bluuebunny/crossref_metadata_2025 huggingface dataset:
Middle‐Range Theory of Disaster Cognitive Readiness in Nursing Practice Through Theory Derivation and Sentence Synthesis
Authors: Hwang Sinwoo , Baek Seoyoung
Published: January 2025

Introduction

Disaster nursing is a complex, dynamic, and resource‐limited working environment, like military operations. As the COVID‐19 outbreak has shown, not only hospitals, but all communities need nurses who can systematically respond to disasters. It is important for nurses to possess the necessary readiness to respond to disasters with confidence and autonomy. However, there is a lack of evidence for a theoretical framework for nurses' cognitive readiness for disaster nursing.

Objective

The purpose of this study was to describe the development of a middle‐range theory about nurse's cognitive readiness in disaster response.

Methods

Fletcher and Wind's model was modified to develop a theoretical framework for disaster cognitive readiness by using theory derivation and sentence synthesis.

Results

In the developed theory, “Disaster cognitive readiness” refers to the cognitive preparedness of nurses for effectively responding to and managing disaster situations which are in high‐stakes, complex environments, achieved through a combination of education, training, and practice in essential skills such as problem‐solving, communication, resilience, and ethics. The theory for disaster cognitive readiness described the competencies: knowledge, problem‐solving, metacognition, decision‐making, adaptability, risk‐communication, resilience, and ethics. The outcomes of disaster cognitive readiness are personal (job satisfaction, professional growth) and organizational (disaster management, disaster resilience) outcomes.

Conclusion

The results of this study are expected to be useful in developing educational and training programs that emphasize the characteristics of disaster nursing competencies and in verifying their effectiveness in enhancing disaster cognitive readiness as well as individual and organizational outcomes.
Ethical Problems and the Role of Expertise in Health Policy: A Case Study of Public Policy Making in Sweden During COVID‐19
Authors: Falkenström Erica , Selberg Rebecca
Published: January 2025

Although the literature widely discusses the role of academics as experts in public policy making, empirical case studies on ethical problems related to the production and implementation of health policy are scarce. During COVID‐19, the Swedish policy document (PD) National Principles for Prioritization in Intensive Care under Extraordinary Conditions was produced in collaboration with 11 academic experts. Based on a case study, this article examines ethical problems related to the production and implementation of this PD by conducting an analysis of key PDs directed at caregivers during this time. Three ethical problems are identified and analyzed, which relate to starting points, the content of the PD, and the implementation. This study provides strong theoretical support for Jonathan Wolff's model of engaged political philosophy, as well as practical support on avoiding undesirable consequences of policy making and preparing academics for expert roles in public policy.

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Does Mobile Money Adoption and Credit Access Improve Enterprise Innovation and Performance in Sierra Leone?
Authors: Djossou Gbetoton Nadege , Sandy James Fomba , Novignon Jacob
Published: January 2025

This study sought to unpack the impact of mobile money adoption and credit constraints on product innovation and performance of Micro, Small, and Medium‐scale Enterprises in Sierra Leone. We used the most recent Sierra Leone Enterprise survey data conducted by the World Bank to monitor enterprises. To achieve the objectives of the study, we used Ordinary Least Squares and nonexperimental techniques (instrumental variable techniques). This allowed us to account for potential endogeneity problems that may bias parameter estimates if not accounted for. Our findings show that mobile money use and credit access significantly enhanced firms' ability to innovate, which then improved their performance. We did not find any statistically significant gender‐related variation in the relationship. Our findings support current policy efforts to revamp financial inclusion in Sierra Leone and highlight the need to tailor services to fully reap the potential gains.
Conceptualising Anti‐Racist Institutionalism
Authors: Eseonu Temidayo
Published: January 2025

Discussions on race, institutions and public administration in scholarly literature have largely originated from a US context; this article argues that new institutionalism needs a race lens outside of this context, allowing for analyses of how institutions can be implicated in the (re)production of racial inequalities in countries with racial regimes. This article suggests focusing on the mechanics of racialisation to understand how racial inequalities are (re)produced. This article makes two theoretical propositions: institutions, as sets of narratives, practices and rules, are racialised, and these institutions can be transformed in pursuit of racial equity. Using qualitative data from a case study of a UK local government's employment service, an expanded theoretical strand of new institutionalism is proposed: anti‐racist institutionalism. This research provides illustrative examples of racialised narratives, and colour‐blind practices and rules such as budgets and performance management measures can have racialised outcomes. Further research is required to understand what institutional change is required to transform these racialised institutions in pursuit of racial equity.
First record of Amblyomma rotundatum (Ixodida: Ixodidae) parasitizing a seabird, the masked booby (Sula dactylatra)
Authors: Acosta Igor C.L. , Martins Thiago F. , Goldberg Daphne W. , Ikeda Joana M.P. , Oliveira Denyiélim E. , Gastal Silvia B. , Labruna Marcelo B.
Published: January 2025

