cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Local and global dynamics in social spider metapopulations
Creators: name: Sharpe, Ruth Victoria
Publisher: name: University of British Columbia
Year: 2017

description: The relative costs and benefits of group living change with group size. In the social spider Anelosimus eximius, as colonies grow, the number of insects captured per capita decreases, but the size of insects increases, causing biomass captured per capita to peak at intermediate colony sizes. One aspect of group living that changes with group size is competition for resources. Whether intraspecific competition occurs via scramble vs. contest competition can affect the stability and survival of the group or population. By feeding large and small prey to artificial colonies of the social spider Anelosimus eximius, we investigated whether prey size could alter the type of competition that takes place and, thus, potentially, influence colony population dynamics. We found that large prey were shared more evenly, and that individuals in poor condition were more likely to feed when prey were large. Next, we investigated whether the condition of individuals vary as a function of colony size by measuring condition of individual spiders in a wide range of nest sizes. We found that, due to reducing per capita food supply as colonies grow, individuals have lower condition in larger colonies. We also found that condition variance decreases with colony size, further suggesting that scramble competition predominates in large colonies. Although dispersing females were larger and in better condition than philopatric ones, nests established by dispersing females had low survival rate, suggesting that dispersal is costly. Dispersers, therefore, likely face multiple constraints. They have to be large enough to stand a chance of survival following dispersal, but, due to dispersal costs and benefits of group living, should not disperse except from large colonies. Diminishing resources in large colonies, however, coupled with scramble competition, should make it hard for individuals to accumulate sufficient resources to disperse. This combination of factors may contribute to the observed sudden extinction of large colonies that fail to disperse representing a paradox of how social spider metapopulations persist. Using an individual-based simulation model, we demonstrate that rare increases in food supply due to environmental stochasticity may precipitate occasional mass dispersal from large colonies, allowing the metapopulation to persist.
Vesicular aptasensor for the detection of thrombin
Creators: name: Müller, Andreas
name: König, Burkhard
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 540 Chemie

description: Self-assembled phospholipid vesicles are functionalized with thrombinbinding aptamers using a thiol-click reaction. The resulting aptasensors signal the binding of the analyte to the vesicle surface by changes of the emission properties of membrane co-embedded reporter dyes.
description: Open-Access-Komponente aus der Nationallizenz
Surface plasmon delocalization in silver nanoparticle aggregates revealed by subdiffraction supercontinuum hot spots
Creators: name: Borys, Nicholas J.
name: Shafran, Eyal
name: Lupton, John M.
Publisher: name: Universität Regensburg
Year: 2013
Subjects: subject: ENHANCED RAMAN-SCATTERING; RESONANCE SPECTROSCOPY; METAL NANOPARTICLES; OPTICAL-PROPERTIES; FIELD; LIGHT; FILMS; LOCALIZATION; MICROSCOPY; SERS
subject: 530 Physik

description: The plasmonic resonances of nanostructured silver films produce exceptional surface enhancement, enabling reproducible single-molecule Raman scattering measurements. Supporting a broad range of plasmonic resonances, these disordered systems are difficult to investigate with conventional far-field spectroscopy. Here, we use nonlinear excitation spectroscopy and polarization anisotropy of single optical hot spots of supercontinuum generation to track the transformation of these plasmon modes as the mesoscopic structure is tuned from a film of discrete nanoparticles to a semicontinuous layer of aggregated particles. We demonstrate how hot spot formation from diffractively-coupled nanoparticles with broad spectral resonances transitions to that from spatially delocalized surface plasmon excitations, exhibiting multiple excitation resonances as narrow as 13 meV. Photon-localization microscopy reveals that the delocalized plasmons are capable of focusing multiple narrow radiation bands over a broadband range to the same spatial region within 6 nm, underscoring the existence of novel plasmonic nanoresonators embedded in highly disordered systems.
The semiclassical propagator in fermionic Fock space
Creators: name: Engl, Thomas
name: Plößl, Peter
name: Urbina, Juan Diego
name: Richter, Klaus
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: Path integral; Semiclassical; Fermions; classical limit
subject: 530 Physik

