1,721,025 research outputs found
Neurogenic potential of human mesenchymal stem cells revisited: analysis by immunostaining, time-lapse video and microarray.
No full textThe possibility of generating neural cells from human bone-marrow-derived mesenchymal stem cells (hMSCs) by simple in vitro treatments is appealing both conceptually and practically. However, whether phenotypic modulations observed after chemical manipulation of such stem cells truly represent a genuine trans-lineage differentiation remains to be established. We have re-evaluated the effects of a frequently reported biochemical approach, based on treatment with butylated hydroxyanisole and dimethylsulphoxide, to bring about such phenotypic conversion by monitoring the morphological changes induced by the treatment in real time, by analysing the expression of phenotype-specific protein markers and by assessing the modulation of transcriptome. Video time-lapse microscopy showed that conversion of mesenchymal stem cells to a neuron-like morphology could be reproduced in normal primary fibroblasts as well as mimicked by addition of drugs eliciting cytoskeletal collapse and disruption of focal adhesion contacts. Analysis of markers revealed that mesenchymal stem cells constitutively expressed multi-lineage traits, including several pertaining to the neural one. However, the applied ;neural induction' protocol neither significantly modulated the expression of such markers, nor induced de novo translation of other neural-specific proteins. Similarly, global expression profiling of over 21,000 genes demonstrated that gene transcription was poorly affected. Most strikingly, we found that the set of genes whose expression was altered by the inductive treatment did not match those sets of genes differentially expressed when comparing untreated mesenchymal stem cells and immature neural tissues. Conversely, by comparing these gene expression profiles with that obtained from comparisons between the same cells and an unrelated non-neural organ, such as liver, we found that the adopted neural induction protocol was no more effective in redirecting human mesenchymal stem cells toward a neural phenotype than toward an endodermal hepatic pathway
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
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_
Full text linkBackground
Exploring cellular responses to stimuli using extensive gene expression profiles has become a routine procedure performed on a daily basis. Raw and processed data from these studies are available on public databases but the opportunity to fully exploit such rich datasets is limited due to the large heterogeneity of data formats. In recent years, several approaches have been proposed to effectively integrate gene expression data for analysis and exploration at a broader level. Despite the different goals and approaches towards gene expression data integration, the first step is common to any proposed method: data acquisition. Although it is seemingly straightforward to extract valuable information from a set of downloaded files, things can rapidly get complicated, especially as the number of experiments grows. Transcriptomic datasets are deposited in public databases with little regard to data format and thus retrieving raw data might become a challenging task. While for RNA-seq experiments such problem is partially mitigated by the fact that raw reads are generally available on databases such as the NCBI SRA, for microarray experiments standards are not equally well established, or enforced during submission, and thus a multitude of data formats has emerged.
Results
COMMAND>_ is a specialized tool meant to simplify gene expression data acquisition. It is a flexible multi-user web-application that allows users to search and download gene expression experiments, extract only the relevant information from experiment files, re-annotate microarray platforms, and present data in a simple and coherent data model for subsequent analysis.
Conclusions
COMMAND>_ facilitates the creation of local datasets of gene expression data coming from both microarray and RNA-seq experiments and may be a more efficient tool to build integrated gene expression compendia. COMMAND>_ is free and open-source software, including publicly available tutorials and documentation
Neurogenic potential of human mesenchymal stem cells revisited: analysis by immunostaining, time-lapse video and microarray
No full textThe possibility of generating neural cells from human
bone-marrow-derived mesenchymal stem cells (hMSCs) by
simple in vitro treatments is appealing both conceptually
and practically. However, whether phenotypic modulations
observed after chemical manipulation of such stem cells
truly represent a genuine trans-lineage differentiation
remains to be established. We have re-evaluated the effects
of a frequently reported biochemical approach, based on
treatment with butylated hydroxyanisole and
dimethylsulphoxide, to bring about such phenotypic
conversion by monitoring the morphological changes
induced by the treatment in real time, by analysing the
expression of phenotype-specific protein markers and by
assessing the modulation of transcriptome. Video timelapse
microscopy showed that conversion of mesenchymal
stem cells to a neuron-like morphology could be
reproduced in normal primary fibroblasts as well as
mimicked by addition of drugs eliciting cytoskeletal
collapse and disruption of focal adhesion contacts. Analysis
of markers revealed that mesenchymal stem cells
constitutively expressed multi-lineage traits, including
several pertaining to the neural one. However, the applied
‘neural induction’ protocol neither significantly modulated
the expression of such markers, nor induced de novo
translation of other neural-specific proteins. Similarly,
global expression profiling of over 21,000 genes
demonstrated that gene transcription was poorly affected.
Most strikingly, we found that the set of genes whose
expression was altered by the inductive treatment did not
match those sets of genes differentially expressed when
comparing untreated mesenchymal stem cells and
immature neural tissues. Conversely, by comparing these
gene expression profiles with that obtained from
comparisons between the same cells and an unrelated nonneural
organ, such as liver, we found that the adopted
neural induction protocol was no more effective in
redirecting human mesenchymal stem cells toward a neural
phenotype than toward an endodermal hepatic pathway.
Key words: Bone-marrow-derived stem cells, Neurogenesis,
Transdifferentiation
Summar
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
Dual RNA-SEQ unearthed the unsuccessful response of a phytopathogenic oomicete to the antagonistic strategies implemented by the biocontrol bacterium Lysobacter capsici AZ78
No full textBackgrounds
The establishment of plant diseases also depends on the outcome of the complex microbial
interactions occurring between pathogenic microorganisms and their antagonists residing in the
rhizosphere.
Objectives
The molecular mechanisms activated in the interaction between the beneficial rhizobacterium
Lysobacter capsici AZ78 and the soilborne phytopathogenic oomycete Phytophthora infestans were
finely dissected using a dual transcriptomic approach.
Methods
Simultaneous transcriptional changes of both L. capsici AZ78 and P. infestans occurring after 6 and
24 h of interaction were analysed. The transcriptional profiling of L. capsici AZ78 was mainly
characterized by the up-regulation of genes involved in the biogenesis of type 4 pilus and lytic
enzymes (cellulases, glucanases and proteases)involved in the host colonization and the subsequent
attack of P. infestans cell wall, respectively. The activation of detoxification processes allowed L.
capsici AZ78 to overcome the defence activity of P. infestans. Moreover, genes deputed to the
antibiotic biosynthesis were up-regulated in L. capsici AZ78 resulting in the up-regulation of genes
involved in programmed cell death in P. infestans. The consequences of the activation of these
processes resulted in the overall down-regulation of primary metabolic pathways in P. infestans, such
as carbohydrate, nucleic acids and protein metabolisms.
Conclusions
The dual transcriptional analysis revealed that the antagonistic activity of L. capsici AZ78 is based on
transcriptional activation of motility, attachment, lytic and antibiotic processes. On the other hand, the
activation of programmed cell death in P. infestans could explain its inability to actively respond to L.
capsici AZ78 attacks
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