bluuebunny/crossref_metadata_2025 huggingface dataset:
Review and Analysis of RGBT Single Object Tracking Methods: A Fusion Perspective
Authors: Zhang Zhihao , Wang Jun , Li Shengjie , Jin Lei , Wu Hao , Zhao Jian , Zhang Bo
Published: March 2024

Visual tracking is a fundamental task in computer vision with significant practical applications in various domains, including surveillance, security, robotics, and human-computer interaction. However, it may face limitations in visible light data, such as low-light environments, occlusion, and camouflage, which can significantly reduce its accuracy. To cope with these challenges, researchers have explored the potential of combining the visible and infrared modalities to improve tracking performance. By leveraging the complementary strengths of visible and infrared data, RGB-infrared fusion tracking has emerged as a promising approach to address these limitations and improve tracking accuracy in challenging scenarios. In this article, we present a review on RGB-infrared fusion tracking. Specifically, we categorize existing RGBT tracking methods into four categories based on their underlying architectures, feature representations, and fusion strategies, namely feature decoupling based method, feature selecting based method, collaborative graph tracking method, and traditional fusion method. Furthermore, we provide a critical analysis of their strengths, limitations, representative methods, and future research directions. To further demonstrate the advantages and disadvantages of these methods, we present a review of publicly available RGBT tracking datasets and analyze the main results on public datasets. Moreover, we discuss some limitations in RGBT tracking at present and provide some opportunities and future directions for RGBT visual tracking, such as dataset diversity, unsupervised and weakly supervised applications. In conclusion, our survey aims to serve as a useful resource for researchers and practitioners interested in the emerging field of RGBT tracking, and to promote further progress and innovation in this area.
Accurate Localization in LOS/NLOS Channel Coexistence Scenarios Based on Heterogeneous Knowledge Graph Inference
Authors: Zhang Bojun , Liu Xiulong , Xie Xin , Tong Xinyu , Jia Yungang , Shi Tuo , Qu Wenyu
Published: March 2024

Accurate localization is one of the basic requirements for smart cities and smart factories. In wireless cellular network localization, the straight-line propagation of electromagnetic waves between base stations and users is called line-of-sight (LOS) wireless propagation. In some cases, electromagnetic wave signals cannot propagate in a straight line due to obstruction by buildings or trees, and these scenarios are usually called non-LOS (NLOS) wireless propagation. Traditional localization algorithms such as TDOA, AOA,
etc.
, are based on LOS channels, which are no longer applicable in environments where NLOS propagation is dominant, and in most scenarios, the number of base stations with LOS channels containing users is often small, resulting in traditional localization algorithms being unable to satisfy the accuracy demand of high-precision localization. In addition, some nonideal factors may be included in the actual system, all of which can lead to localization accuracy degradation. Therefore, the approach developed in this paper uses knowledge graph and graph neural network (GNN) technology to model communication data as knowledge graphs, and it adopts the knowledge graph inference technique based on a heterogeneous graph attention mechanism to infer unknown data representations in complex scenarios based on the known data and the relationships between the data to achieve high-precision localization in scenarios with LOS/NLOS channel coexistence. We experimentally demonstrate a spatial 2D localization accuracy level of approximately 10 meters on multiple datasets and find that our proposed algorithm has higher accuracy and stronger robustness than the state-of-the-art algorithms.
Diabetes and obesity pathophysiology as a teaching tool to emphasize physiology core concepts
Authors: Remmelgas Brandon , Lowes Shanna L. , Bates Holly E.
Published: March 2024

Students often struggle with integration of physiological systems. Type 2 diabetes mellitus and obesity are two related diseases that are useful to explore the interdependence of physiological systems and multiple physiology core concepts. Deep learning about these diseases has the potential to dramatically improve the health care system of the future.
Best practices for data management and sharing in experimental biomedical research
Authors: Cunha-Oliveira Teresa , Ioannidis John P. A. , Oliveira Paulo J.
Published: March 2024

Effective data management is crucial for scientific integrity and reproducibility, a cornerstone of scientific progress. Well-organized and well-documented data enable validation and building on results. Data management encompasses activities including organization, documentation, storage, sharing, and preservation. Robust data management establishes credibility, fostering trust within the scientific community and benefiting researchers’ careers. In experimental biomedicine, comprehensive data management is vital due to the typically intricate protocols, extensive metadata, and large datasets. Low-throughput experiments, in particular, require careful management to address variations and errors in protocols and raw data quality. Transparent and accountable research practices rely on accurate documentation of procedures, data collection, and analysis methods. Proper data management ensures long-term preservation and accessibility of valuable datasets. Well-managed data can be revisited, contributing to cumulative knowledge and potential new discoveries. Publicly funded research has an added responsibility for transparency, resource allocation, and avoiding redundancy. Meeting funding agency expectations increasingly requires rigorous methodologies, adherence to standards, comprehensive documentation, and widespread sharing of data, code, and other auxiliary resources. This review provides critical insights into raw and processed data, metadata, high-throughput versus low-throughput datasets, a common language for documentation, experimental and reporting guidelines, efficient data management systems, sharing practices, and relevant repositories. We systematically present available resources and optimal practices for wide use by experimental biomedical researchers.
Optimized Distance-Based Algorithm for Cloud Space—Tourist Route Recommendation for Heritage Town, Pondicherry, India
Authors: Lakshmanan Lakshmi , A Madhumathi , Pandian R Sudhakara , S Subhashini , Paraman Sivakumar , K Velmurugan , Di Bona Gianpaolo
Published: March 2024

