Application of product dioids for dead token detection in interval P-time event graphs

Linear description of interval P-time event graphs using a product idempotent semiring is proposed and applied to dead token detection. The dependence of dead token on initial condition is studied using residuation theory. Finally, the relationship with the spectral theory of matrices over product semirings is discusse

Modeling sea-salt aerosols in the atmosphere: 2. Atmospheric concentrations and fluxes

Atmospheric sea-salt aerosol concentrations are studied using both long-term observations and model simulations of Na+ at seven stations around the globe. Good agreement is achieved between observations and model predictions in the northern hemisphere. A stronger seasonal variation occurs in the high-latitude North Atlantic than in regions close to the equator and in high-latitude southern hemisphere. Generally, concentrations are higher for both boreal and austral winters. With the model, the production flux and removal flux at the atmosphere-ocean interface was calculated and used to estimate the global sea-salt budget. The flux also shows seasonal variation similar to that of sea-salt concentration. Depending on the geographic location, the model predicts that dry deposition accounts for 60–70% of the total sea-salt removed from the atmosphere while in-cloud and below-cloud precipitation scavenging accounts for about 1% and 28–39% of the remainder, respectively. The total amount of sea-salt aerosols emitted from the world oceans to the atmosphere is estimated to be in the vicinity of 1.17×1016 g yr−1. Approximately 99% of the sea-salt aerosol mass generated by wind falls back to the sea with about 1–2% remaining in the atmosphere to be exported from the original grid square (300×300 km). Only a small portion of that exported (∼4%) is associated with submicron particles that are likely to undergo long-range transport

Dendritic Spine Shape Analysis: A Clustering Perspective

Functional properties of neurons are strongly coupled with their morphology. Changes in neuronal activity alter morphological characteristics of dendritic spines. First step towards understanding the structure-function relationship is to group spines into main spine classes reported in the literature. Shape analysis of dendritic spines can help neuroscientists understand the underlying relationships. Due to unavailability of reliable automated tools, this analysis is currently performed manually which is a time-intensive and subjective task. Several studies on spine shape classification have been reported in the literature, however, there is an on-going debate on whether distinct spine shape classes exist or whether spines should be modeled through a continuum of shape variations. Another challenge is the subjectivity and bias that is introduced due to the supervised nature of classification approaches. In this paper, we aim to address these issues by presenting a clustering perspective. In this context, clustering may serve both confirmation of known patterns and discovery of new ones. We perform cluster analysis on two-photon microscopic images of spines using morphological, shape, and appearance based features and gain insights into the spine shape analysis problem. We use histogram of oriented gradients (HOG), disjunctive normal shape models (DNSM), morphological features, and intensity profile based features for cluster analysis. We use x-means to perform cluster analysis that selects the number of clusters automatically using the Bayesian information criterion (BIC). For all features, this analysis produces 4 clusters and we observe the formation of at least one cluster consisting of spines which are difficult to be assigned to a known class. This observation supports the argument of intermediate shape types.Comment: Accepted for BioImageComputing workshop at ECCV 201

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

The three-dimensional arrangement of the human genome comprises a complex network of structural and regulatory chromatin loops important for coordinating changes in transcription during human development. To better understand the mechanisms underlying context-specific 3D chromatin structure and transcription during cellular differentiation, we generated comprehensive in situ Hi-C maps of DNA loops during human monocyte-to-macrophage differentiation. We demonstrate that dynamic looping events are regulatory rather than structural in nature and uncover widespread coordination of dynamic enhancer activity at preformed and acquired DNA loops. Enhancer-bound loop formation and enhancer-activation of preformed loops represent two distinct modes of regulation that together form multi-loop activation hubs at key macrophage genes. Activation hubs connect 3.4 enhancers per promoter and exhibit a strong enrichment for Activator Protein 1 (AP-1) binding events, suggesting multi-loop activation hubs driven by cell-type specific transcription factors may represent an important class of regulatory chromatin structures for the spatiotemporal control of transcription

Prospects for measuring the gravitational free-fall of antihydrogen with emulsion detectors

