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Deep learning in integrating spatial transcriptomics with other modalities.
Brief Bioinform
November 2024
State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Xuanwu District, Nanjing 210096, China.
Spatial transcriptomics technologies have been extensively applied in biological research, enabling the study of transcriptome while preserving the spatial context of tissues. Paired with spatial transcriptomics data, platforms often provide histology and (or) chromatin images, which capture cellular morphology and chromatin organization. Additionally, single-cell RNA sequencing (scRNA-seq) data from matching tissues often accompany spatial data, offering a transcriptome-wide gene expression profile of individual cells.
View Article and Find Full Text PDFCellMsg: graph convolutional networks for ligand-receptor-mediated cell-cell communication analysis.
Brief Bioinform
November 2024
College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China.
The role of cell-cell communications (CCCs) is increasingly recognized as being important to differentiation, invasion, metastasis, and drug resistance in tumoral tissues. Developing CCC inference methods using traditional experimental methods are time-consuming, labor-intensive, cannot handle large amounts of data. To facilitate inference of CCCs, we proposed a computational framework, called CellMsg, which involves two primary steps: identifying ligand-receptor interactions (LRIs) and measuring the strength of LRIs-mediated CCCs.
View Article and Find Full Text PDFTowards Modern Care and Education for Persons with visual Impairments in Poland: Elżbieta Róża Czacka (1876-1961) and Her Contribution to the Development of Typhlology-Religious Inspirations.
J Relig Health
January 2025
Faculty of Educational Studies, Adam Mickiewicz University, Poznań, Poland.
The aim of this study is to show the relationship between spirituality and the development of modern typhlology focused on supporting people with visual impairments. The text presents the silhouette of Mother Rose Czacka, the sources of her Catholic spirituality and the development of typhlological thought related to her, as well as Dzieło Lasek, which is an emanation of these relationships. The aim of this study is to show the relationship between spirituality and the development of modern typhlology focused on supporting people with visual impairments.
View Article and Find Full Text PDFPrognostic impact and risk factors of severe neutropenia in the early phase of treatment with trifluridine-tipiracil for metastatic colorectal cancer patients: a single-center retrospective study.
Int J Colorectal Dis
January 2025
Department of Surgery, Japan Community Healthcare Organization Tokuyama Central Hospital, 1-1 Koda-Cho, Shunan, Yamaguchi, 745-0822, Japan.
Purpose: We aimed to identify the risk factors for severe neutropenia in the early phase of trifluridine-tipiracil (FTD/TPI) treatment, and their impact on overall survival (OS).
Methods: This single-center retrospective study included patients with unresectable metastatic colorectal cancer who were treated with FTD/TPI. The primary endpoint was OS, and the secondary endpoint was severe neutropenia during the first and second cycles of FTD/TPI.
The petunia heavy metal P-type ATPase PhHMA5II1 interacts with copper chaperons and regulate Cu detoxification.
Plant Cell Rep
January 2025
School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
An endoplasmic reticulum-localized Cu transporter, PhHMA5II1, interacts with copper chaperones and plays an important role in Cu detoxification in petunia. Copper (Cu) is an essential element for plant growth but toxic when present in excess. In this study we present the functional characterization of a petunia (Petunia hybrida) P-type heavy-metal ATPases (HMAs), PhHMA5II1.
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