description: We present a rigorous derivation of a semiclassical propagator for anticommuting (fermionic) degrees of freedom, starting from an exact representation in terms of Grassmann variables. As a key feature of our approach the anticommuting variables are integrated out exactly, and an exact path integral representation of the fermionic propagator in terms of commuting variables is constructed. Since our approach is not based on auxiliary (Hubbard-Stratonovich) fields, it surpasses the calculation of fermionic determinants yielding a standard form $\int {\cal D}[\psi,\psi^{*}] {\rm e}^{i R[\psi,\psi^{*}]}$ with real actions for the propagator. These two features allow us to provide a rigorous definition of the classical limit of interacting fermionic fields and therefore to achieve the long-standing goal of a theoretically sound construction of a semiclassical van Vleck-Gutzwiller propagator in fermionic Fock space. As an application, we use our propagator to investigate how the different universality classes (orthogonal, unitary and symplectic) affect generic many-body interference effects in the transition probabilities between Fock states of interacting fermionic systems.
Effective Polyakov-loop theory for pure Yang-Mills from strong coupling expansion
Creators: name: Langelage, Jens
name: Lottini, Stefano
name: Philipsen, Owe
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Lattice Yang-Mills theories at finite temperature can be mapped onto effective 3d spin systems, thus facilitating their numerical investigation. Using strong-coupling expansions we derive effective actions for Polyakov loops in the $SU(2)$ and $SU(3)$ cases and investigate the effect of higher order corrections. Once a formulation is obtained which allows for Monte Carlo analysis, the nature of the phase transition in both classes of models is investigated numerically, and the results are then used to predict -- with an accuracy within a few percent -- the deconfinement point in the original 4d Yang-Mills pure gauge theories, for a series of values of $N_τ$ at once.
description: 14 pages, 7 figures. Proceedings for The XXVIII International Symposium on Lattice Field Theory, Lattice2010, Villasimius, Italy
Cubic Rashba Spin-Orbit Interaction of a Two-Dimensional Hole Gas in a Strained-Ge/SiGe Quantum Well
Creators: name: Moriya, Rai
name: Sawano, Kentarou
name: Hoshi, Yusuke
name: Masubuchi, Satoru
name: Shiraki, Yasuhiro
name: Wild, Andreas
name: Neumann, Christian
name: Abstreiter, Gerhard
name: Bougeard, Dominique
name: Koga, Yasuhiro
name: Machida, Tomoki
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 530 Physik

description: The spin-orbit interaction (SOI) of a two-dimensional hole gas in the inversion symmetric semiconductor Ge is studied in a strained-Ge/SiGe quantum well structure. We observe weak antilocalization (WAL) in the magnetoconductivity measurement, revealing that the WAL feature can be fully described by the k-cubic Rashba SOI theory. Furthermore, we demonstrate electric field control of the Rashba SOI. Our findings reveal that the heavy hole (HH) in strained Ge is a purely cubic Rashba system, which is consistent with the spin angular momentum m_{j}=±3/2 nature of the HH wave function.
Generalized Geologic Map for Land-Use Planning: Rockcastle County, Kentucky
Creators: name: Carey, Daniel I.
Publisher: name: Kentucky Geological Survey, University of Kentucky
Year: 2007

description: Abstract:
This map is not intended to be used for selecting individual sites. Its purpose is to inform land-use planners, government officials, and the public in a general way about geologic bedrock conditions that affect the selection of sites for various purposes. The properties of thick soils may supercede those of the underlying bedrock and should be considered on a site-to-site basis. At any site, it is important to understand the characteristics of both the soils and the underlying rock.
Quantitative version of the Kipnis-Varadhan theorem and Monte Carlo approximation of homogenized coefficients
Creators: name: Gloria, Antoine
name: Mourrat, Jean-Christophe
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: This article is devoted to the analysis of a Monte Carlo method to approximate effective coefficients in stochastic homogenization of discrete elliptic equations. We consider the case of independent and identically distributed coefficients, and adopt the point of view of the random walk in a random environment. Given some final time t>0, a natural approximation of the homogenized coefficients is given by the empirical average of the final squared positions re-scaled by t of n independent random walks in n independent environments. Relying on a quantitative version of the Kipnis-Varadhan theorem combined with estimates of spectral exponents obtained by an original combination of PDE arguments and spectral theory, we first give a sharp estimate of the error between the homogenized coefficients and the expectation of the re-scaled final position of the random walk in terms of t. We then complete the error analysis by quantifying the fluctuations of the empirical average in terms of n and t, and prove a large-deviation estimate, as well as a central limit theorem. Our estimates are optimal, up to a logarithmic correction in dimension 2.
description: Published in at http://dx.doi.org/10.1214/12-AAP880 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Fabry-Pérot Interference in Gapped Bilayer Graphene with Broken Anti-Klein Tunneling
Creators: name: Varlet, Anastasia
name: Liu, Ming-Hao
name: Krueckl, Viktor
name: Bischoff, Dominik
name: Simonet, Pauline
name: Watanabe, Kenji
name: Taniguchi, Takashi
name: Richter, Klaus
name: Ensslin, Klaus
name: Ihn, Thomas
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 530 Physik
subject: 72.80.Vp, 73.23.-b

