Discrimination of outer membrane proteins with improved performance

<p>Abstract</p> <p>Background</p> <p>Outer membrane proteins (OMPs) perform diverse functional roles in Gram-negative bacteria. Identification of outer membrane proteins is an important task.</p> <p>Results</p> <p>This paper presents a method for distinguishing outer membrane proteins (OMPs) from non-OMPs (that is, globular proteins and inner membrane proteins (IMPs)). First, we calculated the average residue compositions of OMPs, globular proteins and IMPs separately using a training set. Then for each protein from the test set, its distances to the three groups were calculated based on residue composition using a weighted Euclidean distance (WED) approach. Proteins from the test set were classified into OMP versus non-OMP classes based on the least distance. The proposed method can distinguish between OMPs and non-OMPs with 91.0% accuracy and 0.639 Matthews correlation coefficient (MCC). We then improved the method by including homologous sequences into the calculation of residue composition and using a feature-selection method to select the single residue and di-peptides that were useful for OMP prediction. The final method achieves an accuracy of 96.8% with 0.859 MCC. In direct comparisons, the proposed method outperforms previously published methods.</p> <p>Conclusion</p> <p>The proposed method can identify OMPs with improved performance. It will be very helpful to the discovery of OMPs in a genome scale.</p

A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in Caenorhabditis elegans

One of the central goals of developmental neurobiology is to describe and understand the multi-tiered molecular events that control the progression of a fertilized egg to a terminally differentiated neuron. In the nematode Caenorhabditis elegans, the progression from egg to terminally differentiated neuron has been visually traced by lineage analysis. For example, the two gustatory neurons ASEL and ASER, a bilaterally symmetric neuron pair that is functionally lateralized, are generated from a fertilized egg through an invariant sequence of 11 cellular cleavages that occur stereotypically along specific cleavage planes. Molecular events that occur along this developmental pathway are only superficially understood. We take here an unbiased, genome-wide approach to identify genes that may act at any stage to ensure the correct differentiation of ASEL. Screening a genome-wide RNAi library that knocks-down 18,179 genes (94% of the genome), we identified 245 genes that affect the development of the ASEL neuron, such that the neuron is either not generated, its fate is converted to that of another cell, or cells from other lineage branches now adopt ASEL fate. We analyze in detail two factors that we identify from this screen: (1) the proneural gene hlh-14, which we find to be bilaterally expressed in the ASEL/R lineages despite their asymmetric lineage origins and which we find is required to generate neurons from several lineage branches including the ASE neurons, and (2) the COMPASS histone methyltransferase complex, which we find to be a critical embryonic inducer of ASEL/R asymmetry, acting upstream of the previously identified miRNA lsy-6. Our study represents the first comprehensive, genome-wide analysis of a single neuronal cell fate decision. The results of this analysis provide a starting point for future studies that will eventually lead to a more complete understanding of how individual neuronal cell types are generated from a single-cell embryo

Neonates’ responses to repeated exposure to a still face

The main aims of the study were to examine whether human neonates' responses to communication disturbance modelled by the still-face paradigm were stable and whether their responses were affected by their previous experience with the still-face paradigm.The still face procedure, as a laboratory model of interpersonal stress, was administered repeatedly, twice, to 84 neonates (0 to 4 day olds), with a delay of an average of 1.25 day.Frame-by-frame analysis of the frequency and duration of gaze, distressed face, crying, sleeping and sucking behaviours showed that the procedure was stressful to them both times, that is, the still face effect was stable after repeated administration and newborns consistently responded to such nonverbal violation of communication. They averted their gaze, showed distress and cried more during the still-face phase in both the first and the second administration. They also showed a carry-over effect in that they continued to avert their gaze and displayed increased distress and crying in the first reunion period, but their gaze behaviour changed with experience, in the second administration. While in the first administration the babies continued averting their gaze even after the stressful still-face phase was over, this carry-over effect disappeared in the second administration, and the babies significantly increased their gaze following the still-face phase.After excluding explanations of fatigue, habituation and random effects, a self-other regulatory model is discussed as a possible explanation for this pattern

Solar Coronal Plumes

Polar plumes are thin long ray-like structures that project beyond the limb of the Sun polar regions, maintaining their identity over distances of several solar radii. Plumes have been first observed in white-light (WL) images of the Sun, but, with the advent of the space era, they have been identified also in X-ray and UV wavelengths (XUV) and, possibly, even in in situ data. This review traces the history of plumes, from the time they have been first imaged, to the complex means by which nowadays we attempt to reconstruct their 3-D structure. Spectroscopic techniques allowed us also to infer the physical parameters of plumes and estimate their electron and kinetic temperatures and their densities. However, perhaps the most interesting problem we need to solve is the role they cover in the solar wind origin and acceleration: Does the solar wind emanate from plumes or from the ambient coronal hole wherein they are embedded? Do plumes have a role in solar wind acceleration and mass loading? Answers to these questions are still somewhat ambiguous and theoretical modeling does not provide definite answers either. Recent data, with an unprecedented high spatial and temporal resolution, provide new information on the fine structure of plumes, their temporal evolution and relationship with other transient phenomena that may shed further light on these elusive features

Kovesi and the Formal and Material Elements of Concepts

Published in Philosophia, December 2011, Volume 39, Issue 4, pp 699-720. doi: 10.1007/s11406-011-9305-x</p

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion