Selective pressures on genomes in molecular evolution

We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression, transmission, and neutrality selection. The first two affect genome length: the pressure to conserve resources by compressing the code, and the pressure to acquire additional information that improves the channel, increasing the rate of information transmission into each offspring. Noisy transmission channels (replication with mutations) gives rise to a third pressure that acts on the actual encoding of information; it maximizes the fraction of mutations that are neutral with respect to the phenotype. This neutrality selection has important implications for the evolution of evolvability. We demonstrate each selective pressure in experiments with digital organisms.Comment: 16 pages, 3 figures, to be published in J. theor. Biolog

Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology

This module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk).
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Semi-rational engineering of cellobiose dehydrogenase for improved hydrogen peroxide production

Abstract Background The ability of fungal cellobiose dehydrogenase (CDH) to generate H2O2 in-situ is highly interesting for biotechnological applications like cotton bleaching, laundry detergents or antimicrobial functionalization of medical devices. CDH’s ability to directly use polysaccharide derived mono- and oligosaccharides as substrates is a considerable advantage compared to other oxidases such as glucose oxidase which are limited to monosaccharides. However CDH’s low activity with oxygen as electron acceptor hampers its industrial use for H2O2 production. A CDH variant with increased oxygen reactivity is therefore of high importance for biotechnological application. Uniform expression levels and an easy to use screening assay is a necessity to facilitate screening for CDH variants with increased oxygen turnover. Results A uniform production and secretion of active Myriococcum thermophilum CDH was obtained by using Saccharomyces cerevisiae as expression host. It was found that the native secretory leader sequence of the cdh gene gives a 3 times higher expression than the prepro leader of the yeast α-mating factor. The homogeneity of the expression in 96-well deep-well plates was good (variation coefficient <15%). A high-throughput screening assay was developed to explore saturation mutagenesis libraries of cdh for improved H2O2 production. A 4.5-fold increase for variant N700S over the parent enzyme was found. For production, N700S was expressed in P. pastoris and purified to homogeneity. Characterization revealed that not only the kcat for oxygen turnover was increased in N700S (4.5-fold), but also substrate turnover. A 3-fold increase of the kcat for cellobiose with alternative electron acceptors indicates that mutation N700S influences the oxidative- and reductive FAD half-reaction. Conclusions Site-directed mutagenesis and directed evolution of CDH is simplified by the use of S. cerevisiae instead of the high-yield-host P. pastoris due to easier handling and higher transformation efficiencies with autonomous plasmids. Twelve clones which exhibited an increased H2O2 production in the subsequent screening were all found to carry the same amino acid exchange in the cdh gene (N700S). The sensitive location of the five targeted amino acid positions in the active site of CDH explains the high rate of variants with decreased or entirely abolished activity. The discovery of only one beneficial exchange indicates that a dehydrogenase’s oxygen turnover is a complex phenomenon and the increase therefore not an easy target for protein engineering.The authors thank the European Commission (FP7 243529-2-COTTONBLEACH) for financial support. CKP thanks the Austrian Science Fund (FWF) for financial support (grant P22094). IK is a member of the doctoral program BioToP (Biomolecular Technology of Proteins) of the Austrian Science Fund (FWF; W1224). MA thanks the Spanish Government for financial support (BIO2010-19697).Peer Reviewe

Attochirp-free High-order Harmonic Generation

A method is proposed for arbitrarily engineering the high-order harmonic generation phase achieved by shaping a laser pulse and employing xuv light or x rays for ionization. This renders the production of bandwidth-limited attosecond pulses possible while avoiding the use of filters for chirp compensation. By adding the first 8 Fourier components to a sinusoidal field of $10^{16}$W/cm$^2$, the bandwidth-limited emission of 8 as is shown to be possible from a Li$^{2+}$ gas. The scheme is extendable to the zs-scale

Changing the Environment Based on Empowerment as Intrinsic Motivation

This is an open access article distributed under the Creative Commons Attribution License CC BY 3.0 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.One aspect of intelligence is the ability to restructure your own environment so that the world you live in becomes more beneficial to you. In this paper we investigate how the information-theoretic measure of agent empowerment can provide a task-independent, intrinsic motivation to restructure the world. We show how changes in embodiment and in the environment change the resulting behaviour of the agent and the artefacts left in the world. For this purpose, we introduce an approximation of the established empowerment formalism based on sparse sampling, which is simpler and significantly faster to compute for deterministic dynamics. Sparse sampling also introduces a degree of randomness into the decision making process, which turns out to beneficial for some cases. We then utilize the measure to generate agent behaviour for different agent embodiments in a Minecraft-inspired three dimensional block world. The paradigmatic results demonstrate that empowerment can be used as a suitable generic intrinsic motivation to not only generate actions in given static environments, as shown in the past, but also to modify existing environmental conditions. In doing so, the emerging strategies to modify an agent’s environment turn out to be meaningful to the specific agent capabilities, i.e., de facto to its embodiment.Peer reviewedFinal Published versio

Alphabetic Letter Identification: Effects of perceivability, similarity, and bias

The legibility of the letters in the Latin alphabet has been measured numerous times since the beginning of\ud experimental psychology. To identify the theoretical mechanisms attributed to letter identification, we report\ud a comprehensive review of literature, spanning more than a century. This review revealed that identification\ud accuracy has frequently been attributed to a subset of three common sources: perceivability, bias, and simi-\ud larity. However, simultaneous estimates of these values have rarely (if ever) been performed. We present the\ud results of two new experiments which allow for the simultaneous estimation of these factors, and examine\ud how the shape of a visual mask impacts each of them, as inferred through a new statistical model. Results showed that the shape and identity of the mask impacted the inferred perceivability, bias, and similarity space of a letter set, but that there were aspects of similarity that were robust to the choice of mask. The results illustrate how the psychological concepts of perceivability, bias, and similarity can be estimated simultaneously, and how each make powerful contributions to visual letter identification

Central Adjudication Identified Additional and Prognostically Important Myocardial Infarctions in Patients Undergoing Percutaneous Coronary Intervention

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Characterization of gold nanorods conjugated with synthetic glycopolymers using an analytical approach based on spICP-SFMS and EAF4-MALS

A new comprehensive analytical approach based on single-particle inductively coupled plasma-sector field mass spectrometry (spICP-SFMS) and electrical asymmetric-flow field-flow-fractionation combined with multi-angle light scattering detection (EAF4-MALS) has been examined for the characterization of galactosamine-terminated poly(N-hydroxyethyl acrylamide)-coated gold nanorods (GNRs) in two different degrees of polymerization (DP) by tuning the feed ratio (short: DP 35; long: DP 60). spICP-SFMS provided information on the particle number concentration, size and size distribution of the GNRs, and was found to be useful as an orthogonal method for fast characterization of GNRs. Glycoconjugated GNRs were separated and characterized via EAF4-MALS in terms of their size and charge and compared to the bare GNRs. In contrast to spICP-SFMS, EAF4-MALS was also able of providing an estimate of the thickness of the glycopolymer coating on the GNRs surface

AOSpine Consensus Paper on Nomenclature for Working-Channel Endoscopic Spinal Procedures

Study Design: International consensus paper on a unified nomenclature for full-endoscopic spine surgery. Objectives: Minimally invasive endoscopic spinal procedures have undergone rapid development during the past decade. Evolution of working-channel endoscopes and surgical instruments as well as innovation in surgical techniques have expanded the types of spinal pathology that can be addressed. However, there is in the literature a heterogeneous nomenclature defining approach corridors and procedures, and this lack of common language has hampered communication between endoscopic spine surgeons, patients, hospitals, and insurance providers. Methods: The current report summarizes the nomenclature reported for working-channel endoscopic procedures that address cervical, thoracic, and lumbar spinal pathology. Results: We propose a uniform system that defines the working-channel endoscope (full-endoscopic), approach corridor (anterior, posterior, interlaminar, transforaminal), spinal segment (cervical, thoracic, lumbar), and procedure performed (eg, discectomy, foraminotomy). We suggest the following nomenclature for the most common full-endoscopic procedures: posterior endoscopic cervical foraminotomy (PECF), transforaminal endoscopic thoracic discectomy (TETD), transforaminal endoscopic lumbar discectomy (TELD), transforaminal lumbar foraminotomy (TELF), interlaminar endoscopic lumbar discectomy (IELD), interlaminar endoscopic lateral recess decompression (IE-LRD), and lumbar endoscopic unilateral laminotomy for bilateral decompression (LE-ULBD). Conclusions: We believe that it is critical to delineate a consensus nomenclature to facilitate uniformity of working-channel endoscopic procedures within academic scholarship. This will hopefully facilitate development, standardization of procedures, teaching, and widespread acceptance of full-endoscopic spinal procedures