description: We report the experimental observation of Fabry-Pérot interference in the conductance of a gate-defined cavity in a dual-gated bilayer graphene device. The high quality of the bilayer graphene flake, combined with the device’s electrical robustness provided by the encapsulation between two hexagonal boron nitride layers, allows us to observe ballistic phase-coherent transport through a 1-μm-long cavity. We confirm the origin of the observed interference pattern by comparing to tight-binding calculations accounting for the gate-tunable band gap. The good agreement between experiment and theory, free of tuning parameters, further verifies that a gap opens in our device. The gap is shown to destroy the perfect reflection for electrons traversing the barrier with normal incidence (anti-Klein tunneling). The broken anti-Klein tunneling implies that the Berry phase, which is found to vary with the gate voltages, is always involved in the Fabry-Pérot oscillations regardless of the magnetic field, in sharp contrast with single-layer graphene.
Multi-wavelength observations revealing the most obscured high energy sources of our Galaxy
Creators: name: Chaty, S.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: A new type of high-energy binary system has been revealed by the INTEGRAL satellite. These sources are being unveiled by means of multi-wavelength optical, near- and mid-infrared observations. Among these sources, two distinct classes are appearing: the first one is constituted of intrinsically obscured high-energy sources, of which IGR J16318-4848 seems to be the most extreme example. The second one is populated by the so-called supergiant fast X-ray transients, with IGR J17544-2619 being the archetype. We first give here a general introduction on INTEGRAL sources, before reporting on multi-wavelength optical to mid-infrared observations of a sample constituted of 21 INTEGRAL sources. We show that in the case of obscured sources our observations suggest the presence of absorbing material (dust and/or cold gas) enshrouding the whole binary system. We finally discuss the nature of these two different types of sources, in the context of high energy binary systems, and give a scenario of unification of all these different types of high energy sources, based on their high energy properties.
description: Contributed talk,19 pages, 2 figures, 1 table
Charge-doping-induced phase transitions in hydrogenated and fluorinated graphene
Creators: name: Wehling, Tim O.
name: Grundkötter-Stock, Bernhard
name: Aradi, B.
name: Frauenheim, Th.
name: Niehaus, Thomas A.
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: 530 Physik

description: We show that charge doping can induce transitions between three distinct adsorbate phases in hydrogenated and fluorinated graphene. By combining ab initio, approximate density functional theory and tight-binding calculations we identify a transition from islands of C8H2 and C8F2 to random adsorbate distributions around a doping level of ±0.05 e/C atom. Furthermore, in situations with random adsorbate coverage, charge doping is shown to trigger a sublattice ordering transition when the doping level exceeds the adsorbate concentration. Rehybridization and lattice distortion energies make graphene, which is covalently functionalized from one side only, most susceptible to these two kinds of phase transitions. The energy gains associated with the clustering and ordering transitions can exceed room temperature thermal energies.
Restoring a life on the margins. How my grandfather’s diaries from his time in solitary confinement have been used in pursuit of post-mortem justice, and why Iceland has more to reckon with than just our tarnished name
Creators: name: Brynjarsson, Tryggvi Rúnar
Publisher: name: University of British Columbia
Year: 2017

description: This M.A. thesis examines the ongoing state-directed initiative to achieve a posthumous exoneration for my grandfather, Tryggvi Rúnar Leifsson, who in 1975 was wrongfully accused, and later convicted, of involvement in the disappearance of one Guðmundur Einarsson. Diaries he wrote during his exceptionally long detention in solitary confinement before his conviction anchor the essay. I discuss how these texts were received by the Icelandic public after my grandfather’s death in 2009—they came out two years later—and how forensic psychologists and legal professionals have used them to access the diarist’s (innocent) persona. I also provide my own introduction of their contents. The original prosecution against my grandfather in the 1970s built on no hard evidence; neither body nor murder weapon ever materialized, most remarkably. Crucial to achieving a guilty verdict was a prejudiced assessment of his (criminal) character. My essay highlights how portions of that same assessment have been repurposed in the current-day pursuit of his exoneration. As a national scandal is made and remade, I take a stand with my namesake against the violent deformities inflicted by plastic psychology.
Symmetric random walks on Homeo+(R)
Creators: name: Deroin, B.
name: Kleptsyn, V.
name: Navas, A.
name: Parwani, K.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Group Theory (math.GR)
subject: Dynamical Systems (math.DS)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60B15, 20P05, 20F60

