1,721,161 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Get PDFWe 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
Transcriptional regulation of TAX1BP2, a putative tumor suppressor in hepatocellular carcinoma
No full textHepatocellular carcinoma (HCC) is one of the most widespread and deadly cancers
in South East Asia, mainly because of the high incidence rate of chronic hepatitis B
virus (HBV) infection. The clinical outcome of HCC patients is often poor due to
the highly metastatic nature and commonly late diagnosis of HCC. Together with a
limited choice of chemotherapy, this makes HCC a serious health threat in Hong
Kong. Thus, better treatment is desperately required for HCC. Centrosomal Tax1-
binding protein 2 （TAX1BP2）protein is a putative tumor suppressor in HCC and
functions to suppress centrosome overduplication. TAX1BP2 is first recognized as
a novel interacting protein of Tax, an oncoprotein encoded in HTLV-I virus, and is
frequently underexpressed in HCC. TAX1BP2 down-regulation is associated with
poorer overall survival of HCC patients.
To understand how TAX1BP2 is downregulated in HCC, we examined the
transcriptional regulation of TAX1BP2. With the epigenetic analysis, including
methylation profile, demethylation and histone acetylation analysis, we ruled out
the possibility of differential epigenetic modification as the major cause for
TAX1BP2 underexpression.
By LASAGNA online software, we predicted the potential transcriptional factors
(TFs) binding sites on TAX1BP2 promoter and showed that deletion of the binding
sites for Hepatocyte Nuclear Factor 4 alpha (HNF4α or HNF4A) caused a drastic
decrease in TAX1BP2 promoter activity. Consistently, ectopic expression of
HNF4α up-regulated the promoter activity and expression levels of TAX1BP2 both transcriptionally and translationally. Inhibition of HNF4α expression by its
antagonist and siRNA also suppressed TAX1BP2 expression. By Chromatin
Immunoprecipitation, we found that HNF4α binds to TAX1BP2 promoter.
Moreover, we demonstrated that down-regulation of HNF4α was related to a poorer
survival outcome of HCC patients. Using the quantitative real-time PCR (qRTPCR),
a positive correlation of TAX1BP2 and HNF4α expression at clinical level
was observed.
Interestingly, ectopic expression of hepatitis B virus X protein (HBx), an
oncoprotein encoded by HBV, was able to suppress HNF4α and TAX1BP2 protein
expression. Furthermore, the HBx-mediated suppression of TAX1BP2 promoter
activity could be rescued by ectopic expression of HNF4α, which suggested that
HBx and HNF4α worked within the same signaling pathway.
This study focuses on the transcriptional regulation of TAX1BP2. Here we provide
the evidence on positive regulation of TAX1BP2 by HNF4α transcription factor.
Furthermore, we showed that HBx suppressed HNF4α, leading to a downregulation
of TAX1BP2. Further studying the HBx/HNF4α/TAX1BP2 pathway
will shed light on the molecular regulatory mechanism of HBV-associated
hepatocarcinogenesis.published_or_final_versionBiomedical SciencesMasterMaster of Philosoph
Functional characterization of the role of NIMA (never in mitosis gene a)-related kinase 2(Nek2) in hepatocellular carcinoma
No full textThe NIMA-related kinase 2 (Nek2), which regulates centrosome cohesion and cell cycle progression, is a potential player in carcinogenesis. Reports have shown that up-regulation of Nek2 has been observed in various types of cancer.
However, the functional roles of Nek2 in hepatocellular carcinoma (HCC) is poorly understood. HCC is a primary liver malignancy that arises from hepatocyte. It is notorious for its chemo-resistance nature and HCC patients generally have poor prognosis. Previously, our laboratory showed that Nek2 mRNA and protein levels are overexpressed in HCC and knockdown of Nek2 inhibited metastasis. Using the same cell line, Nek2 was found to be involved in the regulation of YAP, a transcriptional factor that control cell proliferation and organ size.
To study the effect of Nek2 in HCC, a stable inducible Nek2 overexpression system was established in different HCC cell lines. Cell growth was inhibited when Nek2 is overexpressed. For the study of centrosome, we observed that higher proportion of cells with centrosome splitting occurred in the Nek2 overexpressing cells in both inducible HepG2 and SMMC-7721 cell lines. Increased cell population with centrosome over-duplication was however observed in U2OS cells when Nek2 is up-regulated. Moreover, cell cycle analysis on induced Nek2 cells revealed an increased in DNA content, suggesting that Nek2 promotes aneuploidy in HCC cells.
