Non-coding RNA

The term non-coding RNA (ncRNA) is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. Although it has been generally assumed that most genetic information is transacted by proteins, recent evidence suggests that the majority of the genomes of mammals and other complex organisms is in fact transcribed into ncRNAs, many of which are alternatively spliced and/or processed into smaller products. These ncRNAs include microRNAs and snoRNAs (many if not most of which remain to be identified), as well as likely other classes of yet-to-be-discovered small regulatory RNAs, and tens of thousands of longer transcripts (including complex patterns of interlacing and overlapping sense and antisense transcripts), most of whose functions are unknown. These RNAs (including those derived from introns) appear to comprise a hidden layer of internal signals that control various levels of gene expression in physiology and development, including chromatin architecture/epigenetic memory, transcription, RNA splicing, editing, translation and turnover. RNA regulatory networks may determine most of our complex characteristics, play a significant role in disease and constitute an unexplored world of genetic variation both within and between species.

Regression with input-dependent noise: A Gaussian process treatment

Gaussian processes provide natural non-parametric prior distributions over regression functions. In this paper we consider regression problems where there is noise on the output, and the variance of the noise depends on the inputs. If we assume that the noise is a smooth function of the inputs, then it is natural to model the noise variance using a second Gaussian process, in addition to the Gaussian process governing the noise-free output value. We show that prior uncertainty about the parameters controlling both processes can be handled and that the posterior distribution of the noise rate can be sampled from using Markov chain Monte Carlo methods. Our results on a synthetic data set give a posterior noise variance that well-approximates the true variance.

Seeing light vs dark lines: psychophysical performance is based on separate channels, limited by noise and uncertainty

Visual detection performance (d') is usually an accelerating function of stimulus contrast, which could imply a smooth, threshold-like nonlinearity in the sensory response. Alternatively, Pelli (1985 Journal of the Optical Society of America A 2 1508 - 1532) developed the 'uncertainty model' in which responses were linear with contrast, but the observer was uncertain about which of many noisy channels contained the signal. Such internal uncertainty effectively adds noise to weak signals, and predicts the nonlinear psychometric function. We re-examined these ideas by plotting psychometric functions (as z-scores) for two observers (SAW, PRM) with high precision. The task was to detect a single, vertical, blurred line at the fixation point, or identify its polarity (light vs dark). Detection of a known polarity was nearly linear for SAW but very nonlinear for PRM. Randomly interleaving light and dark trials reduced performance and rendered it non-linear for SAW, but had little effect for PRM. This occurred for both single-interval and 2AFC procedures. The whole pattern of results was well predicted by our Monte Carlo simulation of Pelli's model, with only two free parameters. SAW (highly practised) had very low uncertainty. PRM (with little prior practice) had much greater uncertainty, resulting in lower contrast sensitivity, nonlinear performance, and no effect of external (polarity) uncertainty. For SAW, identification was about v2 better than detection, implying statistically independent channels for stimuli of opposite polarity, rather than an opponent (light - dark) channel. These findings strongly suggest that noise and uncertainty, rather than sensory nonlinearity, limit visual detection.

Effect of β-adrenoceptor antagonists on autonomic control of ciliary smooth muscle

Purpose: Pharmacological intervention with peripheral sympathetic transmission at ciliary smooth muscle neuro-receptor junctions has been used against a background of controlled parasympathetic activity to investigate the characteristics of autonomic control of ocular accommodation. Methods: A continuously recording infrared optometer was used to measure accommodation on a group of five visually normal emmetropic subjects under open- and closed-loop conditions. A double-blind protocol between saline, timolol and betaxolol was used to differentiate between the localised action on ciliary smooth muscle and effects induced by changes in stimulus conditions. Data were collected before and 45 min following the instillation of saline, timolol or betaxolol. Open-loop post-task decay was investigated following 3 min sustained near fixation of a stimulus placed 3 D above the subject's pre-task tonic accommodation level. Closed-loop dynamic responses were recorded for each treatment condition while subjects viewed sinusoidally (0.05-0.6 Hz) or stepwise vergence-modulated targets over a 2 D range (2-4 D). Results: Open-loop data demonstrate a rapid post-task regression to pre-task tonic accommodation levels for saline and betaxolol control conditions. A slow positive post-task shift was induced by timolol indicating that sympathetic inhibition contributes to accommodative adaptation during sustained near vision. Closed-loop accommodation responses to temporally modulated sinusoidal stimuli showed characteristic features for both saline and betaxolol control conditions. Timolol induced a reduced gain for low- and mid-temporal frequencies (< 0.3 Hz) but did not affect the response at higher temporal frequencies. Response times to stepwise stimuli increased following the instillation of timolol for the near-to-far fixation condition compared with the controls and was related to the period of sustained prior fixation. Conclusions: Modulation of accommodation under open- and closed-loop conditions by a non-selective β-blocker is consistent with the temporal and inhibitory features of sympathetic innervation to ciliary smooth muscle. Although parasympathetic innervation predominates there is evidence to support a role for sympathetic innervation in the control of ocular accommodation. © 2002 The College of Optometrists.