description: We study symmetric random walks on finitely generated groups of orientation-preserving homeomorphisms of the real line. We establish an oscillation property for the induced Markov chain on the line that implies a weak form of recurrence. Except for a few special cases, which can be treated separately, we prove a property of "global stability at a finite distance": roughly speaking, there exists a compact interval such that any two trajectories get closer and closer whenever one of them returns to the compact interval. The probabilistic techniques employed here lead to interesting results for the study of group actions on the line. For instance, we show that under a suitable change of the coordinates, the drift of every point becomes zero provided that the action is minimal. As a byproduct, we recover the fact that every finitely generated group of homeomorphisms of the real line is topologically conjugate to a group of (globally) Lipschitz homeomorphisms. Moreover, we show that such a conjugacy may be chosen in such a way that the displacement of each element is uniformly bounded.
Taxonomy of Social Network Data Types
Creators: name: Richthammer, Christian
name: Netter, Michael
name: Riesner, Moritz
name: Sänger, Johannes
name: Pernul, Günther
Publisher: name: Universität Regensburg
Year: 2014
Subjects: subject: Taxonomy; Privacy; Data types; Online social networks; Social identity management; Classification; Privacy relevance metric
subject: 004 Informatik

description: Online social networks (OSNs) have become an integral part of social interaction and communication between people. Reasons include the ubiquity of OSNs that is offered through mobile devices and the possibility to bridge spatial and temporal communication boundaries. However, several researchers have raised privacy concerns due to the large amount of user data shared on OSNs. Yet, despite the large body of research addressing OSN privacy issues, little differentiation of data types on social network sites is made and a generally accepted classification and terminology for such data is missing. The lack of a terminology impedes comparability of related work and discussions among researchers, especially in the case of privacy implications of different data types. To overcome these shortcomings, this paper develops a well-founded terminology based on a thorough literature analysis and a conceptualization of typical OSN user activities. The terminology is organized hierarchically resulting in a taxonomy of data types. The paper furthermore discusses and develops a metric to assess the privacy relevance of different data types. Finally, the taxonomy is applied to the five major OSNs to evaluate its generalizability.
Inhibited spontaneous emission of quantum dots observed in a 3D photonic band gap
Creators: name: Leistikow, M. D.
name: Mosk, A. P.
name: Yeganegi, E.
name: Huisman, S. R.
name: Lagendijk, A.
name: Vos, W. L.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We present time-resolved emission experiments of semiconductor quantum dots in silicon 3D inverse-woodpile photonic band gap crystals. A systematic study is made of crystals with a range of pore radii to tune the band gap relative to the emission frequency. The decay rates averaged over all dipole orientations are inhibited by a factor of 10 in the photonic band gap and enhanced up to 2? outside the gap, in agreement with theory. We discuss the effects of spatial inhomogeneity, nonradiative decay, and transition dipole orientations on the observed inhibition in the band gap.
description: 5 figures, update author list
Fermi-LAT results on Galactic Plane gamma-ray Transient Sources
Creators: name: Chaty, Sylvain
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The Large Area Telescope on the Fermi gamma-ray Space Telescope provides unprecedented sensitivity for all-sky monitoring of gamma-ray activity. It has detected a few Galactic sources, including 2 gamma-ray binaries and a microquasar. In addition, it is an adequate telescope to detect other transient sources. The observatory scans the entire sky every three hours and allows a general search for flaring activity on daily timescales. This search is conducted automatically as part of the ground processing of the data and allows a fast response to transient events, typically less than a day. Most of the outbursts detected are spatially associated with known blazars, but in several cases during the first years of observations, gamma-ray flares occurring near the Galactic plane did not reveal any initially compelling counterparts. This prompted follow-up observations in X-ray, optical, and radio to attempt to identify the origin of the emission and probe the possible existence of a class of transient gamma-ray sources in the Galaxy. Here we report on these LAT events and the results of the multiwavelength counterpart searches.
description: Invited review, 7 pages, 3 figures
Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays
Creators: name: Moll, Anton G.
name: Lindenmeyer, Maja T.
name: Kretzler, Matthias
name: Nelson, Peter J.
name: Zimmer, Ralf
name: Cohen, Clemens D.
Publisher: name: Universität Regensburg
Year: 2009
Subjects: subject: 610 Medizin
subject: ATP Binding Cassette Transporter 1
subject: ATP-Binding Cassette Transporters/genetics
subject: Cohort Studies
subject: DNA Probes
subject: Diabetic Nephropathies/metabolism
subject: Gene Expression Profiling/methods
subject: Humans
subject: Kidney/metabolism
subject: Kidney Transplantation
subject: Oligonucleotide Array Sequence Analysis
subject: Phosphoprotein Phosphatases/genetics
subject: Plasminogen/genetics
subject: RNA Splicing
subject: RNA, Messenger/genetics
subject: Reverse Transcriptase Polymerase Chain Reaction
subject: Sequence Alignment
subject: Tissue Donors
subject: Transcription, Genetic

description: BACKGROUND: Alternative mRNA processing mechanisms lead to multiple transcripts (i.e. splice isoforms) of a given gene which may have distinct biological functions. Microarrays like Affymetrix GeneChips measure mRNA expression of genes using sets of nucleotide probes. Until recently probe sets were not designed for transcript specificity. Nevertheless, the re-analysis of established microarray data using newly defined transcript-specific probe sets may provide information about expression levels of specific transcripts. METHODOLOGY/PRINCIPAL FINDINGS: In the present study alignment of probe sequences of the Affymetrix microarray HG-U133A with Ensembl transcript sequences was performed to define transcript-specific probe sets. Out of a total of 247,965 perfect match probes, 95,008 were designated "transcript-specific", i.e. showing complete sequence alignment, no cross-hybridization, and transcript-, not only gene-specificity. These probes were grouped into 7,941 transcript-specific probe sets and 15,619 gene-specific probe sets, respectively. The former were used to differentiate 445 alternative transcripts of 215 genes. For selected transcripts, predicted by this analysis to be differentially expressed in the human kidney, confirmatory real-time RT-PCR experiments were performed. First, the expression of two specific transcripts of the genes PPM1A (PP2CA_HUMAN and P35813) and PLG (PLMN_HUMAN and Q5TEH5) in human kidneys was determined by the transcript-specific array analysis and confirmed by real-time RT-PCR. Secondly, disease-specific differential expression of single transcripts of PLG and ABCA1 (ABCA1_HUMAN and Q5VYS0_HUMAN) was computed from the available array data sets and confirmed by transcript-specific real-time RT-PCR. CONCLUSIONS: Transcript-specific analysis of microarray experiments can be employed to study gene-regulation on the transcript level using conventional microarray data. In this study, predictions based on sufficient probe set size and fold-change are confirmed by independent means.
Sparse Inverse Covariance Selection via Alternating Linearization Methods
Creators: name: Scheinberg, Katya
name: Ma, Shiqian
name: Goldfarb, Donald
Publisher: name: arXiv
Year: 2010
Subjects: subject: Machine Learning (cs.LG)
subject: Optimization and Control (math.OC)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Gaussian graphical models are of great interest in statistical learning. Because the conditional independencies between different nodes correspond to zero entries in the inverse covariance matrix of the Gaussian distribution, one can learn the structure of the graph by estimating a sparse inverse covariance matrix from sample data, by solving a convex maximum likelihood problem with an $\ell_1$-regularization term. In this paper, we propose a first-order method based on an alternating linearization technique that exploits the problem's special structure; in particular, the subproblems solved in each iteration have closed-form solutions. Moreover, our algorithm obtains an $ε$-optimal solution in $O(1/ε)$ iterations. Numerical experiments on both synthetic and real data from gene association networks show that a practical version of this algorithm outperforms other competitive algorithms.
Protein-Protein Interaction Analysis by Docking
Creators: name: Fink, Florian
name: Ederer, Stephan
name: Gronwald, Wolfram
Publisher: name: Universität Regensburg
Year: 2009
Subjects: subject: protein-protein docking; verification of protein interactions; 3D protein structures
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin

description: Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general applicability of our approach.
Indigenous peoples and international human rights law : mining, multinational corporations and the struggles of indigenous peoples in Peru
Creators: name: Munarriz, Gerardo J.
Publisher: name: University of British Columbia
Year: 2017