N/A
New host and geographic records of Amblyomma geoemydae (Cantor) (Ixodidae: Amblyomminae) from southern China and Southeast Asia
Authors: Amarga Ace Kevin S. , Robbins Richard G. , Tseng Hui-Yun , Lin Si-Min
Published: January 2025

N/A
Complete mitochondrial genome and phylogenetic analysis of Nothrus silvestris Nicolet, 1855 (Acari, Oribatida, Nothridae)
Authors: Ge Xueying , Liu Dong
Published: January 2025

In this study, we report the complete mitogenome of Nothrus silvestris Nicolet, 1855 (Acari, Oribatida, Nothridae) sequenced from Illumina sequencing data. The full length of this mitogenome is 14,592 bp with the nucleotide composition A (41.0%), C (22.2%), G (13.1%), and T (23.7%). The N. silvestris mitogenome comprises 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region. To elucidate the phylogenetic position of N. silvestris, a phylogenetic tree of 77 mite species were analyzed by maximum likelihood (ML) methods. According to phylogenetic analysis based on 13 protein-coding genes of mitogenomes, N. silvestris and Nothrus reticulatus were found the most basal Crotonioidea in the given dataset. This mitogenome not only enriches the genetic information of Nothridae, but also will be useful in the phylogenic and evolutional studies on oribatid mites.
AAV-based gene delivery of antimicrobial peptides to combat drug-resistant pathogens
Authors: Baindara Piyush , Roy Dinata , Boosani Chandra S. , Mandal Santi M. , Green Jonathan A.
Published: January 2025

Antimicrobial peptides (AMPs) have emerged as potential alternatives to conventional antibiotics due to their novelty and multiple mechanisms of action. Because they are peptides, AMPs are amenable to bioengineering and suitable for cloning and expression at large production scales. However, the efficient delivery of AMPs is an unaddressed issue, particularly due to their large size, possible toxicities, and the development of adverse immune responses. Here, we have reviewed the possibilities of adeno-associated virus (AAV)-based localized gene delivery of AMPs for the treatment of infectious diseases with a special focus on respiratory infections. By discussing the gene delivery mechanism of AAV and the accompanying technical and therapeutic challenges with AMPs, we describe a foundation that emphasizes the use of viral vector-based gene delivery of AMPs for disease treatment.
Spatiotemporal crash outliers are also noteworthy: evidence from 13 years of pedestrian-vehicle crashes in North Carolina
Authors: Song Li , Lin Yixuan , Xu Guixin , Zhang Xuequan , Liu Wei , Liu Bing , Chen Guojun
Published: January 2025

Introduction

Previous research usually focused on high-frequency crash clusters (surrounded by high-frequency crashes), which overlooked outlier locations where high-frequency crashes were surrounded by low-frequency crashes. Neglecting spatiotemporal outliers might overlook critical factors for safety improvements.

Methods

Using pedestrian-vehicle crash data in North Carolina from 2007 to 2019, this study proposes an enhanced spatiotemporal analysis framework (combined with Approximate Nearest Neighbour and the Global Moran I index) to distinguish spatiotemporal crash outliers from aggregated/dispersed patterns. Random parameters ordered logit models with heterogeneity in means are used to model ordered injury severities, identify significant factors and explore in-depth heterogeneity across observations.

Results

Likelihood ratio test results indicate significant instability exists in factors across four spatiotemporal patterns: high-low outlier, low-high outlier, high-high cluster and low-low cluster. Also, spatiotemporal variations and shifts in the proportion of crashes that suffer more severe injuries are founded on the marginal effects of several factors. Specific countermeasures and policy guidance are suggested under different patterns. In high-low outliers, drunk drivers increase the probability of more severe crash outcomes in public vehicular areas from 16.3% to 92.8%. Meanwhile, in low-high outliers, 64.8% of the crashes with speed limits between 45 and 75 mph would result in more severe outcomes. By increasing the mean, older pedestrians, drunk pedestrians and urban areas increase this proportion to 91.6%, 87.2% and 78.2%, respectively.