Architecture, often regarded as a three-dimensional art form, relies on a multitude of abstractions during the design process. In this context, architectural elements are effectively represented through vector-based data processing techniques, offering a canvas for creative exploration. To further our understanding of spatial configurations and generate multiple design insights, mathematical structures known as graphs come into play. Graph theory, a fundamental component of this process, it is a mathematical field that studies relationships and connections between objects using vertices and edges, finding applications in computer science, network analysis, and more finds application in architectural design. This study delves into the application of graph theory in the analytical exploration of urban networks, with a focus on tourism parameters in the picturesque town of Pondicherry, Tamil Nadu, India. Traditionally, urban network analysis seeks to determine the shortest distance between origin and destination, a metric rooted in accessibility. However, in leisure destinations, a novel approach involving an optimized distance-based algorithm is introduced. This innovative methodology aims to facilitate efficient access to all tourist destinations within the spatial extent while minimizing discrete physical distances. To illustrate this concept, we take the iconic French Quarters in the White Town of Pondicherry as a case study. By applying the optimized distance-based algorithm, we endeavor to uncover the most efficient route for tourists to navigate and leisurely explore the area. The outcome of this analysis reveals a path graph structure, which, when compared to a circular graph structure, demonstrates superior efficiency in guiding tourists through the space. The implications of this tourist route extend beyond the realm of tourism itself. It has the potential to enhance the organization of tourist activities, allowing stakeholders to manage and regulate the flow of visitors. Additionally, it presents an opportunity to promote and develop the region’s often-underestimated tourist destinations, which can, in turn, have a positive impact on the local economy. In summary, the integration of graph theory into architectural and urban design methodologies enriches the approach to tourism and offers a holistic perspective on spatial optimization.
Figure 3 from The Next-Generation Oral Selective Estrogen Receptor Degrader Camizestrant (AZD9833) Suppresses ER+ Breast Cancer Growth and Overcomes Endocrine and CDK4/6 Inhibitor Resistance
Authors: Lawson Mandy , Cureton Natalie , Ros Susana , Cheraghchi-Bashi Azadeh , Urosevic Jelena , D'Arcy Sophie , Delpuech Oona , DuPont Michelle , Fisher David I. , Gangl Eric T. , Lewis Hilary , Trueman Dawn , Wali Neha , Williamson Stuart C. , Moss Jennifer , Montaudon Elodie , Derrien Heloise , Marangoni Elisabetta , Miragaia Ricardo J. , Gagrica Sladjana , Morentin-Gutierrez Pablo , Moss Thomas A. , Maglennon Gareth , Sutton Daniel , Polanski Radoslaw , Rosen Alan , Cairns Jonathan , Zhang Pei , Sánchez-Guixé Mònica , Serra Violeta , Critchlow Susan E. , Scott James S. , Lindemann Justin P.O. , Barry Simon T. , Klinowska Teresa , Morrow Christopher J. , Carnevalli Larissa S.
Published: March 2024

Camizestrant has superior in vivo activity to fulvestrant in ESR1wt and ESR1m PDX models (1). A, Waterfall plot representing the growth of 28 of ER+ breast cancer PDX treated with camizestrant 10 mg/kg daily; bars are colored according to ESR1 mutational status and other genomic characteristics annotated at the top. The percentage change calculated from the initial volume at day of treatment is shown. Data represent mean ± SE of the mean. B, Waterfall plot representing the growth of 25 PDX treated with fulvestrant 5 mg/kg weekly. N/A denotes models where the head-to-head arm was not available. The percentage of change calculated from the initial volume at day of treatment is shown. Data represent mean ± SE of the mean. C, Pie chart indicates the proportions of PDX models sensitive or insensitive to camizestrant and/or fulvestrant. The antitumor response of camizestrant versus fulvestrant monotherapy is represented as the percentage of tumor change compared with the initial tumor volume, benchmarked to vehicle changes. D, Correlation of fulvestrant PDX antitumor response (y-axis) versus camizestrant (x-axis) in 25 PDX, represented as the percentage of tumor volume change compared with the initial tumor volume. Data represent mean. The boxes indicate the percentage change from baseline ≤100%; the percentage of models sensitive only to fulvestrant or camizestrant, or sensitive to both is represented in each box.
Table S3 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: March 2024

Pharmacokinetic properties of LY3214996 and abemaciclib
Table S2 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: March 2024

