Defect turbulence and generalized statistical mechanics

We present experimental evidence that the motion of point defects in thermal convection patterns in an inclined fluid layer is well-described by Tsallis statistics with an entropic index $q \approx 1.5$. The dynamical properties of the defects (anomalous diffusion, shape of velocity distributions, power law decay of correlations) are in good agreement with typical predictions of nonextensive models, over a range of driving parameters

Entropy-scaling search of massive biological data

Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo

Estimation of Tracheid Morphological Characteristics of Green Pinus Taeda L. Radial Strips by Near Infrared Spectroscopy

The application of near infrared (NIR) spectroscopy to the green wood of radial samples (simulated increment cores) and the development of calibrations for the prediction of several tracheid morphological characteristics are described. Twenty Pinus taeda L. (loblolly pine) radial samples were characterized in terms of coarseness, perimeter, radial and tangential diameter, specific surface, and wall thickness. NIR spectra were obtained in 10-mm steps from the radial-longitudinal and transverse face of each sample and were used to generate calibrations for each property. NIR spectra were collected from all samples when the wood was green (moisture content ranged from approximately 100 to 154%), and when dried to approximately 7% moisture content. The relationships between measured and NIR-estimates for green wood were strong for coarseness, specific surface, and wall thickness, with coefficients of determination (R2) ranging from 0.89 to 0.73. Differences between calibrations developed using radial-longitudinal and transverse face NIR spectra were generally small. Dry wood calibrations demonstrated strong relationships for all parameters apart from perimeter and radial diameter; R2 ranged from 0.59 to 0.91. Calibrations were tested on an independent set; relationships for coarseness, specific surface, and wall thickness were strong. Good calibrations can be obtained for some tracheid morphological characteristics using NIR spectra collected from the surface of green P. taeda wood

Cross-cultural adaptation and psychometric evaluation of the isiZulu 20-item Toronto Alexithymia Scale : preliminary findings.

Masters Degree. University of KwaZulu-Natal, Durban.According to prevalence studies, 1 in 3 South Africans will present with a diagnosable mental disorder throughout the course of their lifetime, whilst over a given period of 12 months, 1 in 6 South Africans will likely present with a mental disorder that is clinically diagnosable. Given the alarming rates of mental illness in South Africa much attention within the literature has focussed on further understanding both its determinants and associated risk factors. Due to its significant associations with several psychiatric and medical conditions, the subject of alexithymia has advanced these aims in the global literature. However, little research on the subject has been undertaken in South Africa, most likely due to the lack of a validated psychometric assessment for detecting and further investigating the issue of alexithymia among patients. Additionally, research also indicates that the measurement of alexithymia is impacted by sociocultural factors that shape it in part. Consequently, this research aimed to address these issues by undertaking a cross-cultural adaptation of the 20-item Toronto Alexithymia Scale (TAS-20) for an isiZulu-speaking sample of university students and evaluating its psychometric properties. This was achieved through three objectives: (1) cultural adaptation and translation of the TAS-20 into isiZulu; (2) evaluating the psychometric properties of the isiZulu translation of the TAS-20; and (3) exploring variation in scores on the isiZulu TAS-20 by gender. The results of the confirmatory factor analyses suggested best global fit for the standard oblique three-factor model with an additional specified covariance between two indicators. Evaluation of local fit supported meaningful parameter estimates, as well as the convergent and discriminant validity for the DIF and DDF latent factors of the model, but failed to support the validity of the EOT latent factor. Reliability analyses similarly demonstrated acceptable reliability for the total isiZulu TAS-20 scale and the DIF and DDF subscales, but failed to do so for the EOT subscale. Lastly, there was tentative indication of significantly elevated levels of alexithymia among female Zulu participants as compared to male Zulu participants. In conclusion, the psychometric evaluation confirmed the factor structure, but failed to fully support the underlying theoretical relationships in the Zulu culture. In convergence with other studies, these findings suggest that sociocultural factors significantly impact upon the construct and assessment of alexithymia. The study suggests the need for a theoretical reconceptualization of alexithymia, factoring in the role of sociocultural factors

Engineering human cell-based, functionally integrated osteochondral grafts by biological bonding of engineered cartilage tissues to bony scaffolds