Conclusion

These findings underscore the importance of strengthening alcohol tests and setting safety crossing facilities for older pedestrians in identified high-speed urban areas. All these propose a calling for spatiotemporal outlier investigation in future crash analysis and prevention.
Upgrading your best chances: postdiagnosis smoking cessation boosts life expectancy of patients with cancer – a systematic review and meta-analysis
Authors: Caini Saverio , Gorini Giuseppe , Del Riccio Marco , Saieva Calogero , Carreras Giulia , Bonomo Pierluigi , Salvestrini Viola , Cattaruzza Maria Sofia , Assedi Melania , D'Ecclesiis Oriana , Gaeta Aurora , Albini Adriana , Masala Giovanna , Gandini Sara
Published: January 2025

Background

Tobacco use is linked to increased cancer risk, and people who smoke represent a large proportion of newly diagnosed patients with cancer. The fact that smoking cessation at the time of diagnosis can improve the patient’s life expectancy is still not broadly understood. We conducted a systematic review and meta-analysis to quantify the survival benefits obtainable by quitting smoking on diagnosis.

We included articles found in MEDLINE and EMBASE until 2 January 2024. We conducted a random effects meta-analysis, studying correlates of between-studies heterogeneity and exploring the presence of publication bias.

There were 36 eligible studies published in 1980–2023, totalling over 17 000 actively smoking patients with cancer. The most studied cancer sites were the lung (n=17) and head and neck (n=14). The median proportion of patients who quit on diagnosis was 42.5%. Postdiagnosis cessation was associated with longer overall survival (summary HR (sHR) 0.71, 95% CI 0.65 to 0.78), progression-free survival (sHR 0.64, 95% CI 0.41 to 0.98), disease-free/recurrence-free survival (sHR 0.59, 95% CI 0.43 to 0.81) and improved local/locoregional control (sHR 0.69, 95% CI 0.50 to 0.94). Heterogeneity was generally large; for overall survival, study results were stronger when properly adjusted but did not vary across cancer sites. There was evidence for publication bias, but the results were only marginally altered on imputation of potentially missing studies.

Postdiagnosis smoking cessation is effective in improving the chances of survival for patients with cancer. Cessation support programmes should be integrated into the routine management of patients with cancer as they may favourably affect survival.
Association between vitamin D status at 3 years and eosinophilic asthma in 6-year-old children with a history of severe bronchiolitis
Authors: Doumat George , El Zein Joumane , Mehta Geneva D , Zhu Zhaozhong , Espinola Janice A , Sullivan Ashley F , Hasegawa Kohei , Camargo Carlos A
Published: January 2025

The association between early childhood serum 25-hydroxyvitamin D (25(OH)D) and eosinophilic asthma remains unclear. We investigated this association using multicentre prospective data from 584 children with a history of bronchiolitis requiring hospitalisation (high-risk population). Low serum 25(OH)D levels (<20 ng/mL) were associated with increased odds of developing eosinophilic asthma (adjusted OR 2.33; 95% CI 1.23, 4.40; p=0.01) as compared with children with serum 25(OH)D of 20–39.9 ng/mL. Our data facilitate further investigation into the potential role of early-life vitamin D supplementation among children with a history of severe bronchiolitis and eosinophilia for preventing childhood asthma.
Design of Unmarked AI Recognition Algorithm for Athletes’ Traditional Sports Actions Based on Attention Mechanism
Authors: Wei Guo , Yi Liu
Published: January 2025

In order to accurately and quickly understand the characteristics and skills of athletes’ traditional sports actions, an unmarked AI recognition algorithm for athletes’ traditional sports actions based on attention mechanism is designed. The lightweight space-time map convolution neural network (ST-GCN) based on attention mechanism in AI technology is used to complete the traditional sports action recognition of athletes. The traditional sports action skeleton map of athletes is constructed as unlabeled samples and input into the ST-GCN network. The time and space characteristics of the input skeleton map are extracted through the time convolution network (TCN) and graph convolution neural network (GCN), respectively. Add graph attention mechanism and channel attention mechanism in the network layer and channel, improve the feature expression ability and action recognition accuracy, and introduce Ghost module to replace the original image convolution work, complete the network lightweight processing, and improve the efficiency of ST-GCN network recognition of sports actions. Complete the classification and recognition of athletes’ traditional sports actions through the standard SoftMax. Experiments show that when the size of the attention mechanism window added in ST-GCN is 1000, the network can have the best performance, and the identified resource cost is relatively minimal. After adding attention mechanism, the F1 score of ST-GCN network in unmarked training is close to 1. The skeleton extraction results of athletes are very accurate, and the algorithm can accurately identify different actions generated by different kinds of movements.
Innovative Education in College English Education: Advancements in Technology and Teaching Methods
Authors: Han Yuqian
Published: January 2025

