovarian cancer among women with endometriosis.
Impact:
Women with endometriosis with high folate diets may be at increased risk of ovarian cancer. Further research is needed on the potential cancer-promoting effects of folate in this group.