description: This thesis examines and questions the role of international human rights law and international economic law in relation to the increasing encroachment and dispossession of Indigenous lands and territories by multinational corporations (MNCs) in the extractive industry. It also aims to explore the role of a national state’s legal framework and policies not only in validating, authorizing and embedding this process, but also in authorizing a growing and pervasive trend of persecution and criminalization of Indigenous communities who challenge and resist MNCs’ operations. The examination of the relationship between national and international law provides a terrain to grasp how international economic law and international human rights law have become part of evolving regulatory architectures of global governance aiming to validate and embed global capital accumulation. Focusing on Peru, this thesis argues that law, particularly international economic law and the legal framework developed in Peru since the 1990s, has played a prominent role in facilitating and embedding multinational corporate investment in the extractive industry, and in weakening the rights of Indigenous and peasant communities to control their land, water and resources. Peru’s legal framework and policies on extractive industries have not only validated the expansion of MNCs operations and dispossession of Indigenous lands, but have also validated a growing trend of persecution and criminalisation of Indigenous communities. While international economic law constitutes, enables and protects MNCs, international human rights law and corporate social responsibility mechanisms are linked to and help to extend the expansion and deepening of global capital accumulation by means of laws and regulations designed to facilitate and remove barriers to the power and mobility of MNCs. Notwithstanding legal and socio-economic barriers, Indigenous communities have mobilized against and resisted MNCs operations. A comparison of three conflicts involving corporate actors and local communities reveals the existence of intense social mobilization and resistance of Indigenous and peasant communities to defend their land rights, their environment and livelihood, their participation in the decision making process and fair distribution of economic benefits.
Joint Structured Models for Extraction from Overlapping Sources
Creators: name: Gupta, Rahul
name: Sarawagi, Sunita
Publisher: name: arXiv
Year: 2010
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: We consider the problem of jointly training structured models for extraction from sources whose instances enjoy partial overlap. This has important applications like user-driven ad-hoc information extraction on the web. Such applications present new challenges in terms of the number of sources and their arbitrary pattern of overlap not seen by earlier collective training schemes applied on two sources. We present an agreement-based learning framework and alternatives within it to trade-off tractability, robustness to noise, and extent of agreement. We provide a principled scheme to discover low-noise agreement sets in unlabeled data across the sources. Through extensive experiments over 58 real datasets, we establish that our method of additively rewarding agreement over maximal segments of text provides the best trade-offs, and also scores over alternatives such as collective inference, staged training, and multi-view learning.
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades
Creators: name: Förster, Frank
name: Liang, Chunguang
name: Shkumatov, Alexander V.
name: Beisser, Daniela
name: Engelmann, Julia C.
name: Schnölzer, Martina
name: Frohme, Marcus
name: Müller, Tobias
name: Schill, Ralph O.
name: Dandekar, Thomas
Publisher: name: Universität Regensburg
Year: 2009
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: 5' Untranslated Regions
subject: Animals
subject: Cluster Analysis
subject: Invertebrates/genetics
subject: Multigene Family
subject: RNA Stability
subject: RNA, Messenger/genetics
subject: Sequence Analysis, RNA
subject: Species Specificity

description: BACKGROUND: Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. RESULTS: To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. CONCLUSION: Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.
Main supplementary tables relating to study methods and results from Is depression associated with reduced optimistic belief updating?
Creators: name: Hobbs, Catherine
name: Vozarova, Petra
name: Sabharwal, Aarushi
name: Shah, Punit
name: Button, Katherine
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: 179999 Psychology and Cognitive Sciences not elsewhere classified
subject: FOS: Psychology

description: Supplementary tables 1-4, 6-16 and supplementary figures 1-3
Inferring cellular networks - a review
Creators: name: Markowetz, Florian
name: Spang, Rainer
Publisher: name: Universität Regensburg
Year: 2007
Subjects: subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Algorithms
subject: Computer Simulation
subject: Gene Expression Profiling/methods
subject: Models, Biological
subject: Oligonucleotide Array Sequence Analysis/methods
subject: Protein Interaction Mapping/methods
subject: Proteome/metabolism
subject: Signal Transduction/physiology

description: In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently used methods can be organized by a few key concepts. The first part of the review deals with conditional independence models including Gaussian graphical models and Bayesian networks. The second part discusses probabilistic and graph-based methods for data from experimental interventions and perturbations.
$\TT^2$-cobordism of Quasitoric 4-Manifolds
Creators: name: Sarkar, Soumen
Publisher: name: arXiv
Year: 2010
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics
subject: 55N22, 57R90

description: We show the $\TT^2$-cobordism group of the category of 4-dimensional quasitoric manifolds is generated by the $\TT^2$-cobordism classes of $\CP^2$. We construct nice oriented $\TT^2$ manifolds with boundary where the boundary is the Hirzebruch surfaces. The main tool is the theory of quasitoric manifolds.
description: 17 pages, 9 figures, many changes
Poisson approximations on the free Wigner chaos
Creators: name: Nourdin, Ivan
name: Peccati, Giovanni
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: We prove that an adequately rescaled sequence $\{F_n\}$ of self-adjoint operators, living inside a fixed free Wigner chaos of even order, converges in distribution to a centered free Poisson random variable with rate $λ>0$ if and only if $φ(F_n^4)-2φ(F_n^3)\rightarrow2λ^2-λ$ (where $φ$ is the relevant tracial state). This extends to a free setting some recent limit theorems by Nourdin and Peccati [Ann. Probab. 37 (2009) 1412-1426] and provides a noncentral counterpart to a result by Kemp et al. [Ann. Probab. 40 (2012) 1577-1635]. As a by-product of our findings, we show that Wigner chaoses of order strictly greater than 2 do not contain nonzero free Poisson random variables. Our techniques involve the so-called "Riordan numbers," counting noncrossing partitions without singletons.
description: Published in at http://dx.doi.org/10.1214/12-AOP815 the Annals of Probability (http://www.imstat.org/aop/) by the Institute of Mathematical Statistics (http://www.imstat.org)
ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly
Creators: name: Thieme, Marian
name: Lottaz, Claudio
name: Niederstätter, Harald
name: Parson, Walther
name: Spang, Rainer
name: Oefner, Peter J.
Publisher: name: Universität Regensburg
Year: 2009
Subjects: subject: 610 Medizin
subject: Base Sequence
subject: Computational Biology/methods
subject: DNA, Mitochondrial/chemistry
subject: Genome, Mitochondrial/genetics
subject: Sequence Analysis, DNA
subject: Software