The teaching and learning of the English language have changed, with technology introducing new aspects and practices. Throughout this study, we examine the impacts brought about by technological innovations and advancements in learning and teaching of English language, specifically, in colleges. With the increasing adoption of digital platforms, Artificial Intelligence (AI)-powered language learning tools, and virtual classrooms, English educators now have access to a wide range of tools to enhance language acquisition, personalized learning, and student engagement. Integration of these technologies alongside adaptive learning techniques, such as flipped classrooms and blended learning models, which emphasize active student participation and individualized feedback are presented in this research work. Through a comprehensive analysis of current teaching practices and their alignment with modern educational technologies, the study identifies key strategies that improve English proficiency and communication skills among students. The findings of this work demonstrate that the application of AI, interactive learning software, and data-driven assessment methods significantly enhance both student outcomes and overall course effectiveness. The study also stresses the need for teacher training and curriculum development to embrace such changes. Therefore, this paper is a useful reference for educators and institutions that wish to modernize college English education, focused on implementing technological tools to enhance the teaching and learning process.
Artificial Intelligence Implementation in Library Information Systems: Current Trends and Future Studies
Authors: Narendra Albertoes Pramoekti , Dewi Christine , Gunawan Lanyta Setyani , Ardi Ambrosius Sindu
Published: January 2025

The field of Library Information Systems (LIS) has transformed with the rise of Artificial Intelligence (AI), enhancing library operations, services, and user experiences. AI improves user satisfaction by streamlining access to resources and providing librarians with tools for collection management, information retrieval, and data-driven decision-making. It enables analysis of user behavior and trends, optimizing resource allocation and collection development. By leveraging AI to assess circulation data and usage patterns, librarians can better anticipate user needs and future trends. This study examines recent advancements in AI integration within LIS over the past five years, focusing on the methodologies, tools, and algorithms used. Through a systematic literature review, the study identifies key trends, challenges, and examples of AI applications in LIS, providing insights and recommendations for future research and implementation.
Antiamnesic and Neurotrophic Effects of Parkia biglobosa (Jacq.) R. Br (Fabaceae) Aqueous Extract on In Vivo and In Vitro Models of Excitotoxicity
Authors: Kandeda Antoine Kavaye , Foutse Liliane Yimta , Tongoue Corneille , Djientcheu Jean Philippe , Dimo Théophile
Published: January 2025

Amnesia is a memory disorder marked by the inability to recall or acquire information. Hence, drugs that also target the neurogenesis process constitute a hope to discover a cure against memory disorders. This study is aimed at evaluating the antiamnesic and neurotrophic effects of the aqueous extract of Parkia biglobosa (P. biglobosa) on in vivo and in vitro models of excitotoxicity. For the in vivo study, 42 adult male rats were divided into six groups of seven rats each and treated daily for 30 days as follows: normal control group (distilled water, 10 mL/kg, po), negative control group (distilled water, 10 mL/kg, po), positive control group (piracetam, 200 mg/kg, po), and 03 test groups (extract, 44, 88, and 176 mg/kg, po). Scopolamine (0.5 mg/kg, ip) was administered once daily, 45 min after these treatments, for 14 days, except in the normal control group. The animals were then subjected to short‐term memory (new object recognition and T‐maze) and long‐term memory (radial arm maze) tests for 15 following days. Animals were then euthanized, and biochemical analyses (neurotransmitters, oxidative status, and neuroinflammation) were performed in the prefrontal cortex, hippocampus, and serum. Histological analysis of these organs was also carried out. In the in vitro study, the effect of the extract (5, 10, 19, 40, 77, 153, 306, 615, 1225, and 2450 μg/mL) was assessed on the viability of primary cortical neurons exposed to L‐glutamate (0.1 mg/mL). Scopolamine induced memory impairment and increased oxidative stress, neuroinflammation, and neuronal loss. P. biglobosa extract (44 mg/kg) reduced (p < 0.001) short‐ and long‐term memory deficit. It also increased (p < 0.01) the concentration of acetylcholine, reduced (p < 0.001) that of malondialdehyde, and limited (p < 0.001) neuroinflammation and neuronal loss (p < 0.001). In addition, the extract (2450 μg/mL) increased (p < 0.001) the percentage of viable cells. These results suggest that the extract has effects on amnesia and neurogenesis. These effects seem to be mediated by antioxidant and anti‐inflammatory modulations.
Data Supplement 1 from Pathogenic Variants in Cancer Susceptibility Genes Predispose to Ductal Carcinoma In Situ of the Breast
Authors: Huang Huaizhi , Couch Ronan E. , Karam Rachid , Hu Chunling , Boddicker Nicholas , Polley Eric C. , Na Jie , Ambrosone Christine B. , Yao Song , Trentham-Dietz Amy , Eliassen A. Heather , Penney Kathryn , Brantley Kristen , Bodelon Clara , Teras Lauren R. , Hodge James , Patel Alpa , Haiman Christopher A. , John Esther M. , Neuhausen Susan L. , Martinez Elena , Lacey James V. , O’Brien Katie M. , Sandler Dale P. , Weinberg Clarice R. , Palmer Julie R. , Bertrand Kimberly A. , Vachon Celine M. , Olson Janet E. , Ruddy Kathryn E. , Anton-Culver Hoda , Ziogas Argyrios , Goldgar David E. , Nathanson Katherine L. , Domchek Susan M. , Weitzel Jeffrey N. , Kraft Peter , Dolinsky Jill S. , Pesaran Tina , Richardson Marcy E. , Yadav Siddhartha , Couch Fergus J.
Published: January 2025

