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Journal articles on the topic 'Gay scéna'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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1

Lamotte, M., G. De Izarra, and C. Jammes. "SCENA: A simulation tool for radiation-induced gas scintillation." Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 982 (December 2020): 164576. http://dx.doi.org/10.1016/j.nima.2020.164576.

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2

Hillje, Roman, Pier Giuseppe Pelicci, and Lucilla Luzi. "Cerebro: interactive visualization of scRNA-seq data." Bioinformatics 36, no. 7 (2019): 2311–13. http://dx.doi.org/10.1093/bioinformatics/btz877.

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Abstract Despite the growing availability of sophisticated bioinformatic methods for the analysis of single-cell RNA-seq data, few tools exist that allow biologists without extensive bioinformatic expertise to directly visualize and interact with their own data and results. Here, we present Cerebro (cell report browser), a Shiny- and Electron-based standalone desktop application for macOS and Windows which allows investigation and inspection of pre-processed single-cell transcriptomics data without requiring bioinformatic experience of the user. Through an interactive and intuitive graphical i

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Li, Ruiyi, Jihong Guan, and Shuigeng Zhou. "Single-cell RNA-seq data clustering: A survey with performance comparison study." Journal of Bioinformatics and Computational Biology 18, no. 04 (2020): 2040005. http://dx.doi.org/10.1142/s0219720020400053.

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Clustering analysis has been widely applied to single-cell RNA-sequencing (scRNA-seq) data to discover cell types and cell states. Algorithms developed in recent years have greatly helped the understanding of cellular heterogeneity and the underlying mechanisms of biological processes. However, these algorithms often use different techniques, were evaluated on different datasets and compared with some of their counterparts usually using different performance metrics. Consequently, there lacks an accurate and complete picture of their merits and demerits, which makes it difficult for users to s

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Fonseca Costa, Sara S., Marc Robinson-Rechavi, and Jürgen A. Ripperger. "Single-cell transcriptomics allows novel insights into aging and circadian processes." Briefings in Functional Genomics 19, no. 5-6 (2020): 343–49. http://dx.doi.org/10.1093/bfgp/elaa014.

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Abstract Aging and circadian rhythms are two biological processes that affect an organism, although at different time scales. Nevertheless, due to the overlap of their actions, it was speculated that both interfere or interact with each other. However, to address this question, a much deeper insight into these processes is necessary, especially at the cellular level. New methods such as single-cell RNA-sequencing (scRNA-Seq) have the potential to close this gap in our knowledge. In this review, we analyze applications of scRNA-Seq from the aging and circadian rhythm fields and highlight new fi

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Song, Hanbing, Hannah N. W. Weinstein, Paul Allegakoen, et al. "Single-cell analysis of cellular state heterogeneity in human localized prostate cancer." Journal of Clinical Oncology 39, no. 6_suppl (2021): 254. http://dx.doi.org/10.1200/jco.2021.39.6_suppl.254.

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254 Background: Prostate cancer is the second most common malignancy in men worldwide. The development of cancer from prostate tissue involves complex interactions of tumor cells with surrounding epithelial and stromal cells and can occur multifocally, suggesting that prostate epithelial cells may undergo cellular state transitions towards carcinogenesis. Previous studies on localized prostate cancer molecular changes have focused on unsorted bulk tissue samples, leaving a gap in our understanding of the cellular heterogeneity in the tumor microenvironment. Single-cell analyses of tumor specim

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Liu, Juntao, Xiangyu Liu, Xianwen Ren, and Guojun Li. "scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions." Bioinformatics 35, no. 21 (2019): 4264–71. http://dx.doi.org/10.1093/bioinformatics/btz240.