description: BACKGROUND: The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt) genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis. RESULTS: We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/. CONCLUSIONS: ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.
Self-Organized Authentication in Mobile Ad-hoc Networks
Creators: name: Caballero-Gil, P.
name: Hernández-Goya, C.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: This work proposes a new distributed and self-organized authentication scheme for Mobile Ad-hoc NETworks (MANETs). Apart from describing all its components, special emphasis is placed on proving that the proposal fulfils most requirements derived from the special characteristics of MANETs, including limited physical protection of broadcast medium, frequent route changes caused by mobility, and lack of structured hierarchy. Interesting conclusions are obtained from an analysis of simulation experiments in different scenarios.
The wind of virtue over the realm : the concept of feng as a legitimizing medium in Hanazono’s prefaces to the Fūgawakashū
Creators: name: Kim, Yoon-Kyung
Publisher: name: University of British Columbia
Year: 2017

description: This thesis explores the political messages contained in the seventeenth imperial anthology of Japanese poetry (waka), the Fūgawakashū (1346). Through reaffirmation of values presented in previous anthologies, imperial waka anthologies served as a source of mutual legitimization for the commissioning regime and the compiling poets. I examine how Retired Emperor Hanazono (1297-1348, r. 1308-1318), as the head of the Jimyōin faction and the guardian of the Kyōgoku school of poetry, establishes ties between the Fūgawakashū and canonical texts of Japan and China to legitimize his Kyōgoku-Jimyōin faction against the rival Nijō-Daikakuji faction. I argue that Hanazono uses the Confucian concept of feng (風, J. fū) as the organizing principle for his claims in the Fūgawakashū. I discuss the origin of the title “fūga,” which pays homage to the Chinese anthology, the Shijing 詩經 (c. 600 BCE). In the two prefaces composed in kana and mana in the fashion of Kokinwakashū (c. 905) and ShinKokinwakashū (1205), Hanazono identifies governance through the virtue of great men, or feng, as the true function of poetry. By reiterating some arguments from the Kokinwakashū and ShinKokinwakashū prefaces and omitting some aspects to which the Nijō school adheres, Hanazono weaves a poetic lineage that connects the Shijing, Kokinwakashū tradition, and the Fūgawakashū. He proclaims his Kyōgoku school to be the legitimate heir to the spirit of feng represented in the canonized Chinese and Japanese anthologies; the commissioning Jimyōin line is the virtuous rulers abiding by the feng. This thesis also offers some explanation as to the strong legitimacy claim and the explicit critique of the rival faction toward the end of the anthology. I follow evidence for Hanazono’s favourable assessment of Emperor GoDaigo in the early years, consider the turn of events from the perspective of the Jimyōin faction, and conclude that Hanazono’s disappointment in GoDaigo’s revolutionary manoeuvres result in the critical tone in the prefaces. By the assessment of Hanazono’s strategies this study offers to depart from the accepted interpretation of the Fūgawakashū as the Kyōgoku school’s innovative compilation and reconfigures the anthology within a longer tradition of Chinese and Japanese canons.
Detection of genomic aberrations in molecularly defined Burkitt's lymphoma by array-based, high resolution, single nucleotide polymorphism analysis
Creators: name: Scholtysik, René
name: Kreuz, Markus
name: Klapper, Wolfram
name: Burkhardt, Birgit
name: Feller, Alfred
name: Hummel, Michael
name: Loeffler, Markus
name: Rosolowski, Maciej
name: Schwaenen, Carsten
name: Spang, Rainer
name: Stein, Harald
name: Thorns, Christoph
name: Trümper, Lorenz
name: Vater, Inga
name: Wessendorf, Swen
name: Zenz, Thorsten
name: Siebert, Reiner
name: Küppers, Ralf
Publisher: name: Universität Regensburg
Year: 2010
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin
subject: Burkitt Lymphoma/pathology
subject: Chromosome Aberrations
subject: E2F2 Transcription Factor/genetics
subject: Gene Dosage
subject: Gene Expression Regulation, Neoplastic
subject: Gene Rearrangement
subject: Genes, Immunoglobulin/genetics
subject: Genome, Human/genetics
subject: Genotype
subject: Humans
subject: In Situ Hybridization, Fluorescence
subject: Loss of Heterozygosity
subject: MicroRNAs/genetics
subject: Oligonucleotide Array Sequence Analysis/methods
subject: Polymorphism, Single Nucleotide
subject: Proto-Oncogene Proteins c-myc/genetics
subject: Reverse Transcriptase Polymerase Chain Reaction
subject: Translocation, Genetic
subject: Uniparental Disomy