Supplemental methods, references and tables
Supplementary Table 1 from Randomized Phase II Study of Durvalumab with or without Tremelimumab in Patients with Metastatic Castration-Resistant Prostate Cancer
Authors: Winquist Eric , Hotte Sebastien J. , Chi Kim , Sridhar Srikala , Ellard Susan , Ong Michael , Iqbal Nayyer , Salim Muhammad , Emmenegger Urban , Gingerich Joel R. , Lalani Aly-Khan , Major Pierre , Kollmannsberger Christian , Yip Steven , Hansen Aaron , Finch Daygen , Canil Christina , Hutchenreuther James , Vera-Badillo Francisco , Smoragiewicz Martin , Cabanero Michael , Tsao Ming-Sound , Ritch Elie , Wyatt Alexander W. , Seymour Lesley
Published: January 2025

Supplementary Table 1. Representativeness of Study Participants.
Supplementary Table S2 from FDA Approval Summary: Olutasidenib for Adult Patients with Relapsed or Refractory Acute Myeloid Leukemia with an Isocitrate Dehydrogenase 1 Mutation
Authors: Woods Ashley C. , Norsworthy Kelly J. , Choe Moran , Gehrke Brenda J. , Chen Haiyan , Vallejo Jonathon , Pan Lili , Jiang Xiling , Li Hongshan , Kraft Jeffrey , Liu Jiang , Charlab Rosane , Okusanya Olanrewaju O. , Booth Brian , Pazdur Richard , Theoret Marc R. , Angelo de Claro R.
Published: January 2025

Information on Grouped Terms
Table 1 from Chemotherapy Drives Tertiary Lymphoid Structures That Correlate with ICI-Responsive TCF1+CD8+ T Cells in Metastatic Ovarian Cancer
Authors: Lanickova Tereza , Hensler Michal , Kasikova Lenka , Vosahlikova Sarka , Angelidou Artemis , Pasulka Josef , Griebler Hannah , Drozenova Jana , Mojzisova Katerina , Vankerckhoven Ann , Laco Jan , Ryska Ales , Dundr Pavel , Kocian Roman , Cibula David , Brtnicky Tomas , Skapa Petr , Jacob Francis , Kovar Marek , Praznovec Ivan , McNeish Iain A. , Halaska Michal J. , Rob Lukas , Coosemans An , Orsulic Sandra , Galluzzi Lorenzo , Spisek Radek , Fucikova Jitka
Published: January 2025

Univariate Cox proportional hazard analyses.
Supplementary Table S1 from FDA Approval Summary: Olutasidenib for Adult Patients with Relapsed or Refractory Acute Myeloid Leukemia with an Isocitrate Dehydrogenase 1 Mutation
Authors: Woods Ashley C. , Norsworthy Kelly J. , Choe Moran , Gehrke Brenda J. , Chen Haiyan , Vallejo Jonathon , Pan Lili , Jiang Xiling , Li Hongshan , Kraft Jeffrey , Liu Jiang , Charlab Rosane , Okusanya Olanrewaju O. , Booth Brian , Pazdur Richard , Theoret Marc R. , Angelo de Claro R.
Published: January 2025

