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Egon Willighagen › Comments

Egon Willighagen
Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions - http://www.citeulike.org/user...
Cell, Vol. 156, No. 1-2. (16 January 2014), pp. 45-68, doi:10.1016/j.cell.2013.12.019 Methylation of cytosines in the mammalian genome represents a key epigenetic modification and is dynamically regulated during development. Compelling evidence now suggests that dynamic regulation of DNA methylation is mainly achieved through a cyclic enzymatic cascade comprised of cytosine methylation, iterative oxidation of methyl group by TET dioxygenases, and restoration of unmodified cytosines by either replication-dependent dilution or DNA glycosylase-initiated base excision repair. In this review, we discuss the mechanism and function of DNA demethylation in mammalian genomes, focusing particularly on how developmental modulation of the cytosine-modifying pathway is coupled to active reversal of DNA methylation in diverse biological processes. Hao Wu, Yi Zhang - Egon Willighagen
Egon Willighagen
Drug helps to clear traumatic memories - http://www.citeulike.org/user...
Nature (16 January 2014), doi:10.1038/nature.2014.14534 Sara Reardon - Egon Willighagen
Egon Willighagen
An event in Maastricht, Netherlands featuring Barry Hardy and Nina Jeliazkova - Egon Willighagen
Egon Willighagen
Updated LinkedIn network map. Even more than before, the color reflect working environments, with new colors for Open PHACTS and Karolinska Institutet. Prediction for 2014: a color for the NanoSafety... - Egon Willighagen
Egon Willighagen
Body-Mass Index and Mortality among Adults with Incident Type 2 Diabetes - http://www.citeulike.org/user...
N Engl J Med, Vol. 370, No. 3. (15 January 2014), pp. 233-244, doi:10.1056/nejmoa1304501 Excess adiposity is a well-established risk factor for premature death in the general population, including death due to cardiovascular disease or cancer.1?4 However, a so-called obesity paradox (i.e., an association between obesity, as compared with normal weight, and reduced mortality) has been reported among patients with heart failure, end-stage renal disease, or hypertension, and, recently, among those with type 2 diabetes.5?12 Most of these studies, however, have been limited by small samples and suboptimal control for smoking status and preexisting chronic conditions. Smoking is a concern in analyses of body weight and mortality because it is associated with . . . Deirdre Tobias, An Pan, Chandra Jackson, Eilis O'Reilly, Eric Ding, Walter Willett, JoAnn Manson, Frank Hu - Egon Willighagen
Barry Hardy
Goodbye Patrik, we will miss you. - http://barryhardy.blogs.com/cheminf...
Patrik has a friendly guy indeed. A loss indeed :( - Egon Willighagen
Egon Willighagen
Reshared post from John May: - https://plus.google.com/1041867...
Would it be theoretically possible if the Debian Project becomes a formal, authorized signing authority? Original Post from John May: One more nail in the coffin for Java Applets.  Blogs.Oracle.Com - Java Platform Group, Product Management blog - Egon Willighagen
Egon Willighagen
Opgerolde chromosomen mag je beschouwen als zelfassemblerende supramoleculaire structuren. Dan is het ineens logisch dat de geometrie altijd zo'n beetje hetzelfde is, schrijft de Spaanse onderzoeker Joan-Ramon Daban in het tijdschrift Interface . - Egon Willighagen
Egon Willighagen
Reshared post from Casper Steinmann: - https://plus.google.com/1041867...
Original Post from Casper Steinmann: If you don't/can't/won't appreciate the underlying complexity, at least you will find it awesome that these computer models learn to walk. http://vimeo.com/79098420 Flexible Muscle-Based Locomotion for Bipedal Creatures - Egon Willighagen
Egon Willighagen
Revisited: Handling SD files with JavaScript in Bioclipse After asking on the Bioclipse users list it... - https://plus.google.com/1041867...
Revisited: Handling SD files with JavaScript in Bioclipse After asking on the Bioclipse users list it turns out there was an unpublished manager method to trigger parsing of the SDF properties (Arvid++), allowing to simplify creation of the index and not needed parsing of the chemical structures into a CDK molecul... Now, there are a million ways of implementing this workflow. If you really want to know, I chose this one because HMDB identifiers is a more prominent ID used in WikiPathways, and for this one, as well as ChEBI, I can use a SD file. For ChemSpider and PubChem identifiers, however, ... - Egon Willighagen
Egon Willighagen
Reshared post from Clarissa Silva: - https://plus.google.com/1041867...