Using confocal co-immunofluorescence staining, I demonstrated that TAX1BP2, a putative tumor suppressor in HCC, is a potential interacting partner of Nek2 at the centrosome. Interestingly, I provided evidence that overexpression of TAX1BP2 can significantly block the effect of Nek2 mediated centrosome separation, suggesting that TAX1BP2 may act downstream of Nek2 signaling. Furthermore, in terms of the mechanism of regulation, I showed that TAX1BP2 is a substrate of Nek2 using in vitro kinase assay. Although several potential Nek2 phosphorylation sites in TAX1BP2 has been predicted, it remains to be determined which phosphorylation site is critical for the regulation of TAX1BP2 by Nek2.
To dissect how Nek2 promotes HCC formation and delineate its signaling pathways, both Flag antibody and biotin ligase affinity pull-down assay were employed. Some potential interacting partners of Nek2 were identified by these affinity pull-down approaches. Such as the CP110, which is involved in centrosome elongation, has been isolated by Flag antibody pull down. In addition, I also isolated several other potential binding partners in biotin ligase pull down. These novel binding partners suggest that Nek2 may play a role in centromere function, apoptosis and centrosome overall structures.
To conclude, Nek2 induces centrosome splitting and aneuploidy in HCC cells, which provides insights to the oncogenic role of Nek2 in HCC. Dysregulation of centrosome owing to the overexpression of Nek2 may be a key event in inducing hepatocarcinogenesis.published_or_final_versionBiomedical SciencesMasterMaster of Philosoph
Functional characterization of polo-like kinase 4 (PLK4) in hepatocellular carcinoma
No full textThe Polo-like Kinase 4 (PLK4), a centrosomal serine-threonine (S/T) kinase, is the master regulator of centrosome duplication. Recent evidence suggested that PLK4 is frequently overexpressed in cancer and overexpression of PLK4 is linked to chemo-resistance and poor prognosis in many types of cancers.
The critical role of PLK4 plays in centriole biogenesis is well established, but its role in carcinogenesis only begun to emerge until recently. In this study, by stable overexpressing or silencing PLK4 in HCC cells, it was showed that PLK4 was critical for their tumorigenicity, migration and invasion. To understand how PLK4 promotes hepatocarcinogenesis, RNA-Seq analysis was performed using the stable PLK4 overexpression or knockdown HCC cells. Interestingly, bioinformatic analysis of RNA-Seq data revealed that the focal adhesion pathway was involved in PLK4 mediated migration. Such result was further validated by immunoblotting showing overexpression of PLK4 activated focal adhesion kinase in HCC cells.
Mechanistically, it was confirmed that Tyrosine Kinase Expressed in Hepatocellular Carcinoma (TEC) is an interacting-partner of PLK4. TEC is a cytoplasmic signal transducer which functional role in HCC remains uncharacterized. ShRNA-mediated knockdown of TEC inhibited tumorigenicity and metastatic potential of HCC cells while overexpression showed reversed behaviors. SiRNA-mediated knockdown of PLK4 in TEC-expressing HCC cells reversed the enhanced cell invasiveness mediated by TEC overexpression, implying that PLK4 was essential for TEC function. By immunofluorescent staining, PLK4 was shown to localize at the centrosome, and overexpression of which induced supernumerary centrosomes in HCC cell lines. Unlike PLK4, overexpression of TEC had no effect in centrosome number. Though TEC was found to localize in cytoplasm, no TEC could be detected at the centrosomes, suggesting that TEC might activate PLK4 in the cytoplasm to enhance invasion. It was further demonstrated that TEC stabilized PLK4 in vivo via phosphorylation at the tyrosine-86 residue inside PLK4 kinase domain. In contrast to wildtype PLK4, overexpression of phospho-defective mutant (Y86F) of PLK4 did not change the invasiveness of HCC cells.
Another chapter of this study focused to explore whether Aurora A (AurkA), a critical mitotic kinase in centrosome biology, is an upstream regulator of PLK4 and TAX1 binding-protein 2 (TAX1BP2) in HCC. Approach using the in vitro kinase assay coupled with mass spectrometry fingerprinting analysis showed that AurkA phosphorylated six S/T residues in the Cryptic-Polo-Box domain of PLK4. The phosphorylation resulted in an inhibition of PLK4 kinase activity demonstrated by in vitro kinase assay and immunoblotting using phospho-specific antibody against the active site of PLK4. It is still unclear what is the major function of this phosphorylation. However, since AurkA and PLK4 are both implicated in cytokinesis, the possibility that AurkA inhibits PLK4 activity to induce cytokinesis failure remains to be explored. Using co-immunofluorescence staining, it was demonstrated that TAX1BP2 localized in close-proximity with AurkA during interphase. In addition, TAX1BP2 was strongly phosphorylated by AurkA in in vitro kinase assay. By means of an overlapping peptide array and in vitro kinase assay, all the potential AurkA phosphorylation sites on TAX1BP2 was examined. Further analysis on the functional role of these phosphorylation on TAX1BP2 in regulating centrosome disjunction should be examined.