Non-curliation of Escherichia coli O78:K80 isolates associated with IS1 insertion in csgB and reduced persistence in poultry infection

The elaboration of curli fimbriae by Escherichia coli is associated with the development of a lacy colony morphology when grown on colonisation factor antigen agar at 25 degrees C. Avian colisepticaemia E. coli isolates screened for curliation by this culture technique showed lacy and smooth colonial morphologies and the genetic basis of the non-curliated smooth colonial phenotype was analysed. Two smooth E. coli O78:K80 isolates possessed about 40 copies of the IS1 element within their respective genomes of which one copy insertionally inactivated the csgB gene, the nucleator gene for curli fibril formation. One of these two isolates also possessed a defective rpoS gene which is a known regulator of curli expression. In the day-old chick model, both smooth isolates were as invasive as a known virulent O78:K80 isolate as determined by extent of liver and spleen colonisation post oral inoculation but were less persistent in terms of caecal colonisation.

Sparse signal representation by adaptive non-uniform B-spline dictionaries on a compact interval

Non-uniform B-spline dictionaries on a compact interval are discussed in the context of sparse signal representation. For each given partition, dictionaries of B-spline functions for the corresponding spline space are built up by dividing the partition into subpartitions and joining together the bases for the concomitant subspaces. The resulting slightly redundant dictionaries are composed of B-spline functions of broader support than those corresponding to the B-spline basis for the identical space. Such dictionaries are meant to assist in the construction of adaptive sparse signal representation through a combination of stepwise optimal greedy techniques.

The slope of the psychometric function and non-stationarity of thresholds in spatiotemporal contrast vision

The slope of the two-interval, forced-choice psychometric function (e.g. the Weibull parameter, ß) provides valuable information about the relationship between contrast sensitivity and signal strength. However, little is known about how or whether ß varies with stimulus parameters such as spatiotemporal frequency and stimulus size and shape. A second unresolved issue concerns the best way to estimate the slope of the psychometric function. For example, if an observer is non-stationary (e.g. their threshold drifts between experimental sessions), ß will be underestimated if curve fitting is performed after collapsing the data across experimental sessions. We measured psychometric functions for 2 experienced observers for 14 different spatiotemporal configurations of pulsed or flickering grating patches and bars on each of 8 days. We found ß ˜ 3 to be fairly constant across almost all conditions, consistent with a fixed nonlinear contrast transducer and/or a constant level of intrinsic stimulus uncertainty (e.g. a square law transducer and a low level of intrinsic uncertainty). Our analysis showed that estimating a single ß from results averaged over several experimental sessions was slightly more accurate than averaging multiple estimates from several experimental sessions. However, the small levels of non-stationarity (SD ˜ 0.8 dB) meant that the difference between the estimates was, in practice, negligible.

Semiparametric smooth-coefficient stoachastic frontier model

This paper proposes a semiparametric smooth-coefficient stochastic production frontier model where all the coefficients are expressed as some unknown functions of environmental factors. The inefficiency term is multiplicatively decomposed into a scaling function of the environmental factors and a standard truncated normal random variable. A testing procedure is suggested for the relevance of the environmental factors. Monte Carlo study shows plausible ¯nite sample behavior of our proposed estimation and inference procedure. An empirical example is given, where both the semiparametric and standard parametric models are estimated and results are compared.

Fast reconstruction of harmonic functions from Cauchy data using the Dirichlet-to-Neumann map and integral equations

We propose and investigate a method for the stable determination of a harmonic function from knowledge of its value and its normal derivative on a part of the boundary of the (bounded) solution domain (Cauchy problem). We reformulate the Cauchy problem as an operator equation on the boundary using the Dirichlet-to-Neumann map. To discretize the obtained operator, we modify and employ a method denoted as Classic II given in [J. Helsing, Faster convergence and higher accuracy for the Dirichlet–Neumann map, J. Comput. Phys. 228 (2009), pp. 2578–2576, Section 3], which is based on Fredholm integral equations and Nyström discretization schemes. Then, for stability reasons, to solve the discretized integral equation we use the method of smoothing projection introduced in [J. Helsing and B.T. Johansson, Fast reconstruction of harmonic functions from Cauchy data using integral equation techniques, Inverse Probl. Sci. Eng. 18 (2010), pp. 381–399, Section 7], which makes it possible to solve the discretized operator equation in a stable way with minor computational cost and high accuracy. With this approach, for sufficiently smooth Cauchy data, the normal derivative can also be accurately computed on the part of the boundary where no data is initially given.