Sad... I really hate it when data is presented without the alternative (man stealing data from other man), but that doesn't make this less sad... Original Post from Clarissa Silva: Celebrating amazing women that made siginifican contributions to science. #sciencesunday   #womeninstem   #womeninscience   #scienceeveryday   women.jpg - Egon Willighagen
Egon Willighagen
Reshared post from Jan Jensen: - https://plus.google.com/1041867...
One important feature of SourceForge is that they keep file releases into eternity. That way,  people can still download the very first releases of Jmol, the CDK, ... this is important for scientific software as much as it is for older literature. GitHub as a "journal" will help, but we should also have libraries start putting GitHub releases on their shelves and perhaps even mirror git repository tags of articles they put in their library. Original Post from Jan Jensen: 11 Jan 2014 on open | science | github | open science | doi | orcid | altmetrics. 3 simple things GitHub can do for science. Introduction. The topic “GitHub for Science” has been explored quite a few times before (1, 2, 3, 4) and with good reason: it is quite exciting to envision what ... - Egon Willighagen
Egon Willighagen
Stacks, Serials, Search Engines, and Students' Success: First-Year Undergraduate Students' Library Use, Academic Achievement, and Retention - http://www.citeulike.org/user...
The Journal of Academic Librarianship (January 2014), doi:10.1016/j.acalib.2013.12.002 Krista Soria, Jan Fransen, Shane Nackerud - Egon Willighagen
Egon Willighagen
Prediction of Drugs Target Groups Based on ChEBI Ontology. - http://www.citeulike.org/user...
BioMed research international, Vol. 2013 (2013), doi:10.1155/2013/132724 Most drugs have beneficial as well as adverse effects and exert their biological functions by adjusting and altering the functions of their target proteins. Thus, knowledge of drugs target proteins is essential for the improvement of therapeutic effects and mitigation of undesirable side effects. In the study, we proposed a novel prediction method based on drug/compound ontology information extracted from ChEBI to identify drugs target groups from which the kind of functions of a drug may be deduced. By collecting data in KEGG, a benchmark dataset consisting of 876 drugs, categorized into four target groups, was constructed. To evaluate the method more thoroughly, the benchmark dataset was divided into a training dataset and an independent test dataset. It is observed by jackknife test that the overall prediction accuracy on the training dataset was 83.12%, while it was 87.50% on the test dataset-the predictor... - Egon Willighagen
Egon Willighagen
Microbiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits - http://www.citeulike.org/user...
Cell (January 2014), doi:10.1016/j.cell.2013.12.016 Filipe De Vadder, Petia Kovatcheva-Datchary, Daisy Goncalves, Jennifer Vinera, Carine Zitoun, Adeline Duchampt, Fredrik Bäckhed, Gilles Mithieux - Egon Willighagen
Egon Willighagen
Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature - http://www.citeulike.org/user...
Nature Communications, Vol. 5 (9 Jan 2014), doi:10.1038/ncomms4012 Advancing the debate on quantum effects in light-initiated reactions in biology requires clear identification of non-classical features that these processes can exhibit and utilise. Here we show that in prototype dimers present in a variety of photosynthetic antennae, efficient vibration-assisted energy transfer in the subpicosecond timescale and at room temperature can manifest and benefit from non-classical fluctuations of collective pigment motions. Non-classicality of initially thermalised vibrations is induced via coherent exciton-vibration interactions and is unambiguously indicated by negativities in the phase-space quasi-probability distribution of the effective collective mode coupled to the electronic dynamics. These quantum effects can be prompted upon incoherent input of excitation. Our results therefore suggest that investigation of the non-classical properties of vibrational motions assisting excitation... - Egon Willighagen
Egon Willighagen
Reshared post from Vedrin Jeliazkov: - https://plus.google.com/1041867...
Original Post from Vedrin Jeliazkov: So, here is the final proof that Erwin Schrödinger got it right when he suggested studying quantum biology in his 1944 book "What Is Life?": "The UCL team found the unambiguous signature of non-classicality is given by a negative joint probability of finding the chromophores with certain relative positions and momenta. In classical physics, probability distributions are always positive." "The negative values in these probability distributions are a manifestation of a truly quantum feature, that is, the coherent exchange of a single quantum of energy," explained Edward O'Reilly (UCL Physics & Astronomy), first author of the study. "When this happens electronic and vibrational degrees of freedom are jointly and transiently in a superposition of quantum states, a feature that can never be predicted with classical physics." Light-gathering macromolecules in plant cells transfer energy by taking advantage of molecular vibrations whose physical... - Egon Willighagen
Egon Willighagen
Reshared post from Mark Fortner: - https://plus.google.com/1041867...
