Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

Motivation: Understanding how proteins recognize their RNA targets is essential to elucidate regulatory processes in the cell. Many RNA-binding proteins (RBPs) form complexes or have multiple domains that allow them to bind to RNA in a multivalent, cooperative manner. They can thereby achieve higher specificity and affinity than proteins with a single RNA-binding domain. However, current approaches to de novo discovery of RNA binding motifs do not take multivalent binding into account. Results: We present Bipartite Motif Finder (BMF), which is based on a thermodynamic model of RBPs with two co-operatively binding RNA-binding domains. We show that bivalent binding is a common strategy among RBPs, yielding higher affinity and sequence specificity. We furthermore illustrate that the spatial geometry between the binding sites can be learned from bound RNA sequences. These discovered bipartite motifs are consistent with previously known motifs and binding behaviors. Our results demonstrate the importance of multivalent binding for RNA-binding proteins and highlight the value of bipartite motif models in representing the multivalency of protein-RNA interactions

A NOVEL METHOD FOR SYNTHESIS OF METASTABLE TETRAGONAL ZIRCONIA NANOPOWDERS AT LOW TEMPERATURES

Zirconia (ZrO2) nanopowder was synthesized using sucrose and fructose as a chelating agent from zirconium hydroxide. The synthesized powders were characterized by X-ray diffraction (XRD), simultaneously thermal analysis (STA), BET surface area, scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The above-experimental results showed that the synthesized powders had particle sizes in the range 40-60 nm and mean crystallite sizes of 7-8 nm. Finally, in this research, chelating agents of sucrose and fructose were compared and the obtained results demonstrated that using fructose, nanopowder of zirconia with tetragonal phase was obtained

A seismic-driven 3D model of rock mechanical facies: An example from the Asmari reservoir, SW Iran

Asmari Formation is one of the most prolific and important hydrocarbon reservoirs in Iran. This formation in the Cheshmeh-Khosh oilfield shows mixed carbonate-siliciclastic lithology and its elastic modulus changes are correlatable with facies changes. To address these changes, we investigated the relation between sedimentary environment (facies) and texture with various elastic moduli. The Young's modulus shows higher correlation with the facies changes. Data from three wells are analyzed and used for the construction of rock mechanical facies. Based on elastic properties, facies and texture changes as well as petrophysical characteristics seven rock mechanical facies (RMFs) are recognized in the studied formation. To predict RMFs at inter-well spaces more efficiently and capturing the lateral formation property variationsa 3D rock mechanical facies model is constructed based on seismic attributes. In this method, RMFs are correlatable between the studied wells and mappable by seismic attribute in the field scale. Finally, the distribution of RMFs and their related properties is investigated in the studied field

Bilingualism Is Associated with a Delayed Onset of Dementia but Not with a Lower Risk of Developing it: a Systematic Review with Meta-Analyses.

Some studies have linked bilingualism with a later onset of dementia, Alzheimer's disease (AD), and mild cognitive impairment (MCI). Not all studies have observed such relationships, however. Differences in study outcomes may be due to methodological limitations and the presence of confounding factors within studies such as immigration status and level of education. We conducted the first systematic review with meta-analysis combining cross-sectional studies to explore if bilingualism might delay symptom onset and diagnosis of dementia, AD, and MCI. Primary outcomes included the age of symptom onset, the age at diagnosis of MCI or dementia, and the risk of developing MCI or dementia. A secondary outcome included the degree of disease severity at dementia diagnosis. There was no difference in the age of MCI diagnosis between monolinguals and bilinguals [mean difference: 3.2; 95% confidence intervals (CI): -3.4, 9.7]. Bilinguals vs. monolinguals reported experiencing AD symptoms 4.7 years (95% CI: 3.3, 6.1) later. Bilinguals vs. monolinguals were diagnosed with dementia 3.3 years (95% CI: 1.7, 4.9) later. Here, 95% prediction intervals showed a large dispersion of effect sizes (-1.9 to 8.5). We investigated this dispersion with a subgroup meta-analysis comparing studies that had recruited participants with dementia to studies that had recruited participants with AD on the age of dementia and AD diagnosis between mono- and bilinguals. Results showed that bilinguals vs. monolinguals were 1.9 years (95% CI: -0.9, 4.7) and 4.2 (95% CI: 2.0, 6.4) older than monolinguals at the time of dementia and AD diagnosis, respectively. The mean difference between the two subgroups was not significant. There was no significant risk reduction (odds ratio: 0.89; 95% CI: 0.68-1.16) in developing dementia among bilinguals vs. monolinguals. Also, there was no significant difference (Hedges' g = 0.05; 95% CI: -0.13, 0.24) in disease severity at dementia diagnosis between bilinguals and monolinguals, despite bilinguals being significantly older. The majority of studies had adjusted for level of education suggesting that education might not have played a role in the observed delay in dementia among bilinguals vs. monolinguals. Although findings indicated that bilingualism was on average related to a delayed onset of dementia, the magnitude of this relationship varied across different settings. This variation may be due to unexplained heterogeneity and different sources of bias in the included studies. Registration: PROSPERO CRD42015019100

