julilili42/papers huggingface dataset:
Integrating information from two pictorial animations: Complexity and cognitive prerequisites influence performance
2010-12-01

Abstract Dividing visual attention between spatially distinct sources of information could either be beneficial (if there is too much information for a single visualization) or detrimental (if interrelated information has to be mentally re‐integrated) for learning. We present a new display technology allowing for the presentation of two distinct animations by avoiding split foci of visual attention: learners are able to switch between animations by moving their head. We examined how 84 naïve learners integrated information in three presentation modes: the ‘vexing‐image’ mode displaying two animations, participants being able to switch between them without shifting the visual focus, a classical ‘split‐screen’ and an ‘overlaid’ condition. Results showed that reduced complexity led to higher performance. Further, we showed that participants with high mental rotation abilities were best in the ‘split‐screen’ mode, whereas participants with low mental rotation abilities benefited most from the ‘vexing‐image’. Theoretical and instructional consequences of these findings are discussed. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Great Apes and New Wars
2010-12-01

In this article, we ask how far armed conflicts in the Virunga Region directly and indirectly contribute to the extinction of the Great Apes and the critically endangered Mountain Gorilla in specific. We introduce the conflict situation in the Democratic Republic of the Congo and the concept of 'New Wars' in order to identify mechanisms linking armed conflict with the situation of these animals. Contrary to prior research, our empirical analysis draws a more complete and up-to-date picture. Latest available data on the animals' distribution and Red List Status are combined with new (geographically disaggregated) conflict data that include low-level as well non-state fighting. We conclude with some policy implications.
Design of the dynamic stability properties of the collective behavior of articulated bipeds
2010-12-01

The control of the collective behavior of multiple interacting agents is a challenging problem in robotics and autonomous systems design. Such behaviors can be characterized by the dynamic interaction between multiple locomoting bipeds with highly nonlinear articulation dynamics. The analysis and design of the stability properties of such complex multi-component systems is a largely unsolved problem. We discuss a first approach to this problem exploiting concepts from Contraction Theory, a recent framework for the analysis of the stability of complex nonlinear dynamical systems. We demonstrate the application of this framework to groups of humanoid agents interacting collectively in different ways, requiring different types of control rules for their propagation in space and their articulation dynamics. We illustrate the framework based on a learning-based realtime-capable architecture for simulation of the kinematics of propagating bipeds, suitable for the reproduction of natural locomotion trajectories and walking styles. Exploiting central theorems from Contraction Theory and nonlinear control, we derive conditions guaranteeing the global exponential stability of the formation of the coordinated multiagent behavior. In addition, we demonstrate that the same approach permits to derive bounds that guarantee minimum convergence speeds for the formation of ordered states for collective behaviors of multiple humanoid agents.
A CG-based Poisson solver on a GPU-cluster
2010-12-01

We describe an experimental system for parallel distributed processing of numerical algorithms. Computations are performed on GPUs, and communication is facilitated using FPGA-adapters and self-developed interconnects. As case study we have implemented a conjugate gradient solver for the Poisson problem in three dimensions. The work focuses on machine architecture and distributed processing with special emphasis on alleviating communication bottlenecks. Also we present the implementation of a matrix-free preconditioner for the Poisson problem which does not add communication overhead.
Textgattungen und Musikgattungen beim Mönch von Salzburg und bei Oswald von Wolkenstein
2010-12-01

The Mönch von Salzburg and Oswald von Wolkenstein were deeply rooted in German traditions of song poetry, the Mönch also in the Latin songs of the church, but both were also open for available elements of the more advanced French and Italian musical culture. The following study attempts a survey of typical relations between musical forms, metrical patterns and literary semantics in the monodic and polyphonic songs of both poets.
A Syntax-first Approach to High-quality Morphological Analysis and Lemma Disambiguation for the TüBa-D/Z Treebank
2010-12-01

Proceedings of the Ninth International Workshop&#13;\\non Treebanks and Linguistic Theories.&#13;\\nEditors: Markus Dickinson, Kaili Müürisep and Marco Passarotti.&#13;\\nNEALT Proceedings Series, Vol. 9 (2010), 233-244.&#13;\\n© 2010 The editors and contributors.&#13;\\nPublished by&#13;\\nNorthern European Association for Language&#13;\\nTechnology (NEALT)&#13;\\nhttp://omilia.uio.no/nealt .&#13;\\nElectronically published at&#13;\\nTartu University Library (Estonia)&#13;\\nhttp://hdl.handle.net/10062/15891 .
Integrative Systems Biology Visualization with MAYDAY
2010-12-01

Summary Visualization is pivotal for gaining insight in systems biology data. As the size and complexity of datasets and supplemental information increases, an efficient, integrated framework for general and specialized views is necessary. MAYDAY is an application for analysis and visualization of general ‘omics’ data. It follows a trifold approach for data visualization, consisting of flexible data preprocessing, highly customizable data perspective plots for general purpose visualization and systems based plots. Here, we introduce two new systems biology visualization tools for MAYDAY. Efficiently implemented genomic viewers allow the display of variables associated with genomic locations. Multiple variables can be viewed using our new track-based ChromeTracks tool. A functional perspective is provided by visualizing metabolic pathways either in KEGG or BioPax format. Multiple options of displaying pathway components are available, including Systems Biology Graphical Notation (SBGN) glyphs. Furthermore, pathways can be viewed together with gene expression data either as heatmaps or profiles. We apply our tools to two ‘omics’ datasets of Pseudomonas aeruginosa. The general analysis and visualization tools of MAYDAY as well as our ChromeTracks viewer are applied to a transcriptome dataset. We furthermore integrate this dataset with a metabolome dataset and compare the activity of amino acid degradation pathways between these two datasets, by visually enhancing the pathway diagrams produced by MAYDAY.
The effect of decompressive craniectomy on CSF pulsatility in experimental communicating hydrocephalus
2010-12-01

Background It has been well established that intracranial pulsatility, whether measured as parenchymal/intraventricular pressure or as cerebrospinal fluid (CSF) flow in the cerebral aqueduct, is often markedly elevated in patients with hydrocephalus. Attempts have been made to use this measure to predict outcome from shunt surgery, but its specificity is still questionable. The question of whether or not intracranial pulsatility plays a causative role in hydrocephalus or is merely an epiphenomenon related to intracranial compliance is similarly an unanswered question. As a first step toward answering this question, we hypothesized that aqueductal pulsatility would be reduced after increasing compliance following decompressive craniectomy. Materials and methods Communicating hydrocephalus was induced by injection of kaolin into the basal cisterns in five (n = 5) adult Sprague-Dawley rats; controls received similar saline injections. Flow pulsatility was studied at two weeks post-injection by cine phase contrast MRI prior to and immediately following bilateral craniectomy. Aqueductal stroke volume before and after craniectomy were compared. To minimize effects of extended anesthesia, the craniectomy was started prior to the first imaging scan without breaking through the bone completely. Animals were then moved to the scanner, imaged for the precraniectomy pulsatility measurements, and returned to the bench to complete the craniectomy. A bone flap (4 x 10 mm) was taken from each side over the parietal lobe. The dura mater was left intact, although small tears in the dura were noticed in some cases. A second scan was then obtained to measure post-craniectomy pulsatility. To ensure similar physiological state for the two scans, animals were intubated throughout and ventilated on O2/isoflurane. Following the second scan, the animals were euthanized.
Transforming Growth Factor-β1 and Laminin-111 Cooperate in the Regulation of Expression of Interleukin-6 and Interleukin-8 in Synovial Fibroblasts.
2010-12-01

In a recent study we showed that binding of synovial fibroblasts (SF) to laminin-111 (LM-111) in the presence of TGF-β1 induced a significant production of IL-16. Here we go on to investigate the regulation of IL-6 and IL-8 in SF by LM-111 and TGF-β1. Changes in steady state mRNA levels encoding the interleukins were investigated by quantitative RT-PCR. We screened for interleukin production by a multiplexed immunoarray and quantified it with ELISA. The biological activity of IL-6 and IL-8 was corroborated by B-lymphocyte proliferation and cell migration assays, respectively. Growth of SF on LM-111 in presence of TGF-β1 induced significant mRNA responses for IL-6 (mean 3.72-fold increase, ± 1.6, p<0.003) and IL-8 (mean 4.5-fold increase, ± 1.6, p<0.001). In the supernatants significantly elevated concentrations of IL-6 (mean 7.9 ± 5 ng/mL, p<0.005) and IL-8 (mean 73.0 ng/mL ± 51, p<0.05) were detected, and they were shown to be biologically active. Binding to LM-111 in the presence of TGF-β1 activates SF for expression of IL-6 and IL-8 and thus may contribute to synovial inflammation and to infiltration of leukocytes.
Phylogenetic Networks
2010-12-02

The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.
Introduction to phylogenetic networks
2010-12-02

In the previous chapter we give a brief introduction to phylogenetic trees. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for datasets whose evolution involve significant amounts of reticulate events caused by hybridization, horizontal gene transfer, recombination, gene conversion or gene duplication and loss [56, 61, 89, 201, 219, 231]. Moreover, even for a set of taxa that have evolved according to a tree-based model of evolution, phylogenetic networks can be usefully employed to explicitly represent conflicts in a dataset that may, for example, be due to mechanisms such as incomplete lineage sorting or to inadequacies of an assumed evolutionary model [125].
Evaluation of Fasting State-/Oral Glucose Tolerance Test-Derived Measures of Insulin Release for the Detection of Genetically Impaired β-Cell Function
2010-12-02

With AUC(Insulin(0-30))/AUC(Glucose(0-30),) CIR, AUC(C-Peptide(0-30))/AUC(Glucose(0-30)), AUC(C-Peptide(0-120))/AUC(Glucose(0-120)), IGI(2), IGI(1), and insulin 30 min, dynamic measures of insulin secretion based on early insulin and C-peptide responses to oral glucose represent measures which are more appropriate to assess genetically determined β-cell dysfunction than fasting measures, i.e., HOMA-B. Genes predominantly influencing the incretin axis may possibly be best detected by AUC(C-Peptide(0-120))/AUC(Glucose(0-120)).
Algorithms and applications
2010-12-02

In this third part of the book we present a wide range of algorithms that have been developed for computing phylogenetic networks from biological data. For many of the methods, we briefly describe an application and provide references to papers that contain more details. The material is organized by type of input, which is either splits (Chapter 7), clusters (Chapter 8), sequences (Chapter 9), distances (Chapter 10), trees (Chapter 11), triples or quartets (Chapter 12). Additionally, we address the problem of drawing phylogenetic networks (Chapter 13) and give an overview of some of the existing software for computing them (Chapter 14).
Evolution of convex lens-shaped networks under the curve shortening flow
2010-12-02

We consider convex symmetric lens-shaped networks in <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="double-struck upper R squared"> <mml:semantics> <mml:msup> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mi mathvariant="double-struck">R</mml:mi> </mml:mrow> <mml:mn>2</mml:mn> </mml:msup> <mml:annotation encoding="application/x-tex">\\mathbb {R}^2</mml:annotation> </mml:semantics> </mml:math> </inline-formula> that evolve under the curve shortening flow. We show that the enclosed convex domain shrinks to a point in finite time. Furthermore, after appropriate rescaling the evolving networks converge to a self-similarly shrinking network, which we prove to be unique in an appropriate class. We also include a classification result for some self-similarly shrinking networks.
Phylogenetic networks from splits
2010-12-02