The main goal of the AEgIS experiment at CERN is to test the weak equivalence principle for antimatter. AEgIS will measure the free-fall of an antihydrogen beam traversing a moir\'e deflectometer. The goal is to determine the gravitational acceleration g for antihydrogen with an initial relative accuracy of 1% by using an emulsion detector combined with a silicon micro-strip detector to measure the time of flight. Nuclear emulsions can measure the annihilation vertex of antihydrogen atoms with a precision of about 1 - 2 microns r.m.s. We present here results for emulsion detectors operated in vacuum using low energy antiprotons from the CERN antiproton decelerator. We compare with Monte Carlo simulations, and discuss the impact on the AEgIS project.Comment: 20 pages, 16 figures, 3 table

(Quantum) Space-Time as a Statistical Geometry of Fuzzy Lumps and the Connection with Random Metric Spaces

We develop a kind of pregeometry consisting of a web of overlapping fuzzy lumps which interact with each other. The individual lumps are understood as certain closely entangled subgraphs (cliques) in a dynamically evolving network which, in a certain approximation, can be visualized as a time-dependent random graph. This strand of ideas is merged with another one, deriving from ideas, developed some time ago by Menger et al, that is, the concept of probabilistic- or random metric spaces, representing a natural extension of the metrical continuum into a more microscopic regime. It is our general goal to find a better adapted geometric environment for the description of microphysics. In this sense one may it also view as a dynamical randomisation of the causal-set framework developed by e.g. Sorkin et al. In doing this we incorporate, as a perhaps new aspect, various concepts from fuzzy set theory.Comment: 25 pages, Latex, no figures, some references added, some minor changes added relating to previous wor

Enumeration of CD4+ T-Cells Using a Portable Microchip Count Platform in Tanzanian HIV-Infected Patients

Background CD4+ T-lymphocyte count (CD4 count) is a standard method used to monitor HIV-infected patients during anti-retroviral therapy (ART). The World Health Organization (WHO) has pointed out or recommended that a handheld, point-of-care, reliable, and affordable CD4 count platform is urgently needed in resource-scarce settings. Methods HIV-infected patient blood samples were tested at the point-of-care using a portable and label-free microchip CD4 count platform that we have developed. A total of 130 HIV-infected patient samples were collected that included 16 de-identified left over blood samples from Brigham and Women's Hospital (BWH), and 114 left over samples from Muhimbili University of Health and Allied Sciences (MUHAS) enrolled in the HIV and AIDS care and treatment centers in the City of Dar es Salaam, Tanzania. The two data groups from BWH and MUHAS were analyzed and compared to the commonly accepted CD4 count reference method (FACSCalibur system). Results The portable, battery operated and microscope-free microchip platform developed in our laboratory (BWH) showed significant correlation in CD4 counts compared with FACSCalibur system both at BWH (r = 0.94, p<0.01) and MUHAS (r = 0.49, p<0.01), which was supported by the Bland-Altman methods comparison analysis. The device rapidly produced CD4 count within 10 minutes using an in-house developed automated cell counting program. Conclusions We obtained CD4 counts of HIV-infected patients using a portable platform which is an inexpensive (<$1 material cost) and disposable microchip that uses whole blood sample (<10 µl) without any pre-processing. The system operates without the need for antibody-based fluorescent labeling and expensive fluorescent illumination and microscope setup. This portable CD4 count platform displays agreement with the FACSCalibur results and has the potential to expand access to HIV and AIDS monitoring using fingerprick volume of whole blood and helping people who suffer from HIV and AIDS in resource-limited settings.Wallace H. Coulter Foundation (Young Investigation Award in Bioengineering Award)National Institutes of Health (U.S.) (NIH R01AI081534)National Institutes of Health (U.S.) (NIH R21AI087107)National Institutes of Health (U.S.) (NIH grant RR016482)National Institutes of Health (U.S.) (grant AI060354)National Institutes of Health (U.S.) (NIH Fogarty Fellowship

Extensive Variation in Chromatin States Across Humans

The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans