Transcriptional dysregulation of coding and non-coding genes in cellular models of Huntington's disease

HD (Huntington's disease) is a late onset heritable neurodegenerative disorder that is characterized by neuronal dysfunction and death, particularly in the cerebral cortex and medium spiny neurons of the striatum. This is followed by progressive chorea, dementia and emotional dysfunction, eventually resulting in death. HD is caused by an expanded CAG repeat in the first exon of the HD gene that results in an abnormally elongated polyQ (polyglutamine) tract in its protein product, Htt (Huntingtin). Wild-type Htt is largely cytoplasmic; however, in HD, proteolytic N-terminal fragments of Htt form insoluble deposits in both the cytoplasm and nucleus, provoking the idea that mutHtt (mutant Htt) causes transcriptional dysfunction. While a number of specific transcription factors and co-factors have been proposed as mediators of mutHtt toxicity, the causal relationship between these Htt/transcription factor interactions and HD pathology remains unknown. Previous work has highlighted REST [RE1 (repressor element 1)-silencing transcription factor] as one such transcription factor. REST is a master regulator of neuronal genes, repressing their expression. Many of its direct target genes are known or suspected to have a role in HD pathogenesis, including BDNF (brain-derived neurotrophic factor). Recent evidence has also shown that REST regulates transcription of regulatory miRNAs (microRNAs), many of which are known to regulate neuronal gene expression and are dysregulated in HD. Thus repression of miRNAs constitutes a second, indirect mechanism by which REST can alter the neuronal transcriptome in HD. We will describe the evidence that disruption to the REST regulon brought about by a loss of interaction between REST and mutHtt may be a key contributory factor in the widespread dysregulation of gene expression in HD.

Alterations in predicted regulatory and coding regions of the sterol 14α-demethylase gene (CYP51) confer decreased azole sensitivity in the oilseed rape pathogen Pyrenopeziza brassicae

The incidence and severity of light leaf spot epidemics caused by the ascomycete fungus Pyrenopeziza brassicae on UK oilseed rape crops is increasing. The disease is currently controlled by a combination of host resistance, cultural practices and fungicide applications. We report decreases in sensitivities of modern UK P. brassicae isolates to the azole (imidazole and triazole) class of fungicides. By cloning and sequencing the P. brassicae CYP51 (PbCYP51) gene, encoding the azole target sterol 14α-demethylase, we identified two non-synonymous mutations encoding substitutions G460S and S508T associated with reduced azole sensitivity. We confirmed the impact of the encoded PbCYP51 changes on azole sensitivity and protein activity by heterologous expression in a Saccharomyces cerevisiae mutant YUG37::erg11 carrying a controllable promoter of native CYP51 expression. In addition, we identified insertions in the predicted regulatory regions of PbCYP51 in isolates with reduced azole sensitivity. The presence of these insertions was associated with enhanced transcription of PbCYP51 in response to sub-inhibitory concentrations of the azole fungicide tebuconazole. Genetic analysis of in vitro crosses of sensitive and resistant isolates confirmed the impact of PbCYP51 alterations in coding and regulatory sequences on a reduced sensitivity phenotype, as well as identifying a second major gene at another locus contributing to resistance in some isolates. The least sensitive field isolates carry combinations of upstream insertions and non-synonymous mutations, suggesting PbCYP51 evolution is on-going and the progressive decline in azole sensitivity of UK P. brassicae populations will continue. The implications for the future control of light leaf spot are discussed.

Reliability comparison of transmit/receive diversity and error control coding in low-power medium access control protocols

Low-power medium access control (MAC) protocols used for communication of energy constraint wireless embedded devices do not cope well with situations where transmission channels are highly erroneous. Existing MAC protocols discard corrupted messages which lead to costly retransmissions. To improve transmission performance, it is possible to include an error correction scheme and transmit/receive diversity. It is possible to add redundant information to transmitted packets in order to recover data from corrupted packets. It is also possible to make use of transmit/receive diversity via multiple antennas to improve error resiliency of transmissions. Both schemes may be used in conjunction to further improve the performance. In this study, the authors show how an error correction scheme and transmit/receive diversity can be integrated in low-power MAC protocols. Furthermore, the authors investigate the achievable performance gains of both methods. This is important as both methods have associated costs (processing requirements; additional antennas and power) and for a given communication situation it must be decided which methods should be employed. The authors’ results show that, in many practical situations, error control coding outperforms transmission diversity; however, if very high reliability is required, it is useful to employ both schemes together.