Gram - positive and gram - negative subcellular localization using rotation forest and physicochemical-based features

The functioning of a protein relies on its location in the cell. Therefore, predicting protein subcellular localization is an important step towards protein function prediction. Recent studies have shown that relying on Gene Ontology (GO) for feature extraction can improve the prediction performance. However, for newly sequenced proteins, the GO is not available. Therefore, for these cases, the prediction performance of GO based methods degrade significantly. Results: In this study, we develop a method to effectively employ physicochemical and evolutionary-based information in the protein sequence. To do this, we propose segmentation based feature extraction method to explore potential discriminatory information based on physicochemical properties of the amino acids to tackle Gram-positive and Gram-negative subcellular localization. We explore our proposed feature extraction techniques using 10 attributes that have been experimentally selected among a wide range of physicochemical attributes. Finally by applying the Rotation Forest classification technique to our extracted features, we enhance Gram-positive and Gram-negative subcellular localization accuracies up to 3.4% better than previous studies which used GO for feature extraction. Conclusion: By proposing segmentation based feature extraction method to explore potential discriminatory information based on physicochemical properties of the amino acids as well as using Rotation Forest classification technique, we are able to enhance the Gram-positive and Gram-negative subcellular localization prediction accuracies, significantly

Intense physical activity is associated with cognitive performance in the elderly

Numerous studies have reported positive impacts of physical activity on cognitive function. However, the majority of these studies have utilised physical activity questionnaires or surveys, thus results may have been influenced by reporting biases. Through the objective measurement of routine levels of physical activity via actigraphy, we report a significant association between intensity, but not volume, of physical activity and cognitive functioning. A cohort of 217 participants (aged 60–89 years) wore an actigraphy unit for 7 consecutive days and underwent comprehensive neuropsychological assessment. The cohort was stratified into tertiles based on physical activity intensity. Compared with individuals in the lowest tertile of physical activity intensity, those in the highest tertile scored 9%, 9%, 6% and 21% higher on the digit span, digit symbol, Rey Complex Figure Test (RCFT) copy and Rey Figure Test 30-min recall test, respectively. Statistically, participants in the highest tertile of physical activity intensity performed significantly better on the following cognitive tasks: digit symbol, RCFT copy and verbal fluency test (all P<0.05). The results indicate that intensity rather than quantity of physical activity may be more important in the association between physical activity and cognitive function

Personality characteristics are independently associated with prospective memory in the laboratory, and in daily life, among older adults

Prospective memory (PM) can deteriorate with age and adversely influence health behaviours. Research suggests that personality is related to PM in healthy young adults, but we know little about the role of personality in the PM amongst older adults. Community-dwelling older adults (N=152) completed the NEO Five-Factor Inventory-3 and PM measures. After adjusting for demographics and general cognition, higher neuroticism and lower levels of openness were independently associated with lower objectively-measured time- and event-based PM. Lower conscientiousness was the only personality predictor of self-reported everyday PM failures. Findings indicate that personality plays a role in PM functioning in the laboratory and daily life