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

Crowdsourced mapping of unexplored target space of kinase inhibitors

Despite decades of intensive search for compounds that modulate the activity of particular protein targets, a large proportion of the human kinome remains as yet undrugged. Effective approaches are therefore required to map the massive space of unexplored compound-kinase interactions for novel and potent activities. Here, we carry out a crowdsourced benchmarking of predictive algorithms for kinase inhibitor potencies across multiple kinase families tested on unpublished bioactivity data. We find the top-performing predictions are based on various models, including kernel learning, gradient boosting and deep learning, and their ensemble leads to a predictive accuracy exceeding that of single-dose kinase activity assays. We design experiments based on the model predictions and identify unexpected activities even for under-studied kinases, thereby accelerating experimental mapping efforts. The open-source prediction algorithms together with the bioactivities between 95 compounds and 295 kinases provide a resource for benchmarking prediction algorithms and for extending the druggable kinome. The IDG-DREAM Challenge carried out crowdsourced benchmarking of predictive algorithms for kinase inhibitor activities on unpublished data. This study provides a resource to compare emerging algorithms and prioritize new kinase activities to accelerate drug discovery and repurposing efforts

Interactive Visual Transformation for Symbolic Representation of Time-oriented Data

Abstract Data Mining on time-oriented data has many real-world applications, like optimizing shift plans for shops or hospitals, or analyzing traffic or climate. As those data are often very large and multi-variate, several methods for symbolic representation of time-series have been proposed. Some of them are statistically robust, have a lower-bound distance measure, and are easy to configure, but do not consider temporal structures and domain knowledge of users. Other approaches, proposed as basis for Apriori pattern finding and similar algorithms, are strongly configurable, but the parametrization is hard to perform, resulting in ad-hoc decisions. Our contribution combines the strengths of both approaches: an interactive visual interface that helps defining event classes by applying statistical computations and domain knowledge at the same time. We are not focused on a particular application domain, but intend to make our approach useful for any kind of time-oriented data

Supplementary Material for: Gesundheitsförderung durch Stress- und Burnout-Prophylaxe mit ätherischen Ölen für alle Berufsgruppen im Wiener Otto-Wagner-Spital

<b><i>Hintergrund: </i></b>Mehr als 50% der Menschen leiden an berufsbedingtem und familiärem Stress, der bei hohem Pegel zu körperlichen, mentalen und sozialen Beeinträchtigungen bis hin zum Burnout-Syndrom führen kann. Die regelmäßige Anwendung von hochwertigen ätherischen Ölen vermag den individuellen Stresspegel deutlich zu senken. In einem Projekt zur Gesundheitsförderung durch Stress- und Burnout-Prophylaxe soll die Stressreduktion durch ätherische Öle bestätigt werden. <b><i>Methodik:</i></b> In das Studienprojekt konnten insgesamt 88 Mitarbeiter des Wiener Otto Wagner Spitals mit auswertbaren Aufnahme- und 55 Mitarbeiter mit auswertbaren Abschluss-Fragebögen aufgenommen werden. Die Teilnehmer erhielten einen SOS-Stress-Deoroller mit 12 ätherischen Ölen, der mindestens 3-mal täglich einen Monat lang an den Pulszonen der Handgelenke aufgetragen wurde. <b><i>Ergebnisse: </i></b>Zum Befragungszeitpunkt 1 am Tag der Aufnahme in die Studie betrug der Stresswert bezogen auf eine Stress-Skala von 1 (gar nicht belastet) bis 10 (sehr stark belastet) im Mittel 6,28, am Ende der Beobachtungszeit 5,24. In der Analyse der körperlichen Beeinträchtigungen durch Stress (SK 1-8) zeigte sich beim Pflegepersonal (p = 0,036) und bei Personen über 50 Jahren (p = 0,012 bzw. 0,025) ein signifikanter Benefit der Aromatherapie. Das Belastungsniveau durch körperlichen, psychischen und sozialen Stress zwischen Befragungszeitpunkt 1 und 2 zeigte deutliche, mitunter signifikante positive Veränderung durch die Anwendung der ätherischen Öle. Bei 27 Teilnehmern konnten die Fragebögen von Zeitpunkt 1 und 2 dem jeweiligen Teilnehmer zugeordnet werden. In dieser Personengruppe zeigten sich sowohl in der Gesamtbelastung wie auch in allen Teilbereichen signifikant positive Ergebnisse der Aromatherapie. <b><i>Schlussfolgerung: </i></b>Ein Großteil der Teilnehmer konnte mittels der ätherischen Öle im SOS-Stress-Deoroller seine Stress-assoziierten Beeinträchtigungen deutlich reduzieren. Es konnten keine allergischen Reaktionen oder Unverträglichkeiten beobachtet werden. Ausgewählte hochwertige ätherische Öle können für die Prophylaxe und Behandlung von Stress und Burnout empfohlen werden