EMBOJ-2024-117209_File list Figure 1G
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ABSTRACT:
ORGANISM(S): Danio rerio (zebrafish) ze
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PROVIDER: S-BSST1414 | biostudies-other |
REPOSITORIES: biostudies-other
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Project description:Neuropathology-based studies in neurosurgically resected brain tissue obtained from carefully examined patients with focal epilepsies remain a treasure box for excellent insights into human neuroscience, including avenues to better understand the neurobiology of human brain organization and neuronal hyperexcitability at the cellular level including glio-neuronal interaction. It also allows to translate results from animal models in order to develop personalized treatment strategies in the near future. A nice example of this is the discovery of a new disease entity in 2017, termed mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy or MOGHE, in the frontal lobe of young children with intractable seizures. In 2021, a brain somatic missense mutation of the galactose transporter SLC35A2 leading to altered glycosylation of lipoproteins in the Golgi apparatus was detected in 50 % of MOGHE samples. In 2023, the first clinical trial evaluated galactose supplementation in patients with histopathologically confirmed MOGHE carrying brain somatic SLC35A2 mutations that were not seizure free after surgery. The promising results of this pilot trial are an example of personalized medicine in the arena of epileptology. Besides this, neuropathological studies of epilepsy samples have revealed many other fascinating results for the main disease categories in focal epilepsies, such as the first deep-learning based classifier for Focal Cortical Dysplasia, or the genomic landscape of cortical malformations showing new candidate genes such as PTPN11, which is associated with ganglioglioma and adverse clinical outcome. This update will also ask why common pathogenic variants accumulate in certain brain regions, e.g., MTOR in the frontal lobe, and BRAF in the temporal lobe. Finally, I will highlight the ongoing discussion addressing commonalities between temporal lobe epilepsy and Alzheimer's disease, the impact of adult neurogenesis and gliogenesis for the initiation and progression of temporal lobe seizures in the human brain as well as the immunopathogenesis of glutamic acid decarboxylase antibody associated temporal lobe epilepsy as a meaningful disease entity. This review will update the reader on some of these fascinating publications from 2022 and 2023 which were selected carefully, yet subjectively, by the author.
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Project description:WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight the continuing efforts supporting WikiPathways, content growth and collaboration among pathway researchers. As an evolving database, there is a growing need for WikiPathways to address and overcome technical challenges. In this direction, WikiPathways has undergone major restructuring, enabling a renewed approach for sharing and curating pathway knowledge, thus providing stability for the future of community pathway curation. The website has been redesigned to improve and enhance user experience. This next generation of WikiPathways continues to support existing features while improving maintainability of the database and facilitating community input by providing new functionality and leveraging automation.
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Project description:Figure-ground (FG) segregation that separates an object from the rest of the image is a fundamental problem in vision science. A majority of neurons in monkey V2 showed the selectivity to border ownership (BO) that indicates which side of a contour owns the border. Although BO could be a precursor of FG segregation, the contribution of BO to FG segregation has not been clarified. Because FG segregation is the perception of the global region that belongs to an object, whereas BO determination provides the local direction of figure (DOF) along a contour, a spatial integration of BO might be expected for the generation of FG. To understand the mechanisms underlying the perception of figural regions, we investigated the interaction between the local BO determination and the global FG segregation through the quantitative analysis of the visual perception and the spatiotemporal characteristics of eye movements. We generated a set of novel stimuli in which translucency induces local DOF along the contour and global FG independently so that DOF and FG could be either consistent or contradictory. The perceptual responses showed better performance in DOF discrimination than FG segregation, supporting distinct mechanisms for the DOF discrimination and the FG segregation. We examined whether the contradiction between DOF and FG modulates the eye movement while participants judged DOF and FG. The duration of the first eye fixation was modulated by the contradiction during FG segregation but not DOF discrimination, suggesting a sequential processing from the BO determination to the FG segregation. These results of human perception and eye fixation provide important clues for understanding the visual processing for FG segregation.
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Project description:Biomedical literature incorporates millions of figures, which are a rich and important knowledge resource for biomedical researchers. Scientists need access to the figures and the knowledge they represent in order to validate research findings and to generate new hypotheses. By themselves, these figures are nearly always incomprehensible to both humans and machines and their associated texts are therefore essential for full comprehension. The associated text of a figure, however, is scattered throughout its full-text article and contains redundant information content. In this paper, we report the continued development and evaluation of several figure summarization systems, the FigSum+ systems, that automatically identify associated texts, remove redundant information, and generate a text summary for every figure in an article. Using a set of 94 annotated figures selected from 19 different journals, we conducted an intrinsic evaluation of FigSum+. We evaluate the performance by precision, recall, F1, and ROUGE scores. The best FigSum+ system is based on an unsupervised method, achieving F1 score of 0.66 and ROUGE-1 score of 0.97. The annotated data is available at figshare.com (http://figshare.com/articles/Figure_Associated_Text_Summarization_and_Evaluation/858903).
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