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Abstract Motivation Full-length transcript reconstruction is essential for single-cell RNA-seq data analysis, but dropout events, which can cause transcripts discarded completely or broken into pieces, pose great challenges for transcript assembly. Currently available RNA-seq assemblers are generally designed for bulk RNA sequencing. To fill the gap, we introduce single-cell RNA-seq assembler, a method that applies explicit strategies to impute lost information caused by dropout events and a combing strategy to infer transcripts using scRNA-seq. Results Extensive evaluations on both simulated

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Chen, Qian, and Yuru Liu. "Heterogeneous groups of alveolar type II cells in lung homeostasis and repair." American Journal of Physiology-Cell Physiology 319, no. 6 (2020): C991—C996. http://dx.doi.org/10.1152/ajpcell.00341.2020.

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Alveoli are the gas-exchanging units of the lung, and the alveolar barrier is often a key battleground where pathogens, allergens, and other insults from the environment are encountered. This is seen in the current coronavirus disease 2019 (COVID-19) pandemic, as alveolar epithelium is one of the major targets of SARS-COV-2, the virus that causes COVID-19. Thus, it is essential to understand the mechanisms in order to maintain the integrity of alveoli epithelium. Alveolar type II (AT2) cells behave as tissue stem cells that repair alveoli epithelium during steady-state replacement and after in

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An, Omer, Kar-Tong Tan, Ying Li, et al. "CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing." International Journal of Molecular Sciences 21, no. 11 (2020): 3828. http://dx.doi.org/10.3390/ijms21113828.

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Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and a significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and shar

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9

Kanagal-Shamanna, Rashmi, Vera Adema, Feiyang Ma, et al. "SF3B1-Mutant Myelodysplastic Syndrome with Ringed Sideroblasts (MDS-RS) at the Single-Cell Level." Blood 136, Supplement 1 (2020): 50–51. http://dx.doi.org/10.1182/blood-2020-141928.

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The biological mechanisms of abnormal terminal erythroid differentiation (TED) in MDS-RS and SF3B1 mutations (SF3B1MT) are largely unknown. This gap in understanding, which has dramatically delayed the design of second-line approaches for SF3B1MT patients whose disease has failed hypomethylating agent (HMA) therapy, is primarily due to a lack of studies molecularly characterizing how SF3B1MTaffect distinct stages of erythropoiesis. Here, we dissected at the single-cell level the cellular and transcriptomic changes induced by SF3B1MT in cells undergoing erythroid differentiation and elucidated

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10

Kinaret, Pia Anneli Sofia, Angela Serra, Antonio Federico, et al. "Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects." Nanomaterials 10, no. 4 (2020): 750. http://dx.doi.org/10.3390/nano10040750.

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The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms’ responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics inte

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11

Joseph, K., L. Vollmer, V. M. Ravi, et al. "OS06.9A Diversity of cellular communication in glioblastoma." Neuro-Oncology 23, Supplement_2 (2021): ii10. http://dx.doi.org/10.1093/neuonc/noab180.032.

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Abstract BACKGROUND Owing to recent advances in understanding of the active functional states exhibited within glioblastoma (GBM), intra-tumoral cellular signaling has moved into focus of neuro-oncological research. In our study, we aim to explore the diversity of transcellular signaling and investigate correlations to transcriptional dynamics and cellular behavior. MATERIAL AND METHODS Electrophysiological mapping of primary GBM cultures was performed by planar microelectrodes, in conjunction with calcium imaging in a human neocortical section based GBM model. Exposure to conditions that are

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12

Jeong, Mira, Sangbae Kim, Yumei Li, Rui Chen, Premal Lulla, and Margaret Goodell. "Single Cell Profiling of DNMT3A-Mutant Progenitors Reveals LY86 As a Novel Pre-Leukemia Marker and Potential Therapeutic Target." Blood 134, Supplement_1 (2019): 2724. http://dx.doi.org/10.1182/blood-2019-123597.

