DNA Molecule Classification Using Feature Primitives

BACKGROUND: We present a novel strategy for classification of DNA molecules using measurements from an alpha-Hemolysin channel detector. The proposed approach provides excellent classification performance for five different DNA hairpins that differ in only one base-pair. For multi-class DNA classification problems, practitioners usually adopt approaches that use decision trees consisting of binary classifiers. Finding the best tree topology requires exploring all possible tree topologies and is computationally prohibitive. We propose a computational framework based on feature primitives that eliminates the need of a decision tree of binary classifiers. In the first phase, we generate a pool of weak features from nanopore blockade current measurements by using HMM analysis, principal component analysis and various wavelet filters. In the next phase, feature selection is performed using AdaBoost. AdaBoost provides an ensemble of weak learners of various types learned from feature primitives. RESULTS AND CONCLUSION: We show that our technique, despite its inherent simplicity, provides a performance comparable to recent multi-class DNA molecule classification results. Unlike the approach presented by Winters-Hilt et al., where weaker data is dropped to obtain better classification, the proposed approach provides comparable classification accuracy without any need for rejection of weak data. A weakness of this approach, on the other hand, is the very "hands-on" tuning and feature selection that is required to obtain good generalization. Simply put, this method obtains a more informed set of features and provides better results for that reason. The strength of this approach appears to be in its ability to identify strong features, an area where further results are actively being sought

The Effects of Time Varying Curvature on Species Transport in Coronary Arteries

Alterations in mass transport patterns of low-density lipoproteins (LDL) and oxygen are known to cause atherosclerosis in larger arteries. We hypothesise that the species transport processes in coronary arteries may be affected by their physiological motion, a factor which has not been considered widely in mass transfer studies. Hence, we numerically simulated the mass transport of LDL and oxygen in an idealized moving coronary artery model under both steady and pulsatile flow conditions. A physiological inlet velocity and a sinusoidal curvature waveform were specified as velocity and wall motion boundary conditions. The results predicted elevation of LDL flux, impaired oxygen flux and low wall shear stress (WSS) along the inner wall of curvature, a predilection site for atherosclerosis. The wall motion induced changes in the velocity and WSS patterns were only secondary to the pulsatile flow effects. The temporal variations in flow and WSS due to the flow pulsation and wall motion did not affect temporal changes in the species wall flux. However, the wall motion did alter the time-averaged oxygen and LDL flux in the order of 26% and 12% respectively. Taken together, these results suggest that the wall motion may play an important role in coronary arterial transport processes and emphasise the need for further investigation

Welcome [by Renaud Dehousse, EUI President]

This contribution was delivered online on 6 May 2021 on the occasion of the hybrid 2021 edition of EUI State of the Union on ‘Europe in a Changing World'

Individual fluid plans versus ad libitum on hydration status in minor professional ice hockey players

Abstract Background Despite exercising in cool environments, ice hockey players exhibit several dehydration risk factors. Individualized fluid plans (IFPs) are designed to mitigate dehydration by matching an individual’s sweat loss in order to optimize physiological systems and performance. Methods A randomized control trial was used to examine IFP versus ad libitum fluid ingestion on hydration in 11 male minor professional ice hockey players (mean age = 24.4 ± 2.6 years, height = 183.0 ± 4.6 cm, weight = 92.9 ± 7.8 kg). Following baseline measures over 2 practices, participants were randomly assigned to either control (CON) or intervention (INT) for 10 additional practices. CON participants were provided water and/or carbohydrate electrolyte beverage to drink ad libitum. INT participants were instructed to consume water and an electrolyte-enhanced carbohydrate electrolyte beverage to match sweat and sodium losses. Urine specific gravity, urine color, and percent body mass change characterized hydration status. Total fluid consumed during practice was assessed. Results INT consumed significantly more fluid than CON (1180.8 ± 579.0 ml vs. 788.6 ± 399.7 ml, p = 0.002). However, CON participants replaced only 25.4 ± 12.9% of their fluid needs and INT 35.8 ± 17.5%. Mean percent body mass loss was not significantly different between groups and overall indicated minimal dehydration (<1.2% loss). Pre-practice urine specific gravity indicated CON and INT began hypohydrated (mean = 1.024 ± 0.007 and 1.024 ± 0.006, respectively) and experienced dehydration during practice (post = 1.026 ± 0.006 and 1.027 ± 0.005, respectively, p < 0.001). Urine color increased pre- to post-practice for CON (5 ± 2 to 6 ± 1, p < 0.001) and INT (5 ± 1 to 6 ± 1, p < 0.001). Conclusions Participants consistently reported to practice hypohydrated. Ad libitum fluid intake was not significantly different than IFP on hydration status. Based on urine measures, both methods were unsuccessful in preventing dehydration during practice, suggesting practice-only hydration is inadequate to maintain euhydration in this population when beginning hypohydrated

Dental Abnormalities in Schimke Immuno-osseous Dysplasia

Described for the first time in 1971, Schimke immuno-osseous dysplasia (SIOD) is an autosomal-recessive multisystem disorder that is caused by bi-allelic mutations of SMARCAL1, which encodes a DNA annealing helicase. To define better the dental anomalies of SIOD, we reviewed the records from SIOD patients with identified bi-allelic SMARCAL1 mutations, and we found that 66.0% had microdontia, hypodontia, or malformed deciduous and permanent molars. Immunohistochemical analyses showed expression of SMARCAL1 in all developing teeth, raising the possibility that the malformations are cell-autonomous consequences of SMARCAL1 deficiency. We also found that stimulation of cultured skin fibroblasts from SIOD patients with the tooth morphogens WNT3A, BMP4, and TGF beta 1 identified altered transcriptional responses, raising the hypothesis that the dental malformations arise in part from altered responses to developmental morphogens. To the best of our knowledge, this is the first systematic study of the dental anomalies associated with SIOD