Noise, Bifurcations, and Modeling of Interacting Particle Systems

We consider the stochastic patterns of a system of communicating, or coupled, self-propelled particles in the presence of noise and communication time delay. For sufficiently large environmental noise, there exists a transition between a translating state and a rotating state with stationary center of mass. Time delayed communication creates a bifurcation pattern dependent on the coupling amplitude between particles. Using a mean field model in the large number limit, we show how the complete bifurcation unfolds in the presence of communication delay and coupling amplitude. Relative to the center of mass, the patterns can then be described as transitions between translation, rotation about a stationary point, or a rotating swarm, where the center of mass undergoes a Hopf bifurcation from steady state to a limit cycle. Examples of some of the stochastic patterns will be given for large numbers of particles

Coherent Pattern Prediction in Swarms of Delay-Coupled Agents

We consider a general swarm model of self-propelling agents interacting through a pairwise potential in the presence of noise and communication time delay. Previous work [Phys. Rev. E 77, 035203(R) (2008)] has shown that a communication time delay in the swarm induces a pattern bifurcation that depends on the size of the coupling amplitude. We extend these results by completely unfolding the bifurcation structure of the mean field approximation. Our analysis reveals a direct correspondence between the different dynamical behaviors found in different regions of the coupling-time delay plane with the different classes of simulated coherent swarm patterns. We derive the spatio-temporal scales of the swarm structures, and also demonstrate how the complicated interplay of coupling strength, time delay, noise intensity, and choice of initial conditions can affect the swarm. In particular, our studies show that for sufficiently large values of the coupling strength and/or the time delay, there is a noise intensity threshold that forces a transition of the swarm from a misaligned state into an aligned state. We show that this alignment transition exhibits hysteresis when the noise intensity is taken to be time dependent

Predicting electrical conductivity in Cu/Nb composites: a combined model-experiment study

The generation of high magnetic fields requires materials with high electric conductivity and good strength properties. Cu/Nb composites are considered to be good candidates for this purpose. In this work we aim to predict, from theory, the dependence of electric conductivity on the microstructure, most notably on the layer thickness and grain sizes. We also conducted experiments to calibrate and validate our simulations. Bimetal interfaces and grain boundaries are confirmed to have the largest impact on conductivity in this composite material. In this approach, a distribution of the layer thickness is accounted for in order to better model the experimentally observed microstructure. Because layer thicknesses below the mean free path of Cu significantly degrade the conductivity, an average layer thickness larger than expected may be needed to meet conductivity requirements in order to minimize these smaller layers in the distribution. We also investigate the effect of variations in volume fraction of Nb and temperature on the material's conductivity.Comment: 19 pages, 5 figures, 2 table

Detection of Dental Fluorosis-Associated Quantitative Trait Loci on Mouse Chromosomes 2 and 11

Systemic exposure to greater than optimal fluoride (F) can lead to dental fluorosis (DF). Parental A/J (DF-susceptible) and 129P3/J (DF-resistant) inbred mice were used for histological studies and to generate F2 progeny. Mice were treated with 0 or 50 ppm F in their drinking water for 60 days. A clinical criterion (modified Thylstrup and Fejerskov categorical scale) was used to assess the severity of DF for each individual F2 animal. Parental strains were subjected to histological examination of maturing enamel. F treatment resulted in accumulation of amelogenins in the maturing enamel of A/J mice. Quantitative trait loci (QTL) detection was performed using phenotypic extreme F2 animals genotyped for 354 single nucleotide polymorphism-based markers distributed throughout the mouse genome followed by χ2 analysis. Significant evidence of association was observed on chromosomes 2 and 11 for a series of consecutive markers (p < 0.0001). Further analyses were performed to examine whether the phenotypic effects were found in both male and female F2 mice or whether there was evidence for gender-specific effects. Analyses performed using the markers on chromosomes 2 and 11 which were significant in the mixed-gender mice were also significant when analyses were limited to only the male or female mice. The QTL detected on chromosomes 2 and 11 which influence the variation in response to fluorosis have their effect in mice of both genders. Finally, the QTL in both chromosomes appear to have an additive effect

