cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A genomic timescale for the origin of eukaryotes
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2001
Subjects: Animals
Archaea
Eubacterium
Eukaryotic Cells
Evolution, Molecular
Genetic Variation
Genome
Genome, Archaeal
Genome, Bacterial
Genome, Protozoan
Giardia
Models, Genetic
Phylogeny

description: Background: Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes. Results: Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (∼4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events. Conclusions: We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell. © 2001 Hedges et al; licensee BioMed Central Ltd.
Leggadina Thomas 1910
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Leggadina

description: Leggadina Thomas, 1910. Ann. Mag. Nat. Hist., ser. 8, 6:606. REVIEWED BY: C. H. S. Watts (CHSW)(Australia); A. C. Ziegler (ACZ)(New Guinea). COMMENT: Included in Pseudomys by Ride, 1970:244, but considered a separate genus by Watts, 1976, Trans. R. Soc. S. Aust., 100:105-108 (who included delicatulus and hermannsburgensis in Leggadina), Mahoney and Posamentier, 1975, Aust. Mammal., 1 (4):334, and Fox and Briscoe, 1980, Aust. Mammal., 3(2): 109-126, who transferred delicatulus and hermannsburgensis to Pseudomys, and are followed here.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 5), pp. 504-560 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 520, DOI: 10.5281/zenodo.7353037
description: {"references": ["Ride, W. D. L. 1970. A guide to the native mammals of Australia. Oxford University Press, Melbourne, 249 pp.", "Watts, C. H. S. 1976. Leggadina lakedownensis, a new species of murid rodent from North Queensland. Transactions of the Royal Society of South Australia, 100: 105 - 108.", "Mahoney, J. A., and H. Posamentier. 1975. The occurrence of the native rodent Pseudomys gracilicaudatus (Gould, 1845) (Rodentia: Muridae) in New South Wales. Journal of the Australian Mammal Society, 1: 333 - 346.", "Fox, B. J., and D. A. Briscoe. 1980. Pseudomys pilligaensis, a new species of murid rodent from the Pilliga Scrub, Northern New South Wales. Australian Mammalogy, 3: 109 - 126."]}
A genomic timescale of prokaryote evolution: Insights into the origin of methanogenesis, phototrophy, and the colonization of land
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2004
Subjects: Bacteria
Biological Evolution
Biomass
Evolution, Molecular
Genomics
Methane
Photosynthesis
Time

description: Background: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (∼7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. Results: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5-3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1-4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8-4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8-3.1 Ga, and an origin of aerobic methanotrophy 2.5-2.8 Ga. Conclusions: Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8-2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations. © 2004 Battistuzzi et al; licensee BioMed Central Ltd.
Analytic PSF Correction for Gravitational Flexion Studies
Creators: name: Levinson, Rebecca Sobel
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Given a galaxy image, one cannot simply measure its flexion. An image's spin one and three shape properties, typically associated with F- and G-flexion, are actually complicated functions of the galaxy's intrinsic shape and the telescope's PSF, in addition to the lensing properties. The same is true for shear. In this work we create a completely analytic mapping from apparent measured galaxy flexions to gravitational flexions by (1) creating simple models for a lensed galaxy and for a PSF whose distortions are dominated by atmospheric smearing and optical aberrations, (2) convolving the two models, and (3) comparing the pre- and post-convolved flexion-like shape variations of the final image. For completeness, we do the same for shear. As expected, telescope astigmatism, coma, and trefoil can corrupt measurements of shear, F- flexion, and G-flexion, especially for small galaxies. We additionally find that PSF size dilutes the flexion signal more rapidly than the shear signal. Moreover, mixing between shears, flexions, and asymmetric aberrations can create additive offsets in lensing measurements that vary with both galaxy size and galaxy ellipticity and flexion values. But all is not lost; by measuring the patterns, we can correct for them.
description: 46 pages, many figures. Corrects erroneous equation 29b in published version with no consequence for any of the conclusions drawn
Group classification of variable coefficient generalized Kawahara equations
Creators: name: Kuriksha, Oksana
name: Pošta, Severin
name: Vaneeva, Olena
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 35A30, 35Q53, 58J70, 35C05

