26 research outputs found
Comparison of Gene Expression Profiles in Chromate Transformed BEAS-2B Cells
Hexavalent chromium [Cr(VI)] is a potent human carcinogen.
Occupational exposure has been associated with increased risk of respiratory
cancer. Multiple mechanisms have been shown to contribute to Cr(VI) induced
carcinogenesis, including DNA damage, genomic instability, and epigenetic
modulation, however, the molecular mechanism and downstream genes mediating
chromium's carcinogenicity remain to be elucidated.We established chromate transformed cell lines by chronic exposure of normal
human bronchial epithelial BEAS-2B cells to low doses of Cr(VI) followed by
anchorage-independent growth. These transformed cell lines not only
exhibited consistent morphological changes but also acquired altered and
distinct gene expression patterns compared with normal BEAS-2B cells and
control cell lines (untreated) that arose spontaneously in soft agar.
Interestingly, the gene expression profiles of six Cr(VI) transformed cell
lines were remarkably similar to each other yet differed significantly from
that of either control cell lines or normal BEAS-2B cells. A total of 409
differentially expressed genes were identified in Cr(VI) transformed cells
compared to control cells. Genes related to cell-to-cell junction were
upregulated in all Cr(VI) transformed cells, while genes associated with the
interaction between cells and their extracellular matrices were
down-regulated. Additionally, expression of genes involved in cell
proliferation and apoptosis were also changed.This study is the first to report gene expression profiling of Cr(VI)
transformed cells. The gene expression changes across individual chromate
exposed clones were remarkably similar to each other but differed
significantly from the gene expression found in anchorage-independent clones
that arose spontaneously. Our analysis identified many novel gene expression
changes that may contribute to chromate induced cell transformation, and
collectively this type of information will provide a better understanding of
the mechanism underlying chromate carcinogenicity
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe