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Egon Willighagen › Comments

Egon Willighagen
The ‘digital natives’ debate: A critical review of the evidence - http://www.citeulike.org/user...
British Journal of Educational Technology, Vol. 39, No. 5. (1 September 2008), pp. 775-786, doi:10.1111/j.1467-8535.2007.00793.x The idea that a new generation of students is entering the education system has excited recent attention among educators and education commentators. Termed ‘digital natives’ or the ‘Net generation’, these young people are said to have been immersed in technology all their lives, imbuing them with sophisticated technical skills and learning preferences for which traditional education is unprepared. Grand claims are being made about the nature of this generational change and about the urgent necessity for educational reform in response. A sense of impending crisis pervades this debate. However, the actual situation is far from clear. In this paper, the authors draw on the fields of education and sociology to analyse the digital natives debate. The paper presents and questions the main claims made about digital natives and analyses the nature of the debate... - Egon Willighagen
Egon Willighagen
Egonw: {{multiple issues| {{Cleanup-spam|date=August 2013}} {{Cleanup-list|date=August 2013}}}} A '''molecule editor''' is a [[computer program]] for creating and modifying representations of [[chemical structure]]s. Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. [[Two-dimensional]] editors generate output used as illustrations or for querying [[chemical database]]s. [[3-D computer graphics|Three-dimensional]] molecule editors are used to build molecular models, usually as part of [[molecular modelling]] software packages. Database molecular editors such as Leatherface,<ref>Kenny, P.W.; Sadowski, J. (2005) [http://dx.doi.org/10... Structure modification in chemical databases] ''Chemoinformatics in drug discovery'' (editor&mdash;Oprea, T.I.), 271-285 (Wiley).</ref> RECAP<ref>Lewell, X.Q.; Judd, D.B; Watson, S.P.; Hann, M.M. (1998) [http://dx.doi.org/10... RECAP-Retrosynthetic Combinatorial Analysis... - Egon Willighagen
Egon Willighagen
CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis - http://www.citeulike.org/user...
PLoS ONE, Vol. 8, No. 12. (5 December 2013), e82160, doi:10.1371/journal.pone.0082160 The high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the cellular machinery. By deciphering the role of important players, including transcription factors, microRNAs, or small molecules, a better understanding of key regulatory processes can be obtained. Various databases contain information on the interactions of regulators with their targets for different organisms, data recently being extended with the results of the ENCODE (Encyclopedia of DNA Elements) project. A systems biology approach integrating our understanding on different regulators is essential in interpreting the regulation of molecular biological processes. We developed CyTargetLinker (http://projects.bigcat.unimaas.nl/cytarg etlinker), a Cytoscape app, for integrating regulatory interactions in network analysis. Recently we released... - Egon Willighagen
Egon Willighagen
Bioinformatics, Vol. 29, No. 10. (15 May 2013), pp. 1350-1351, doi:10.1093/bioinformatics/btt138 Summary: Cytoscape is an open source software tool for biological network visualization and analysis, which can be extended with independently developed apps. We launched the Cytoscape App Store to highlight the important features that apps add to Cytoscape, enable researchers to find and install apps they need and help developers promote their apps. Samad Lotia, Jason Montojo, Yue Dong, Gary Bader, Alexander Pico - Egon Willighagen
Egon Willighagen
In Chemometrics with R (2011), doi:10.1007/978-3-642-17841-2 Ron Wehrens - Egon Willighagen
Egon Willighagen
Uncovering global SUMOylation signaling networks in a site-specific manner - http://www.citeulike.org/user...
Nature Structural &#38; Molecular Biology, Vol. 21, No. 10. (14 September 2014), pp. 927-936, doi:10.1038/nsmb.2890 High-resolution MS identifies >4,300 SUMOylation sites in >1,600 proteins in human cells under standard growth conditions and after proteasome inhibition or heat shock. The data reveal cross-talk between SUMO and other post-translational modifications. Ivo Hendriks, Rochelle D'Souza, Bing Yang, Matty Verlaan-de Vries, Matthias Mann, Alfred Vertegaal - Egon Willighagen
Egon Willighagen
Accessing biological data in R with semantic web technologies - http://www.citeulike.org/user...
PeerJ PrePrints (31 December 2013), doi:10.7287/peerj.preprints.185 Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library. Results. We here present three examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a... - Egon Willighagen
Egon Willighagen
Egon Willighagen
Obesity accelerates epigenetic aging of human liver - http://www.citeulike.org/user...
