A novel approach to detect hot-spots in large-scale multivariate data

Background: Progressive advances in the measurement of complex multifactorial components of biological processes involving both spatial and temporal domains have made it difficult to identify the variables (genes, proteins, neurons etc.) significantly changed activities in response to a stimulus within large data sets using conventional statistical approaches. The set of all changed variables is termed hot-spots. The detection of such hot spots is considered to be an NP hard problem, but by first establishing its theoretical foundation we have been able to develop an algorithm that provides a solution. Results: Our results show that a first-order phase transition is observable whose critical point separates the hot-spot set from the remaining variables. Its application is also found to be more successful than existing approaches in identifying statistically significant hot-spots both with simulated data sets and in real large-scale multivariate data sets from gene arrays, electrophysiological recording and functional magnetic resonance imaging experiments. Conclusion: In summary, this new statistical algorithm should provide a powerful new analytical tool to extract the maximum information from complex biological multivariate data

Osteoporotic and Neoplastic Compression Fracture Classification on Longitudinal CT

Classification of vertebral compression fractures (VCF) having osteoporotic or neoplastic origin is fundamental to the planning of treatment. We developed a fracture classification system by acquiring quantitative morphologic and bone density determinants of fracture progression through the use of automated measurements from longitudinal studies. A total of 250 CT studies were acquired for the task, each having previously identified VCFs with osteoporosis or neoplasm. Thirty-six features or each identified VCF were computed and classified using a committee of support vector machines. Ten-fold cross validation on 695 identified fractured vertebrae showed classification accuracies of 0.812, 0.665, and 0.820 for the measured, longitudinal, and combined feature sets respectively.Comment: Contributed 4-Page Paper to be presented at the 2016 IEEE International Symposium on Biomedical Imaging (ISBI), April 13-16, 2016, Prague, Czech Republi

The M33 Synoptic Stellar Survey. II. Mira Variables

We present the discovery of 1847 Mira candidates in the Local Group galaxy M33 using a novel semi-parametric periodogram technique coupled with a Random Forest classifier. The algorithms were applied to ~2.4x10^5 I-band light curves previously obtained by the M33 Synoptic Stellar Survey. We derive preliminary Period-Luminosity relations at optical, near- & mid-infrared wavelengths and compare them to the corresponding relations in the Large Magellanic Cloud.Comment: Includes small corrections to match the published versio

The Hydrodynamic Interaction in Polymer Solutions Simulated with Dissipative Particle Dynamics

We analyzed extensively the dynamics of polymer chains in solutions simulated with dissipative particle dynamics (DPD), with a special focus on the potential influence of a low Schmidt number of a typical DPD fluid on the simulated polymer dynamics. It has been argued that a low Schmidt number in a DPD fluid can lead to underdevelopment of the hydrodynamic interaction in polymer solutions. Our analyses reveal that equilibrium polymer dynamics in dilute solution, under a typical DPD simulation conditions, obey the Zimm model very well. With a further reduction in the Schmidt number, a deviation from the Zimm model to the Rouse model is observed. This implies that the hydrodynamic interaction between monomers is reasonably developed under typical conditions of a DPD simulation. Only when the Schmidt number is further reduced, the hydrodynamic interaction within the chains becomes underdeveloped. The screening of the hydrodynamic interaction and the excluded volume interaction as the polymer volume fraction is increased are well reproduced by the DPD simulations. The use of soft interaction between polymer beads and a low Schmidt number do not produce noticeable problems for the simulated dynamics at high concentrations, except that the entanglement effect which is not captured in the simulations.Comment: 27 pages, 13 page

Stellar origin of 15N-rich presolar SiC grains of type AB: Supernovae with explosive hydrogen burning

© 2017. The American Astronomical Society. All rights reserved. We report C, N, and Si isotopic data for 59 highly 13 C-enriched presolar submicron-to micron-sized SiC grains from the Murchison meteorite, including eight putative nova grains (PNGs) and 29 15 N-rich ( 14 N/ 15 N ≤ solar) AB grains, and their Mg-Al, S, and Ca-Ti isotope data when available. These 37 grains are enriched in 13 C, 15 N, and 26 Al with the PNGs showing more extreme enhancements. The 15 N-rich AB grains show systematically higher 26 Al and 30 Si excesses than the 14 N-rich AB grains. Thus, we propose to divide the AB grains into groups 1 ( 14 N/ 15 N < solar) and 2 ( 14 N/ 15 N ≥ solar). For the first time, we have obtained both S and Ti isotopic data for five AB1 grains and one PNG and found 32 S and/or 50 Ti enhancements. Interestingly, one AB1 grain had the largest 32 S and 50 Ti excesses, strongly suggesting a neutron-capture nucleosynthetic origin of the 32 S excess and thus the initial presence of radiogenic 32 Si (t 1/2 = 153 years). More importantly, we found that the 15 N and 26 Al excesses of AB1 grains form a trend that extends to the region in the N-Al isotope plot occupied by C2 grains, strongly indicating a common stellar origin for both AB1 and C2 grains. Comparison of supernova models with the AB1 and C2 grain data indicates that these grains came from supernovae that experienced H ingestion into the He/C zones of their progenitors

Spin relaxation and coherence times for electrons at the Si/SiO2 interface

While electron spins in silicon heterostructures make attractive qubits, little is known about the coherence of electrons at the Si/SiO2 interface. We report spin relaxation (T1) and coherence (T2) times for mobile electrons and natural quantum dots at a 28Si/SiO2 interface. Mobile electrons have short T1 and T2 of 0.3 us at 5 K. In line with predictions, confining electrons and cooling increases T1 to 0.8 ms at 350 mK. In contrast, T2 for quantum dots is around 10 us at 350 mK, increasing to 30 us when the dot density is reduced by a factor of two. The quantum dot T2 is shorter than T1, indicating that T2 is not controlled by T1 at 350 mK but is instead limited by an extrinsic mechanism. The evidence suggests that this extrinsic mechanism is an exchange interaction between electrons in neighboring dots.Comment: Extended with more experiments and rewritten. 6 pages, 5 figures, to be submitted to Phys. Rev.

Functional redundancy of EGF-CFC genes in epiblast and extraembryonic patterning during early mouse embryogenesis

AbstractDuring early mouse embryogenesis, multiple patterning and differentiation events require the activity of Nodal, a ligand of the transforming growth factor-beta (TGFβ) family. Although Nodal signaling is known to require activity of EGF-CFC co-receptors in many contexts, it has been unclear whether all Nodal signaling in the early mouse embryo is EGF-CFC dependent. We have investigated the double null mutant phenotypes for the EGF-CFC genes Cripto and Cryptic, which encode co-receptors for Nodal, and have found that they have partially redundant functions in early mouse development. Expression of Cripto and Cryptic is non-overlapping prior to gastrulation, since Cripto is expressed solely in the epiblast whereas Cryptic is expressed in the primitive endoderm of the late blastocyst and the visceral endoderm after implantation. Despite these non-overlapping expression patterns, Cripto; Cryptic double mutants display severe defects in epiblast, extraembryonic ectoderm, and anterior visceral endoderm (AVE), resulting in phenotypes that are highly similar to those of Nodal null mutants. Our results indicate that both Cripto and Cryptic function non-cell-autonomously during normal development, and that most if not all Nodal activity in early mouse embryogenesis is EGF-CFC-dependent