Subgroup Analysis of Efficacy
Supplementary Data1 from Chemotherapy Drives Tertiary Lymphoid Structures That Correlate with ICI-Responsive TCF1+CD8+ T Cells in Metastatic Ovarian Cancer
Authors: Lanickova Tereza , Hensler Michal , Kasikova Lenka , Vosahlikova Sarka , Angelidou Artemis , Pasulka Josef , Griebler Hannah , Drozenova Jana , Mojzisova Katerina , Vankerckhoven Ann , Laco Jan , Ryska Ales , Dundr Pavel , Kocian Roman , Cibula David , Brtnicky Tomas , Skapa Petr , Jacob Francis , Kovar Marek , Praznovec Ivan , McNeish Iain A. , Halaska Michal J. , Rob Lukas , Coosemans An , Orsulic Sandra , Galluzzi Lorenzo , Spisek Radek , Fucikova Jitka
Published: January 2025

Supplemental material, figures and tables
Supplementary Figure S9 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Supplementary Figure S9. Cell-free DNA methylation analysis of differentially accessible transcription factor binding sites. The box and whisker plots summarize methylation levels in plasma cfDNA from AR/enhancer altered versus wild-type mCRPC patients after z-score transformation of the 10,000 TF binding sites corresponding to each of the top 20 TFs that are (A) most accessible and (B) least accessible in cfDNA from AR/enhancer altered lethal high-risk mCRPC patients. p values were calculated by the Mann-Whitney U test. cfDNA, cell-free DNA; mCRPC, metastatic castration-resistant prostate cancer; TF, transcription factor.
Supplementary Figure S8 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Supplementary Figure S8. Transcription factor analysis in localized prostate cancer versus blood. Log2 fold change of the 20 TFs with most accessible and least accessible binding sites in plasma cell-free DNA (see Fig. 4E, Table S12 and Table S13) in localized prostate adenocarcinoma tumors from TCGA (n = 496) versus blood samples from GTEX (n = 337) (Methods). p value was calculated by Student’s t test. GTEX, Genotype-Tissue Expression project; TCGA, The Cancer Atlas Genome Atlas project; TF, transcription factor.
Figure 3 from Chemotherapy Drives Tertiary Lymphoid Structures That Correlate with ICI-Responsive TCF1+CD8+ T Cells in Metastatic Ovarian Cancer
Authors: Lanickova Tereza , Hensler Michal , Kasikova Lenka , Vosahlikova Sarka , Angelidou Artemis , Pasulka Josef , Griebler Hannah , Drozenova Jana , Mojzisova Katerina , Vankerckhoven Ann , Laco Jan , Ryska Ales , Dundr Pavel , Kocian Roman , Cibula David , Brtnicky Tomas , Skapa Petr , Jacob Francis , Kovar Marek , Praznovec Ivan , McNeish Iain A. , Halaska Michal J. , Rob Lukas , Coosemans An , Orsulic Sandra , Galluzzi Lorenzo , Spisek Radek , Fucikova Jitka
Published: January 2025

NACT-mediated adjuvanticity positively impacts the density of follicular T cells (TFH) and in situ activation of intratumoral B cells in mHGSOC. A–C, Representative image (A) and box plots showing the density of CD4+ cells (B) and CXCR5+PD1+FoxP3−CD4+ TFH cells (C) in the pTME and mTME of chemo-naïve and treated HGSOC (study cohort 1 and 2). Box plots: lower quartile, median, upper quartile; whiskers, minimum, maximum. Statistical significance was calculated by the Mann–Whitney test. P values are indicated. D and E, Dot plot (D) and box plot (E) showing expression profile of gene signatures of B-cell subtypes, e.g., plasma cells (PC), germinal center (GC), and memory B cells within pTME and mTME HGSOC tumor samples with/without NACT. Box plots: lower quartile, median, upper quartile; whiskers, minimum, maximum. Statistical significance was calculated by two-sided Mann–Whitney test. P values are indicated. F and G, Representative image (F) and density of CD68+CD163+ TAMs in pTME and mTME of chemo naïve and treated HGSOC (G). Mean and SEM are shown. Statistical significance was calculated by two-sided Mann–Whitney test. P values are indicated.
Supplementary Figure S3 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Supplementary Figure S3. Kaplan-Meier analysis of an additional cohort of 27 patients with oligometastatic mCRPC, stratified by AR enhancer amplification status in plasma cell-free DNA. (A) Progression-free survival, (B) radiographic progression-free survival, and (C) overall survival. p values were calculated by the log-rank test.
Supplementary Figure S2 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Supplementary Figure S2. Kaplan-Meier analysis based on plasma collected prior to first-line androgen receptor-signaling inhibitor (ARSI) treatment according to (A,B) Androgen receptor (AR) gene body status and (C,D) AR enhancer region status in 63 patients with metastatic castration-resistant prostate cancer (mCRPC). p values were calculated by the log-rank test and hazard ratios (HRs) by the Mantel-Haenszel method.
Supplementary Figure S11 from Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer
Authors: Chauhan Pradeep S. , Alahi Irfan , Sinha Savar , Ledet Elisa M. , Mueller Ryan , Linford Jessica , Shiang Alexander L. , Webster Jace , Greiner Lilli , Yang Breanna , Ni Gabris , Dang Ha X. , Saha Debanjan , Babbra Ramandeep K. , Feng Wenjia , Harris Peter K. , Qaium Faridi , Duose Dzifa Y. , Alexander Sanchez E. , Sherry Alexander D. , Jaeger Ellen B. , Miller Patrick J. , Caputo Sydney A. , Orme Jacob J. , Lucien Fabrice , Park Sean S. , Tang Chad , Pachynski Russell K. , Sartor Oliver , Maher Christopher A. , Chaudhuri Aadel A.
Published: January 2025

