Evaluation of two interaction techniques for visualization of dynamic graphs

Several techniques for visualization of dynamic graphs are based on different spatial arrangements of a temporal sequence of node-link diagrams. Many studies in the literature have investigated the importance of maintaining the user's mental map across this temporal sequence, but usually each layout is considered as a static graph drawing and the effect of user interaction is disregarded. We conducted a task-based controlled experiment to assess the effectiveness of two basic interaction techniques: the adjustment of the layout stability and the highlighting of adjacent nodes and edges. We found that generally both interaction techniques increase accuracy, sometimes at the cost of longer completion times, and that the highlighting outclasses the stability adjustment for many tasks except the most complex ones.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Lead-zinc mining and home-grown foodstuffs (Eastern FYR Macedonia)

Comunicação oral da qual só está disponível o resumo.Mining accompany our civilization since evolution. Since the “Copper (Chalcolithic) Age” and later “Golden Age”, mining activities have created great wealth. Unfortunately, beside wealth the exploitation of metal rich ores, have been almost always correlated with a negative impact to the nearby ecosystems. In this study a broad area around the active Pb-Zn Sasa mine (NE FYR Macedonia) was characterized, to evaluate the contents of some Potentially Toxic Elements (PTE). The PTE were determined in the surrounding fresh waters (lake and rivers), soils and the home-grown vegetables. The evaluation of the potential hazardous ef ects of the PTE, especially on humans, is a key goal. The PTE’s were determined by ICP-AES and ICP-MS. Furthermore also detailed questionnaires were applied among the local inhabitants. Sequential extraction analyses of selected soil samples revealed that the majority of PTE was bounded to water soluble and exchangeable fraction, which shows that those elements (Ag, As, Cd, Cu, Mo, Ni, Pb, Sb and Zn) are therefore very easily mobile and consequently available to plants. According to the applied questionnaires, the consumption of home-grown foodstuf s is high, and certain vegetables, such as tomatoes, peppers, salads, etc., are consumed every day or even more than once a day. Chemical evaluation of PTE in home-grown vegetables revealed that the most crucial PTE’s (those which heavily exceed upper allowable limits) are Cd, Co, Cu, Pb and Zn, and are closely followed by Cr and As. The calculated Health Risk Index (HRI) shows extremely high estimated values, both for adults and children. As the study area is surrounded by rich metallogenic ore deposits, is expected that the natural background is slightly higher than elsewhere. Nevertheless, the concentrations of PTE’s in waters used for irrigation which were increased and the wind-blown (aeorogenic) PTE’s pollution from the nearby tailings dam, both increases the PTE contents in the studied foodstuf s. Thus, the health of inhabitants in this area is of high concern

The Contribution of 17beta-Hydroxysteroid Dehydrogenase Type 1 to the Estradiol-Estrone Ratio in Estrogen-Sensitive Breast Cancer Cells

Estrone and estradiol are both estrogens with estrone being the less potent form and estradiol being the most potent estrogen. The binding of the latter to cellular regulatory elements stimulates the proliferation of breast cancer cells. A high ratio of estradiol/estrone is related to increased cell proliferation, and is of great importance to understanding of breast cancer mechanisms. 17beta-hydroxysteroid dehydrogenase type 1 and type 2 play important roles in the activation of estrone and inactivation of estradiol. Breast cancer cells T47D, MCF-7, BT 20, and JEG 3 as control cells, were chosen to evaluate the contribution of these two enzymes to the ratio. Twenty four hours after addition of different concentrations of estrone and estradiol, the ratio stabilized to around 9/1 in breast cancer cell lines with high expression of type 1 (T47D, BT 20, and JEG 3), whereas it approached 1/5 in cells with low expression of type 1 (MCF-7). The estradiol/estrone concentration ratio was modified to 9/1 in MCF-7 and HEK-293 cells over-expressing type 1. In T47D and BT 20, this ratio was decreased from 9/1 to nearly 1/5 (19/81 and 17/83 respectively) after type 1 knockdown by specific siRNAs. Type 2 is mainly involved in the conversion of estradiol into estrone. This ratio was decreased from 9/1 to 7/3 after over-expression of type 2 in MCF-7 cells already over-expressing type 1. The ratio was further decreased by the addition of the oxidative cofactor, NAD, to the cell culture to facilitate the estradiol to estrone conversion catalyzed by type 2. These results demonstrate that the estradiol/estrone ratio is controlled by both type 1 and type 2 with an additional contribution by NAD, although type 1 is the first determining factor in the cellular environment compared with type 2 and cofactors. Moreover, kinetic studies were carried out in intact cells as a new approach, using HEK-293 cells over-expressing type 1 and T47D breast cancer cells

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole genome mutation screening in Candida albicans and aeruginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion: We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens

Expression analysis of estrogen-metabolizing enzymes in human endometrial cancer.

Estrogen-dependent endometrial cancer is related to unopposed and prolonged estrogen stimulation. We examined the expression of estrogen-metabolizing enzymes in correlation with the ERα and ERβ estrogen receptors in human endometrial Ishikawa adenocarcinoma cells and in endometrial cancer specimens and adjacent normal endometrium from the same patients. Real-time PCR analysis revealed that both estrogen receptors and selected estrogen-metabolizing enzymes were expressed in the Ishikawa cells and in endometrial tissue. We detected higher expression of ERα than ERβ, higher expression of sulfatase than sulfotransferase and low expression of aromatase in the Ishikawa cells and the tissue, as well as higher levels of type 2 17β-hydroxysteroid dehydrogenase (17β-HSD) in normal and diseased tissue than in the Ishikawa cells. When we compared the expression in endometrial cancer samples and in the adjacent normal endometrium, ERα and ERβ, sulfatase and sulfotransferase were seen to be downregulated in the majority of the cancerous tissue specimens

Novel estrogen-related genes and potential biomarkers of ovarian endometriosis identified by differential expression analysis.

In the search for novel biomarkers of endometriosis, we selected 152 genes from the GeneLogic database based on results of genome-wide expression analysis of ovarian endometriosis, plus 20 genes related to estrogen metabolism and action. We then performed low-density array analysis of these 172 genes on 11 ovarian endometriosis samples and 9 control endometrium samples. Principal component analysis of the gene expression levels showed clear separation between the endometriosis and control groups. We identified 78 genes as differentially expressed. Based on Ingenuity pathway analysis, these differentially expressed genes were arranged into groups according to biological function. These analyses revealed that 32 differentially expressed genes are estrogen related, 23 of which have not been reported previously in connection with endometriosis. Functional annotation showed that 25 and 22 genes are associated with the biological terms "secreted" and "extracellular region", respectively. Differential expression of 4 out of 5 genes related to estrogen metabolism and action (ESR1, ESR2, PGR and BGN) was also confirmed by immunohistochemistry. Our study thus reveals differential expression of several genes that have not previously been associated with endometriosis and that encode potential novel biomarkers and drug targets