Joint multiple dictionary learning for tensor sparse coding

Traditional dictionary learning algorithms are used for finding a sparse representation on high dimensional data by transforming samples into a one-dimensional (1D) vector. This 1D model loses the inherent spatial structure property of data. An alternative solution is to employ Tensor Decomposition for dictionary learning on their original structural form —a tensor— by learning multiple dictionaries along each mode and the corresponding sparse representation in respect to the Kronecker product of these dictionaries. To learn tensor dictionaries along each mode, all the existing methods update each dictionary iteratively in an alternating manner. Because atoms from each mode dictionary jointly make contributions to the sparsity of tensor, existing works ignore atoms correlations between different mode dictionaries by treating each mode dictionary independently. In this paper, we propose a joint multiple dictionary learning method for tensor sparse coding, which explores atom correlations for sparse representation and updates multiple atoms from each mode dictionary simultaneously. In this algorithm, the Frequent-Pattern Tree (FP-tree) mining algorithm is employed to exploit frequent atom patterns in the sparse representation. Inspired by the idea of K-SVD, we develop a new dictionary update method that jointly updates elements in each pattern. Experimental results demonstrate our method outperforms other tensor based dictionary learning algorithms.

A new argument from interpersonal variation to subjectivism about color: a response to Gómez-Torrente

I describe a new, comparative, version of the argument from interpersonal variation to subjectivism about color. The comparative version undermines a recent objectivist response to standard versions of that argument (Gómez-Torrente 2014).

Exploring combinations of different color and facial expression stimuli for gaze-independent BCIs

Background: Some studies have proven that a conventional visual brain computer interface (BCI) based on overt attention cannot be used effectively when eye movement control is not possible. To solve this problem, a novel visual-based BCI system based on covert attention and feature attention has been proposed and was called the gaze-independent BCI. Color and shape difference between stimuli and backgrounds have generally been used in examples of gaze-independent BCIs. Recently, a new paradigm based on facial expression changes has been presented, and obtained high performance. However, some facial expressions were so similar that users couldn't tell them apart, especially when they were presented at the same position in a rapid serial visual presentation (RSVP) paradigm. Consequently, the performance of the BCI is reduced. New Method: In this paper, we combined facial expressions and colors to optimize the stimuli presentation in the gaze-independent BCI. This optimized paradigm was called the colored dummy face pattern. It is suggested that different colors and facial expressions could help users to locate the target and evoke larger event-related potentials (ERPs). In order to evaluate the performance of this new paradigm, two other paradigms were presented, called the gray dummy face pattern and the colored ball pattern. Comparison with Existing Method(s): The key point that determined the value of the colored dummy faces stimuli in BCI systems was whether the dummy face stimuli could obtain higher performance than gray faces or colored balls stimuli. Ten healthy participants (seven male, aged 21–26 years, mean 24.5 ± 1.25) participated in our experiment. Online and offline results of four different paradigms were obtained and comparatively analyzed. Results: The results showed that the colored dummy face pattern could evoke higher P300 and N400 ERP amplitudes, compared with the gray dummy face pattern and the colored ball pattern. Online results showed that the colored dummy face pattern had a significant advantage in terms of classification accuracy (p < 0.05) and information transfer rate (p < 0.05) compared to the other two patterns. Conclusions: The stimuli used in the colored dummy face paradigm combined color and facial expressions. This had a significant advantage in terms of the evoked P300 and N400 amplitudes and resulted in high classification accuracies and information transfer rates. It was compared with colored ball and gray dummy face stimuli.

