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Abstract: The suffix tree is an extremely important data structure in bioinformatics. Classical implementations require much space, which renders them useless to handle large sequence collections. Recent research has obtained various compressed representations for suffix trees, with widely different space-time tradeoffs. In this paper we show how the use of range min-max trees yields novel representations achieving practical space/time tradeoffs. In addition, we show how those trees can be modified to index highly repetitive collections, obtaining the first compressed suffix tree representation that effectively adapts to that scenario.

Abstract: It is my great pleasure to announce a newly launched open access journal, Cosmetics, published by MDPI, dedicated to this fascinating world. Do we need a new journal in this area? This was the question I had in mind before starting the project and I will try to answer in the following paragraphs. [...]

Abstract: The Upper Ordovician (Edenian) Lindsay Formation of the Ottawa Embayment represents the final stage of carbonate platform development in the Taconic foreland periphery inboard of the northern Appalachian orogen. The succession overlies a narrow (~60 km) axis of a Neoproterozoic Laurentian rift extending across the Grenville orogen. The Lindsay Formation consists of a lower heavily bioturbated skeletal limestone that represents a warm-water shoal facies following an underlying outer ramp stratigraphy, and an upper division of renewed deep-water deposition with organic-rich shale and fossiliferous lime mudstone. Pyritic deep-water black shale of the westerly advancing Taconic foreland basin disconformably overlies this platform succession. Stratigraphic correlation through the central embayment identifies likely synsedimentary faults and seaward-directed erosion bounding the Lindsay Formation in a region of older Ordovician faults and a change in the lithotectonic character of the crystalline basement. The Late Ordovician shallowing and localization of structural/erosional features are interpreted to record a structural hinge: a local accommodation to, first, foreland periphery uplift, then rapid subsidence related to westerly diachronous foreland subsidence through the platform interior. Spatial association of structures of differing ages suggests that reactivation of inherited weakened crust influenced Late Ordovician sedimentary patterns.

Abstract: The Critical Assessment of Small Molecule Identification (CASMI) contest was developed to provide a systematic comparative evaluation of strategies applied for the annotation and identification of small molecules. The authors participated in eleven challenges in both category 1 (to deduce a molecular formula) and category 2 (to deduce a molecular structure) related to high resolution LC-MS data. For category 1 challenges, the PUTMEDID_LCMS workflows provided the correct molecular formula in nine challenges; the two incorrect submissions were related to a larger mass error in experimental data than expected or the absence of the correct molecular formula in a reference file applied in the PUTMEDID_LCMS workflows. For category 2 challenges, MetFrag was applied to construct in silico fragmentation data and compare with experimentally-derived MS/MS data. The submissions for three challenges were correct, and for eight challenges, the submissions were not correct; some submissions showed similarity to the correct structures, while others showed no similarity. The low number of correct submissions for category 2 was a result of applying the assumption that all chemicals were derived from biological samples and highlights the importance of knowing the origin of biological or chemical samples studied and the metabolites expected to be present to define the correct chemical space to search in annotation processes.

Abstract: In this paper, we introduce an adaptive type-2 fuzzy logic controller (FLC) for flexible-joint manipulators with structured and unstructured dynamical uncertainties. Simplified interval fuzzy sets are used for real-time efficiency, and internal stability is enhanced by adopting a trade-off strategy between the manipulator’s and the actuators’ velocities. Furthermore, the control scheme is independent of the computationally expensive noisy torque and acceleration signals. The controller is validated through a set of numerical simulations and by comparing it against its type-1 counterpart. The ability of the adaptive type-2 FLC in coping with large magnitudes of uncertainties yields an improved performance. The stability of the proposed control system is guaranteed using Lyapunov stability theory.

Abstract: In this paper, we demonstrate how a network of dendrites can be used to build the state decoding block of a wordspotter similar to a Hidden Markov Model (HMM) classifier structure. We present simulation and experimental data for a single line dendrite and also experimental results for a dendrite-based classifier structure. This work builds on previously demonstrated building blocks of a neural network: the channel, synapses and dendrites using CMOS circuits. These structures can be used for speech and pattern recognition. The computational efficiency of such a system is >10 MMACs/μW as compared to Digital Systems which perform 10 MMACs/mW.

Abstract: 4,4′-Dithiodipyridine (dtdp), also termed 4,4′-dipyridyldisulfide, is a bridging ligand of the 4,4′-bipyridine type. The introduction of the disulfide moiety inevitably leads to a relatively rigid angular structure, which exhibits axial chirality. More than 90 metal complexes containing the dtdp ligand have been crystallographically characterised until now. This review focuses on the preparation and structural diversity of discrete and polymeric metallosupramolecular assemblies constructed from dtdp as bridging ligands. These encompass metallamacrocycles with M₂L₂ topology and coordination polymers with periodicity in one or two dimensions. One-dimensional coordination polymers represent the vast majority of the metallosupramolecular structures obtained from dtdp. These include repeated rhomboids, zigzag, helical and arched chains among other types. In this contribution, we make an attempt to provide a comprehensive account of the structural data that are currently available for metallosupramolecular assemblies based on the bent bridging ligand dtdp.

Abstract: While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation—if not adequately minimized by effective normalization—may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes.

Abstract: The hallmark of our species is our ability to hybridize symbolic thinking with behavioral output. We began with the symmetrical hand axe around 1.7 mya and have progressed, slowly at first, then with greater rapidity, to producing increasingly more complex hybridized products. We now live in the age where our drive to hybridize has pushed us to the brink of a neuroscientific revolution, where for the first time we are in a position to willfully alter the brain and hence, our behavior and evolution. Nootropics, transcranial direct current stimulation (tDCS), transcranial magnetic stimulation (TMS), deep brain stimulation (DBS) and invasive brain mind interface (BMI) technology are allowing humans to treat previously inaccessible diseases as well as open up potential vistas for cognitive enhancement. In the future, the possibility exists for humans to hybridize with BMIs and mobile architectures. The notion of self is becoming increasingly extended. All of this to say: are we in control of our brains, or are they in control of us?

Abstract: This review summarizes the state of the art in the synthesis of well-defined glycopolymers by Reversible-Deactivation Radical Polymerization (RDRP) from its inception in 1998 until August 2012. Glycopolymers architectures have been successfully synthesized with four major RDRP techniques: Nitroxide-mediated radical polymerization (NMP), cyanoxyl-mediated radical polymerization (CMRP), atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT) polymerization. Over 140 publications were analyzed and their results summarized according to the technique used and the type of monomer(s) and carbohydrates involved. Particular emphasis was placed on the experimental conditions used, the structure obtained (comonomer distribution, topology), the degree of control achieved and the (potential) applications sought. A list of representative examples for each polymerization process can be found in tables placed at the beginning of each section covering a particular RDRP technique.