description: The present findings suggest that uniparental disomies do not play a major role in the pathogenesis of Burkitt's lymphoma, whereas some genes may contribute to the development of this lymphoma through gene dosage effects. Amplifications of the polymerase iota gene may be functionally linked with increased genomic alterations in Burkitt's lymphoma. The pattern and rarity of chromosomal changes detectable, even at the high resolution employed here, together with aberrations of genes regulating MYC activity, support the hypothesis that deregulation of the MYC pathway is the major force driving the pathogenesis of Burkitt's lymphoma, but show that this deregulation is more complex than previously known.
Panspermia, Past and Present: Astrophysical and Biophysical Conditions for the Dissemination of Life in Space
Creators: name: Wesson, Paul S.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Astronomically, there are viable mechanisms for distributing organic material throughout the Milky Way. Biologically, the destructive effects of ultraviolet light and cosmic rays means that the majority of organisms arrive broken and dead on a new world. The likelihood of conventional forms of panspermia must therefore be considered low. However, the information content of dam-aged biological molecules might serve to seed new life (necropanspermia).
description: Accepted for publication in Space Science Reviews
Protein structure calculation with a max-min ant system
Creators: name: Gimmler, Jens
name: Gronwald, Wolfram
name: Möller, Heiko M.
name: Exner, Thomas E.
Publisher: name: Universität Regensburg
Year: 2009
Subjects: subject: 500 Naturwissenschaften
subject: 570 Biowissenschaften, Biologie
subject: 610 Medizin

description: Poster presentation
Use of a porous membrane for gas bubble removal in microfluidic channels: physical mechanisms and design criteria
Creators: name: Xu, Jie
name: Vaillant, Regis
name: Attinger, Daniel
Publisher: name: arXiv
Year: 2010
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: We demonstrate and explain a simple and efficient way to remove gas bubbles from liquid-filled microchannels, by integrating a hydrophobic porous membrane on top of the microchannel. A prototype chip is manufactured in hard, transparent polymer with the ability to completely filter gas plugs out of a segmented flow at rates up to 7.4 microliter/s per mm2 of membrane area. The device involves a bubble generation section and a gas removal section. In the bubble generation section, a T-junction is used to generate a train of gas plugs into a water stream. These gas plugs are then transported towards the gas removal section, where they slide along a hydrophobic membrane until complete removal. The system has been successfully modeled and four necessary operating criteria have been determined to achieve a complete separation of the gas from the liquid. The first criterion is that the bubble length needs to be larger than the channel diameter. The second criterion is that the gas plug should stay on the membrane for a time sufficient to transport all the gas through the membrane. The third criterion is that the gas plug travel speed should be lower than a critical value: otherwise a stable liquid film between the bubble and the membrane prevents mass transfer. The fourth criterion is that the pressure difference across the membrane should not be larger than the Laplace pressure to prevent water from leaking through the membrane.
Covariance estimation for distributions with $2+\varepsilon$ moments
Creators: name: Srivastava, Nikhil
name: Vershynin, Roman
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: We study the minimal sample size N=N(n) that suffices to estimate the covariance matrix of an n-dimensional distribution by the sample covariance matrix in the operator norm, with an arbitrary fixed accuracy. We establish the optimal bound N=O(n) for every distribution whose k-dimensional marginals have uniformly bounded $2+\varepsilon$ moments outside the sphere of radius $O(\sqrt{k})$. In the specific case of log-concave distributions, this result provides an alternative approach to the Kannan-Lovasz-Simonovits problem, which was recently solved by Adamczak et al. [J. Amer. Math. Soc. 23 (2010) 535-561]. Moreover, a lower estimate on the covariance matrix holds under a weaker assumption - uniformly bounded $2+\varepsilon$ moments of one-dimensional marginals. Our argument consists of randomizing the spectral sparsifier, a deterministic tool developed recently by Batson, Spielman and Srivastava [SIAM J. Comput. 41 (2012) 1704-1721]. The new randomized method allows one to control the spectral edges of the sample covariance matrix via the Stieltjes transform evaluated at carefully chosen random points.
description: Published in at http://dx.doi.org/10.1214/12-AOP760 the Annals of Probability (http://www.imstat.org/aop/) by the Institute of Mathematical Statistics (http://www.imstat.org)