Original Post from Mark Fortner: Some more info on the TRAIL-nanoparticle conjugate. #cancer Nanoparticles Search and Destroy Tumor-Causing Cells in Bloodstream — NOVA Next | PBS - Egon Willighagen
Egon Willighagen
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again - http://www.citeulike.org/user...
BMC Bioinformatics, Vol. 15, No. Suppl 1. (2014), S11, doi:10.1186/1471-2105-15-s1-s11 BACKGROUND:The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment.RESULTS:The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using... - Egon Willighagen
Egon Willighagen
Sometime biology can be quite enjoyable :) - https://plus.google.com/1041867...
Sometime biology can be quite enjoyable :) Tigerfish swallows swallows after grabbing them out of the air over African lake. - Egon Willighagen
Egon Willighagen
Reshared post from Alan Cann: - https://plus.google.com/1041867...
Who wants to learn a bit of #WikiPathways  drawing and wants to convert this into a machine readable entry in the database?Learn all about how to draw pathways here: http://wikipathways.org/index... Original Post from Alan Cann: Obesity: The emerging neurobiology of calorie addiction http://elife.elifesciences.org/content... F1.medium.gif - Egon Willighagen
Egon Willighagen
QSAR Modeling: Where Have You Been? Where Are You Going To? - http://www.citeulike.org/user...
J. Med. Chem. (18 December 2013), doi:10.1021/jm4004285 Quantitative structure?activity relationship modeling is one of the major computational tools employed in medicinal chemistry. However, throughout its entire history it has drawn both praise and criticism concerning its reliability, limitations, successes, and failures. In this paper, we discuss (i) the development and evolution of QSAR; (ii) the current trends, unsolved problems, and pressing challenges; and (iii) several novel and emerging applications of QSAR modeling. Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR models. We hope that this Perspective will help communications between computational and experimental chemists toward collaborative development and use of QSAR models. We also believe that the guidelines presented here will help journal editors and reviewers... - Egon Willighagen
Egon Willighagen
Genome-wide localization of small molecules - http://www.citeulike.org/user...
Nat Biotech, Vol. 32, No. 1. (15 January 2014), pp. 92-96, doi:10.1038/nbt.2776 Lars Anders, Matthew Guenther, Jun Qi, Zi Fan, Jason Marineau, Peter Rahl, Jakob Loven, Alla Sigova, William Smith, Tong Lee, James Bradner, Richard Young - Egon Willighagen
Egon Willighagen
Reshared post from Mark Fortner: - https://plus.google.com/1041867...
And so the smart phone industry will safe the environment... Original Post from Mark Fortner: Battery advance could boost renewable energy take-up http://www.bbc.co.uk/news... Battery advance boost to renewables - Egon Willighagen
Egon Willighagen
Reshared post from Numberphile: - https://plus.google.com/1041867...
Wow, infinite is even infinitely more weird than I knew... addition up all positive numbers into infinity is a negative number, -1/12 . !!! Original Post from Numberphile: Hope you have all seen our Grandi's Series video from a while ago?  One minus one plus one minus one - Numberphile ASTOUNDING: 1 + 2 + 3 + 4 + 5 + ... = -1/12 - Egon Willighagen
Egon Willighagen
An Evaluation of the Left-Brain vs. Right-Brain Hypothesis with Resting State Functional Connectivity Magnetic Resonance Imaging - http://www.citeulike.org/user...
PLoS ONE, Vol. 8, No. 8. (14 August 2013), e71275, doi:10.1371/journal.pone.0071275 Lateralized brain regions subserve functions such as language and visuospatial processing. It has been conjectured that individuals may be left-brain dominant or right-brain dominant based on personality and cognitive style, but neuroimaging data has not provided clear evidence whether such phenotypic differences in the strength of left-dominant or right-dominant networks exist. We evaluated whether strongly lateralized connections covaried within the same individuals. Data were analyzed from publicly available resting state scans for 1011 individuals between the ages of 7 and 29. For each subject, functional lateralization was measured for each pair of 7266 regions covering the gray matter at 5-mm resolution as a difference in correlation before and after inverting images across the midsagittal plane. The difference in gray matter density between homotopic coordinates was used as a regressor to reduce... - Egon Willighagen
Egon Willighagen
Teacher and student perceptions of the development of learner autonomy; a case study in the biological sciences - http://www.citeulike.org/user...