description: An exhaustive group classification of variable coefficient generalized Kawahara equations is carried out. As a result, we derive new variable coefficient nonlinear models admitting Lie symmetry extensions. All inequivalent Lie reductions of these equations to ordinary differential equations are performed. We also present some examples on the construction of exact and numerical solutions.
description: 18 pages, 5 figures; the version accepted to J. Phys. A: Math. Theor
Exploring structural patterns in the uptake of scientific publications in policy-related documents using the Overton altmetrics database: the case of universities in Flanders, Belgium
Creators: name: Jonker, Hans
name: Vanlee, Florian
Publisher: name: Zenodo
Year: 2022

description: The performance evaluations of universities and academics are undergoing unprecedented expansion. Excellence in academia might not naturally translate into societal impact; alternative assessment instruments have been developed in recent years, aimed at extending conceptions of academic excellence. New metric techniques like altmetrics play a key role in capturing non-academic engagement of research in a broad range of sources, meant as a complement to traditional indicators. Just as citations are seen as indicative of a degree of academic recognition, references to scientific publications in non-scholarly sources are seen as indicative of a certain societal recognition they enjoy. However, their partial reliance on social media like Twitter makes them prone to manipulations like academic spamming. References to scientific publications cited in policy documents seem a promising avenue for application in research evaluation, as these are presumably more likely to signal a direct SIUR and seem less prone to questionable practices. Novel databases like Overton allow for detailed analysis of research uptake in more than six million policy-related documents from countries worldwide. But because the ability to measure and analyze citations to academic works in policy documents has only recently become a technical possibility, questions remain as to which and whose research appears in those documents. More research is needed that focuses on unexpected biases these objects might generate; moreover, gender and seniority of researchers appearing in Overton have not been thoroughly investigated.
Avalanche localization and crossover scaling in amorphous plasticity
Creators: name: Budrikis, Zoe
name: Zapperi, Stefano
Publisher: name: arXiv
Year: 2013
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We perform large scale simulations of a two dimensional lattice model for amorphous plasticity with random local yield stresses and long-range quadrupolar elastic interactions. We show that as the external stress increases towards the yielding phase transition, the scaling behavior of the avalanches crosses over from mean-field theory to a different universality class. This behavior is associated with strain localization, which significantly depends on the short-range properties of the interaction kernel.
description: 8 pages, 11 figures
Long cycles in random subgraphs of graphs with large minimum degree
Creators: name: Riordan, Oliver
Publisher: name: arXiv
Year: 2013
Subjects: subject: Combinatorics (math.CO)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 05C80

description: Let $G$ be any graph of minimum degree at least $k$, and let $G_p$ be the random subgraph of $G$ obtained by keeping each edge independently with probability $p$. Recently, Krivelevich, Lee and Sudakov showed that if $pk\to\infty$ then with probability tending to 1 $G_p$ contains a cycle of length at least $(1-o(1))k$. We give a much shorter proof of this result, also based on depth-first search.
description: 4 pages, 1 figure; figure reoriented
title: Study of Allosteric Polymer Mechanochemistry
Creators: name: Wongjan, Watsuwach
Publisher: name: University of Liverpool Repository
Year: 2024

description: The distribution of forces along stretched polymer chains by cooperative or anti-cooperative activation of mechanophores has never been explored since there are current limitations in designing a suitable mechanophore for force distribution quantification and the suitable chemical system for the experimental demonstration. In order to explore this question, a novel mechanophore, stiff stilbene, was designed, synthesized and incorporated into a linear polymer chain. The study aims to assess its force-coupled reactivity using SMFS and use this information to describe the force distribution within a more complex polymer architecture.
A guide to phylogenetic metrics for conservation, community ecology and macroecology
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2017
Subjects: biodiversity hotspots
biogeography
community assembly
conservation
diversity metrics
evolutionary history
phylogenetic diversity
prioritization
range size

