Optical encoding of microbeads for gene screening: alternatives to microarrays

Rapid access to genetic information is central to the revolution presently occurring in the pharmaceutical industry, particularly In relation to novel drug target identification and drug development. Genetic variation, gene expression, gene function and gene structure are just some of the important research areas requiring efficient methods of DNA screening. Here, we highlight state-of-the-art techniques and devices for gene screening that promise cheaper and higher-throughput yields than currently achieved with DNA microarrays. We include an overview of existing and proposed bead-based strategies designed to dramatically increase the number of probes that can be interrogated in one assay. We focus, in particular, on the issue of encoding and/or decoding (bar-coding) large bead-based libraries for HTS.

High-fidelity Z-measurement error encoding of optical qubits

We demonstrate a quantum error correction scheme that protects against accidental measurement, using a parity encoding where the logical state of a single qubit is encoded into two physical qubits using a nondeterministic photonic controlled-NOT gate. For the single qubit input states vertical bar 0 >, vertical bar 1 >, vertical bar 0 > +/- vertical bar 1 >, and vertical bar 0 > +/- i vertical bar 1 > our encoder produces the appropriate two-qubit encoded state with an average fidelity of 0.88 +/- 0.03 and the single qubit decoded states have an average fidelity of 0.93 +/- 0.05 with the original state. We are able to decode the two-qubit state (up to a bit flip) by performing a measurement on one of the qubits in the logical basis; we find that the 64 one-qubit decoded states arising from 16 real and imaginary single-qubit superposition inputs have an average fidelity of 0.96 +/- 0.03.

Attachment insecurity as a filter in the decoding and encoding of nonverbal behavior in close relationships

In this article, I have focused my comments on the possible associations between the cognitions related to different attachment styles, and the impact that those cognitions are likely to have on nonverbal encoding and decoding. I see attachment insecurity as acting as a filter, distorting both encoding and decoding processes. In terms of decoding, an insecure individual may appraise the situation as more threatening than it actually is, may see the attachment figure as more or less available than he or she actually is, and may make an inappropriate decision about the viability or desirability of seeking proximity to the attachment figure. Attachment insecurity is also likely to inhibit the distressed individual from expressing their distress in a way that is understood by the attachment figure and that increases the likelihood that the attachment figure will engage in supportive behavior.

Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides

Background: Approximately 40% of mammalian mRNA sequences contain AUG trinucleotides upstream of the main coding sequence, with a quarter of these AUGs demarcating open reading frames of 20 or more codons. In order to investigate whether these open reading frames may encode functional peptides, we have carried out a comparative genomic analysis of human and mouse mRNA 'untranslated regions' using sequences from the RefSeq mRNA sequence database. Results: We have identified over 200 upstream open reading frames which are strongly conserved between the human and mouse genomes. Consensus sequences associated with efficient initiation of translation are overrepresented at the AUG trinucleotides of these upstream open reading frames, while comparative analysis of their DNA and putative peptide sequences shows evidence of purifying selection. Conclusion: The occurrence of a large number of conserved upstream open reading frames, in association with features consistent with protein translation, strongly suggests evolutionary maintenance of the coding sequence and indicates probable functional expression of the peptides encoded within these upstream open reading frames.

Intelligent encoding of concepts in web development retrieval

The main aim of the proposed approach presented in this paper is to improve Web information retrieval effectiveness by overcoming the problems associated with a typical keyword matching retrieval system, through the use of concepts and an intelligent fusion of confidence values. By exploiting the conceptual hierarchy of the WordNet (G. Miller, 1995) knowledge base, we show how to effectively encode the conceptual information in a document using the semantic information implied by the words that appear within it. Rather than treating a word as a string made up of a sequence of characters, we consider a word to represent a concept.

Publication practices of English language occupational therapy journals

The aim of this study was to determine the characteristics and publication practices of English language occupational therapy journals. An adapted version of the Survey of Editors Regarding Publishing Practices was posted to the editors of English language occupational therapy journals (n = 14) in September 2001. The response rate was 92.9% (n = 13). Journals were published on average 4.77 times per year and comprised 89% text and 10% advertising. The preferred average length of manuscripts was 20 pages using American Psychological Association format. The average acceptance rate of unsolicited manuscripts was 46.6%. All the journals were peer-reviewed publications and 80% were research oriented. The most frequently cited reasons for rejection of manuscripts were methodology problems, poorly developed idea, poorly written and data interpretation problems. The professional focus of published manuscripts was on research and the clinical foci were on paediatrics, gerontology and physical medicine. The study concludes that there are a variety of publishing opportunities available to occupational therapists. It is essential that prospective authors consult the journal guidelines for authors, including the types of manuscript accepted.

Preface - Special issue on environmental toxicology of metals and metalloids

Following the Ninth International Congress of Toxicology (ICT-IX) and its satellite meeting ‘The International Conference on the Environmental Toxicology of Metals and Metalloids’ held in 2001 in Australia, a special issue on Arsenic was published in July 2002 (Toxicology Letters, 133(1), 1–120, 2002). We felt that it was timely to follow up with a special issue covering a wider range of metals and metalloids. Participants from the above conferences were invited to contribute to this special issue on ‘Environmental Toxicology of Metals and Metalloids’. This special issue consists of 11 manuscripts, representing up to date studies on a number of important harmful elements including aluminium, arsenic, cadmium, selenium, tin (tributyltin) and zinc. It illustrates the multidisciplinary nature of modern research in environmental toxicology involving chemical, biological and molecular technological approaches. It has been our great pleasure to produce this special issue. We would like to thank the authors for their contributions. We greatly appreciate the guidance and assistance provided by Dr J.P. Kehrer (Managing Editor), Dr Lulu Stader (Senior Publishing Editor) and their colleagues at Elsevier Science.

The morals of metaphysics: Kant's 'Groundwork' as intellectual paideia

To approach philosophy as a way of working on the self means to begin not with the experience it clarifies and the subject it discovers, but with the acts of self‐transformation it requires and the subjectivity it seeks to fashion. Commenting on the variety of spiritual exercises to be found in the ancient schools, Pierre Hadot remarks that: Some, like Plutarch’s ethismoi, designed to curb curiosity, anger or gossip, were only practices intended to ensure good moral habits. Others, particularly the meditations of the Platonic tradition, demanded a high degree of mental concentration. Some, like the contemplation of nature as practiced in all philosophical schools, turned the soul toward the cosmos, while still others—rare and exceptional—led to a transfiguration of the personality, as in the experiences of Plotinus. We also saw that the emotional tone and notional content of these exercises varied widely from one philosophical school to another: from the mobilization of energy and consent to destiny of the Stoics, to the relaxation and detachment of the Epicureans, to the mental concentration and renunciation of the sensible world among the Platonists.1 While successfully applied to ancient philosophy,2 this approach has not been widely exploited in the history of philosophy more broadly. There is, however, at least one study of medieval metaphysics in these terms,3 and there are some important discussions of early modern Stoicism and Epicureanism.4 And a recent study of Hume shows the fruitfulness of the approach for Enlightenment philosophy.5 It is all the more surprising then that there seems to have been no serious attempt to approach Kant’s moral philosophy in this way.

Learning the dynamics of embedded clauses

Recent work by Siegelmann has shown that the computational power of recurrent neural networks matches that of Turing Machines. One important implication is that complex language classes (infinite languages with embedded clauses) can be represented in neural networks. Proofs are based on a fractal encoding of states to simulate the memory and operations of stacks. In the present work, it is shown that similar stack-like dynamics can be learned in recurrent neural networks from simple sequence prediction tasks. Two main types of network solutions are found and described qualitatively as dynamical systems: damped oscillation and entangled spiraling around fixed points. The potential and limitations of each solution type are established in terms of generalization on two different context-free languages. Both solution types constitute novel stack implementations - generally in line with Siegelmann's theoretical work - which supply insights into how embedded structures of languages can be handled in analog hardware.