A database of microRNA expression patterns in Xenopus laevis

MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAs we have looked at show expression in the heart. Our results have been made freely available as a resource in both XenMARK and Xenbase

'So wide and varied': The origins and character of British information science

This paper examines some characteristics of the ‘British School’ of information science. Three main forces driving the development of the new subject in Britain are identified: the documentation movement; special libraries; and the need for better treatment of scientific and technical information. Five characteristics which, taken together, distinguish the early British approach to information science from those adopted elsewhere are identified: its subject-based nature; its broad approach to information and information science; its status as an academic subject with a strong professional remit; its involvement with, but distinction from, information technology; and its involvement with memory institutions. Lessons are drawn for the future development of the information sciences

Effect of Pictorial Depth Cues, Binocular Disparity Cues and Motion Parallax Depth Cues on Lightness Perception in Three-Dimensional Virtual Scenes

Surface lightness perception is affected by scene interpretation. There is some experimental evidence that perceived lightness under bi-ocular viewing conditions is different from perceived lightness in actual scenes but there are also reports that viewing conditions have little or no effect on perceived color. We investigated how mixes of depth cues affect perception of lightness in three-dimensional rendered scenes containing strong gradients of illumination in depth.Observers viewed a virtual room (4 m width x 5 m height x 17.5 m depth) with checkerboard walls and floor. In four conditions, the room was presented with or without binocular disparity (BD) depth cues and with or without motion parallax (MP) depth cues. In all conditions, observers were asked to adjust the luminance of a comparison surface to match the lightness of test surfaces placed at seven different depths (8.5-17.5 m) in the scene. We estimated lightness versus depth profiles in all four depth cue conditions. Even when observers had only pictorial depth cues (no MP, no BD), they partially but significantly discounted the illumination gradient in judging lightness. Adding either MP or BD led to significantly greater discounting and both cues together produced the greatest discounting. The effects of MP and BD were approximately additive. BD had greater influence at near distances than far.These results suggest the surface lightness perception is modulated by three-dimensional perception/interpretation using pictorial, binocular-disparity, and motion-parallax cues additively. We propose a two-stage (2D and 3D) processing model for lightness perception

Identifying protein complexes directly from high-throughput TAP data with Markov random fields

<p>Abstract</p> <p>Background</p> <p>Predicting protein complexes from experimental data remains a challenge due to limited resolution and stochastic errors of high-throughput methods. Current algorithms to reconstruct the complexes typically rely on a two-step process. First, they construct an interaction graph from the data, predominantly using heuristics, and subsequently cluster its vertices to identify protein complexes.</p> <p>Results</p> <p>We propose a model-based identification of protein complexes directly from the experimental observations. Our model of protein complexes based on Markov random fields explicitly incorporates false negative and false positive errors and exhibits a high robustness to noise. A model-based quality score for the resulting clusters allows us to identify reliable predictions in the complete data set. Comparisons with prior work on reference data sets shows favorable results, particularly for larger unfiltered data sets. Additional information on predictions, including the source code under the GNU Public License can be found at http://algorithmics.molgen.mpg.de/Static/Supplements/ProteinComplexes.</p> <p>Conclusion</p> <p>We can identify complexes in the data obtained from high-throughput experiments without prior elimination of proteins or weak interactions. The few parameters of our model, which does not rely on heuristics, can be estimated using maximum likelihood without a reference data set. This is particularly important for protein complex studies in organisms that do not have an established reference frame of known protein complexes.</p

Understanding Action and Adventure Sports Participation-An Ecological Dynamics Perspective.