Raw log2LFQ values for kinases profiled by MIB/MS
Figure S9 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: March 2024

Kaplan Meier Survival Curve and Tolerability
Figure S7 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: March 2024

DNSC Colony Forming Assay Matrix, ipNF05.5 Western Blots, and ipNF95.6 Western Blots
Figure S4 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: March 2024

SPI1 Mouse and ETV4 Human IHC Cytonuclear Analysis
Figure S12 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: March 2024

Ki67 Mouse IHC Analysis
Figure S11 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: March 2024

DEG Tables and Volcano Plots
Figure S1 from Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: March 2024

Hallmark KRAS Pathway Heatmap and Top DEGs
TABLE 3 from CALGB 80802 (Alliance): Impact of Sorafenib with and without Doxorubicin on Hepatitis C Infection in Patients with Advanced Hepatocellular Carcinoma
Authors: Abou-Alfa Ghassan K. , Geyer Susan M. , Nixon Andrew B. , Innocenti Federico , Shi Qian , Kumthekar Priya , Jacobson Sawyer , El Dika Imane , Yaqubie Amin , Lopez Juan , Huang Binhui , Tang Yi-Wei , Wen Yujia , Schwartz Lawrence H. , El-Khoueiry Anthony B. , Knox Jennifer J. , Rajdev Lakshmi , Bertagnolli Monica M. , Meyerhardt Jeffrey A. , O'Reilly Eileen M. , Venook Alan P.
Published: March 2024

Cox proportional hazards model results for PFS and the influence of genotype classification. Separation reflects different models for different breakdowns of genotype group
Table S4 from Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation
Authors: Carroll Christopher , Manaprasertsak Auraya , Boffelli Castro Arthur , van den Bos Hilda , Spierings Diana C.J. , Wardenaar René , Bukkuri Anuraag , Engström Niklas , Baratchart Etienne , Yang Minjun , Biloglav Andrea , Cornwallis Charlie K. , Johansson Bertil , Hagerling Catharina , Arsenian-Henriksson Marie , Paulsson Kajsa , Amend Sarah R. , Mohlin Sofie , Foijer Floris , McIntyre Alan , Pienta Kenneth J. , Hammarlund Emma U.
Published: March 2024

Table S4: Well counts for single cell colonies two months after cisplatin treatment.
Supplementary Figure 4 from CALGB 80802 (Alliance): Impact of Sorafenib with and without Doxorubicin on Hepatitis C Infection in Patients with Advanced Hepatocellular Carcinoma
Authors: Abou-Alfa Ghassan K. , Geyer Susan M. , Nixon Andrew B. , Innocenti Federico , Shi Qian , Kumthekar Priya , Jacobson Sawyer , El Dika Imane , Yaqubie Amin , Lopez Juan , Huang Binhui , Tang Yi-Wei , Wen Yujia , Schwartz Lawrence H. , El-Khoueiry Anthony B. , Knox Jennifer J. , Rajdev Lakshmi , Bertagnolli Monica M. , Meyerhardt Jeffrey A. , O'Reilly Eileen M. , Venook Alan P.
Published: March 2024

Supplementary Figure 4. Kaplan-Meier curves for the overall survival distributions for patients who have detectable (HCV-D) vs. undetectable (HCV-UN) HCV titer levels on their first evaluated sample, by treatment arm.
Table S1 from Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation
Authors: Carroll Christopher , Manaprasertsak Auraya , Boffelli Castro Arthur , van den Bos Hilda , Spierings Diana C.J. , Wardenaar René , Bukkuri Anuraag , Engström Niklas , Baratchart Etienne , Yang Minjun , Biloglav Andrea , Cornwallis Charlie K. , Johansson Bertil , Hagerling Catharina , Arsenian-Henriksson Marie , Paulsson Kajsa , Amend Sarah R. , Mohlin Sofie , Foijer Floris , McIntyre Alan , Pienta Kenneth J. , Hammarlund Emma U.
Published: March 2024

Table S1: LD50 values for cell lines after 72h cisplatin treatment.
Methods S1 from Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation
Authors: Carroll Christopher , Manaprasertsak Auraya , Boffelli Castro Arthur , van den Bos Hilda , Spierings Diana C.J. , Wardenaar René , Bukkuri Anuraag , Engström Niklas , Baratchart Etienne , Yang Minjun , Biloglav Andrea , Cornwallis Charlie K. , Johansson Bertil , Hagerling Catharina , Arsenian-Henriksson Marie , Paulsson Kajsa , Amend Sarah R. , Mohlin Sofie , Foijer Floris , McIntyre Alan , Pienta Kenneth J. , Hammarlund Emma U.
Published: March 2024

Methods S1: Filtration of treated cells
FIGURE 3 from CALGB 80802 (Alliance): Impact of Sorafenib with and without Doxorubicin on Hepatitis C Infection in Patients with Advanced Hepatocellular Carcinoma
Authors: Abou-Alfa Ghassan K. , Geyer Susan M. , Nixon Andrew B. , Innocenti Federico , Shi Qian , Kumthekar Priya , Jacobson Sawyer , El Dika Imane , Yaqubie Amin , Lopez Juan , Huang Binhui , Tang Yi-Wei , Wen Yujia , Schwartz Lawrence H. , El-Khoueiry Anthony B. , Knox Jennifer J. , Rajdev Lakshmi , Bertagnolli Monica M. , Meyerhardt Jeffrey A. , O'Reilly Eileen M. , Venook Alan P.
Published: March 2024

Kaplan–Meier curves for the OS distributions for patients who had detectable (HCV-d) versus undetectable (HCV-UN) HCV titer levels on their first evaluated sample. The HR based on a corresponding Cox proportional hazards model was 1.14 for those with HCV-UN (vs. HCV-d), 95% CI: 0.58–2.23 (P = 0.70).
Figure S9 from Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation
Authors: Carroll Christopher , Manaprasertsak Auraya , Boffelli Castro Arthur , van den Bos Hilda , Spierings Diana C.J. , Wardenaar René , Bukkuri Anuraag , Engström Niklas , Baratchart Etienne , Yang Minjun , Biloglav Andrea , Cornwallis Charlie K. , Johansson Bertil , Hagerling Catharina , Arsenian-Henriksson Marie , Paulsson Kajsa , Amend Sarah R. , Mohlin Sofie , Foijer Floris , McIntyre Alan , Pienta Kenneth J. , Hammarlund Emma U.
Published: March 2024

Figure S9: Transcription factors regulating downregulated genes in HCC1806 cells surviving 10 DPT as quantified using RNAseq and CHEA3 analysis.
Figure S8 from Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation
Authors: Carroll Christopher , Manaprasertsak Auraya , Boffelli Castro Arthur , van den Bos Hilda , Spierings Diana C.J. , Wardenaar René , Bukkuri Anuraag , Engström Niklas , Baratchart Etienne , Yang Minjun , Biloglav Andrea , Cornwallis Charlie K. , Johansson Bertil , Hagerling Catharina , Arsenian-Henriksson Marie , Paulsson Kajsa , Amend Sarah R. , Mohlin Sofie , Foijer Floris , McIntyre Alan , Pienta Kenneth J. , Hammarlund Emma U.
Published: March 2024

Figure S8: Pathways downregulated in HCC1806 cells surviving 10 DPT, as quantified with RNAseq and Reactome analysis.
Figure S3 from Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation
Authors: Carroll Christopher , Manaprasertsak Auraya , Boffelli Castro Arthur , van den Bos Hilda , Spierings Diana C.J. , Wardenaar René , Bukkuri Anuraag , Engström Niklas , Baratchart Etienne , Yang Minjun , Biloglav Andrea , Cornwallis Charlie K. , Johansson Bertil , Hagerling Catharina , Arsenian-Henriksson Marie , Paulsson Kajsa , Amend Sarah R. , Mohlin Sofie , Foijer Floris , McIntyre Alan , Pienta Kenneth J. , Hammarlund Emma U.
Published: March 2024

Figure S3: Cell diameter distributions for cell lines HCC1806, HCT116, and 786-0
FIGURE 3 from Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation
Authors: Carroll Christopher , Manaprasertsak Auraya , Boffelli Castro Arthur , van den Bos Hilda , Spierings Diana C.J. , Wardenaar René , Bukkuri Anuraag , Engström Niklas , Baratchart Etienne , Yang Minjun , Biloglav Andrea , Cornwallis Charlie K. , Johansson Bertil , Hagerling Catharina , Arsenian-Henriksson Marie , Paulsson Kajsa , Amend Sarah R. , Mohlin Sofie , Foijer Floris , McIntyre Alan , Pienta Kenneth J. , Hammarlund Emma U.
Published: March 2024

Cisplatin treatment of HCC1806 cells induced an altered transcriptome. A, Visualization of clusters of genetically similar cell populations (HCC1806) when untreated (red), and when resilient to treatment and large at 0 DPT (yellow), 5 DPT (green), and 10 DPT (blue). The PCA based on differentially expressed genes from the RNA-seq data. B, Visualization of gene expression of HCC1806 cells when untreated, surviving treatment at 0 DPT, 5 DPT, 10 DPT, and as progeny. Heat maps of the differentially expressed gene data. C, Visualization of downregulated and upregulated genes (fold change vs. adjusted P-value) in drug-resilient and transiently large HCC1806 cells at 10 DPT, compared with untreated control cells. D, Pathways upregulated in HCC1806 cells surviving at 10 DPT, as quantified with RNA-seq and Reactome analysis. E, Transcription factors regulating upregulated genes in HCC1806 cells surviving 10 DPT as quantified using RNA-seq and CHEA3 analysis.
FIGURE 2 from Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation
Authors: Carroll Christopher , Manaprasertsak Auraya , Boffelli Castro Arthur , van den Bos Hilda , Spierings Diana C.J. , Wardenaar René , Bukkuri Anuraag , Engström Niklas , Baratchart Etienne , Yang Minjun , Biloglav Andrea , Cornwallis Charlie K. , Johansson Bertil , Hagerling Catharina , Arsenian-Henriksson Marie , Paulsson Kajsa , Amend Sarah R. , Mohlin Sofie , Foijer Floris , McIntyre Alan , Pienta Kenneth J. , Hammarlund Emma U.
Published: March 2024