Taken together, this study identified two mechanisms in which phosphorylation of PLK4 by TEC and AurkA modulate the stability and activity of PLK4. Functionally, TEC stabilizes PLK4 in HCC to promote cell invasiveness, while the significance of AurkA mediated PLK4 inhibition and TAX1BP2 phosphorylation warrant further investigation.published_or_final_versionBiomedical SciencesDoctoralDoctor of Philosoph
Characterization of upstream and downstream signaling pathway of P21-activated kinase 4 through TAX1 binding protein 2 and INKA1 in cancer metastasis
No full textP21 activated protein kinase 4 (PAK4) regulates various cellular processes including cell migration, cell cycle progression, and cell survival. PAK4 overexpression, which has been reported in diverse cancer cell lines and various clinical samples, including hepatocellular carcinoma (HCC) and pancreatic cancer, is associated with poor survival and more aggressive tumor behaviors in patients. TAX1 binding protein 2 (TAX1BP2), which is an alternative splicing variant of ciliary rootlet coiled-coil protein, was first identified as a novel interacting protein of human T-lymphocyte virus I (HTLV-1) coded oncoprotein TAX. Further studies revealed that TAX1BP2 was frequently underexpressed in HCC, and its underexpression was associated with a poorer prognosis. In terms of tumor-suppressive activity, TAX1BP2 was found to upregulate p53 tumor suppressor and p21wa1f/cip1 cell cycle inhibitor in a p38 MAPK dependent manner.
In the current study, I characterized the interaction of PAK4 and TAX1BP2 both in vitro and in cells. PAK4 phosphorylated TAX1BP2 at serine 387 promoted the protein degradation of TAX1BP2 through the ubiquitin-proteasome pathway, which resulted in attenuation of the proliferation and migration inhibition functions of TAX1BP2. Meanwhile, the centrosome targeting domain of PAK4 was mapped to the 100-300 a.a. region of PAK4, which was crucial for the interaction between PAK4 and TAX1BP2.
Because of the important roles of PAK4 in tumorigenesis and cancer metastasis, PAK4 can be a good target for cancer therapy. However, no safe PAK4 inhibitor is available clinically so far. Excitingly, an endogenous PAK4 inhibitor, INKA1 was identified recently. It was reported that the functional domains of INKA1 inhibited the kinase activity of PAK4 in vitro. It is still unclear whether INKA1 could suppress PAK4 activity in cancer cells. Therefore, in this study, I characterized the PAK4 kinase inhibition functions of INKA1. Firstly, the interaction of PAK4 and INKA1 was confirmed in HCC and pancreatic cancer cells. Secondly, the kinase activity of PAK4 was inhibited by full-length INKA1 and the functional domains of INKA1 in vitro and in cells. Based on the amino acid sequence of the PAK4 inhibitory domain of INKA1, I designed a small peptide, which efficiently inhibited the PAK4 activity in cells. With the clinical data analysis, I found that INKA1 underexpression was associated with patients’ survival in pancreatic cancer. More importantly, the tumorigenic activity of pancreatic cancer cells, including proliferation, anchorage-independent growth, migration, and invasion, were suppressed by INKA1. Meanwhile, matrix metalloproteinase-2 (MMP2) was significantly suppressed by INKA1 in pancreatic cells via inhibiting the activation of NF-κB signaling. Interestingly, INKA1 was also a phosphorylation substrate of PAK4, and the PAK4 phosphorylation attenuated the PAK4 inhibitory function of INKA1. Finally, I identified four novel INKA1-interacting proteins, and these proteins may cooperate with INKA1 to suppress PAK4 activity.
In summary, the present study characterized the interactions of PAK4 with its downstream effector TAX1BP2 and endogenous inhibitor INKA1. The findings advance our understanding of PAK4 and provide important insight on the development of PAK4 as a therapeutic target for cancers.published_or_final_versionBiomedical SciencesDoctoralDoctor of Philosoph
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