In this study, we aimed at developing and validating a technique for the engineering of osteochondral grafts based on the biological bonding of a chondral layer with a bony scaffold by cell-laid extracellular matrix. Osteochondral composites were generated by combining collagen-based matrices (Chondro-Gide) containing human chondrocytes with devitalized spongiosa cylinders (Tutobone) using a fibrin gel (Tisseel). We demonstrate that separate pre-culture of the chondral layer for 3 days prior to the generation of the composite allows for (i) more efficient cartilaginous matrix accumulation than no pre-culture, as assessed histologically and biochemically, and (ii) superior biological bonding to the bony scaffold than 14 days of pre-culture, as assessed using a peel-off mechanical test, developed to measure integration of bilayered materials. The presence of the bony scaffold induced an upregulation in the infiltrated cells of the osteoblast-related gene bone sialoprotein, indicative of the establishment of a gradient of cell phenotypes, but did not affect per se the quality of the cartilaginous matrix in the chondral layer. The described strategy to generate osteochondral plugs is simple to be implemented and--since it is based on clinically compliant cells and materials--is amenable to be readily tested in the clinic

Modelling train delays with q-exponential functions

We demonstrate that the distribution of train delays on the British railway network is accurately described by q-exponential functions. We explain this by constructing an underlying superstatistical model.Comment: 12 pages, 5 figure

Effects of Live Music Therapy on Autonomic Stability in Preterm Infants:A Cluster-Randomized Controlled Trial

Unbuffered stress levels may negatively influence preterm-infants’ autonomic nervous system (ANS) maturation, thus affecting neurobehavior and psycho-emotional development. Music therapy (MT) is an evidence-based treatment modality in neonatal care. When coupled with skin-to-skin care (SSC), it may reduce stress responses in both preterm infants and their parents and enhance family-centered care. Accordingly, we aimed to compare the effects of combined MT and SSC and SSC alone on ANS stabilization in preterm infants. In a single-center, cluster-randomized trial design, ten two-month time-clusters were randomized to either combined MT and SSC or SSC alone. Families of preterm infants were offered two sessions of the allocated condition in the NICU, and a three-month follow up session at home. The primary outcome variable was stabilization of the ANS, defined by change in the high frequency (HF) power of heart rate variability (HRV) during the second session. Secondary outcomes included other HRV measures, parent–infant attachment, and parental anxiety at each session. Sixty-eight families were included. MT combined with SSC improved infants’ ANS stability, as indicated by a greater increase in HF power during MT compared to SSC alone (mean difference 5.19 m2/Hz, SE = 1.27, p < 0.001) (95% confidence interval 0.87 to 2.05). Most secondary outcomes were not significantly different between the study groups. MT contributes to preterm-infants’ autonomic stability, thus laying an important foundation for neuro-behavioral and psycho-emotional development. Studies evaluating longer-term effects of MT on preterm infants’ development are warranted

Stretched exponentials from superstatistics

Distributions exhibiting fat tails occur frequently in many different areas of science. A dynamical reason for fat tails can be a so-called superstatistics, where one has a superposition of local Gaussians whose variance fluctuates on a rather large spatio-temporal scale. After briefly reviewing this concept, we explore in more detail a class of superstatistics that hasn't been subject of many investigations so far, namely superstatistics for which a suitable power beta^eta of the local inverse temperature beta is chi^2-distributed. We show that eta >0 leads to power law distributions, while eta <0 leads to stretched exponentials. The special case eta=1 corresponds to Tsallis statistics and the special case eta=-1 to exponential statistics of the square root of energy. Possible applications for granular media and hydrodynamic turbulence are discussed.Comment: 10 pages. Proceedings of NEXT-SigmaPhi conference, Kolymbari, 13-18 August 200

Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region.

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.We would like to thank the KAUST BioScience Core Lab and S. Neelamegam for 454 library generation and sequencing. We would also like to thank Y. Sawall and A. Al-Sofyani for provision and collection of coral samples, and three anonymous reviewers for helpful comments. This project was funded by a KAUST Academic Excellence Alliance (AEA) Award to CRV and CJH, baseline research funds to CRV and a National Science Foundation grant to TCL (OCE-09287664).This is the final published version. It first appeared at http://onlinelibrary.wiley.com/doi/10.1111/mec.12869/abstract