Locally Estimating Core Numbers

Graphs are a powerful way to model interactions and relationships in data from a wide variety of application domains. In this setting, entities represented by vertices at the "center" of the graph are often more important than those associated with vertices on the "fringes". For example, central nodes tend to be more critical in the spread of information or disease and play an important role in clustering/community formation. Identifying such "core" vertices has recently received additional attention in the context of {\em network experiments}, which analyze the response when a random subset of vertices are exposed to a treatment (e.g. inoculation, free product samples, etc). Specifically, the likelihood of having many central vertices in any exposure subset can have a significant impact on the experiment. We focus on using $k$-cores and core numbers to measure the extent to which a vertex is central in a graph. Existing algorithms for computing the core number of a vertex require the entire graph as input, an unrealistic scenario in many real world applications. Moreover, in the context of network experiments, the subgraph induced by the treated vertices is only known in a probabilistic sense. We introduce a new method for estimating the core number based only on the properties of the graph within a region of radius $\delta$ around the vertex, and prove an asymptotic error bound of our estimator on random graphs. Further, we empirically validate the accuracy of our estimator for small values of $\delta$ on a representative corpus of real data sets. Finally, we evaluate the impact of improved local estimation on an open problem in network experimentation posed by Ugander et al.Comment: Main paper body is identical to previous version (ICDM version). Appendix with additional data sets and enlarged figures has been added to the en

Competition and Conflict: Ludic Structures and Strategies in Late Medieval Iberian Romance

The current dissertation analyzes the ludic foundations of the conflictive moments found within Juan Rodríguez del Padrón's Siervo libre de amor, Juan de Flores' Grimalte y Gradissa, Diego de San Pedro's Cárcel de amor, and Garci Rodríguez de Montalvo's Amadís de Gaula. Building on the notion that there is a special reciprocal bond between the concepts of conflict and play, I assert that this binary phenomenon forms the foundation of the Sentimental and Chivalric sub-genres of late medieval Iberia, thus requiring a reclassification of the works under a ludic fiction category. My analysis draws from multiple twentieth and twenty-first century theories on conflict and play in order to analyze plot creation, character motivation and interaction, as well as authorial messaging. My approach attempts to situate the works not only in recent debates about the boundaries and limitations of both sub-genres, but also within the socio-cultural framework of late fifteenth-century Iberia

A practical fpt algorithm for Flow Decomposition and transcript assembly

The Flow Decomposition problem, which asks for the smallest set of weighted paths that "covers" a flow on a DAG, has recently been used as an important computational step in transcript assembly. We prove the problem is in FPT when parameterized by the number of paths by giving a practical linear fpt algorithm. Further, we implement and engineer a Flow Decomposition solver based on this algorithm, and evaluate its performance on RNA-sequence data. Crucially, our solver finds exact solutions while achieving runtimes competitive with a state-of-the-art heuristic. Finally, we contextualize our design choices with two hardness results related to preprocessing and weight recovery. Specifically, $k$-Flow Decomposition does not admit polynomial kernels under standard complexity assumptions, and the related problem of assigning (known) weights to a given set of paths is NP-hard.Comment: Introduces software package Toboggan: Version 1.0. http://dx.doi.org/10.5281/zenodo.82163

Role for polo-like kinase 4 in mediation of cytokinesis.

The mitotic protein polo-like kinase 4 (PLK4) plays a critical role in centrosome duplication for cell division. By using immunofluorescence, we confirm that PLK4 is localized to centrosomes. In addition, we find that phospho-PLK4 (pPLK4) is cleaved and distributed to kinetochores (metaphase and anaphase), spindle midzone/cleavage furrow (anaphase and telophase), and midbody (cytokinesis) during cell division in immortalized epithelial cells as well as breast, ovarian, and colorectal cancer cells. The distribution of pPLK4 midzone/cleavage furrow and midbody positions pPLK4 to play a functional role in cytokinesis. Indeed, we found that inhibition of PLK4 kinase activity with a small-molecule inhibitor, CFI-400945, prevents translocation to the spindle midzone/cleavage furrow and prevents cellular abscission, leading to the generation of cells with polyploidy, increased numbers of duplicated centrosomes, and vulnerability to anaphase or mitotic catastrophe. The regulatory role of PLK4 in cytokinesis makes it a potential target for therapeutic intervention in appropriately selected cancers