Drug-resilient cells exhibit one to two whole-genome duplications with high fidelity. A, Copy numbers in untreated and treated surviving HCC1806 cells 5 DPT, as visualized with AneuFinder (reads per 10 Mb over total amount of reads) from scWGS each row representing a single nucleus. B, Ratio of DNA content within each cell in untreated and surviving HCC1806 cells 5 DPT. The heat maps show the normalized read depth (reads per 10 Mb bins over total amount of reads in the cell) of scWGS, where blue areas show a lower number of reads, and red areas show a higher number of reads. The blocks R1, R2, and R3 in the left represent replicates 1, 2, and 3, respectively. C, Copy number of chromosome X in untreated (CTL), surviving HCC1806 cells at 5 DPT and their progeny, as visualized with chromosomal FISH of cells in interphase.
Supplementary Figure 9 from Gigaxonin Suppresses Epithelial-to-Mesenchymal Transition of Human Cancer Through Downregulation of Snail
Authors: Veena Mysore S. , Gahng Jungmo J. , Alani Mustafa , Ko Albert Y. , Basak Saroj K. , Liu Isabelle Y. , Hwang Kimberly J. , Chatoff Jenna R. , Venkatesan Natarajan , Morselli Marco , Yan Weihong , Ali Ibraheem , Kaczor-Urbanowicz Karolina Elżbieta , Gowda Bhavani Shankara , Frost Patrick , Pellegrini Matteo , Moatamed Neda A. , Wilczynski Sharon P. , Bomont Pascale , Wang Marilene B. , Shin Daniel Sanghoon , Srivatsan Eri S.
Published: March 2024

Synonymous exome duplication sequences in ME180 and GAN edited cell lines
Supplementary Figure 12 from Gigaxonin Suppresses Epithelial-to-Mesenchymal Transition of Human Cancer Through Downregulation of Snail
Authors: Veena Mysore S. , Gahng Jungmo J. , Alani Mustafa , Ko Albert Y. , Basak Saroj K. , Liu Isabelle Y. , Hwang Kimberly J. , Chatoff Jenna R. , Venkatesan Natarajan , Morselli Marco , Yan Weihong , Ali Ibraheem , Kaczor-Urbanowicz Karolina Elżbieta , Gowda Bhavani Shankara , Frost Patrick , Pellegrini Matteo , Moatamed Neda A. , Wilczynski Sharon P. , Bomont Pascale , Wang Marilene B. , Shin Daniel Sanghoon , Srivatsan Eri S.
Published: March 2024

expression of GAN, senescence and autophagy genes
Data from CALGB 80802 (Alliance): Impact of Sorafenib with and without Doxorubicin on Hepatitis C Infection in Patients with Advanced Hepatocellular Carcinoma
Authors: Abou-Alfa Ghassan K. , Geyer Susan M. , Nixon Andrew B. , Innocenti Federico , Shi Qian , Kumthekar Priya , Jacobson Sawyer , El Dika Imane , Yaqubie Amin , Lopez Juan , Huang Binhui , Tang Yi-Wei , Wen Yujia , Schwartz Lawrence H. , El-Khoueiry Anthony B. , Knox Jennifer J. , Rajdev Lakshmi , Bertagnolli Monica M. , Meyerhardt Jeffrey A. , O'Reilly Eileen M. , Venook Alan P.
Published: March 2024

Abstract
Sorafenib blocks nonstructural protein 5A (NS5A)-recruited c-Raf–mediated hepatitis C virus (HCV) replication and gene expression. Release of Raf-1-Ask-1 dimer and inhibition of Raf-1 via sorafenib putatively differ in the presence or absence of doxorubicin. Cancer and Leukemia Group B (CALGB) 80802 (Alliance) randomized phase III trial of doxorubicin plus sorafenib versus sorafenib in patients with advanced hepatocellular carcinoma (HCC), showed no improvement in median overall survival (OS). Whether HCV viral load impacts therapy and whether any correlation between HCV titers and outcome based on HCV was studied. In patients with HCV, HCV titer levels were evaluated at baseline and at multiple postbaseline timepoints until disease progression or treatment discontinuation. HCV titer levels were evaluated in relation to OS and progression-free survival (PFS). Among 53 patients with baseline HCV data, 12 patients had undetectable HCV (HCV-UN). Postbaseline HCV titer levels did not significantly differ between treatment arms. One patient in each arm went from detectable to HCV-UN with greater than 2 log-fold titer levels reduction. Aside from these 2 HCV-UN patients, HCV titers remained stable on treatment. Patients who had HCV-UN at baseline were 3.5 times more likely to progress and/or die from HCC compared with HCV detectable (HR = 3.51; 95% confidence interval: 1.58–7.78; P = 0.002). HCV titer levels remained unchanged, negating any sorafenib impact onto HCV titer levels. Although an overall negative phase III study, patients treated with doxorubicin plus sorafenib and sorafenib only, on CALGB 80802 had worse PFS if HCV-UN. Higher levels of HCV titers at baseline were associated with significantly improved PFS.
Significance:
Sorafenib therapy for HCC may impact HCV replication and viral gene expression. In HCV-positive patients accrued to CLAGB 80802 phase III study evaluating the addition of doxorubicin to sorafenib, HCV titer levels were evaluated at baseline and different timepoints. Sorafenib did not impact HCV titer levels. Despite an improved PFS in patients with detectable higher level HCV titers at baseline, no difference in OS was noted.
Prevalence of Renal Neoplasia in Autosomal Dominant Polycystic Kidney Disease: Systematic Review and Meta-Analysis
Authors: Drake Anna M. , Paynter Jessica A. , Yim Arthur , Tempo Jake A. , Manning Todd G. , Brennan Janelle , Qin Kirby R.
Published: March 2024

Background: Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited condition; however, its relationship with renal cell carcinoma (RCC) remains unclear. This paper aims to establish the prevalence of RCC and its subtypes amongst ADPKD patients. Methods: A database search was conducted to retrieve studies reporting RCC occurrence within ADPKD patients until July 2023. Key outcomes included number and subtype of RCC cases, and number of RCCs presenting incidentally. A random-effects meta-analysis was performed. Results: Our search yielded 569 articles, 16 met the inclusion criteria. Nephrectomy specimens from 1,147 ADPKD patients were identified. Of studies reporting per-kidney results (n = 13), 73 RCCs were detected amongst 1,493 kidneys, equating to a per-kidney prevalence of 4.3% (95% CI, 3.1–5.7, I2 = 15.7%). 75 ADPKD patients were found to have RCC (75/1,147), resulting in a per-person prevalence of 5.7% (95% CI, 3.7–7.9, I2 = 40.3%) (n = 16). As 7 patients had bilateral disease, 82 RCCs were detected in total. Of these, 39 were clear cell RCC, 35 were papillary and 8 were other. As such, papillary RCCs made up 41.1% (95% CI, 25.9–56.9, I2 = 18.1%) of detected cancers. The majority of RCCs were detected incidentally (72.5% [95% CI, 43.7–95.1, I2 = 66.9%]). Conclusion: ADPKD appears to be associated with the papillary RCC subtype. The clinical implications of these findings are unclear, however, may become apparent as outcomes and life expectancy amongst APDKD patients improve.
Implicit Bias versus Intentional Belief: When Morally Elevated
Leadership Drives Transformational Change
Authors: Sigur Wanda A. , Donofrio Nicholas M.
Published: March 2024

The twenty-first century is witnessing rapid and deep change in the global economy. These changes require innovation-driven solutions and motivated, skilled workforces. The talents of every person will be required to support performance in every domain, and deliberate actions must be taken to address impediments to full engagement. Even with clear government policy and significant investments in encouraging representation and inclusion of diversity of race, sexual orientation, gender identity, and ability, progress continues to lag. This essay captures promising practices and recommendations for structural or systemic change punctuated with stories of leadership driven by the belief that implementing strategies to disrupt the effects of implicit bias are important to develop diverse, fully engaged populations.
Probing the Structure and Functional Properties of the Dropout-Induced Correlated Variability in Convolutional Neural Networks
Authors: Pan Xu , Coen-Cagli Ruben , Schwartz Odelia
Published: March 2024

Computational neuroscience studies have shown that the structure of neural variability to an unchanged stimulus affects the amount of information encoded. Some artificial deep neural networks, such as those with Monte Carlo dropout layers, also have variable responses when the input is fixed. However, the structure of the trial-by-trial neural covariance in neural networks with dropout has not been studied, and its role in decoding accuracy is unknown. We studied the above questions in a convolutional neural network model with dropout in both the training and testing phases. We found that trial-by-trial correlation between neurons (i.e., noise correlation) is positive and low dimensional. Neurons that are close in a feature map have larger noise correlation. These properties are surprisingly similar to the findings in the visual cortex. We further analyzed the alignment of the main axes of the covariance matrix. We found that different images share a common trial-by-trial noise covariance subspace, and they are aligned with the global signal covariance. This evidence that the noise covariance is aligned with signal covariance suggests that noise covariance in dropout neural networks reduces network accuracy, which we further verified directly with a trial-shuffling procedure commonly used in neuroscience. These findings highlight a previously overlooked aspect of dropout layers that can affect network performance. Such dropout networks could also potentially be a computational model of neural variability.
From Reluctance to Reliance: Opium Smuggling in 18th-Century Macao
Authors: Canton-Alvarez Jose A.
Published: March 2024