Fluoride Modulates Parathyroid Hormone Secretion in vivo and in vitro

The study objective was to investigate fluoride’s effects on iPTH secretion. Thryo-parathyroid complexes (TPCs) from C3H (n=18) and B6 (n=18) mice were cultured in Ca2+ optimized medium. TPCs were treated with 0, 250 or 500µM NaF for 24hrs and secreted iPTH assayed by ELISA. C3H (n=78) and B6 (n=78) mice were gavaged once with distilled or with fluoride (0.001mg [F−]/g body weight) water. At serial time points (0.5–96hrs) serum iPTH, fluoride, total calcium, phosphorus and magnesium levels were determined. Expression of genes involved in mineral regulation via bone-parathyroid-kidney (BPK) axis such as: Pth, Casr, Vdr, Pthlh, Fgf23, αKlotho, Fgf1rc, Tnfs11, Pth1r, Slc34a1, Slc9a3r1, Clcn5 and Pdzk1 were determined in TPCs, humerii and kidneys at 24hrs. An in vitro decrease in iPTH was seen in C3H and B6 TPC at 500µM (p<0.001). In vivo levels of serum fluoride peaked at 0.5hr in both C3H (p=0.002) and B6 (p=0.01). In C3H, iPTH decreased at 24hrs (p<0.0001) returning to baseline at 48hrs. In B6, iPTH increased at 12hrs (p<0.001) returning to baseline at 24hrs. Serum total calcium, phosphorus and magnesium did not change significantly. Pth, Casr, αKlotho, Fgf1rc, Vdr and Pthlh were significantly up-regulated in C3H TPC as compared to B6. Conclusions, fluoride’s effects on TPC in vitro were equivalent between the two mouse strains. However, fluoride demonstrated an early strain dependent effect on iPTH secretion in vivo. Both strains demonstrated a differences in the expression of genes involved in BPK axis suggesting a possible role in physiologic handling of fluoride

A database accelerator for energy-efficient query processing and optimization

Data processing on a continuously growing amount of information and the increasing power restrictions have become an ubiquitous challenge in our world today. Besides parallel computing, a promising approach to improve the energy efficiency of current systems is to integrate specialized hardware. This paper presents a Tensilica RISC processor extended with an instruction set to accelerate basic database operators frequently used in modern database systems. The core was taped out in a 28 nm SLP CMOS technology and allows energy-efficient query processing as well as query optimization by applying selectivity estimation techniques. Our chip measurements show an 1000x energy improvement on selected database operators compared to state-of-the-art systems

Phenotypic Variation of Fluoride Responses between Inbred Strains of Mice

Excessive systemic exposure to fluoride (F) can lead to disturbances in bone homeostasis and dental enamel development. We have previously shown strain-specific responses to F in the development of dental fluorosis (DF) and in bone formation/mineralization. The current study was undertaken to further investigate F responsive variations in bone metabolism and to determine possible relationships with DF susceptibility. Seven-week-old male mice from FVB/NJ, C57BL/6J, C3H/HeJ, A/J, 129S1/SvImJ, AKR/J, DBA/2J, and BALB/cByJ inbred strains were exposed to NaF (0 or 50 ppm as F–) in drinking water for 60 days. Sera were collected for F, Ca, Mg, PO4, iPTH, sRANKL, and ALP levels. Bone marrow cells were subjected to ex vivo cell culture for osteoclast potential and CFU colony assays (CFU-fibroblast, CFU-osteoblast, CFU-erythrocyte/granulocyte/macrophage/megakaryocyte, CFU-granulocyte/macrophage, CFU-macrophage, and CFU-granulocyte). Femurs and vertebrae were subjected to micro-CT analyses, biomechanical testing, and F, Mg, and Ca content assays. DF was evaluated using quantitative fluorescence and clinical criteria. Strain-specific responses to F were observed for DF, serum studies, ex vivo cell culture studies, and bone quality. Among the strains, there were no patterns or significant correlations between DF severity and the actions of F on bone homeostasis (serum studies, ex vivo assays, or bone quality parameters). The genetic background continues to play a role in the actions of F on tooth enamel development and bone homeostasis. F exposure led to variable phenotypic responses between strains involving dental enamel development and bone metabolism

DAPHNE: An Open and Extensible System Infrastructure for Integrated Data Analysis Pipelines

Integrated data analysis (IDA) pipelines—that combine data management (DM) and query processing, high-performance computing (HPC), and machine learning (ML) training and scoring—become increasingly common in practice. Interestingly, systems of these areas share many compilation and runtime techniques, and the used—increasingly heterogeneous—hardware infrastructure converges as well. Yet, the programming paradigms, cluster resource management, data formats and representations, as well as execution strategies differ substantially. DAPHNE is an open and extensible system infrastructure for such IDA pipelines, including language abstractions, compilation and runtime techniques, multi-level scheduling, hardware (HW) accelerators, and computational storage for increasing productivity and eliminating unnecessary overheads. In this paper, we make a case for IDA pipelines, describe the overall DAPHNE system architecture, its key components, and the design of a vectorized execution engine for computational storage, HW accelerators, as well as local and distributed operations. Preliminary experiments that compare DAPHNE with MonetDB, Pandas, DuckDB, and TensorFlow show promising results

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead