Braids, Shuffles and Symmetrizers

Multiplicative analogues of the shuffle elements of the braid group rings are introduced; in local representations they give rise to certain graded associative algebras (b-shuffle algebras). For the Hecke and BMW algebras, the (anti)-symmetrizers have simple expressions in terms of the multiplicative shuffles. The (anti)-symmetrizers can be expressed in terms of the highest multiplicative 1-shuffles (for the Hecke and BMW algebras) and in terms of the highest additive 1-shuffles (for the Hecke algebras). The spectra and multiplicities of eigenvalues of the operators of the multiplication by the multiplicative and additive 1-shuffles are examined.Comment: 18 page

Time separation as a hidden variable to the Copenhagen school of quantum mechanics

The Bohr radius is a space-like separation between the proton and electron in the hydrogen atom. According to the Copenhagen school of quantum mechanics, the proton is sitting in the absolute Lorentz frame. If this hydrogen atom is observed from a different Lorentz frame, there is a time-like separation linearly mixed with the Bohr radius. Indeed, the time-separation is one of the essential variables in high-energy hadronic physics where the hadron is a bound state of the quarks, while thoroughly hidden in the present form of quantum mechanics. It will be concluded that this variable is hidden in Feynman's rest of the universe. It is noted first that Feynman's Lorentz-invariant differential equation for the bound-state quarks has a set of solutions which describe all essential features of hadronic physics. These solutions explicitly depend on the time separation between the quarks. This set also forms the mathematical basis for two-mode squeezed states in quantum optics, where both photons are observable, but one of them can be treated a variable hidden in the rest of the universe. The physics of this two-mode state can then be translated into the time-separation variable in the quark model. As in the case of the un-observed photon, the hidden time-separation variable manifests itself as an increase in entropy and uncertainty.Comment: LaTex 10 pages with 5 figure. Invited paper presented at the Conference on Advances in Quantum Theory (Vaxjo, Sweden, June 2010), to be published in one of the AIP Conference Proceedings serie

Modeling perennial groundcover effects on annual maize grain crop growth with the Agricultural Production Systems sIMulator

The inclusion of perennial groundcover (PGC) in maize production offers a tenable solution to natural resources-related concerns associated with conventional maize; however, insight into system management and key information gaps is needed to guide future research. We therefore extended the Agricultural Production Systems sIMulator (APSIM) to an annual and perennial intercrop by integrating annual and perennial APSIM modules. These were parameterized for Kentucky bluegrass (KB) (Poa pratensis L.) or creeping red fescue (CF) (Festuca rubra L.) as PGC using a three-year dataset. Our objectives for this intercropping modeling study were to: i) simultaneously model a PGC and annual cash crop using APSIM software; ii) utilize APSIM to understand interactive processes in the maize-PGC system; and iii) utilize the calibrated model to explore both production and environmental benefits via scenario modeling. For objective I, the integrated model successfully predicted maize total aboveground biomass (TAB) (relative root mean square error, RRMSE of 13- 27%) and PGC above- and belowground tissue N concentration (RRMSE of 11-18%). The calibrated model effectively captured observed trends in PGC biomass accumulation and soil nitrate (NO3). For objective II, model analysis showed that competition for light was the primary maize yield penalty factor from PGC, while water and N impacted maize yield later in the maize growing season. In objective III, we concluded that effective PGC suppression produces minimal maize yield loss and significant environmental benefits; conversely, poor groundcover suppression may produce unfavorable environmental consequences and decrease maize grain yield. Effective PGC suppression is key for long-term system success

Should we welcome robot teachers?

Abstract Current uses of robots in classrooms are reviewed and used to characterise four scenarios: (s1) Robot as Classroom Teacher; (s2) Robot as Companion and Peer; (s3) Robot as Care-eliciting Companion; and (s4) Telepresence Robot Teacher. The main ethical concerns associated with robot teachers are identified as: privacy; attachment, deception, and loss of human contact; and control and accountability. These are discussed in terms of the four identified scenarios. It is argued that classroom robots are likely to impact children’s’ privacy, especially when they masquerade as their friends and companions, when sensors are used to measure children’s responses, and when records are kept. Social robots designed to appear as if they understand and care for humans necessarily involve some deception (itself a complex notion), and could increase the risk of reduced human contact. Children could form attachments to robot companions (s2 and s3), or robot teachers (s1) and this could have a deleterious effect on their social development. There are also concerns about the ability, and use of robots to control or make decisions about children’s behaviour in the classroom. It is concluded that there are good reasons not to welcome fully fledged robot teachers (s1), and that robot companions (s2 and 3) should be given a cautious welcome at best. The limited circumstances in which robots could be used in the classroom to improve the human condition by offering otherwise unavailable educational experiences are discussed