description: © 2016 The Authors. The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α-diversity metrics these are PD (Faith’s phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.
Leggadina forresti
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Leggadina
Leggadina forresti

description: Leggadina forresti (Thomas, 1906). Abstr. Proc. Zool. Soc. Lond., 32:6. TYPE LOCALITY: Australia, Northern Territory, Alexandria. DISTRIBUTION: Arid parts of Western Australia, Northern Territory, South Australia, Queensland and New South Wales (Australia). COMMENT: Includes messorius, waitei, and berneyi; see Ride, 1970:246-247. ISIS NUMBER: 5301410011057006001 as Pseudomys forresti.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 5), pp. 504-560 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 520, DOI: 10.5281/zenodo.7353037
description: {"references": ["Ride, W. D. L. 1970. A guide to the native mammals of Australia. Oxford University Press, Melbourne, 249 pp."]}
A hypothetical molecular mechanism for TRPV1 activation that invokes rotation of an S6 asparagine
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2018
Subjects: Asparagine
Molecular Dynamics Simulation
Protein Conformation
Rotation
TRPV Cation Channels

description: © 2018 Kasimova et al. The transient receptor potential channel vanilloid type 1 (TRPV1) is activated by a variety of endogenous and exogenous stimuli and is involved in nociception and body temperature regulation. Although the structure of TRPV1 has been experimentally determined in both the closed and open states, very little is known about its activation mechanism. In particular, the conformational changes that occur in the pore domain and result in ionic conduction have not yet been identified. Here we suggest a hypothetical molecular mechanism for TRPV1 activation, which involves rotation of a conserved asparagine in S6 from a position facing the S4-S5 linker toward the pore. This rotation is associated with hydration of the pore and dehydration of the four peripheral cavities located between each S6 and S4-S5 linker. In light of our hypothesis, we perform bioinformatics analyses of TRP and other evolutionary related ion channels, evaluate newly available structures, and reexamine previously reported water accessibility and mutagenesis experiments. These analyses provide several independent lines of evidence to support our hypothesis. Finally, we show that our proposed molecular mechanism is compatible with the prevailing theory that the selectivity filter acts as a secondary gate in TRPV1.
Cosmology with Minkowski functionals and moments of the weak lensing convergence field
Creators: name: Petri, Andrea
name: Haiman, Zoltán
name: Hui, Lam
name: May, Morgan
name: Kratochvil, Jan M.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We compare the efficiency of moments and Minkowski functionals (MFs) in constraining the subset of cosmological parameters (Omega_m,w,sigma_8) using simulated weak lensing convergence maps. We study an analytic perturbative expansion of the MFs in terms of the moments of the convergence field and of its spatial derivatives. We show that this perturbation series breaks down on smoothing scales below 5', while it shows a good degree of convergence on larger scales (15'). Most of the cosmological distinguishing power is lost when the maps are smoothed on these larger scales. We also show that, on scales comparable to 1', where the perturbation series does not converge, cosmological constraints obtained from the MFs are approximately 1.5-2 times better than the ones obtained from the first few moments of the convergence distribution --- provided that the latter include spatial information, either from moments of gradients, or by combining multiple smoothing scales. Including either a set of these moments or the MFs can significantly tighten constraints on cosmological parameters, compared to the conventional method of using the power spectrum alone.
description: 16 pages, 9 figures, 6 tables
A large-scale evaluation of computational protein function prediction
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Algorithms
Animals
Computational Biology
Databases, Protein
Exoribonucleases
Forecasting
Humans
Molecular Biology
Molecular Sequence Annotation
Proteins
Species Specificity

description: Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. © 2013 Nature America, Inc. All rights reserved.
A likelihood approach to estimate the number of co-infections
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2014
Subjects: Algorithms
Coinfection
Genetic Loci
Humans
Likelihood Functions
Malaria
Microsatellite Repeats
Models, Theoretical

