A multistage mathematical approach to automated clustering of high-dimensional noisy data

A critical problem faced in many scientific fields is the adequate separation of data derived from individual sources. Often, such datasets require analysis of multiple features in a highly multidimensional space, with overlap of features and sources. The datasets generated by simultaneous recording from hundreds of neurons emitting phasic action potentials have produced the challenge of separating the recorded signals into independent data subsets (clusters) corresponding to individual signal-generating neurons. Mathematical methods have been developed over the past three decades to achieve such spike clustering, but a complete solution with fully automated cluster identification has not been achieved. We propose here a fully automated mathematical approach that identifies clusters in multidimensional space through recursion, which combats the multidimensionality of the data. Recursion is paired with an approach to dimensional evaluation, in which each dimension of a dataset is examined for its informational importance for clustering. The dimensions offering greater informational importance are given added weight during recursive clustering. To combat strong background activity, our algorithm takes an iterative approach of data filtering according to a signal-to-noise ratio metric. The algorithm finds cluster cores, which are thereafter expanded to include complete clusters. This mathematical approach can be extended from its prototype context of spike sorting to other datasets that suffer from high dimensionality and background activity.National Institutes of Health (U.S.) (Grant R01 MH060379)United States. Defense Advanced Research Projects AgencyUnited States. Army Research Office (Grant W911NF-10-1-0059)Cure Huntington’s Disease Initiative, Inc. (Grant A-5552

Duality and ontology

A ‘duality’ is a formal mapping between the spaces of solutions of two empirically equivalent theories. In recent times, dualities have been found to be pervasive in string theory and quantum field theory. Naïvely interpreted, duality-related theories appear to make very different ontological claims about the world—differing in e.g. space-time structure, fundamental ontology, and mereological structure. In light of this, duality-related theories raise questions familiar from discussions of underdetermination in the philosophy of science: in the presence of dual theories, what is one to say about the ontology of the world? In this paper, we undertake a comprehensive and non-technical survey of the landscape of possible ontological interpretations of duality-related theories. We provide a significantly enriched and clarified taxonomy of options—several of which are novel to the literature

Relativistic Diskoseismology. I. Analytical Results for 'Gravity Modes'

We generalize previous calculations to a fully relativistic treatment of adiabatic oscillations which are trapped in the inner regions of accretion disks by non-Newtonian gravitational effects of a black hole. We employ the Kerr geometry within the scalar potential formalism of Ipser and Lindblom, neglecting the gravitational field of the disk. This approach treats perturbations of arbitrary stationary, axisymmetric, perfect fluid models. It is applied here to thin accretion disks. Approximate analytic eigenfunctions and eigenfrequencies are obtained for the most robust and observable class of modes, which corresponds roughly to the gravity (internal) oscillations of stars. The dependence of the oscillation frequencies on the mass and angular momentum of the black hole is exhibited. These trapped modes do not exist in Newtonian gravity, and thus provide a signature and probe of the strong-field structure of black holes. Our predictions are relevant to observations which could detect modulation of the X-ray luminosity from stellar mass black holes in our galaxy and the UV and optical luminosity from supermassive black holes in active galactic nuclei.Comment: 31 pages, 6 figures, uses style file aaspp4.sty, prepared with the AAS LATEX macros v4.0, significant revision of earlier submission to include modes with axial index m>

Immunologic markers of progression to acquired immunodeficiency syndrome are time-dependent and illness-specific

Krämer A, Biggar RJ, Hampl H, et al. Immunologic markers of progression to acquired immunodeficiency syndrome are time-dependent and illness-specific. American Journal of Epidemiology. 1992;136(1):71-80.Since prevalent cohorts may be biased by the duration of human immunodeficiency virus (HIV) infection (onset bias), it is useful to assess the potential predictive value of markers in incident cohorts of HIV-positive subjects for whom the date of seroconversion is known or can reliably be estimated. Of 131 homosexual men with HIV-1 seroconversion from New York City and Washington, DC, who were evaluated annually beginning in 1982, 60 developed acquired immunodeficiency syndrome (AIDS) by the end of 1989. The prognostic significance of immunologic markers (proportion of CD4+ T-lymphocytes, neopterin, ß2-microglobulin, serum interferon, and anti-p24 antibody) and of a virologic marker (HIV p24 antigen) was determined using measurements made at defined time intervals after the known or estimated date of HIV seroconversion. When measurements made 3 years after seroconversion were used, all markers except anti-p24 antibody were found to be significant estimators of AIDS risk in univariate analyses. In multivariate Cox regression modeling, the maximum information was obtained by including neopterin, interferon, and the CD4+ T-lymphocyte proportion. The predictive value of markers after HIV seroconversion could change considerably from one interval to another. Elevated levels of ß2-microglobulin and neopterin significantly predicted the development of Kaposi‘s sarcoma. These two markers were highly correlated (r=0. 74). The authors conclude that immunologic markers can be important for an HIV staging system for estimating prognosis and facilitating early therapeutic intervention in HIV-positive patients