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Acute Myeloid Leukemia (AML) is a clonal disease of the hematopoietic system that initiated and sustained by self-renewing hematopoietic stem and progenitor cells (HSPC). Mutations in the de novo DNA methyltransferase 3A (DNMT3A) gene occur in approximately 25% of adult acute myeloid leukemias (AML). Although the mechanisms through which such mutations promote leukemogenesis remain unclear, we have previously shown that loss of the DNMT3A can inhibit normal hematopoietic differentiation (Challen, Nature Genetics, 2011), accounting for the emergence of DNMT3A-HSC clones as a predisposition to h

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13

Weber, S., C. G. Anchang, S. Rauber, et al. "SAT0302 INNATE LYMPHOID CELLS INDUCE A FIBROTIC PHENOTYPE OF FIBROBLASTS." Annals of the Rheumatic Diseases 79, Suppl 1 (2020): 1096.2–1096. http://dx.doi.org/10.1136/annrheumdis-2020-eular.5804.

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Background:Fibrotic diseases are characterized by excessive extracellular matrix production as a result of immune-mediated permanent fibroblast activation. Innate lymphoid cells type II (ILC2) are an only recently discovered cell type involved in barrier integrity and tissue homeostasis. There is upcoming evidence that ILC2s play a central role in mediating fibrotic diseases.Objectives:The aim of the study was to further elucidate the role of ILC2s in fibrotic tissue remodeling and fibroblast activation.Methods:Skin biopsies of patients with systemic sclerosis (SSc) or sclerodermatous chronic

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14

Yu, Jovian, Xiufen Chen, James Godfrey, et al. "Single-Cell Analysis of the Classical Hodgkin Lymphoma Immune Environment Reveals a Clonally-Expanded CD8+ T Cell Population with a Cytotoxic Phenotype." Blood 136, Supplement 1 (2020): 40–41. http://dx.doi.org/10.1182/blood-2020-137171.

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Introduction: Classical Hodgkin lymphoma (cHL) is characterized by a robust and complex immune cell infiltrate and the rare presence of malignant Hodgkin-Reed-Sternberg (HRS) cells. At the genetic level, HRS cells recurrently acquire alterations that lead to defective antigen presentation (β2 microglobulin mutations) and mediate T cell dysfunction (PD-L1 copy gains/amplifications) in order to subvert host immune surveillance. The clinical relevance of PD-L1 protein over-expression in cHL is clear, as response rates to PD-1 blockade therapy are extremely high among patients with relapsed/refrac

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15

Tang, Guoqiang, Martyn P. Clark, and Simon Michael Papalexiou. "The use of serially complete station data to improve the temporal continuity of gridded precipitation and temperature estimates." Journal of Hydrometeorology, April 12, 2021. http://dx.doi.org/10.1175/jhm-d-20-0313.1.

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AbstractStations are an important source of meteorological data, but often suffer from missing values and short observation periods. Gap filling is widely used to generate serially complete datasets (SCDs), which are subsequently used to produce gridded meteorological estimates. However, the value of SCDs in spatial interpolation is scarcely studied. Based on our recent efforts to develop a SCD over North America (SCDNA), we explore the extent to which gap filling improves gridded precipitation and temperature estimates. We address two specific questions: (1) Can SCDNA improve the statistical

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16

Sun, Shiquan, Jiaqiang Zhu, Ying Ma, and Xiang Zhou. "Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis." Genome Biology 20, no. 1 (2019). http://dx.doi.org/10.1186/s13059-019-1898-6.

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Abstract Background Dimensionality reduction is an indispensable analytic component for many areas of single-cell RNA sequencing (scRNA-seq) data analysis. Proper dimensionality reduction can allow for effective noise removal and facilitate many downstream analyses that include cell clustering and lineage reconstruction. Unfortunately, despite the critical importance of dimensionality reduction in scRNA-seq analysis and the vast number of dimensionality reduction methods developed for scRNA-seq studies, few comprehensive comparison studies have been performed to evaluate the effectiveness of d

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17

Hurskainen, Maria, Ivana Mižíková, David P. Cook, et al. "Single cell transcriptomic analysis of murine lung development on hyperoxia-induced damage." Nature Communications 12, no. 1 (2021). http://dx.doi.org/10.1038/s41467-021-21865-2.