Open Babel: An open chemical toolbox

Background: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendorneutral formats. Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license fro

Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis

<p>Abstract</p> <p>Background</p> <p>One of the challenges of bioinformatics remains the recognition of short signal sequences in genomic DNA such as donor or acceptor splice sites, splicing enhancers or silencers, translation initiation sites, transcription start sites, transcription factor binding sites, nucleosome binding sites, miRNA binding sites, or insulator binding sites. During the last decade, a wealth of algorithms for the recognition of such DNA sequences has been developed and compared with the goal of improving their performance and to deepen our understanding of the underlying cellular processes. Most of these algorithms are based on statistical models belonging to the family of Markov random fields such as position weight matrix models, weight array matrix models, Markov models of higher order, or moral Bayesian networks. While in many comparative studies different learning principles or different statistical models have been compared, the influence of choosing different prior distributions for the model parameters when using different learning principles has been overlooked, and possibly lead to questionable conclusions.</p> <p>Results</p> <p>With the goal of allowing direct comparisons of different learning principles for models from the family of Markov random fields based on the <it>same a-priori information</it>, we derive a generalization of the commonly-used product-Dirichlet prior. We find that the derived prior behaves like a Gaussian prior close to the maximum and like a Laplace prior in the far tails. In two case studies, we illustrate the utility of the derived prior for a direct comparison of different learning principles with different models for the recognition of binding sites of the transcription factor Sp1 and human donor splice sites.</p> <p>Conclusions</p> <p>We find that comparisons of different learning principles using the same a-priori information can lead to conclusions different from those of previous studies in which the effect resulting from different priors has been neglected. We implement the derived prior is implemented in the open-source library Jstacs to enable an easy application to comparative studies of different learning principles in the field of sequence analysis.</p

Bifurcation study of a neural field competition model with an application to perceptual switching in motion integration.

Perceptual multistability is a phenomenon in which alternate interpretations of a fixed stimulus are perceived intermittently. Although correlates between activity in specific cortical areas and perception have been found, the complex patterns of activity and the underlying mechanisms that gate multistable perception are little understood. Here, we present a neural field competition model in which competing states are represented in a continuous feature space. Bifurcation analysis is used to describe the different types of complex spatio-temporal dynamics produced by the model in terms of several parameters and for different inputs. The dynamics of the model was then compared to human perception investigated psychophysically during long presentations of an ambiguous, multistable motion pattern known as the barberpole illusion. In order to do this, the model is operated in a parameter range where known physiological response properties are reproduced whilst also working close to bifurcation. The model accounts for characteristic behaviour from the psychophysical experiments in terms of the type of switching observed and changes in the rate of switching with respect to contrast. In this way, the modelling study sheds light on the underlying mechanisms that drive perceptual switching in different contrast regimes. The general approach presented is applicable to a broad range of perceptual competition problems in which spatial interactions play a role

Gene Expression Dynamics During Bone Healing and Osseointegration

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141010/1/jper1007.pd

Unifying generative and discriminative learning principles

<p>Abstract</p> <p>Background</p> <p>The recognition of functional binding sites in genomic DNA remains one of the fundamental challenges of genome research. During the last decades, a plethora of different and well-adapted models has been developed, but only little attention has been payed to the development of different and similarly well-adapted learning principles. Only recently it was noticed that discriminative learning principles can be superior over generative ones in diverse bioinformatics applications, too.</p> <p>Results</p> <p>Here, we propose a generalization of generative and discriminative learning principles containing the maximum likelihood, maximum a posteriori, maximum conditional likelihood, maximum supervised posterior, generative-discriminative trade-off, and penalized generative-discriminative trade-off learning principles as special cases, and we illustrate its efficacy for the recognition of vertebrate transcription factor binding sites.</p> <p>Conclusions</p> <p>We find that the proposed learning principle helps to improve the recognition of transcription factor binding sites, enabling better computational approaches for extracting as much information as possible from valuable wet-lab data. We make all implementations available in the open-source library Jstacs so that this learning principle can be easily applied to other classification problems in the field of genome and epigenome analysis.</p