In Chapter 5, we introduced splits and split networks and presented the Buneman graph as the canonical split network associated with a given set of splits. Splits can be computed from many different types of data, as we discuss in some of the following chapters. The focus of this chapter is on the problem of computing a split network N for a given set of splits S on X. We present two different approaches. The first is the convex hull algorithm that computes the Buneman graph and can be applied to any set of splits, using an exponential number of nodes and edges in the worst case [11]. It is also used in Section 9.4 to compute median networks. The second is the circular network algorithm, which can be applied to any set of circular splits and produces an outer-labeled planar network with only a quadratic number of nodes and edges [62].
Phylogenetic networks from trees
2010-12-02

In this chapter, we look at a number of methods that take as input one or more phylogenetic trees and compute as output a phylogenetic network. We first discuss methods for computing consensus trees and consensus split networks from unrooted phylogenetic trees, and then briefly touch on doing the same for rooted phylogenetic trees. We then present an algorithm for computing a minimum hybridization network for two trees. The two last topics in this section both address the issue of gene duplications. First we discuss how to compute a phylogenetic network for a given multi-labeled phylogenetic tree. Then we discuss an approach used for computing an optimal duplication-loss-transfer scenario that reconciles a gene tree with a species tree.
Phylogenetic networks from sequences
2010-12-02

In this chapter we describe a number of methods that require sequences, or more precisely, a multiple sequence alignment, as input. To this end, we first introduce the useful concept of a condensed alignment and briefly discuss the relationship between binary sequences and splits. We then discuss a number of methods that can be used to compute unrooted phylogenetic networks from sequences, including the median network, quasi-median network and median-joining methods. Finally, we look at two different ways of computing rooted networks from sequences, both aimed at explaining differences in terms of mutations and recombinations.
Clusters and rooted phylogenetic networks
2010-12-02

The concept of a cluster plays a fundamental role in classification: For a set of taxa X we may want to group some of the elements together in the form of a cluster, for example, because they share an attribute that distinguishes them from other elements. In the context of phylogenetic analysis, clusters should be clades or monophyletic groups that reflect the evolutionary history of a set of taxa.
Splits and unrooted phylogenetic networks
2010-12-02

The concept of a split plays an important role in the mathematics of phylogeny. It is motivated by the simple, but crucial, observation that every edge e in an unrooted phylogenetic tree T defines a bipartition of the underlying taxon set X into two non-empty and disjoint subsets, A and B, known as a split. The splits of an unrooted phylogenetic tree uniquely define the topology of the tree and splits are used, for example, to compare different trees or to compute consensus trees. Any set of splits that is compatible corresponds to a phylogenetic tree and so one possible way to generalize from trees to networks is to consider sets of splits that are incompatible.
Phylogenetic networks from clusters
2010-12-02

In this chapter, we present some methods for computing phylogenetic networks from clusters. Clusters, as opposed to splits, are inherently rooted and this explains why all methods presented in this chapter produce rooted phylogenetic networks. We first briefly mention the cluster-popping algorithm for computing a cluster network, and then present a divide-and-conquer approach for computing rooted phylogenetic networks. Based on this, we discuss how to compute minimum galled trees, galled networks and level-k networks from clusters.
Preface
2010-12-02

The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. The concept of a rooted tree is very simple and has proved to be extremely useful in many application domains. However, the truth is rarely pure and never simple.
Theory
2010-12-02

In this second part of the book we develop the theoretical foundations for phylogenetic networks. First we study splits and unrooted phylogenetic networks (Chapter 5). The mathematical and computational aspects of such networks have been worked out in detail over the last 20 years. The existing algorithms are routinely used in numerous publications in systematic biology. Then we turn to clusters and rooted phylogenetic networks (Chapter 6). Their theory is still under development and widely used methods for the computation of rooted phylogenetic networks have yet to emerge.
Drawing phylogenetic networks
2010-12-02

The algorithms presented in the previous chapters compute a phylogenetic tree or network as a labeled graph, possibly with edge lengths. In this chapter, we discuss the problem of assigning coordinates to the nodes (and sometimes also to points along the edges) of a given phylogenetic tree or network so that it can be drawn by a computer program. The results presented here are based on [62, 77, 124].
Introduction
2010-12-02