Supplementary Figure S11. Cell-free DNA methylation levels of the top 10 least stem-like signature genes in plasma. The box and whisker plots summarize the promoter methylation rates for the top 10 least stem-like genes in plasma cfDNA from AR/enhancer altered versus wild-type mCRPC patients. p values were calculated by the Student’s t test. cfDNA, cell-free DNA; mCRPC, metastatic castration-resistant prostate cancer; TF, transcription factor.
Supplementary Video S1 from BRAF Deletion in Adult Patients with Langerhans Cell Histiocytosis Correlates with Multisystem Disease and Poor Outcomes
Authors: Lang Min , Chang Long , Cai Hao , Lin He , Liu Zheng-zheng , Duan Ming-hui , Zhou Dao-bin , Cao Xin-xin
Published: January 2025

Supplementary Video S1. The function complex (BRAF-MEK-14-3-3) predicted by Alphafold3.
Supplementary Table S1 from BRAF Deletion in Adult Patients with Langerhans Cell Histiocytosis Correlates with Multisystem Disease and Poor Outcomes
Authors: Lang Min , Chang Long , Cai Hao , Lin He , Liu Zheng-zheng , Duan Ming-hui , Zhou Dao-bin , Cao Xin-xin
Published: January 2025

Supplementary Table S1. 183 candidate genes for target sequencing.
Supplementary Figure S4 from BRAF Deletion in Adult Patients with Langerhans Cell Histiocytosis Correlates with Multisystem Disease and Poor Outcomes
Authors: Lang Min , Chang Long , Cai Hao , Lin He , Liu Zheng-zheng , Duan Ming-hui , Zhou Dao-bin , Cao Xin-xin
Published: January 2025

Supplementary Figure S4. The function complex (BRAF-MEK-14-3-3) predicted by Alphafold3 [PyMOL(TM) 2.5.3 - Incentive Product Copyright (C) Schrodinger, LLC.].
Supplementary Figure S3 from BRAF Deletion in Adult Patients with Langerhans Cell Histiocytosis Correlates with Multisystem Disease and Poor Outcomes
Authors: Lang Min , Chang Long , Cai Hao , Lin He , Liu Zheng-zheng , Duan Ming-hui , Zhou Dao-bin , Cao Xin-xin
Published: January 2025

Supplementary Figure S3. Prognosis of adult patients with LCH according to BRAFV600E status.
Supplementary Figure S2 from BRAF Deletion in Adult Patients with Langerhans Cell Histiocytosis Correlates with Multisystem Disease and Poor Outcomes
Authors: Lang Min , Chang Long , Cai Hao , Lin He , Liu Zheng-zheng , Duan Ming-hui , Zhou Dao-bin , Cao Xin-xin
Published: January 2025

Supplementary Figure S2. Initial treatments of adult patients with LCH.
Supplementary Table S8 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Subgroup analysis of the association between DLRI risk groups and disease-free survival in other clinical characteristics in the external validation set 2.
Supplementary Figure S1 from BRAF Deletion in Adult Patients with Langerhans Cell Histiocytosis Correlates with Multisystem Disease and Poor Outcomes
Authors: Lang Min , Chang Long , Cai Hao , Lin He , Liu Zheng-zheng , Duan Ming-hui , Zhou Dao-bin , Cao Xin-xin
Published: January 2025