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AbstractDuring late lung development, alveolar and microvascular development is finalized to enable sufficient gas exchange. Impaired late lung development manifests as bronchopulmonary dysplasia (BPD) in preterm infants. Single-cell RNA sequencing (scRNA-seq) allows for assessment of complex cellular dynamics during biological processes, such as development. Here, we use MULTI-seq to generate scRNA-seq profiles of over 66,000 cells from 36 mice during normal or impaired lung development secondary to hyperoxia with validation of some of the findings in lungs from BPD patients. We observe dynam

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18

Quint, Wim H., Kirke C. D. Tadema, Erik de Vrieze, et al. "Loss of Gap Junction Delta-2 (GJD2) gene orthologs leads to refractive error in zebrafish." Communications Biology 4, no. 1 (2021). http://dx.doi.org/10.1038/s42003-021-02185-z.

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AbstractMyopia is the most common developmental disorder of juvenile eyes, and it has become an increasing cause of severe visual impairment. The GJD2 locus has been consistently associated with myopia in multiple independent genome-wide association studies. However, despite the strong genetic evidence, little is known about the functional role of GJD2 in refractive error development. Here, we find that depletion of gjd2a (Cx35.5) or gjd2b (Cx35.1) orthologs in zebrafish, cause changes in the biometry and refractive status of the eye. Our immunohistological and scRNA sequencing studies show th

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Pique-Regi, Roger, Roberto Romero, Adi L. Tarca, et al. "Single cell transcriptional signatures of the human placenta in term and preterm parturition." eLife 8 (December 12, 2019). http://dx.doi.org/10.7554/elife.52004.

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More than 135 million births occur each year; yet, the molecular underpinnings of human parturition in gestational tissues, and in particular the placenta, are still poorly understood. The placenta is a complex heterogeneous organ including cells of both maternal and fetal origin, and insults that disrupt the maternal-fetal dialogue could result in adverse pregnancy outcomes such as preterm birth. There is limited knowledge of the cell type composition and transcriptional activity of the placenta and its compartments during physiologic and pathologic parturition. To fill this knowledge gap, we

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20

Zańko, Piotr, and Mirosław Pęczak. "Underground po Śląsku." Sprawy Narodowościowe, no. 50 (December 31, 2018). http://dx.doi.org/10.11649/sn.1739.

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Underground music scene in SilesiaUpper Silesia is usually associated with the historical land situated in southern Poland with highly developed industry, mainly mines and steelworks. The inhabitants of Upper Silesia are perceived as conservatist. In spite of that, it is Upper Silesia, precisely Gliwice, where the most vigorous underground music scene in communist Poland was created at the beginning of the 1980s. The Gliwice Alternative Scene was focused around student clubs in Gliwice with „Gwarek” as the representative one. In this article we will show the artistic legacy of chosen musical b

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21

Qu, Lili, Chuan Li, Alyssa Matz, et al. "Abstract 16504: Low Disturbed Flow Induces Dynamic Immune Compartment Alterations in Atherogenesis as Revealed by Single Cell Rna-seq." Circulation 142, Suppl_3 (2020). http://dx.doi.org/10.1161/circ.142.suppl_3.16504.

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Low disturbed blood flow (LDF) is a critical contributing factor to atherogenesis but its direct impact on the immune compartment was not well-depict. To fill this knowledge gap, we adopted scRNA-seq to capture sheer-stress induced immune responses during atherogenesis. A partial carotid artery ligation (PCAL) model was selected for its paired comparison of carotid arteries with normal flow (NF) or LDF. Indeed, we observed drastic changes in both endothelial and immune compartment. Macrophages were the most significantly increased population induced by LDF (from 4% to 12% of CD45+ cells) with

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