The Radio Light Curve of the Gamma-Ray Nova in V407 Cyg: Thermal Emission from the Ionized Symbiotic Envelope, Devoured from Within by the Nova Blast

We present multi-frequency radio observations of the 2010 nova event in the symbiotic binary V407 Cygni, obtained with the Karl G. Jansky Very Large Array and spanning 1-45 GHz and 17-770 days following discovery. This nova---the first ever detected in gamma rays---shows a radio light curve dominated by the wind of the Mira giant companion, rather than the nova ejecta themselves. The radio luminosity grew as the wind became increasingly ionized by the nova outburst, and faded as the wind was violently heated from within by the nova shock. This study marks the first time that this physical mechanism has been shown to dominate the radio light curve of an astrophysical transient. We do not observe a thermal signature from the nova ejecta or synchrotron emission from the shock, due to the fact that these components were hidden behind the absorbing screen of the Mira wind. We estimate a mass loss rate for the Mira wind of Mdot_w ~ 10^-6 M_sun/yr. We also present the only radio detection of V407 Cyg before the 2010 nova, gleaned from unpublished 1993 archival VLA data, which shows that the radio luminosity of the Mira wind varies by a factor of >~20 even in quiescence. Although V407 Cyg likely hosts a massive accreting white dwarf, making it a candidate progenitor system for a Type Ia supernova, the dense and radially continuous circumbinary material surrounding V407 Cyg is inconsistent with observational constraints on the environments of most Type Ia supernovae.Comment: Resubmitted to ApJ after incorporating referee's comment

Radio studies of novae: a current status report and highlights of new results

Novae, which are the sudden visual brightening triggered by runaway thermonuclear burning on the surface of an accreting white dwarf, are fairly common and bright events. Despite their astronomical significance as nearby laboratories for the study of nuclear burning and accretion phenomena, many aspects of these common stellar explosions are observationally not well-constrained and remain poorly understood. Radio observations, modeling and interpretation can potentially play a crucial role in addressing some of these puzzling issues. In this review on radio studies of novae, we focus on the possibility of testing and improving the nova models with radio observations, and present a current status report on the progress in both the observational front and theoretical developments. We specifically address the issues of accurate estimation of ejecta mass, multi-phase and complex ejection phenomena, and the effect of a dense environment around novae. With highlights of new observational results, we illustrate how radio observations can shed light on some of these long-standing puzzles.Comment: 19 pages, 4 figures. Review article published in the Bulletin of the Astronomical Society of India (BASI) special issue on nova

Efficient depletion of host DNA contamination in malaria clinical sequencing.

The cost of whole-genome sequencing (WGS) is decreasing rapidly as next-generation sequencing technology continues to advance, and the prospect of making WGS available for public health applications is becoming a reality. So far, a number of studies have demonstrated the use of WGS as an epidemiological tool for typing and controlling outbreaks of microbial pathogens. Success of these applications is hugely dependent on efficient generation of clean genetic material that is free from host DNA contamination for rapid preparation of sequencing libraries. The presence of large amounts of host DNA severely affects the efficiency of characterizing pathogens using WGS and is therefore a serious impediment to clinical and epidemiological sequencing for health care and public health applications. We have developed a simple enzymatic treatment method that takes advantage of the methylation of human DNA to selectively deplete host contamination from clinical samples prior to sequencing. Using malaria clinical samples with over 80% human host DNA contamination, we show that the enzymatic treatment enriches Plasmodium falciparum DNA up to ∼9-fold and generates high-quality, nonbiased sequence reads covering >98% of 86,158 catalogued typeable single-nucleotide polymorphism loci

Advances in mesenchymal stem cell-mediated gene therapy for cancer

Mesenchymal stem cells have a natural tropism for tumours and their metastases, and are also considered immunoprivileged. This remarkable combination of properties has formed the basis for many studies investigating their potential as tumour-specific delivery vehicles for suicide genes, oncolytic viruses and secreted therapeutic proteins. The aim of the present review is to discuss the range of approaches that have been used to exploit the tumour-homing capacity of mesenchymal stem cells for gene delivery, and to highlight advances required to realize the full potential of this promising approach