description: The number of co-infections of a pathogen (multiplicity of infection or MOI) is a relevant parameter in epidemiology as it relates to transmission intensity. Notably, such quantities can be built into a metric in the context of disease control and prevention. Having applications to malaria in mind, we develop here a maximum-likelihood (ML) framework to estimate the quantities of interest at low computational and no additional costs to study designs or data collection. We show how the ML estimate for the quantities of interest and corresponding confidence-regions are obtained from multiple genetic loci. Assuming specifically that infections are rare and independent events, the number of infections per host follows a conditional Poisson distribution. Under this assumption, we show that a unique ML estimate for the parameter (λ) describing MOI exists which is found by a simple recursion. Moreover, we provide explicit formulas for asymptotic confidence intervals, and show that profile-likelihood-based confidence intervals exist, which are found by a simple twodimensional recursion. Based on the confidence intervals we provide alternative statistical tests for the MOI parameter. Finally, we illustrate the methods on three malaria data sets. The statistical framework however is not limited to malaria. © 2014 Schneider, Escalante.
Leggadina lakedownensis Watts 1976
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Leggadina
Leggadina lakedownensis

description: Leggadina lakedownensis Watts, 1976. Trans. R. Soc. S. Aust., 100(2): 105. TYPE LOCALITY: Australia, Queensland, Lakeland Downs. DISTRIBUTION: Cooktown region, N. Queensland (Australia).
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 5), pp. 504-560 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 520, DOI: 10.5281/zenodo.7353037
Motile bacteria, active biohybrids and cellular physiology
Creators: name: Le Nagard, Lucas
Publisher: name: The University of Edinburgh
Year: 2023
Subjects: flagella
propulsion
lipid membranes
sugar consumption