Supplementary Figure S1. The distribution of myeloid-associated mutations based on age at diagnosis. The relationship between myeloid-associated mutations and age at diagnosis.
Supplementary Table S6 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Univariate CoxPH regression analysis of DLRI risk groups and other clinical characteristics in the external validation set 2.
Supplementary Table S9 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

[89Zr]trastuzumab (ZrT) class and metabolic response signatures
Supplementary Table S8 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Gene set enrichment analysis on Reactome gene sets, comparing, within the 89Zr-trastuzumab class “high”, metabolic response (positive normalized enrichment score – NES) and lack of metabolic response (negative NES).
Supplementary Table S3 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Comparison of clinical characteristics for the external validation set 2 patients with different DLRI risk groups.
Supplementary Table S7 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Gene set enrichment analysis on Hallmark gene sets, comparing, within the 89Zr-trastuzumab class “high”, metabolic response (positive normalized enrichment score – NES) and lack of metabolic response (negative NES).
Supplementary Table S2 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Comparison of immunohistochemical index for the internal validation set 2 patients with different DLRI risk groups.
Supplementary Table S6 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Gene set enrichment analysis on Reactome gene sets, comparing metabolic response (positive normalized enrichment score – NES) and lack of metabolic response (negative NES).
Supplementary Table S11 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Net reclassification index and integrated discrimination improvement statistics in the internal validation set 2.
Supplementary Table S5 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Gene set enrichment analysis on Hallmark gene sets, comparing metabolic response (positive normalized enrichment score – NES) and lack of metabolic response (negative NES).
Supplementary Table S4 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Gene set enrichment analysis on Reactome gene sets, on genes ranked based on the correlation between gene expression and FDG-PET uptake described by SUVmax (positive normalized enrichment score – NES – for positive correlation, negative NES for negative correlation).
Supplementary Table S3 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Gene set enrichment analysis on Hallmark gene sets, on genes ranked based on the correlation between gene expression and FDG-PET uptake described by SUVmax (positive normalized enrichment score – NES – for positive correlation, negative NES for negative correlation).
Supplementary Table S2 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Gene set enrichment analysis on Reactome gene sets, comparing 89Zr-trastuzumab classes “high” (positive normalized enrichment score – NES) and “low” (negative NES).
Supplementary Methods S1 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Supplementary Methods
Supplementary Figure s5 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Perform image testing for web applications to ensure their proper functionality.
Supplementary Figure S6 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Forest plots for pCR in I-SPY2, HER2-positive population, multivariable analysis controlling for hormone receptor status and treatment arm.
Supplementary Figure S6 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

Deep learning radiomic feature selection and the establishment of DLRS using the LASSO Cox regression model.
Supplementary Figure S4 from An Artificial Intelligence–Driven Preoperative Radiomic Subtype for Predicting the Prognosis and Treatment Response of Patients with Papillary Thyroid Carcinoma
Authors: Li Qiang , Zhang Weituo , Liao Tian , Gao Yi , Zhang Yanzhi , Jin Anqi , Ma Ben , Qu Ning , Zhang Huan , Zheng Xiangqian , Li Dapeng , Yun Xinwei , Zhao Jingzhu , Yu Herbert , Gao Ming , Wang Yu , Qian Biyun
Published: January 2025

The specific operational diagrams for the website's predictive classification results.
Supplementary Figure S4 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Comparison of abundance scores of immune populations and stromal cell types with MCP-counter according to A, ZrT class (dichotomized into “high” and “low”), and B, metabolic response.
Supplementary Figure S3 from Integrating Molecular Imaging and Transcriptomic Profiling in Advanced HER2-Positive Breast Cancer Receiving Trastuzumab Emtansine: An Analysis of the ZEPHIR Clinical Trial
Authors: Rediti Mattia , Fimereli Danai , Mileva Magdalena , Wimana Zéna , Venet David , Flamen Patrick , Guiot Thomas , de Vries Elisabeth G.E. , Schröder Carolien P. , Menke-van der Houven van Oordt Catharina Willemien , Maetens Marion , Majjaj Samira , Larsimont Denis , Rothé Françoise , Sotiriou Christos , Gebhart Géraldine
Published: January 2025

Levels of TILs (%) according to ZrT class (dichotomized into “high” and “low”), and metabolic response.