Proceedings of the National Academy of Sciences (13 October 2014), 201412759, doi:10.1073/pnas.1412759111 Steve Horvath, Wiebke Erhart, Mario Brosch, Ole Ammerpohl, Witigo von Schönfels, Markus Ahrens, Nils Heits, Jordana Bell, Pei-Chien Tsai, Tim Spector, Panos Deloukas, Reiner Siebert, Bence Sipos, Thomas Becker, Christoph Röcken, Clemens Schafmayer, Jochen Hampe - Egon Willighagen
Egon Willighagen
Visual Workflows for 13C-Metabolic Flux Analysis - http://www.citeulike.org/user...
Bioinformatics (7 October 2014), doi:10.1093/bioinformatics/btu585 Motivation: The precise quantification of intracellular metabolic flow rates is of fundamental importance in bio(techno)logy and medical research. The gold standard in the field is metabolic flux analysis (MFA) with 13C-labeling experiments. 13C-MFA workflows orchestrate several, mainly human-in-the-loop software applications, integrating them with plenty of heterogeneous information. In practice, this had posed a major practical barrier for evaluating, interpreting, and understanding isotopic data from carbon labeling experiments.Results: Graphical modeling, interactive model exploration, and visual data analysis are the key to overcome this limitation. We have developed a first-of-its-kind graphical tool suite providing scientists with an integrated software framework for all aspects of 13C-MFA. Almost 30 modules (plugins) have been implemented for the Omix visualization software. Several advanced graphical workflows... - Egon Willighagen
Egon Willighagen
Long-echo time MR spectroscopy for skeletal muscle acetylcarnitine detection. - http://www.citeulike.org/user...
The Journal of clinical investigation (1 October 2014) Animal models suggest that acetylcarnitine production is essential for maintaining metabolic flexibility and insulin sensitivity. Because current methods to detect acetylcarnitine involve biopsy of the tissue of interest, noninvasive alternatives to measure acetylcarnitine concentrations could facilitate our understanding of its physiological relevance in humans. Here, we investigated the use of long-echo time (TE) proton magnetic resonance spectroscopy (1H-MRS) to measure skeletal muscle acetylcarnitine concentrations on a clinical 3T scanner. We applied long-TE 1H-MRS to measure acetylcarnitine in endurance-trained athletes, lean and obese sedentary subjects, and type 2 diabetes mellitus (T2DM) patients to cover a wide spectrum in insulin sensitivity. A long-TE 1H-MRS protocol was implemented for successful detection of skeletal muscle acetylcarnitine in these individuals. There were pronounced differences in insulin... - Egon Willighagen
Egon Willighagen
Scientific Lenses to Support Multiple Views over Linked Chemistry Data - http://www.citeulike.org/user...
In The Semantic Web – ISWC 2014, Vol. 8796 (2014), pp. 98-113, doi:10.1007/978-3-319-11964-9_7 When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over the data with no way of varying the notion of equivalence to be applied. In this paper, we present an approach to enable applications to choose the equivalence criteria to apply between datasets. Thus, supporting multiple dynamic views over the Linked Data. For chemical data, we show that multiple sets of links can be automatically generated according to different equivalence criteria and published with semantic descriptions capturing their context and interpretation. This approach has been applied within a large scale public-private data integration platform for drug discovery. To cater for... - Egon Willighagen
Egon Willighagen
Reshared post from Graham Steel: - https://plus.google.com/1041867...
This is not a reincarnation of the fake DOI? Original Post from Graham Steel: Elsevier are now charging $30 for blank PDF's. http://www.sciencedirect.com/science... blankpage2.png - Egon Willighagen
Egon Willighagen
This page is intentionally left blank - http://www.citeulike.org/user...
In Verified Syntheses of Zeolitic Materials (2001), 267, doi:10.1016/b978-044450703-7/50187-3 - Egon Willighagen
Egon Willighagen
2014 update! Well done! This web page is the home of the LOD cloud diagram. This image shows datasets that have been published in Linked Data format, by contributors to the Linking Open Data community project and other individuals and organisations. It is based on metadata collected and curated by contributors to the ... - Egon Willighagen
Egon Willighagen
Reshared post from NextMove Software: - https://plus.google.com/1041867...
