1,720,986 research outputs found
PrestoCell: A persistence-based clustering approach for rapid and robust segmentation of cellular morphology in three-dimensional data
Full text linkLight microscopy methods have continued to advance allowing for unprecedented analysis of various cell types in tissues including the brain. Although the functional state of some cell types such as microglia can be determined by morphometric analysis, techniques to perform robust, quick, and accurate measurements have not kept pace with the amount of imaging data that can now be generated. Most of these image segmentation tools are further burdened by an inability to assess structures in three-dimensions. Despite the rise of machine learning techniques, the nature of some biological structures prevents the training of several current day implementations. Here we present PrestoCell, a novel use of persistence-based clustering to segment cells in light microscopy images, as a customized Python-based tool that leverages the free multidimensional image viewer Napari. In evaluating and comparing PrestoCell to several existing tools, including 3DMorph, Omipose, and Imaris, we demonstrate that PrestoCell produces image segmentations that rival these solutions. In particular, our use of cell nuclei information resulted in the ability to correctly segment individual cells that were interacting with one another to increase accuracy. These benefits are in addition to the simplified graphically based user refinement of cell masks that does not require expensive commercial software licenses. We further demonstrate that PrestoCell can complete image segmentation in large samples from light sheet microscopy, allowing quantitative analysis of these large datasets. As an open-source program that leverages freely available visualization software, with minimum computer requirements, we believe that PrestoCell can significantly increase the ability of users without data or computer science expertise to perform complex image analysis
Isolation and Characterization of Extracellular Vesicles from Cerebrospinal fluid
No full textDuring the last years research in the field of extracellular vesicles (EVs) has gained high interest for diagnostic and therapeutic approaches. Especially in regard to neurological diseases EVs from Cerebrospinal fluid (CSF) represent a new tool to obtain insights into cellular processes of the brain as so called “liquid biopsies”. Therefore it is essential to develop highly standardized isolation and characterization procedures for clinical EV research. Currently most purification methods rely on ultracentrifugation or immunoaffinity protocols. Since these approaches are very labour intensive and suffer from methodological drawbacks, they cannot be easily performed in standard clinical settings. Hence, alternative isolation methods have to be investigated. The field of commercially available EV purification kits has rapidly increased in the last years, leading to a multitude of studies with EV research. To achieve comparability in this field the International Society for Extracellular Vesicles (ISEV) released guidelines for standardized EV research.
For this reasons we decided to compare two commercially available purification methods, precipitation and ultrafiltration, to establish which method gave higher yields and lower impurity content. The final method had to be robust and reliable as well as applicable in a standard clinical laboratory. To perform high scientific standards, we characterized the preparations according to ISEV guidelines, not only to perform comparisons between the methods but also to guarantee comparability in the research field. We found that precipitation is the most suitable method for our purpose since it isolates considerable amounts of EVs from CSF with acceptable purity and discards large amounts of contaminating molecules. After establishing a standard operating protocol (SOP), we performed isolation procedures with CSF samples from seven individuals to show standardization of the final SOP. These results suggest that our final isolation method can be used for further downstream analysis and clinical EV research. It might therefore represent the next step in research of EVs from cerebrospinal fluid
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Mechanisms of aberrant HTT splicing and its implications on RNA homeostasis in Huntington’s disease
No full textHuntington disease (HD) is an autosomal dominant monogenic neurological disorder. The elongation of the CAG repeat in exon 1 of huntingtin (HTT) leads to the production of a short novel HTT isoform called HTT1a. HTT1a is a functional polyadenylated mRNA that contains the sequences of HTT exon 1 and a part of intron 1. Both the HTT1a mRNA as well as the encoded HTT exon 1 protein are known to be toxic. The generation of HTT1a is CAG repeat length dependent but the exact mechanism leading to HTT1a production remains unknown. In addition, it is unclear whether there is a tissue specific expression profile of HTT1a outside of the brain. Thus, a first approach in this study was to detect HTT1a in several different tissues and cell types. In addition to the involvement of the splicing machinery also regulators of transcription like R-loops and epigenetic modifications could contribute to the generation of HTT1a. Therefore, the involvement of DNA methylation, histone H3K27 trimethylations and R-loops at the HTT1a genomic region was analysed. The role of R-loops and epigenetics is not only interesting with regards to the production of HTT1a but also general transcriptional dysregulation in HD. Hence, the genome wide distribution of differentially methylated regions (DMRs), H3K27me3 marks and R-loops was investigated. For the detection of the HTT1a transcript in human peripheral tissues and brain a highly sensitive digital PCR (dPCR) assay was established. The analysis of transcriptional changes, epigenetics and R-loops was performed in primary human fibroblasts derived from healthy controls, adult onset and juvenile onset HD patients. Amplification-free, long read Nanopore sequencing was used for the analysis of the transcriptome and methylome. R-loops and H3K27me3 were detected by the novel method Cleavage under targets and tagmentation (CUT&Tag). Using dPCR, the HTT1a transcript could be detected not only in human post-mortem tissue in several brain regions but also in human muscle tissue, peripheral blood mononuclear cells (PBMCs) and fibroblasts. A significant, positive linear correlation between the expression levels of HTT1a and the CAG repeat length was found in the motor cortex and in PBMCs. Consequently, the measurement of HTT1a levels in easily accessible PBMCs could be a feasible biomarker in studies aiming at HTT lowering. The analysis of DNA methylation, H3K27me3 and R-loops in HTT exon 1 and intron 1 resulted in no significant differences neither between control and adult onset nor control and juvenile onset HD human fibroblasts. Based on the data obtained, the effect of the studied epigenetic factors on the generation of HTT1a in fibroblasts could not be clarified. However, fibroblasts are much less affected by transcriptional and possibly also epigenetic changes in HD than neurons and therefore these factors may well play a role in the generation of HTT1a in neuronal cells. On the genome wide level, the biggest differences in the transcriptome, epigenome and R-loops were found between control and juvenile onset HD fibroblasts. In contrast, HD mutation state was associated with fewer significant differences in the transcriptome, epigenome and R-loops. This was most likely due to the distinct findings in adult and juvenile onset HD fibroblasts. Overall, the number of significant differentially expressed genes or enriched epigenetic/R-loop regions was low. Only a few genes were identified that had a significant differentially enriched region of more than one type. Moreover, the overlap of genes with significant differentially enriched epigenetic or R-loop regions and differentially expressed genes was low. Nevertheless, TBX5 which was found to be significantly upregulated on the transcript level in juvenile onset HD fibroblasts also
showed reduced H3K27me3 and DNA methylation, an epigenetic state associated with active transcription, at its transcription start site. TBX5, encoding T-box binding transcription
factor 5, is interacting with transcription factors involved in HD pathogenesis. Consequently, TBX5 might be an interesting candidate to study in the context of transcriptional dysregulation in HD. The gene ontology and pathway enrichment analysis of the differentially expressed genes and genes containing at least one DMR or differential H3K27me3 region or R-loop resulted in multiple inconclusive pathways and processes. However, SUZ12 and EZH2 were identified as potential regulators in all juvenile HD onset gene sets. This is especially interesting as they are both part of the polycomb repressive complex 2, which is discussed to play a role in transcriptional dysregulation in HD. To sum up, in this work the CAG length dependent expression of HTT1a in PBMCs was shown which implies the assessment of HTT1a as potential future biomarker in clinical HD studies. Additionally, this study could further broaden the knowledge about transcriptional dysregulation in HD by analysing genome wide changes in epigenetic marks and R-loops
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