In the first part of this book we give an introduction to basic concepts from graph theory and systematics (Chapter 1). We briefly discuss the problem of aligning molecular sequences (Chapter 2) and give a more detailed introduction to the computation of phylogenetic trees from aligned sequences and distances (Chapter 3). Finally, we give a brief introduction to the computation of phylogenetic networks, which also serves as an overview for the material presented in the second and third parts of the book (Chapter 4).
Non-convergence of the critical cooling time-scale for fragmentation of self-gravitating discs
2010-12-03

Abstract We carry out a resolution study on the fragmentation boundary of self-gravitating discs. We perform three-dimensional Smoothed Particle Hydrodynamics simulations of discs to determine whether the critical value of the cooling time-scale in units of the orbital time-scale, βcrit, converges with increasing resolution. Using particle numbers ranging from 31 250 to 16 million (the highest resolution simulations to date) we do not find convergence. Instead, fragmentation occurs for longer cooling time-scales as the resolution is increased. These results suggest that at the very least, the critical value of the cooling time-scale is longer than previously thought. However, the absence of convergence also raises the question of whether or not a critical value exists. In light of these results, we caution against using cooling time-scale or gravitational stress arguments to deduce whether gravitational instability may or may not have been the formation mechanism for observed planetary systems.
Posaconazole: clinical pharmacokinetics and drug interactions
2010-12-03

Summary Posaconazole represents an antifungal extended‐spectrum triazole whose absolute bioavailability following oral drug administration is considerably variable. Special conditions including increased gastric pH values, malabsorption syndrome, diarrhoea, intake on an empty stomach and some concomitantly administered potent enzyme‐inducing drugs may contribute to lower drug plasma levels than expected. As a consequence, establishment of Therapeutic Drug Monitoring (TDM) has been proposed to be beneficial in patients receiving antifungal prophylaxis or therapy with posaconazole. Based on its considerable CYP3A inhibiting potency, posaconazole may significantly increase plasma concentrations of concomitantly applied drugs which undergo an extensive first‐pass effect through gut and liver. More intensified posaconazole TDM may help to estimate the extent of drug interaction more accurately.
Detection of very-high-energyγ-ray emission from the vicinity of PSR B1706–44 and G 343.1–2.3 with H.E.S.S.
2010-12-03

The gamma-ray pulsar PSR B1706-44 and the adjacent supernova remnant (SNR)\\ncandidate G343.1-2.3 were observed by H.E.S.S. during a dedicated observation\\ncampaign in 2007. As a result of this observation campaign, a new source of\\nvery-high-energy (VHE; E &gt; 100 GeV) gamma-ray emission, HESS J1708-443, was\\ndetected with a statistical significance of 7 sigma, although no significant\\npoint-like emission was detected at the position of the energetic pulsar\\nitself. In this paper, the morphological and spectral analyses of the\\nnewly-discovered TeV source are presented. The centroid of HESS J1708-443 is\\nconsiderably offset from the pulsar and located near the apparent center of the\\nSNR, at RA(J2000) = 17h08m11s +/- 17s and Dec(J2000) = -44d20' +/- 4'. The\\nsource is found to be significantly more extended than the H.E.S.S. point\\nspread function (~0.1 deg), with an intrinsic Gaussian width of 0.29 deg +/-\\n0.04 deg. Its integral flux between 1 and 10 TeV is ~ 3.8 x 10^-12 ph cm^-2\\ns^-1, equivalent to 17% of the Crab Nebula flux in the same energy range. The\\nmeasured energy spectrum is well-fit by a power law with a relatively hard\\nphoton index Gamma = 2.0 +/- 0.1 (stat) +/- 0.2 (sys). Additional\\nmulti-wavelength data, including 330 MHz VLA observations, were used to\\ninvestigate the VHE gamma-ray source's possible associations with the pulsar\\nwind nebula of PSR B1706-44 and/or with the complex radio structure of the\\npartial shell-type SNR G343.1-2.3.\\n