This paper critically appraises the role of the opium trade in the politics of 18th-century Macao. By examining previously unexplored Portuguese accounts on opium smuggling, this study contributes new insights into the shift in attitudes of the Macanese authorities towards the opium trade in this period, which subsequently aided further European opium smuggling in the Pearl River Delta. Thus, this paper fills an important gap in our understanding of the transformation that took place in the period before opium became a bone of contention between the Qing dynasty and European powers, on the eve of the Opium Wars.
Praised and Maligned: Receptions of Erasmus’ Paraphrases on the New Testament
Authors: Bloemendal Jan
Published: March 2024

Erasmus was not only the first to have the Greek text of the New Testament printed together with his Latin translation, but he also paraphrased the books of the New Testament—with the exception of the Apocalypse. These Paraphrases were highly successful as evidenced by their many editions and translations. Even an English translation was to be found in every parish in the Church of England. There was also opposition. Theologians from Spain and France scrutinized them for Lutheran ideas, and, of course, found them. However, the interest in the paraphrases was not diminished by this criticism and they had an intense reception in the sixteenth century and a long-lasting one stretching after Erasmus’ death. Parts were included in commentaries on the New Testament, sometimes with reference to the original author, more often without his name.
Chinese Civilians Beyond the Palisade: an Inquiry on the Opening of Northern Manchuria to Han Commoners in the Yongzheng era
Authors: Sepe Agostino
Published: March 2024

Even before the Qianlong ban of 1740 (fengjin zhengce 封禁政策), which officially and thoroughly prohibited Han civilians’ migration to Manchuria, the Qing rulers’ attitude toward the phenomenon was, most of the time, a negative one. Generally speaking, the court meant to preserve the territory to the imperial family themselves and the Manchu people. More specifically, as the policies addressing southern Manchuria (present day Liaoning province) changed over time, as the rulers’ wish to keep the place to their own people clashed with concerns about repopulation and land reclamation – for which Chinese settlers could be a resource, spontaneous settling in the northern part of the region (bianwai 邊外, “beyond the (Willow) Palisade”) was always formally forbidden. Such a difference was clearly reflected by the local administrative structures. The Chinese-fashioned system, zhouxianzhi 州縣制, was present in southern Manchuria since 1653, whereas it was established in Jilin only in Yongzheng era. Emperors Kangxi and Qianlong controlled or opposed the growth of the Chinese civil population in Manchuria. As a consequence, they kept unaltered or weakened the Chinese branch of the local government while making efforts to develop the local Eight Banners’ structures. Yongzheng’ policies were headed toward a different direction. Not only did the sovereign enlarge the civil administration in Liaoning; even more significantly, he ordered the foundation of three civil administrative centres in northern Manchuria – Yongji 永吉, Changning 長寧 and Taining 泰寧, which were in charge of the increasing civil population. Neither in China nor in western studies such policies have been attached the importance they are worth of. In addition, Qing sources such as Veritable Records, Gazetteers and the Collected Statutes provide very scarce information on such maneuver. By resorting to archival sources, both in Chinese and in Manchu, this work aims at researching into the rationales and the decision making process which lead to a brief but important interruption of the main trend of Qing rule of their motherland.
Reappraisal of Eiconaxius farreae Ortmann, 1891 and Eiconaxius mortenseni Sakai, 1992 (Decapoda: Axiidea: Axiidae), with description of a new species from Japan
Authors: KOMAI TOMOYUKI
Published: March 2024

The sponge associated axiid shrimp Eiconaxius farreae Ortmann, 1891 was originally described based on specimens from Sagami Bay, central Japan. Morphological examination of many specimens of Eiconaxius collected from Sagami Bay and nearby areas, and genetic data from the mitochondrial COI and 16S rRNA genes have revealed that three species are represented. This finding led to a reappraisal of the identity of E. farreae and E. mortenseni Sakai, 1992, also originally described from Sagami Bay. It has been clarified that two species (E. farreae and an undescribed species) were mixed in the syntype material of E. farreae, and consequently, a lectotype of E. farreae is designated in the interest of nomenclatural stability. Here, E. farreae and E. mortenseni are redescribed, and the third species is described as new, E. reconditus. The new species is morphologically very similar to E. mortenseni. Differentiating characters among closely allied species are reassessed. Previous records of E. farreae are reviewed in light of the present findings.
Studies of Raspy Crickets: The Status of the Wingless American gryllacridines (Orthoptera: Gryllacrididae)
Authors: CADENA-CASTAÑEDA OSCAR J. , QUINTANA-ARIAS RONALD FERNANDO
Published: March 2024