Potent suppression of vascular smooth muscle cell migration and human neointimal hyperplasia by KV1.3 channel blockers

Aim - The aim of the study was to determine the potential for KV1 potassium channel blockers as inhibitors of human neoinitimal hyperplasia. Methods and results - Blood vessels were obtained from patients or mice and studied in culture. Reverse transcriptasepolymerase chain reaction and immunocytochemistry were used to detect gene expression. Whole-cell patch-clamp, intracellular calcium measurement, cell migration assays, and organ culture were used to assess channel function.  KV1.3 was unique among the  KV1 channels in showing preserved and up-regulated expression when the vascular smooth muscle cells switched to the proliferating phenotype. There was strong expression in neointimal formations. Voltage-dependent potassium current in proliferating cells was sensitive to three different blockers of  KV1.3 channels. Calcium entry was also inhibited. All three blockers reduced vascular smooth muscle cell migration and the effects were non-additive. One of the blockers (margatoxin) was highly potent, suppressing cell migration with an IC of 85 pM. Two of the blockers were tested in organ-cultured human vein samples and both inhibited neointimal hyperplasia. Conclusion - KV1.3 potassium channels are functional in proliferating mouse and human vascular smooth muscle cells and have positive effects on cell migration. Blockers of the channels may be useful as inhibitors of neointimal hyperplasia and other unwanted vascular remodelling events. © 2010 The Author.

From Spanish paintings to murder:topic transitions in casual conversations between native and non-native speakers of English

This article explores some of the strategies used by international students of English to manage topic shifts in casual conversations with English-speaking peers. It therefore covers aspects of discourse which have been comparatively under-researched, and where research has also tended to focus on the problems rather than the communicative achievements of non-native speakers. A detailed analysis of the conversations under discussion, which were recorded by the participants themselves, showed that they all flowed smoothly, and this was in large measure due to the ways in which topic shifts were managed. The paper will focus on a very distinct type of topic shift, namely that of topic transitions, which enable a smooth flow from one topic to another, but which do not explicitly signal that a shift is taking place. It will examine how the non-native speakers achieved coherence in the topic transitions which they initiated, which strategies or procedures they employed, and show how their initiations were effective in enabling the proposed topic to be understood, taken up and developed. It therefore adds to our understanding of the interactional achievements of international speakers in informal, social contexts. © 2013 Elsevier B.V.

Representable Banach Spaces and Uniformly Gateaux-Smooth Norms

It is proved that a representable non-separable Banach space does not admit uniformly Gâteaux-smooth norms. This is true in particular for C(K) spaces where K is a separable non-metrizable Rosenthal compact space.

Double-Wavelet Neuron Based on Analytical Activation Functions

In this paper a new double-wavelet neuron architecture obtained by modification of standard wavelet neuron, and its learning algorithm are proposed. The offered architecture allows to improve the approximation properties of wavelet neuron. Double-wavelet neuron and its learning algorithm are examined for forecasting non-stationary chaotic time series.

Decomposition of Boolean Functions – Recognizing a Good Solution by Traces

The problem of sequent two-block decomposition of a Boolean function is regarded in case when a good solution does exist. The problem consists mainly in finding an appropriate weak partition on the set of arguments of the considered Boolean function, which should be decomposable at that partition. A new fast heuristic combinatorial algorithm is offered for solving this task. At first the randomized search for traces of such a partition is fulfilled. The recognized traces are represented by some "triads" - the simplest weak partitions corresponding to non-trivial decompositions. After that the whole sought-for partition is restored from the discovered trace by building a track initialized by the trace and leading to the solution. The results of computer experiments testify the high practical efficiency of the algorithm.

Non-verbal signalling in digital discourse:the case of letter repetition

This study focuses on the interactional functions of non-standard spelling, in particular letter repetition, used in text-based computer-mediated communication as a means of non-verbal signalling. The aim of this paper is to assess the current state of non-verbal cue research in computer-mediated discourse and demonstrate the need for a more comprehensive and methodologically rigorous exploration of written non-verbal signalling. The study proposes a contextual and usage-centered view of written paralanguage. Through illustrative, close linguistic analyses the study proves that previous approaches to non-standard spelling based on their relation to the spoken word might not account for the complexities of this CMC cue, and in order to further our understanding of their interactional functions it is more fruitful to describe the role they play during the contextualisation of the verbal messages. The interactional sociolinguistic approach taken in the analysis demonstrates the range of interactional functions letter repetition can achieve, including contribution to the inscription of socio-emotional information into writing, to the evoking of auditory cues or to a display of informality through using a relaxed writing style.