Overview of (pro-)Lie group structures on Hopf algebra character groups

Character groups of Hopf algebras appear in a variety of mathematical and physical contexts. To name just a few, they arise in non-commutative geometry, renormalisation of quantum field theory, and numerical analysis. In the present article we review recent results on the structure of character groups of Hopf algebras as infinite-dimensional (pro-)Lie groups. It turns out that under mild assumptions on the Hopf algebra or the target algebra the character groups possess strong structural properties. Moreover, these properties are of interest in applications of these groups outside of Lie theory. We emphasise this point in the context of two main examples: The Butcher group from numerical analysis and character groups which arise from the Connes--Kreimer theory of renormalisation of quantum field theories.Comment: 31 pages, precursor and companion to arXiv:1704.01099, Workshop on "New Developments in Discrete Mechanics, Geometric Integration and Lie-Butcher Series", May 25-28, 2015, ICMAT, Madrid, Spai

MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

Background: Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results: MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft Excel spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion: The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data

Aggrecan, link protein and tenascin-R are essential components of the perineuronal net to protect neurons against iron-induced oxidative stress

In Alzheimer’s disease (AD), different types of neurons and different brain areas show differential patterns of vulnerability towards neurofibrillary degeneration, which provides the basis for a highly predictive profile of disease progression throughout the brain that now is widely accepted for neuropathological staging. In previous studies we could demonstrate that in AD cortical and subcortical neurons are constantly less frequently affected by neurofibrillary degeneration if they are enwrapped by a specialized form of the hyaluronan-based extracellular matrix (ECM), the so called ‘perineuronal net’ (PN). PNs are basically composed of large aggregating chondroitin sulphate proteoglycans connected to a hyaluronan backbone, stabilized by link proteins and cross-linked via tenascin-R (TN-R). Under experimental conditions in mice, PN-ensheathed neurons are better protected against iron-induced neurodegeneration than neurons without PN. Still, it remains unclear whether these neuroprotective effects are directly mediated by the PNs or are associated with some other mechanism in these neurons unrelated to PNs. To identify molecular components that essentially mediate the neuroprotective aspect on PN-ensheathed neurons, we comparatively analysed neuronal degeneration induced by a single injection of FeCl3 on four different mice knockout strains, each being deficient for a different component of PNs. Aggrecan, link protein and TN-R were identified to be essential for the neuroprotective properties of PN, whereas the contribution of brevican was negligible. Our findings indicate that the protection of PN-ensheathed neurons is directly mediated by the net structure and that both the high negative charge and the correct interaction of net components are essential for their neuroprotective function

Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes

Background: The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of functionally described domains. If these variants promote an organism's ecological fitness, they are likely to be conserved in the genome of its progeny and the population at large. The genetic composition of microbial communities in their native ecosystems is accessible through metagenomics. We hypothesize the co-variation of protein domain sequences across metagenomes from similar ecosystems will provide insights into their potential roles and aid further investigation. Methodology/Principal findings: We calculated the correlation of Pfam protein domain sequences across the Global Ocean Sampling metagenome collection, employing conservative detection and correlation thresholds to limit results to well-supported hits and associations. We then examined intercorrelations between domains of unknown function (DUFs) and domains involved in known metabolic pathways using network visualization and cluster-detection tools. We used a cautious "guilty-by-association'' approach, referencing knowledge-level resources to identify and discuss associations that offer insight into DUF function. We observed numerous DUFs associated to photobiologically active domains and prevalent in the Cyanobacteria. Other clusters included DUFs associated with DNA maintenance and repair, inorganic nutrient metabolism, and sodium-translocating transport domains. We also observed a number of clusters reflecting known metabolic associations and cases that predicted functional reclassification of DUFs. Conclusion/Significance: Critically examining domain covariation across metagenomic datasets can grant new perspectives on the roles and associations of DUFs in an ecological setting. Targeted attempts at DUF characterization in the laboratory or in silico may draw from these insights and opportunities to discover new associations and corroborate existing ones will arise as more large-scale metagenomic datasets emerge

The Relationship between Physical Growth and Infant Behavioral Development in Rural Guatemala

The present study investigated the relationship between a number of anthropometric indices and behavioral development during the first 2 years of life in rural Guatemala. Length and weight were the indices most strongly correlated with behavioral development. If the effect of the infant\u27s length and weight was statistically controlled for, none of the other anthropometric variables explained a significant proportion of the variance in behavioral development. Con- trolling for length (or weight) assessed at the same age as the behavioral assessment, length (or weight) for younger ages was not significantly correlated with behavioral development. Changes in length or weight over time were correlated with changes in behavioral performance. We were unable to explain the association between physical growth and behavioral development by a number of variables including gestational age, nutrient intake, prevalence of disease, and familial characteristics

A Mole for Warm Magnetic and Optical Measurements of LHC Dipoles

A new rotating coil probe (a mole) has been developed for the simultaneous measurement of the magnetic field and magnetic axis of warm superconducting LHC dipoles and associated corrector windings. The mole houses a radial rotating coil and travels inside the magnet aperture by means of an externally driven two-way traction belt. The coil is rotated by an on-board piezo motor, being tested in view of future devices for cold measurements as the only type of motor compatible with strong magnetic fields. A virtual light spot is generated in the coil center by a LED source. The position of this light spot is measured from the outside by a system including a telescope, a CCD camera and a DSP. Jigs on reference granite tables are used to transfer the optical measurements to the magnet fiducials. We describe here the main characteristics and performance of the mol

Individual decision making and the evolutionary roots of institutions

Just as many aspects of individual decisions are sometimes called unconscious or automatic, we know that some institutions have evolved through unconscious, nondeliberative mechanisms. Their function can also be largely nondeliberative, as in the case of some institutions that may structure behavior without requiring any reflection on the part of the participants. On the other hand, political institutions exist for the purpose of bringing deliberative mechanisms to bear on institutions in the hope of changing them for the better. The immense project of building an integrated explanation of institutions from individual brains to nations-has only barely begun. In this chapter, we report on our discussions that attempted to sketch the mechanisms that connect individuals to large-scale institutions. We begin with a discussion of current thought on the design of individual decision making. If institutions regulate behavior, then presumably the mechanisms that have evolved to produce individual behavior will be relevant to the broader enterprise of integrating these two scales of explanation. Then we explore ways in which institutions may have evolved, both as a result of individual decision making and as a result of processes distinct from those that govern individual behavior. We approach this topic from two perspectives. Seen one way, unconscious psychological forces constrain the design of institutions, sometimes powerfully. Seen another way, unconscious population-level processes create functional institutional design that few social architects could conceive of with their individual deliberate faculties

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets

In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyers using faceted browsing. Using this approach we have developed the Ontogrator platform, which allows for rapid retrieval of data in a way that would be familiar to any online shopper. Using Knowledge Organization Systems (KOS), especially ontologies, Ontogrator uses text mining to mark up data and faceted browsing to help users navigate, query and retrieve data. Ontogrator offers the potential to impact scientific research in two major ways: 1) by significantly improving the retrieval of relevant information; and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. This implementation demonstrates the power of ontogration and highlights that the usefulness of this approach is fully dependent on both the quality of data and the KOS (ontologies) used. Ideally, the use and further expansion of this collaborative system will help to surface issues associated with the underlying quality of annotation and could lead to a systematic means for accessing integrated data resources