Studies in Higher Education (7 January 2014), pp. 1-12, doi:10.1080/03075079.2013.842216 Biology teachers in a UK university expressed a majority view that student learning autonomy increases with progression through university. A minority suggested that pre-existing diversity in learning autonomy was more important and that individuals not cohorts differ in their learning autonomy. They suggested that personal experience prior to university and age were important and that mature students are more autonomous than 18?20 year olds. Our application of an autonomous learning scale (ALS) to four year-groups of biology students confirmed that the learning autonomy of students increases through their time at university but not that mature students are necessarily more autonomous than their younger peers. It was evident however that year of study explained relatively little (<?10%) of total variation in ALS scores in this student population, which suggests that personal and... - Egon Willighagen
Egon Willighagen
Kinetics of the formation and secretion of the aniline metabolite 4-aminophenol and its conjugates by isolated rat hepatocytes - http://www.citeulike.org/user...
Xenobiotica, Vol. 14, No. 5. (1 January 1984), pp. 409-416, doi:10.3109/00498258409151429 1. The rates of secretion of 4-aminophenol and its sulphate and glucuronide conjugate were determined in cultures of rat hepatocytes with aniline and 4-aminophenol as substrates. 2. When 4-aminophenol (300 ?M) was used as substrate, 4-aminophenol disappeared from the medium within 30 min. Secretion of conjugates continued for more than 60 min, when 70% of the 4-aminophenol had been secreted as conjugates. 3. At a low concn. of 4-aminophenol, the sulphate ester was the main metabolite, while secretion of the glucuronide showed a more than proportional rise (?lag phase?) with increasing substrate concn. At higher concn. (>300?M) about equal amounts of both conjugates were formed. 4. Without inorganic sulphate, sulphation of 4-aminophenol was greatly diminished and the lag phase in glucuronide secretion was not found. 5. With 1 him aniline as substrate up to 300 ?M of conjugated 4-aminophenol was... - Egon Willighagen
Egon Willighagen
The Inhibitory Effects of Bioactive Compounds of Tomato Juice Binding to Hepatic HMGCR: In Vivo Study and Molecular Modelling - http://www.citeulike.org/user...
PLoS ONE, Vol. 9, No. 1. (2 January 2014), e83968, doi:10.1371/journal.pone.0083968 The hypocholesterolemic effect of tomato juice has been investigated in an intervention study with rats, along with the possible inhibition effect of bioactive tomato compounds binding to the HMGCR enzyme. Two experimental groups (n = 8 Sprague-Dawley rats) were fed ad libitum for five weeks, with water or tomato juice provided to the control and intervention groups, respectively. Total, LDL and HDL cholesterol, and total triglycerides were analysed in plasma, and the lycopene content and the expression and activity of the enzyme HMGCR were determined in liver samples. A computational molecular modelling was carried out to determine the interactions between HMGCR and lycopene, chlorogenic acid and naringenin. Total, LDL and HDL cholesterol were significantly lower in the intervention group after the intake of tomato juice. In addition, a significant reduction in HMGCR activity was observed, although... - Egon Willighagen
Egon Willighagen
N6-methyladenosine-dependent regulation of messenger RNA stability - http://www.citeulike.org/user...
Nature, Vol. 505, No. 7481. (27 November 2013), pp. 117-120, doi:10.1038/nature12730 N6-methyladenosine (m6A) is the most prevalent internal (non-cap) modification present in the messenger RNA of all higher eukaryotes. Although essential to cell viability and development, the exact role of m6A modification remains to be determined. The recent discovery of two m6A demethylases in mammalian cells highlighted the importance of m6A in basic biological functions and disease. Here we show that m6A is selectively recognized by the human YTH domain family 2 (YTHDF2) reader protein to regulate mRNA degradation. We identified over 3,000 cellular RNA targets of YTHDF2, most of which are mRNAs, but which also include non-coding RNAs, with a conserved core motif of G(m6A)C. We further establish the role of YTHDF2 in RNA metabolism, showing that binding of YTHDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies. The... - Egon Willighagen
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