Tensor LRR and sparse coding-based subspace clustering

Subspace clustering groups a set of samples from a union of several linear subspaces into clusters, so that the samples in the same cluster are drawn from the same linear subspace. In the majority of the existing work on subspace clustering, clusters are built based on feature information, while sample correlations in their original spatial structure are simply ignored. Besides, original high-dimensional feature vector contains noisy/redundant information, and the time complexity grows exponentially with the number of dimensions. To address these issues, we propose a tensor low-rank representation (TLRR) and sparse coding-based (TLRRSC) subspace clustering method by simultaneously considering feature information and spatial structures. TLRR seeks the lowest rank representation over original spatial structures along all spatial directions. Sparse coding learns a dictionary along feature spaces, so that each sample can be represented by a few atoms of the learned dictionary. The affinity matrix used for spectral clustering is built from the joint similarities in both spatial and feature spaces. TLRRSC can well capture the global structure and inherent feature information of data, and provide a robust subspace segmentation from corrupted data. Experimental results on both synthetic and real-world data sets show that TLRRSC outperforms several established state-of-the-art methods.

COLOR STABILITY OF DENTAL CERAMICS SUBMITTED TO ARTIFICIAL ACCELERATED AGING AFTER REPEATED FIRINGS

Statement of problem. Color stability is an important factor to ensure the long-term clinical success of ceramic restorations. There is a lack of information on how color is affected by fabrication procedures, such as the number of firings. Purpose. The purpose of this study was to evaluate the effects that the number of firings and type of substrate have on the color stability of dental ceramic submitted to artificial accelerated aging. Material and methods. Sixty specimens were fabricated: 30 metal ceramic (Verabond II + IPS d.SIGN) and 30 all-ceramic (IPS d.SIGN). Specimens were divided into 3 groups (n=10), and submitted to 2, 3, or 4 firings (+/- 900 degrees C), respectively, according to the manufacturer`s instructions. Color readings were obtained with a spectro photometer before and after artificial accelerated aging, and L*, a*, and b* coordinates and total color variation (Delta E) were analyzed (2-way ANOVA, Bonferroni, (alpha=05). Results. For metal ceramic specimens, differences for the L* coordinates were significant (P<.05) only for the group submitted to 3 firings. With respect to the all-ceramic specimens, smaller L* coordinates were obtained for greater a* and b* coordinates, indicating that the greater the number of firings, the darker and more reddish/yellowish the specimen. All Delta E values, for all groups, were below 1.0. All-ceramic specimens submitted to 3 and 4 firings presented Delta E means differing statistically (P<.05) from those of the metal ceramic group. Conclusions. The type of substrate and number of firings affected the color stability of the ceramic material tested. Artificial accelerated aging did not produce perceptible color stability changes (Delta E<1.0). (J Prosthet Dent 2009-101:13-18)

The effect of the degree of hydrolysis of the PVA and the plasticizer concentration on the color, opacity, and thermal and mechanical properties of films based on PVA and gelatin blends

The objective of this work was to study the color, opacity, crystallinity, and the thermal and mechanical properties of films based on blends of gelatin and five different types of PVA [poly(vinyl alcohol)], with and without a plasticizer. The effect of the degree of hydrolysis of the PVA and the glycerol concentration on these properties was studied using colorimetry, differential scanning calorimetry (DSC), X-ray diffraction (XRD) and tensile mechanical tests. All films were essentially colorless (Delta E* < 5) and with low opacity ( Y <= 2.1). The DSC results were typical of partially crystalline materials, showing some phase separation characterized by a glass transition (T(g) = 40-55 degrees C), related to the amorphous part of the material, followed by two endothermic peaks related to the melting (T(m) = 100-160 and 170-210 degrees C) of the crystallites. The XRD results confirmed the crystallinity of the films. The film produced with PVA Celvol((R)) 418 (DH = 91.8%) showed the highest tensile resistance (tensile strength = 38 MPa), for films without plasticizer. However, with glycerol, the above-mentioned PVA and the PVA Celvol((R)) 504 produced the least resistant films of all the PVA types. But, although the mechanical properties of the blended films depended on the type of PVA used, there was no direct relationship between these properties and the degree of hydrolysis of the PVA. The properties studied were more closely dependent on the glycerol concentration. Finally, the mechanical resistance of the films presented a linear relationship with the glass transition temperature of the films. (c) 2007 Elsevier Ltd. All rights reserved.