description: This thesis investigates bacterial motility from active matter and physiological perspectives using experiments and theoretical modelling. In the first part, I design and characterize a system made of motile Escherichia coli encapsulated in giant lipid vesicles. For slightly deflated vesicles, the bacteria extrude active membrane tubes that can propel the vesicles. I show that the propulsion arises from a physical coupling between the lipid membrane tubes and the flagella of the encapsulated bacteria and develop a simple theoretical model to estimate the propulsive force. In a second part, I present two studies using motility as a tool to gain insight into bacterial physiology. First, I study the motility of dense suspensions of Escherichia coli fermenting glucose. Using new experimental data gathered by others, I develop a semi-empirical model that quantitatively links the swimming speed of the bacteria to the concentration of protonated organic acids in anaerobic conditions. Secondly, I focus on bacterial motility during complete starvation. Combining single-cell and population-level experiments, I show that Escherichia coli maintains a motile phenotype in the early stages of starvation, but that the swimming speed and motile fraction decay over a few tens of hours. I show that the complete decay of motility in these conditions happens on a much faster timescale than cell death. Interestingly, while swimming speed and flagellar motor measurements both show that the motility fully decays in about 24 h in these conditions, they seem to return different temporal dynamics.
Potentially Singular Solutions of the 3D Incompressible Euler Equations
Creators: name: Luo, Guo
name: Hou, Thomas Y.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Numerical Analysis (math.NA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Whether the 3D incompressible Euler equations can develop a singularity in finite time from smooth initial data is one of the most challenging problems in mathematical fluid dynamics. This work attempts to provide an affirmative answer to this long-standing open question from a numerical point of view, by presenting a class of potentially singular solutions to the Euler equations computed in axisymmetric geometries. The solutions satisfy a periodic boundary condition along the axial direction and no-flow boundary condition on the solid wall. The equations are discretized in space using a hybrid 6th-order Galerkin and 6th-order finite difference method, on specially designed adaptive (moving) meshes that are dynamically adjusted to the evolving solutions. With a maximum effective resolution of over $(3 \times 10^{12})^{2}$ near the point of the singularity, we are able to advance the solution up to $τ_{2} = 0.003505$ and predict a singularity time of $t_{s} \approx 0.0035056$, while achieving a \emph{pointwise} relative error of $O(10^{-4})$ in the vorticity vector $ω$ and observing a $(3 \times 10^{8})$-fold increase in the maximum vorticity $\|ω\|_{\infty}$. The numerical data are checked against all major blowup (non-blowup) criteria, including Beale-Kato-Majda, Constantin-Fefferman-Majda, and Deng-Hou-Yu, to confirm the validity of the singularity. A local analysis near the point of the singularity also suggests the existence of a self-similar blowup in the meridian plane.
description: version 1: 81 pages, 86 figures; version 2: 57 pages, 44 figures, removed part of the technical details and streamlined the presentation
MPEC 2025-C84 : 2022 LJ15
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2025
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
The effects of structure anisotropy on lensing observables in an exact general relativistic setting for precision cosmology
Creators: name: Troxel, M. A.
name: Ishak, Mustapha
name: Peel, Austin
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The study of relativistic, higher order and nonlinear effects has become necessary in recent years in the pursuit of precision cosmology. We develop and apply here a framework to study gravitational lensing in exact models in general relativity that are not restricted to homogeneity and isotropy, and where full nonlinearity and relativistic effects are included. We apply the framework to a specific, anisotropic galaxy cluster model which is based on a modified NFW halo density profile and described by the Szekeres metric. We examine the effects of increasing levels of anisotropy in the galaxy cluster on lensing observables like the convergence and shear for various lensing geometries, finding a strong nonlinear response in both the convergence and shear for rays passing through anisotropic regions of the cluster. Deviation from the expected values in a spherically symmetric structure are asymmetric with respect to path direction and thus will persist as a statistical effect when averaged over some ensemble of such clusters. The resulting relative difference in various geometries can be as large as approximately 2%, 8%, and 24% in the measure of convergence for levels of anisotropy of 5%, 10%, and 15%, respectively, as a fraction of total cluster mass. For the total magnitude of shear, the relative difference can grow near the center of the structure to be as large as 15%, 32%, and 44% for the same levels of anisotropy, averaged over the two extreme geometries. The convergence is impacted most strongly for rays which pass in directions along the axis of maximum dipole anisotropy in the structure, while the shear is most strongly impacted for rays which pass in directions orthogonal to this axis, as expected. These effects due to anisotropic structures will affect lensing measurements and must be fully examined in an era of precision cosmology.
description: 26 pages, 8 figures, matches version published in JCAP
Exactly solvable counting statistics in weakly coupled open interacting spin systems
Creators: name: Buca, Berislav
name: Prosen, Tomaz
Publisher: name: arXiv
Year: 2013
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the full counting statistics for interacting quantum many-body spin systems weakly coupled to the environment. In the leading order in the system-bath coupling we derive exact spin current statistics for a large class of parity symmetric spin-1/2 systems driven by a pair of Markovian baths with local coupling operators. Interestingly, in this class of systems the leading order current statistics are universal and do not depend on details of the Hamiltonian. Furthermore, in the specific case of symmetrically boundary driven anisotropic Heisenberg ($XXZ$) spin 1/2 chain we derive explicitly the third-order non-linear corrections to the current statistics.
description: 4 pages in RevTex, with 1 pdf figure, version as accepted by Phys. Rev. Lett
Lemniscomys Trouessart 1881
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Lemniscomys

description: Lemniscomys Trouessart, 1881. Bull. Soc. d'Etudes Sci. Angers, 10: 124. REVIEWED BY: E. Van der Straeten (EVS). COMMENT: L. striatus species complex revised by Van der Straeten, 1975, Unpubl. Ph.D. Dissertation, Antwerp, and Van der Straeten and Verheyen, 1980, Mammalia, 44:73-82. ISIS NUMBER: 5301410011028000000.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 5), pp. 504-560 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 520, DOI: 10.5281/zenodo.7353037
description: {"references": ["Van der Straeten, E. 1975. Lemniscomys bellieri, a new species of Muridae from the Ivory Coast (Mammalia, Muridae). Revue de Zoologie Africaine, 89: 906 - 908.", "Van der Straeten, E., and W. N. Verheyen. 1980. Relations biometriques dans le groupe specifique Lemniscomys striatus (Mammalia, Muridae). Mammalia, 44: 73 - 82."]}
Lemniscomys barbarus
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Lemniscomys
Lemniscomys barbarus