Molecular Profiling of Neurons Based on Connectivity

The complexity and cellular heterogeneity of neural circuitry presents a major challenge to understanding the role of discrete neural populations in controlling behavior. While neuroanatomical methods enable high-resolution mapping of neural circuitry, these approaches do not allow systematic molecular profiling of neurons based on their connectivity. Here, we report the development of an approach for molecularly profiling projective neurons. We show that ribosomes can be tagged with a camelid nanobody raised against GFP and that this system can be engineered to selectively capture translating mRNAs from neurons retrogradely labeled with GFP. Using this system, we profiled neurons projecting to the nucleus accumbens. We then used an AAV to selectively profile midbrain dopamine neurons projecting to the nucleus accumbens. By comparing the captured mRNAs from each experiment, we identified a number of markers specific to VTA dopaminergic projection neurons. The current method provides a means for profiling neurons based on their projections

Effects of Non-Thermal Plasma on Mammalian Cells

Thermal plasmas and lasers have been widely used in medicine to cut, ablate and cauterize tissues through heating; in contrast, non-thermal plasma produces no heat, so its effects can be selective. In order to exploit the potential for clinical applications, including wound healing, sterilization, blood coagulation, and cancer treatment, a mechanistic understanding of the interaction of non-thermal plasma with living tissues is required. Using mammalian cells in culture, it is shown here that non-thermal plasma created by dielectric barrier discharge (DBD) has dose-dependent effects that range from increasing cell proliferation to inducing apoptosis. It is also shown that these effects are primarily due to formation of intracellular reactive oxygen species (ROS). We have utilized γ-H2AX to detect DNA damage induced by non-thermal plasma and found that it is initiated by production of active neutral species that most likely induce formation of organic peroxides in cell medium. Phosphorylation of H2AX following non-thermal plasma treatment is ATR dependent and ATM independent, suggesting that plasma treatment may lead to replication arrest or formation of single-stranded DNA breaks; however, plasma does not lead to formation of bulky adducts/thymine dimers

FORGE: An eLearning Framework for Remote Laboratory Experimentation on FIRE Testbed Infrastructure

The Forging Online Education through FIRE (FORGE) initiative provides educators and learners in higher education with access to world-class FIRE testbed infrastructure. FORGE supports experimentally driven research in an eLearning environment by complementing traditional classroom and online courses with interactive remote laboratory experiments. The project has achieved its objectives by defining and implementing a framework called FORGEBox. This framework offers the methodology, environment, tools and resources to support the creation of HTML-based online educational material capable accessing virtualized and physical FIRE testbed infrastruc- ture easily. FORGEBox also captures valuable quantitative and qualitative learning analytic information using questionnaires and Learning Analytics that can help optimise and support student learning. To date, FORGE has produced courses covering a wide range of networking and communication domains. These are freely available from FORGEBox.eu and have resulted in over 24,000 experiments undertaken by more than 1,800 students across 10 countries worldwide. This work has shown that the use of remote high- performance testbed facilities for hands-on remote experimentation can have a valuable impact on the learning experience for both educators and learners. Additionally, certain challenges in developing FIRE-based courseware have been identified, which has led to a set of recommendations in order to support the use of FIRE facilities for teaching and learning purposes

Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus

© 2021, The Author(s). Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments

The Basics of American Government

Newly revised, The Basics of American Government offers a comprehensive overview of the American political system for students taking introductory courses in American national government and combines the best aspects of both a traditional textbook and a reader. The Basics of American Government is a collaborative effort among eight current and one former faculty members in the Department of Political Science & Criminal Justice at the University of North Georgia. Most of its chapters offer a piece of original scholarship as a case study bolstering the material in the chapter. Additionally, most chapters present a civic engagement-type exercise and discussion questions that are challenging and engaging, and help foster student participation in the political system. The purpose of this book is to offer a no-frills, low-cost, yet comprehensive overview of the American political system for students taking introductory courses in American national government. A print version of this book is available for $27.99. Contact the University of North Georgia Press for details and ordering information. [email protected] | 706-864-1556https://digitalcommons.northgeorgia.edu/books/1004/thumbnail.jp