Previous research has considered action and adventure sports using a variety of associated terms and definitions which has led to confusing discourse and contradictory research findings. Traditional narratives have typically considered participation exclusively as the pastime of young people with abnormal characteristics or personalities having unhealthy and pathological tendencies to take risks because of the need for thrill, excitement or an adrenaline 'rush'. Conversely, recent research has linked even the most extreme forms of action and adventure sports to positive physical and psychological health and well-being outcomes. Here, we argue that traditional frameworks have led to definitions, which, as currently used by researchers, ignore key elements constituting the essential merit of these sports. In this paper, we suggest that this lack of conceptual clarity in understanding cognitions, perception and action in action and adventure sports requires a comprehensive explanatory framework, ecological dynamics which considers person-environment interactions from a multidisciplinary perspective. Action and adventure sports can be fundamentally conceptualized as activities which flourish through creative exploration of novel movement experiences, continuously expanding and evolving beyond predetermined environmental, physical, psychological or sociocultural boundaries. The outcome is the emergence of a rich variety of participation styles and philosophical differences within and across activities. The purpose of this paper is twofold: (a) to point out some limitations of existing research on action and adventure sports; (b) based on key ideas from emerging research and an ecological dynamics approach, to propose a holistic multidisciplinary model for defining and understanding action and adventure sports that may better guide future research and practical implications

The effects of emotional states and traits on time perception

Background: Models of time perception share an element of scalar expectancy theory known as the internal clock, containing specific mechanisms by which the brain is able to experience time passing and function effectively. A debate exists about whether to treat factors that influence these internal clock mechanisms (e.g., emotion, personal- ity, executive functions, and related neurophysiological components) as arousal- or attentional-based factors. Purpose: This study investigated behavioral and neurophysiological responses to an affective time perception Go/ NoGo task, taking into account the behavioral inhibition (BIS) and behavioral activation systems (BASs), which are components of reinforcement sensitivity theory. Methods: After completion of self-report inventories assessing personality traits, electroencephalogram (EEG/ERP) and behavioral recordings of 32 women and 13 men recruited from introductory psychology classes were completed during an affective time perception Go/NoGo task. This task required participants to respond (Go) and inhibit (NoGo) to positive and negative affective visual stimuli of various durations in comparison to a standard duration. Results: Higher BAS scores (especially BAS Drive) were associated with overestimation bias scores for positive stimuli, while BIS scores were not correlated with overestimation bias scores. Furthermore, higher BIS Total scores were associ- ated with higher N2d amplitudes during positive stimulus presentation for 280 ms, while higher BAS Total scores were associated with higher N2d amplitudes during negative stimuli presentation for 910 ms. Discussion: Findings are discussed in terms of arousal-based models of time perception, and suggestions for future research are considered

A Global Clustering Algorithm to Identify Long Intergenic Non-Coding RNA - with Applications in Mouse Macrophages

Identification of diffuse signals from the chromatin immunoprecipitation and high-throughput massively parallel sequencing (ChIP-Seq) technology poses significant computational challenges, and there are few methods currently available. We present a novel global clustering approach to enrich diffuse CHIP-Seq signals of RNA polymerase II and histone 3 lysine 4 trimethylation (H3K4Me3) and apply it to identify putative long intergenic non-coding RNAs (lincRNAs) in macrophage cells. Our global clustering method compares favorably to the local clustering method SICER that was also designed to identify diffuse CHIP-Seq signals. The validity of the algorithm is confirmed at several levels. First, 8 out of a total of 11 selected putative lincRNA regions in primary macrophages respond to lipopolysaccharides (LPS) treatment as predicted by our computational method. Second, the genes nearest to lincRNAs are enriched with biological functions related to metabolic processes under resting conditions but with developmental and immune-related functions under LPS treatment. Third, the putative lincRNAs have conserved promoters, modestly conserved exons, and expected secondary structures by prediction. Last, they are enriched with motifs of transcription factors such as PU.1 and AP.1, previously shown to be important lineage determining factors in macrophages, and 83% of them overlap with distal enhancers markers. In summary, GCLS based on RNA polymerase II and H3K4Me3 CHIP-Seq method can effectively detect putative lincRNAs that exhibit expected characteristics, as exemplified by macrophages in the study