description: Lemniscomys barbarus (Linnaeus, 1766). Syst. Nat., 12 th ed., Laddenda. TYPE LOCALITY: Morocco (= “Barbaria"). DISTRIBUTION: Tunisia; Algeria; Morocco; W. Sahara; Senegal; Gambia; Nigeria; Cameroun; Sudan; Ethiopia; Kenya; N. Uganda; Tanzania; E. Zaire. ISIS NUMBER: 5301410011028001001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 5), pp. 504-560 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 520, DOI: 10.5281/zenodo.7353037
Bifurcations of relative equilibria near zero momentum in Hamiltonian systems with spherical symmetry
Creators: name: Montaldi, James
Publisher: name: arXiv
Year: 2013
Subjects: subject: Dynamical Systems (math.DS)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 70H33, 58F14, 37J20

description: For Hamiltonian systems with spherical symmetry there is a marked difference between zero and non-zero momentum values, and amongst all relative equilibria with zero momentum there is a marked difference between those of zero and those of non-zero angular velocity. We use techniques from singularity theory to study the family of relative equilibria that arise as a symmetric Hamiltonian which has a group orbit of equilibria with zero momentum is perturbed so that the zero-momentum relative equilibrium are no longer equilibria. We also analyze the stability of these perturbed relative equilibria, and consider an application to satellites controlled by means of rotors.
description: 24 pp; to appear in J. Geometric Mechanics
A longitudinal study of post-traumatic growth and psychological distress in colorectal cancer survivors
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2015
Subjects: Adult
Aged
Aged, 80 and over
Colorectal Neoplasms
Emotional Adjustment
Female
Humans
Longitudinal Studies
Male
Middle Aged
Quality of Life
Stress, Psychological
Surveys and Questionnaires
Young Adult

description: © 2015 Occhipinti et al. The stability of post-traumatic growth overtime and the relationship between post-traumatic growth and traditional distress outcomes remains unclear. We tracked post-traumatic growth in a population-based sample of colorectal cancer patients from soon after diagnosis to five years subsequently to assess the heterogeneity of a post-traumatic growth response to cancer over time and describe the simultaneous and longitudinal relationships between post-traumatic growth and psychological distress. 1966 colorectal patients who were five months post diagnosis were assessed six times over a five year period. There was considerable heterogeneity associated with both psychological distress and benefit finding scores over time. However, both for benefit finding and psychological distress, the variation in individual scores suggested an underlying positive linear trend and both lagged and lagged change components. Specifically, benefit finding and psychological distress are mutual leading indicators of each other. First, benefit finding served as a leading indicator of distress, in that increases in reported benefit finding from year to year predicted higher future increases in psychological distress. As well, in an inverse relationship, psychological distress served as a leading indicator of benefit finding, such that increases in reported distress from year to year predicted lower future increases in benefit finding. Post-traumatic growth may reflect patients coping efforts to enhance perceptions of wellbeing in response to escalating cancer-related threats, acting as harbinger of increasing trajectories of psychological distress. This explanation is consistent with a cognitive dissonance response in which threats to the integrity of the self then lead to a tendency to accentuate positive aspects of the self.
Lemniscomys bellieri Van der Straeten 1975
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Lemniscomys
Lemniscomys bellieri

description: Lemniscomys bellieri Van der Straeten, 1975. Rev. Zool. Afr., 89:906. TYPE LOCALITY: Ivory Coast, Ayeremou (= Lamto). DISTRIBUTION: Guinea; Doka Woodland (Ivory Coast).
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 5), pp. 504-560 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 520, DOI: 10.5281/zenodo.7353037
Asynchronous Gossip for Averaging and Spectral Ranking
Creators: name: Borkar, Vivek S.
name: Makhijani, Rahul
name: Sundaresan, Rajesh
Publisher: name: arXiv
Year: 2013
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Information Theory (cs.IT)
subject: Systems and Control (eess.SY)
subject: Optimization and Control (math.OC)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Mathematics

description: We consider two variants of the classical gossip algorithm. The first variant is a version of asynchronous stochastic approximation. We highlight a fundamental difficulty associated with the classical asynchronous gossip scheme, viz., that it may not converge to a desired average, and suggest an alternative scheme based on reinforcement learning that has guaranteed convergence to the desired average. We then discuss a potential application to a wireless network setting with simultaneous link activation constraints. The second variant is a gossip algorithm for distributed computation of the Perron-Frobenius eigenvector of a nonnegative matrix. While the first variant draws upon a reinforcement learning algorithm for an average cost controlled Markov decision problem, the second variant draws upon a reinforcement learning algorithm for risk-sensitive control. We then discuss potential applications of the second variant to ranking schemes, reputation networks, and principal component analysis.
description: 14 pages, 7 figures. Minor revision
Lemniscomys griselda
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Lemniscomys
Lemniscomys griselda

description: Lemniscomys griselda (Thomas, 1904). Ann. Mag. Nat. Hist., ser. 7, 13:414. TYPE LOCALITY: Angola, Jinga country, Muene Coshi. DISTRIBUTION: Angola. COMMENT: Formerly included linulus and rosalia; see Van der Straeten, 1980, Rev. Zool. Afr„ 94: 185-201, Van der Straeten and Verheyen, 1980, Mammalia, 44:73, and Van der Straeten, 1980, Ann. Cape Prov. Mus. Nat. Hist., 13(5):55-62. ISIS NUMBER: 5301410011028002001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Rodentia (Part 5), pp. 504-560 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on pages 520-521, DOI: 10.5281/zenodo.7353037
description: {"references": ["Van der Straeten, E., and W. N. Verheyen. 1980. Relations biometriques dans le groupe specifique Lemniscomys striatus (Mammalia, Muridae). Mammalia, 44: 73 - 82."]}
The loop effects on the chargino decays $\tildeχ_1^\pm\to \tildeχ_1^0 f f^\prime$ in the MSSM
Creators: name: Xu, Qing-jun
name: Xu, Shu-sheng
name: Xiao, Zhen-jun
name: Jin, Li-gang
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The lighter chargino three body decays $\tildeχ_1^\pm\to \tildeχ_1^0 f f^\prime$ via the $W^\pm$ boson and the charged Higgs boson $H^\pm$ are studied in the R-parity conserved Minimal Supersymmetric Standard Model (MSSM). We treat $\tilde χ_1^\pm$ decays as production and decay of $W^\pm$ and $H^\pm$: i.e., $\tildeχ_1^\pm \to \tildeχ_1^0 W^\pm (H^\pm) \to \tildeχ_1^0 f f^\prime$. Both higgsino-like and wino-like $\tilde χ_1^\pm$ decays are well investigated. These decays are calculated at 1-loop level and the loop corrections are found to be less than three percent.The signal of the charged Higgs $H^\pm$ production from $\tilde χ_1^\pm$ decays are discussed. It will offer important information about the chargino and neutralino sector, as well as the charged Higgs sector in the MSSM.
description: 13 pages, 3 figures
Modeling Radiometric Uncertainty for Vision with Tone-mapped Color Images
Creators: name: Chakrabarti, Ayan
name: Xiong, Ying
name: Sun, Baochen
name: Darrell, Trevor
name: Scharstein, Daniel
name: Zickler, Todd
name: Saenko, Kate
Publisher: name: arXiv
Year: 2013
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: To produce images that are suitable for display, tone-mapping is widely used in digital cameras to map linear color measurements into narrow gamuts with limited dynamic range. This introduces non-linear distortion that must be undone, through a radiometric calibration process, before computer vision systems can analyze such photographs radiometrically. This paper considers the inherent uncertainty of undoing the effects of tone-mapping. We observe that this uncertainty varies substantially across color space, making some pixels more reliable than others. We introduce a model for this uncertainty and a method for fitting it to a given camera or imaging pipeline. Once fit, the model provides for each pixel in a tone-mapped digital photograph a probability distribution over linear scene colors that could have induced it. We demonstrate how these distributions can be useful for visual inference by incorporating them into estimation algorithms for a representative set of vision tasks.
$B_{1g}$-like pairing states in two-leg ladder iron superconductors
Creators: name: Lv, Weicheng
name: Moreo, Adriana
name: Dagotto, Elbio
Publisher: name: arXiv
Year: 2013
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Motivated by the recent report of superconductivity in Fe-based ladder materials, we study the pairing state of a multi-orbital t-J model defined on two-leg ladders using the standard mean-field theory. We find that the superconducting order parameters change sign between the $d_{xz}$ and $d_{yz}$ orbitals in most of the phase diagram. By analogy with the two-dimensional Fe planes, we conclude that the leading pairing channel of this state belongs to the $B_{1g}$ symmetry class, which is distinct from the common $s_{\pm}$ gap with the $A_{1g}$ symmetry. By smoothly interpolating from planes into ladders, we show that a first-order transition occurs between these two competing phases when the dimension of the system is reduced.
description: 10 pages, 11 figures, minor changes
A Loss-Of-Function Analysis Reveals That Endogenous Rem2 Promotes Functional Glutamatergic Synapse Formation and Restricts Dendritic Complexity
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2013
Subjects: Animals
Base Sequence
Cells, Cultured
DNA Primers
Dendrites
Glutamic Acid
HEK293 Cells
Hippocampus
Humans
Monomeric GTP-Binding Proteins
RNA Interference
Synapses

