Predicting coaxial helical stacking in RNA junctions

RNA junctions are important structural elements that form when three or more helices come together in space in the tertiary structures of RNA molecules. Determining their structural configuration is important for predicting RNA 3D structure. We introduce a computational method to predict, at the secondary structure level, the coaxial helical stacking arrangement in junctions, as well as classify the junction topology. Our approach uses a data mining approach known as random forests, which relies on a set of decision trees trained using length, sequence and other variables specified for any given junction. The resulting protocol predicts coaxial stacking within three- and four-way junctions with an accuracy of 81% and 77%, respectively; the accuracy increases to 83% and 87%, respectively, when knowledge from the junction family type is included. Coaxial stacking predictions for the five to ten-way junctions are less accurate (60%) due to sparse data available for training. Additionally, our application predicts the junction family with an accuracy of 85% for three-way junctions and 74% for four-way junctions. Comparisons with other methods, as well applications to unsolved RNAs, are also presented. The web server Junction-Explorer to predict junction topologies is freely available at: http://bioinformatics.njit.edu/junction

Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number

Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of high-resolution structures, hydrodynamic radius and diffusion coefficient of evolutionary conserved RNA single strands (ssRNA) were calculated. The diffusion coefficients D of 17–174 nucleotides (nt) containing ssRNA depended on the number of nucleotides N with D = 4.56 × 10−10 N−0.39 m2 s−1. The hydrodynamic radius RH depended on N with RH = 5.00 × 10−10 N0.38 m. An average ratio of the radius of gyration and the hydrodynamic radius of 0.98 ± 0.08 was calculated in solution. The empirical law was tested by in solution measured hydrodynamic radii and radii of gyration and was found to be highly consistent with experimental data of evolutionary conserved ssRNA. Furthermore, the hydrodynamic behaviour of several evolutionary unevolved ribonucleic acids could be predicted. Based on atom-level shell-modelling of high-resolution structures and experimental hydrodynamic data, empirical models are proposed, which enable to predict the translational diffusion coefficient and molecular size of short RNA single strands solely on the basis of the polymer size

Construct validity of a continuous metabolic syndrome score in children

<p>Abstract</p> <p>Objective</p> <p>The primary purpose of this study was to examine the construct validity of a continuous metabolic syndrome score (cMetS) in children. The secondary purpose was to identify a cutpoint value(s) for an adverse cMetS based on receiver operating characteristic (ROC) curve analysis.</p> <p>Methods</p> <p>378 children aged 7 to 9 years were assessed for the metabolic syndrome which was determined by age-modified cutpoints. High-density-lipoprotein cholesterol, triglycerides, the homeostasis assessment model of insulin resistance, mean arterial pressure, and waist circumference were used to create a cMetS for each subject.</p> <p>Results</p> <p>About half of the subjects did not possess any risk factors while about 5% possessed the metabolic syndrome. There was a graded relationship between the cMetS and the number of adverse risk factors. The cMetS was lowest in the group with no adverse risk factors (-1.59 ± 1.76) and highest in those possessing the metabolic syndrome (≥3 risk factors) (7.05 ± 2.73). The cutoff level yielding the maximal sensitivity and specificity for predicting the presence of the metabolic syndrome was a cMetS of 3.72 (sensitivity = 100%, specificity = 93.9%, and the area of the curve = 0.978 (0.957-0.990, 95% confidence intervals).</p> <p>Conclusion</p> <p>The results demonstrate the construct validity for the cMetS in children. Since there are several drawbacks to identifying a single cut-point value for the cMetS based on this sample, we urge researchers to use the approach herein to validate and create a cMetS that is specific to their study population.</p

Revised Proposal for the Prevention of Low Bone Mass in Patients with Classic Galactosemia

Decreased bone mass is frequently encountered in classic galactosemia, an inborn error of galactose metabolism. This decrease is most prominent in adults, but is already seen in prepubertal children with increased risk of osteoporosis and fractures later in life. Therefore, bone health in patients with classic galactosemia is increasingly monitored. Although the pathophysiological mechanism is still not fully understood, several factors could negatively affect bone metabolism in this disease. Patients are at risk of nutritional deficiencies due to the galactose-restricted diet. Primary ovarian insufficiency (POI) in female patients also contributes to decreased bone mass. Furthermore, patients with classic galactosemia might be less physically active due to motor or neurological impairments. A disease-specific intrinsic abnormality has been suggested as well. This revised proposal is an update of the 2007 recommendations. In this current approach, we advise comprehensive dietary evaluation, optimization of calcium intake if needed, monitoring and if necessary supplementation of vitamin D, hormonal status evaluation and hormone replacement therapy (HRT) consideration, as well as a regular exercise and assessment of skeletal deformities and clinically significant fractures. We propose bone mineral density (BMD) assessment by serial DXA scans of the lumbar spine, femoral neck, and total hip in adults and lumbar spine and total body less head (TBLH) in children

Beyond tourism-based economic development: city-regions and transient custom

[Departement_IRSTEA]TerritoiresInternational audienceMany localities are able to survive without competitive export industries. The economic base of regional development rests upon various wage and non-wage external incomes. However, suitable regional data are often unavailable, and particularly those related to external consumer spending in urban regions and short-stay tourism. Three geo-localized databases are here combined into a circular-flow template from former consumer spending to the final wage income. By doing so, the paper contributes to identifying transient custom' as a new inflow driving local development and it provides a first estimate of its magnitude, using the Paris Region as a case study