Visualization of Big Spatial Data using Coresets for Kernel Density Estimates

The size of large, geo-located datasets has reached scales where visualization of all data points is inefficient. Random sampling is a method to reduce the size of a dataset, yet it can introduce unwanted errors. We describe a method for subsampling of spatial data suitable for creating kernel density estimates from very large data and demonstrate that it results in less error than random sampling. We also introduce a method to ensure that thresholding of low values based on sampled data does not omit any regions above the desired threshold when working with sampled data. We demonstrate the effectiveness of our approach using both, artificial and real-world large geospatial datasets

Why is Open Source Software Viable? A Study of Intrinsic Motivation, Personal Needs and Future Returns

Traditional business models for software development are currently being challenged by the phenomenon of open source software where communities of programmers leverage the Internet to develop free software without receiving any direct compensation. To understand the success and the prospects of open source software it is necessary to examine the motivation of the participants in open source projects. This paper presents a theoretical model to study the three main factors leading to participation in open source projects: intrinsic motivation, personal need and expectation of future returns. Implications of the model are derived and their significance discussed. We conclude that open source software will be an enduring alternative to traditional software development and that it is possible to combine aspects of both development approaches

The C-terminus of p63 contains multiple regulatory elements with different functions

The transcription factor p63 is expressed as at least six different isoforms, of which two have been assigned critical biological roles within ectodermal development and skin stem cell biology on the one hand and supervision of the genetic stability of oocytes on the other hand. These two isoforms contain a C-terminal inhibitory domain that negatively regulates their transcriptional activity. This inhibitory domain contains two individual components: one that uses an internal binding mechanism to interact with and mask the transactivation domain and one that is based on sumoylation. We have carried out an extensive alanine scanning study to identify critical regions within the inhibitory domain. These experiments show that a stretch of ~13 amino acids is crucial for the binding function. Further, investigation of transcriptional activity and the intracellular level of mutants that cannot be sumoylated suggests that sumoylation reduces the concentration of p63. We therefore propose that the inhibitory function of the C-terminal domain is in part due to direct inhibition of the transcriptional activity of the protein and in part due to indirect inhibition by controlling the concentration of p63. Keywords: p63, transcriptional regulation, auto-inhibition, sumoylatio

ALADIN-α\alpha -- An open-source MATLAB toolbox for distributed non-convex optimization

This paper introduces an open-source software for distributed and decentralized non-convex optimization named ALADIN-$\alpha$. ALADIN-$\alpha$ is a MATLAB implementation of the Augmented Lagrangian Alternating Direction Inexact Newton (ALADIN) algorithm, which is tailored towards rapid prototyping for non-convex distributed optimization. An improved version of the recently proposed bi-level variant of ALADIN is included enabling decentralized non-convex optimization. A collection of application examples from different applications fields including chemical engineering, robotics, and power systems underpins the application potential of ALADIN-$\alpha$

ALADIN-α—An open-source MATLAB toolbox for distributed non-convex optimization

This article introduces an open-source software for distributed and decentralized non-convex optimization named ALADIN-α. ALADIN-α is a MATLAB implementation of tailored variants of the Augmented Lagrangian Alternating Direction Inexact Newton (ALADIN) algorithm. It is user interface is convenient for rapid prototyping of non-convex distributed optimization algorithms. An improved version of the recently proposed bi-level variant of ALADIN is included enabling decentralized non-convex optimization with reduced information exchange. A collection of examples from different applications fields including chemical engineering, robotics, and power systems underpins the potential of ALADIN-α

JNET: Learning User Representations via Joint Network Embedding and Topic Embedding

User representation learning is vital to capture diverse user preferences, while it is also challenging as user intents are latent and scattered among complex and different modalities of user-generated data, thus, not directly measurable. Inspired by the concept of user schema in social psychology, we take a new perspective to perform user representation learning by constructing a shared latent space to capture the dependency among different modalities of user-generated data. Both users and topics are embedded to the same space to encode users' social connections and text content, to facilitate joint modeling of different modalities, via a probabilistic generative framework. We evaluated the proposed solution on large collections of Yelp reviews and StackOverflow discussion posts, with their associated network structures. The proposed model outperformed several state-of-the-art topic modeling based user models with better predictive power in unseen documents, and state-of-the-art network embedding based user models with improved link prediction quality in unseen nodes. The learnt user representations are also proved to be useful in content recommendation, e.g., expert finding in StackOverflow

Monte Carlo implementation of supercoiled double-stranded DNA

Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending constrained by hydrogen bonds formed between DNA complementary nucleotide bases. Three evident regimes are found in extension versus torsion and/or force versus extension plots: a low-force regime in which over- and underwound molecules behave similarly under stretching; an intermediate-force regime in which chirality appears for negatively and positively supercoiled DNA and extension of underwound molecule is insensitive to the supercoiling degree of the polymer; and a large-force regime in which plectonemic DNA is fully converted to extended DNA and supercoiled DNA behaves quite like a torsionless molecule. The striking coincidence between theoretic calculations and recent experimental measurement of torsionally stretched DNA [Strick et al., Science {\bf 271}, 1835 (1996), Biophys. J. {\bf 74}, 2016 (1998)] strongly suggests that the interplay between base-stacking interaction and permanent hydrogen-bond constraint takes an important role in understanding the novel properties of elasticity of supercoiled DNA polymer.Comment: 21 pages, 6 PS figures. To appear at Biophys.

Acute and Chronic Dosing of a High-Affinity Rat/Mouse Chimeric Transferrin Receptor Antibody in Mice

Non-invasive brain delivery of neurotherapeutics is challenging due to the blood-brain barrier. The revived interest in transferrin receptor antibodies (TfRMAbs) as brain drug-delivery vectors has revealed the effect of dosing regimen, valency, and affinity on brain uptake, TfR expression, and Fc-effector function side effects. These studies have primarily used monovalent TfRMAbs with a human constant region following acute intravenous dosing in mice. The effects of a high-affinity bivalent TfRMAb with a murine constant region, without a fusion partner, following extravascular dosing in mice are, however, not well characterized. Here we elucidate the plasma pharmacokinetics and safety of a high-affinity bivalent TfRMAb with a murine constant region following acute and chronic subcutaneous dosing in adult C57BL/6J male mice. Mice received a single (acute dosing) 3 mg/kg dose, or were treated for four weeks (chronic dosing). TfRMAb and control IgG1 significantly altered reticulocyte counts following acute and chronic dosing, while other hematologic parameters showed minimal change. Chronic TfRMAb dosing did not alter plasma- and brain-iron measurements, nor brain TfR levels, however, it significantly increased splenic-TfR and -iron. Plasma concentrations of TfRMAb were significantly lower in mice chronically treated with IgG1 or TfRMAb. Overall, no injection related reactions were observed in mic