description: Rem2 is a member of the RGK family of small Ras-like GTPases whose expression and function is regulated by neuronal activity in the brain. A number of questions still remain as to the endogenous functions of Rem2 in neurons. RNAi-mediated Rem2 knockdown leads to an increase in dendritic complexity and a decrease in functional excitatory synapses, though a recent report challenged the specificity of Rem2-targeted RNAi reagents. In addition, overexpression in a number of cell types has shown that Rem2 can inhibit voltage-gated calcium channel (VGCC) function, while studies employing RNAi-mediated knockdown of Rem2 have failed to observe a corresponding enhancement of VGCC function. To further investigate these discrepancies and determine the endogenous function of Rem2, we took a comprehensive, loss-of-function approach utilizing two independent, validated Rem2-targeted shRNAs to analyze Rem2 function. We sought to investigate the consequence of endogenous Rem2 knockdown by focusing on the three reported functions of Rem2 in neurons: regulation of synapse formation, dendritic morphology, and voltage-gated calcium channels. We conclude that endogenous Rem2 is a positive regulator of functional, excitatory synapse development and a negative regulator of dendritic complexity. In addition, while we are unable to reach a definitive conclusion as to whether the regulation of VGCCs is an endogenous function of Rem2, our study reports important data regarding RNAi reagents for use in future investigation of this issue. © 2013 Moore et al.
Generalized north-south dynamics on the space of geodesic currents
Creators: name: Uyanik, Caglar
Publisher: name: arXiv
Year: 2013
Subjects: subject: Geometric Topology (math.GT)
subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: Primary 20F65, Secondary 57M, 37D

description: We prove uniform north-south dynamics type results for the action of $φ\in Out(F_{N})$ on the space of projectivized geodesic currents $\mathbb{P}Curr(S)=\mathbb{P}Curr(F_{N})$, where $φ$ is induced by a pseudo-Anosov homeomorphism on a compact surface S with boundary such that $π_{1}(S)=F_{N}$. As an application, we show that for a subgroup $H\le Out(F_N)$, containing an iwip, either $H$ contains a hyperbolic iwip or $H$ is contained in the image in $Out(F_N)$ of the mapping class group of a surface with a single boundary component.
description: 20 pages, 2 figures, v3: Minor corrections
A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses
Creators: name: (:Unkn) Unknown
Publisher: name: My University
Year: 2011
Subjects: wild horse
next-generation sequencing
mitochondrial DNA
nuclear DNA
phylogeny

description: The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered-two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117-0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow. © The Author(s) 2010.