Excellent post showing that data analysis requires thinking about how you represent your problem. In other words, it really matters how you represent your data, what analysis you can do, and therefore, what hypothesis you can answer. Original Post from NextMove Software: If we know some activity orders as a starting point, our ability to predict is much improved... There is a 2008 paper by the folks at Abbott that Roger refers to as “the paper that killed matched pairs for activity data”. This is the Hajduk and Sauer paper which looked at matched pair transformations across 84K compounds and 30 protein targets, and found that the potency changes associated ... - Egon Willighagen
Egon Willighagen
Me is thinking old editions of the CRC Handbook of Chemistry and Physics... - https://plus.google.com/1041867...
Me is thinking old editions of the CRC Handbook of Chemistry and Physics... Announcing BookLiberator Beta — the affordable, low-tech book digitizer that's made of wood, looks good in your living room or library, and can scan 600-900 pages per hour! Order now from our online store. We're very pleased to announce the availability of BookLiberator Beta kits. - Egon Willighagen
Egon Willighagen
New nanomaterials increasingly find their way to the European market, because of their unique applications. Understanding the safety of nanomaterials is therefore of utmost importance. This post-doc position takes responsibility of the development new intelligent methods that aim to understand the toxicity issues of nanomaterials. The project will explore and ... - Egon Willighagen
Egon Willighagen
It must be hard to be an "industry" representative, if you represent companies willing to engage in ... - https://plus.google.com/1041867...
It must be hard to be an "industry" representative, if you represent companies willing to engage in these kind of things... :( (HT Dana on CHMINF-L mailing list) The case brings up larger questions about the reliability of self-reporting - Egon Willighagen
David Bradley
Top 10 Facebook updates to make me unfollow you - http://www.sciencetext.com/top-10-...
1. Post like this one. - Egon Willighagen
Egon Willighagen
Neutral molecular cluster formation of sulfuric acid–dimethylamine observed in real time under atmospheric conditions - http://www.citeulike.org/user...
Proceedings of the National Academy of Sciences (06 October 2014), 201404853, doi:10.1073/pnas.1404853111 Andreas Kürten, Tuija Jokinen, Mario Simon, Mikko Sipilä, Nina Sarnela, Heikki Junninen, Alexey Adamov, João Almeida, Antonio Amorim, Federico Bianchi, Martin Breitenlechner, Josef Dommen, Neil Donahue, Jonathan Duplissy, Sebastian Ehrhart, Richard Flagan, Alessandro Franchin, Jani Hakala, Armin Hansel, Martin Heinritzi, Manuel Hutterli, Juha Kangasluoma, Jasper Kirkby, Ari Laaksonen, Katrianne Lehtipalo, Markus Leiminger, Vladimir Makhmutov, Serge Mathot, Antti Onnela, Tuukka Petäjä, Arnaud Praplan, Francesco Riccobono, Matti Rissanen, Linda Rondo, Siegfried Schobesberger, John Seinfeld, Gerhard Steiner, António Tomé, Jasmin Tröstl, Paul Winkler, Christina Williamson, Daniela Wimmer, Penglin Ye, Urs Baltensperger, Kenneth Carslaw, Markku Kulmala, Douglas Worsnop, Joachim Curtius - Egon Willighagen
Egon Willighagen
Amino acids involved in stabilizing sulfuric acids droplets ... mmm... more nano! - https://plus.google.com/1041867...
Amino acids involved in stabilizing sulfuric acids droplets ... mmm... more nano! Amines in de atmosfeer houden zwavelzuurmoleculen bij elkaar en werken zo de vorming van wolken in de hand. Een internationaal gezelschap heeft dat experimenteel vastgesteld, zo valt te lezen in PNAS . - Egon Willighagen
Egon Willighagen
Rise of the Rest: The Growing Impact of Non-Elite Journals - http://www.citeulike.org/user...
(8 Oct 2014) In this paper, we examine the evolution of the impact of non-elite journals. We attempt to answer two questions. First, what fraction of the top-cited articles are published in non-elite journals and how has this changed over time. Second, what fraction of the total citations are to non-elite journals and how has this changed over time. We studied citations to articles published in 1995-2013. We computed the 10 most-cited journals and the 1000 most-cited articles each year for all 261 subject categories in Scholar Metrics. We marked the 10 most-cited journals in a category as the elite journals for the category and the rest as non-elite. There are two conclusions from our study. First, the fraction of top-cited articles published in non-elite journals increased steadily over 1995-2013. While the elite journals still publish a substantial fraction of high-impact articles, many more authors of well-regarded papers in diverse research fields are choosing other venues. The... - Egon Willighagen
Egon Willighagen
Cholestenoic acids regulate motor neuron survival via liver X receptors - http://www.citeulike.org/user...
Journal of Clinical Investigation (1 October 2014), doi:10.1172/jci68506 Spyridon Theofilopoulos, William Griffiths, Peter Crick, Shanzheng Yang, Anna Meljon, Michael Ogundare, Satish Kitambi, Andrew Lockhart, Karin Tuschl, Peter Clayton, Andrew Morris, Adelaida Martinez, Ashwin Reddy, Andrea Martinuzzi, Maria Bassi, Akira Honda, Tatsuki Mizuochi, Akihiko Kimura, Hiroshi Nittono, Giuseppe De Michele, Rosa Carbone, Chiara Criscuolo, Joyce Yau, Jonathan Seckl, Rebecca Schüle, Ludger Schöls, Andreas Sailer, Jens Kuhle, Matthew Fraidakis, Jan-Åke Gustafsson, Knut Steffensen, Ingemar Björkhem, Patrik Ernfors, Jan Sjövall, Ernest Arenas, Yuqin Wang - Egon Willighagen
Egon Willighagen
Product of the NanoSafety Cluster Database working group. - https://plus.google.com/1041867...
Product of the NanoSafety Cluster Database working group. Summary of the Spring 2014 NSC Database Survey - Egon Willighagen
Egon Willighagen
Summary of the Spring 2014 NSC Database Survey - http://www.citeulike.org/user...
(2014), doi:10.6084/m9.figshare.1195888 The NanoSafety Cluster Database working group organized in Spring 2014 a survey for the community to summarize the current state of databases and including questions of a more technical nature. This survey is a first in a biannual continuous effort and attempt to collect, organise and share up-to-date information about NanoSafety related databases worldwide. For example, it included questions about application programming interfaces, database schema, supported input and output formats, etc. This document summarizes the responses we received before August 2014. Axel Mustad, Bart Smeets, Nina Jeliazkova, Vedrin Jeliazkov, Egon Willighagen - Egon Willighagen
Egon Willighagen
Computational Derivation of Structural Alerts from Large Toxicology Datasets - http://www.citeulike.org/user...
J. Chem. Inf. Model. (2 October 2014), doi:10.1021/ci500314a Structural alerts have been one of the backbones of computational toxicology and have applications in many areas including cosmetic, environmental and pharmaceutical toxicology. The development of structural alerts has always involved a manual analysis of existing data related to a relevant endpoint followed by the determination of substructures that appear to be related to a specific outcome. The substructures are then analyzed for their utility in posterior validation studies which at times have stretched over years or even decades. With higher throughput methods now being employed in many areas of toxicology, data sets are growing at an unprecedented rate. This growth has made manual analysis of data sets impractical in many cases. This report outlines a fully automatic method that highlights significant substructures for toxicologically-important data sets. The method identifies important substructures by computationally... - Egon Willighagen
Egon Willighagen
Butyrate and other short-chain fatty acids increase the rate of lipolysis in 3T3-L1 adipocytes - http://www.citeulike.org/user...
PeerJ, Vol. 2 (07 October 2014), e611, doi:10.7717/peerj.611 John Rumberger, Jonathan Arch, Allan Green - Egon Willighagen
Egon Willighagen
Size dependency variation in lattice parameter and valency states in nanocrystalline cerium oxide - http://www.citeulike.org/user...
Applied Physics Letters, Vol. 87, No. 13. (26 September 2005), 133113, doi:10.1063/1.2061873 A correlation between the particle size and the lattice parameter has been established in nanocerium oxide particles ( 3 – 30 nm ) . The variation in the lattice parameter is attributed to the lattice strain induced by the introduction of Ce 3 + due to the formation of oxygen vacancies. Lattice strain was observed to decrease with an increase in the particle size. Ce 3 + ions concentration increased from 17% to 44% with the reduction in the particle size. Sameer Deshpande, Swanand Patil, Satyanarayana Kuchibhatla, Sudipta Seal - Egon Willighagen
Egon Willighagen
I am not at all fond of terminology if you have perfectly good means to communicate the meaning. So, I rather say: “what is missing” than “gap analysis”. About the same number of characters, but the... - Egon Willighagen
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