Color inheritance and pigment characterization of red (wild-type), greenish-brown, and green strains of Gracilaria birdiae (Gracilariales, Rhodophyta)

Species of Gracilaria are some of the most useful algae in the world for the production of agar. As a consequence of its economic importance, the genus has been the subject of many studies worldwide. Color variants of Gracilaria birdiae have been found in the natural population on the Brazilian coast, and they have also been isolated from plants cultivated in laboratory. These findings raised new questions regarding intraspecific variation and the prospects of cultivating such variants for their agar production. Therefore, this work aimed to determine the mode of color inheritance for two G. birdiae strains: a greenish-brown strain (gb) found in a natural population and a green strain (gr) which had arisen as a spontaneous mutation in a red plant cultured in the laboratory. The pigment contents of these strains, as well as the red wildtype (rd), were also characterized. Crosses between female and male plants of the same color (rd, gr, or gb) and between different colors were performed. Crosses between plants of the same color showed tetrasporophytic and gametophytic descendents of the parental color. Recessive nuclear inheritance was found in the greenish-brown strain, and cytoplasmic maternal inheritance was found in the green strain; both had lower phycoerythrin and higher concentrations of allophycocyanin and phycocyanin than the wild-type. Chlorophyll a contents were similar among all strains. Taken together, our results contribute to knowledge about the variability of this important red algae. In addition, since greenish-brown and green strains showed stability of color, both could be selected and tested in experimental sea cultivation to evaluate if mutants have advantageous performance when compared with red strain.

Coding behavioural data for cladistic analysis: using dynamic homology without parsimony

Many of the controversies around the concept of homology rest on the subjectivity inherent to primary homology propositions. Dynamic homology partially solves this problem, but there has been up to now scant application of it outside of the molecular domain. This is probably because morphological and behavioural characters are rich in properties, connections and qualities, so that there is less space for conflicting character delimitations. Here we present a new method for the direct optimization of behavioural data, a method that relies on the richness of this database to delimit the characters, and on dynamic procedures to establish character state identity. We use between-species congruence in the data matrix and topological stability to choose the best cladogram. We test the methodology using sequences of predatory behaviour in a group of spiders that evolved the highly modified predatory technique of spitting glue onto prey. The cladogram recovered is fully compatible with previous analyses in the literature, and thus the method seems consistent. Besides the advantage of enhanced objectivity in character proposition, the new procedure allows the use of complex, context-dependent behavioural characters in an evolutionary framework, an important step towards the practical integration of the evolutionary and ecological perspectives on diversity. (C) The Willi Hennig Society 2010.

The non-coding RNA BC1 is down-regulated in the hippocampus of Wistar Audiogenic Rat (WAR) strain after audiogenic kindling

The aim of this study was to identify molecular pathways involved in audiogenic seizures in the epilepsy-prone Wistar Audiogenic Rat (WAR). For this, we used a suppression-subtractive hybridization (SSH) library from the hippocampus of WARs coupled to microarray comparative gene expression analysis, followed by Northern blot validation of individual genes. We discovered that the levels of the non-protein coding (npc) RNA BC1 were significantly reduced in the hippocampus of WARs submitted to repeated audiogenic seizures (audiogenic kindling) when compared to Wistar resistant rats and to both naive WARs and Wistars. By quantitative in situ hybridization, we verified lower levels of BC1 RNA in the GD-hilus and significant signal ratio reduction in the stratum radiatum and stratum pyramidale of hippocampal CA3 subfield of audiogenic kindled animals. Functional results recently obtained in a BC1-/- mouse model and our current data are supportive of a potential disruption in signaling pathways, upstream of BC1, associated with the seizure susceptibility of WARs. (C) 2010 Elsevier B.V. All rights reserved.