1,721,073 research outputs found
sj-pdf-1-jhc-10.1369_00221554211047287 – Supplemental material for Rejuvenated Vintage Tissue Sections Highlight Individual Antigen Fate During Processing and Long-term Storage
No full textSupplemental material, sj-pdf-1-jhc-10.1369_00221554211047287 for Rejuvenated Vintage Tissue Sections Highlight Individual Antigen Fate During Processing and Long-term Storage by Francesco Mascadri, Maddalena M. Bolognesi, Daniela Pilla and Giorgio Cattoretti in Journal of Histochemistry & Cytochemistry</p
Antibodies validated for routinely processed tissue unpredictably stain frozen tissue sections.
No full textBackground: Antibody validation for tissue staining is required for reproducibility and criteria to ensure validity have been published recently. The majority of these recommendations imply the use of routinely processed tissue (FFPE).
Materials & Methods: We applied to lightly fixed frozen sections a panel of 126 antibodies validated for FFPE with extended criteria.
Results: Less than 30% performed conservatively with all fixations, 35% preferred one fixation over another, 13% gave non-specific staining, 23% did not stain at all.
Conclusions: Individual antibody variability of the paratope fitness for the fixed antigen may be the cause. Re-validation of established antibody panels is required when applied to sections whose fixation and processing is different from the tissue where they have been initially validated.
These are supplementary Data to the manuscript. In addition Tabel 1 and Supplementary Table 1 are provided in Excel format
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
A DNA damage response-like phenotype defines a third of colon cancers at onset. Supplementary data.
No full textThese are supplemental data to the manuscript entitled: A DNA damage response-like phenotype defines a novel subset of colon cancer. A third of de-novo presentations of colorectal cancer display foci of positivity for ℽH2AX, pCHK2, pNBS1 in the absence of apoptosis or senescence associated p21/CDKN1A. This phenotype is reminiscent of an ongoing DNA damage response (DDR). The TP53 status, the chromosome 20q amplification or the microsatellite instability gene status did not correlate with the DDR phenotype, except for a preferential association with MSH2/MSH6 inactivation and conserved MLH1. Additional lesions of DDR-associated genes may be responsible for this phenotype, which is absent from the remaining cases in this cohort. The outcome, after adjuvant treatment with DNA-damaging drugs, did not differentiate this group from the remaining cases. DDR+ colorectal cancers may be amenable to personalized therapy by targeting the DDR
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
BRAQUE: Bayesian Reduction for Amplified Quantization in UMAP Embedding. Supplementary data.
No full textWe propose a Bayesian Reduction for Amplified Quantization in Umap Embedding (BRAQUE) as an integrative novel approach, from data preprocessing to phenotype classification. BRAQUE starts with an innovative preprocessing, named Lognormal Shrinkage, able to enhance input fragmentation by fitting a lognormal mixture model and shrinking each component towards its median, in order to help further clustering step in finding more separated and clear clusters. The BRAQUE’s pipeline consist of a dimensionality reduction step performed using UMAP, and a clustering performed using HDBSCAN on UMAP embedding. These SUPPLEMENTAL DATA contain the csv image data files for seven lymphoid tissues, the antibody list and an MTA agreement letter for the CyBorgh software
The immune landscape of uterine leiomyosarcomas
No full textPersonalized immune intervention to release and redirect the T cells against a tumor has shown substantial progress in aggressive tumors such as melanoma and lung cancer, despite the fact that predictors of sustained response are still unclear. Data on less common histotypes are scanty. Among soft tissue sarcomas, uterine leiomyosarcomas (ULMS) have a dire prognosis, yet therapeutic advances are needed in order to improve the actual treatment. Immune checkpoint inhibitor therapy has been applied to exceptionally few cases, of which the immune cell composition was not examined in detail. We analyzed in situ the inflammatory infiltrate of 21 untreated ULMS in high-dimensional, single cell phenotyping on routinely processed tissue, directed at the characterization of lymphoid cells and macrophages. T-lymphoid cells displayed a composite phenotype common to all tumors, suggestive of antigen-exposure; in about half of the cases containing sufficient lymphocytes, we found evidence of exhaustion and a CD8+ TCF7+ phenotype, this latter associated with T-cell reactivation. To the contrary, myelomonocytic cells had case-specific individual combinations of phenotypes and subsets. We identified five distinct monocyte-macrophage cell types: histiocytes, phagocytes, tumor-associated macrophages, inflammatory monocytes and myelomonocytic cells of undefined phenotype. Immunosuppressive molecules (TIM3, B7H3, VISTA, PD1, PDL1) were heterogeneously expressed in inflammatory and endothelial cells. The heterogeneity and phenotype of the monocyte-macrophage population may represents a challenge for which we provide an initial understanding
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
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