In this contribution based on the American wingless gryllacridines, the two genera described for the New World Camptonotus and Neoeremus are defined and differentiated, resulting in three additional genera: Neortus stat. resurr., Fiancogryllacris n. gen. and Camposgryllacris n. gen. The species of these genera were described at the end of the 19th century and the beginning of the 20th century, and in most taxa, there are no records since their description, so the iNaturalist platform provided additional distributional data for some species. Taxonomic keys are provided for the identification of the genera and species studied. Finally, the evolutionary interpretation of the appearance and disappearance of wings in leaf-rolling crickets are discussed.
Use of bitemporal NACA score documentation in prehospital emergency medical services– a retrospective study
Authors: Eichinger Michael , Reiterer Sandro , Rief Martin , Eichlseder Michael , Pichler Alexander , Zoidl Philipp , Prause Gerhard
Published: March 2024

Background

The assessment of illness severity in the prehospital setting is essential for guiding appropriate medical interventions. The National Advisory Committee for Aeronautics (NACA) score is a validated tool commonly used for this purpose. However, the potential benefits of using bitemporal documentation of NACA scores to capture the dynamic changes in emergency situations remain uncertain. The objective of this study was to evaluate the potential benefit of bitemporal NACA score documentation in the prehospital setting, specifically in assessing the dynamic changes of emergencies and facilitating quality improvement through enhanced documentation practices.

Methods

In this retrospective study, data from prehospital emergency patients were analyzed who received care from the physician response unit between January 1, 2018, and May 31, 2021. Patient demographics, NACA scores, indications for emergency care, and changes in NACA scores were extracted from medical records. Statistical analyses were performed to examine the associations between NACA scores, emergency categories, indications, and changes in NACA scores.

Results

The study included 4005 patients, predominantly categorized as NACA III (33.7% at initial assessment, 41.8% at subsequent assessment) and NACA IV (31.6% at initial assessment, 22.4% at subsequent assessment). There was a significant improvement in NACA scores during the provision of prehospital care (p < 0.01). Notably, prehospital emergencies attributed to internal medical, neurological, traumatic, and paediatric causes demonstrated significant improvements in NACA scores (p < 0.01). Gender-specific differences were also observed.

Conclusion

Our study suggests that the bitemporal documentation of NACA scores can be advantageous in the prehospital setting and may have implications for research, practice, and policy.
High genetic diversity of the himalayan marmot relative to plague outbreaks in the Qinghai-Tibet Plateau, China
Authors: Ma Ying , Liu Pengbo , Li Ziyan , Yue Yujuan , Zhao Yanmei , He Jian , Zhao Jiaxin , Song Xiuping , Wang Jun , Liu Qiyong , Lu Liang
Published: March 2024

Plague, as an ancient zoonotic disease caused by Yersinia pestis, has brought great disasters. The natural plague focus of Marmota himalayana in the Qinghai-Tibet Plateau is the largest, which has been constantly active and the leading source of human plague in China for decades. Understanding the population genetics of M. himalayana and relating that information to the biogeographic distribution of Yersinia pestis and plague outbreaks are greatly beneficial for the knowledge of plague spillover and arecrucial for pandemic prevention. In the present research, we assessed the population genetics of M. himalayana. We carried out a comparative study of plague outbreaks and the population genetics of M. himalayana on the Qinghai-Tibet Plateau. We found that M. himalayana populations are divided into two main clusters located in the south and north of the Qinghai-Tibet Plateau. Fourteen DFR genomovars of Y. pestis were found and exhibited a significant region-specific distribution. Additionally, the increased genetic diversity of plague hosts is positively associated with human plague outbreaks. This insight gained can improve our understanding of biodiversity for pathogen spillover and provide municipally directed targets for One Health surveillance development, which will be an informative next step toward increased monitoring of M. himalayana dynamics.
Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study
Authors: Fang Lucheng , Tuohuti Aikebaier , Cai Wanyue , Chen Xiong
Published: March 2024

Objective

To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA.

Methods

Before adeno-tonsillectomy, we collected throat swab samples from different parts of the oropharynx and nasopharynx of 30 OSA patients and 10 non-OSA patients and collected throat swab samples from the oropharynx of the above patients one month after the adeno-tonsillectomy. The 16 S rRNA V3–V4 region was sequenced to identify the microbial communities. The correlation analysis was conducted based on clinical characteristics.

Results

There was a significant difference of alpha diversity in different parts of the upper airway of pediatric OSA, but this difference was not found in children with non-OSA. Beta diversity was significantly different between non-OSA and pediatric OSA. At the genus level, the composition of flora in different parts is different between non-OSA and pediatric OSA. The correlation analysis revealed that the relative abundance of Neisseria was significantly correlated with obstructive apnea hypopnea index. Furthermore, the functional prediction revealed that pathways related to cell proliferation and material metabolism were significantly different between non-OSA and pediatric OSA. Besides, the adeno-tonsillectomy has minimal impact on oral microbiota composition in short term.

Conclusion

The changes in upper airway microbiome are highly associated with pediatric OSA. The relative abundance of some bacteria was significantly different between OSA and non-OSA. These bacteria have the potential to become new diagnostic and early warning biomarkers.