cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Embedding high-level quantum mechanical approaches within linear-scaling density functional theory
Creators: name: Charlton, Robert John
Publisher: name: Imperial College London
Year: 2019

description: Advances in computational methods in recent decades have significantly expanded the range of problems in condensed matter physics that can be tackled from first principles. Linear-scaling density functional theory methods enable quantum mechanical calculations to be performed on systems containing tens of thousands of atoms, with modern approaches capable of reproducing the accuracy of plane wave DFT approaches. This opens up the possibility of treating highly complex molecular systems such as doped organic molecular crystals that require the dopant molecule to be contained within a large periodic structure. One example of such a system is pentacene in p-terphenyl, a system that finds use as a room-temperature maser. Understanding the maser mechanism requires both a highly accurate description of the pentacene molecule and a computationally efficient approach that can correctly capture the impact of the p-terphenyl host on the active pentacene subsystem. Quantum embedding allows an accurate but expensive hybrid functional to be embedded within a cheaper semi-local functional, for maximum combination of accuracy and efficiency in a DFT-in-DFT framework. In this dissertation we consider the implementation of embedded mean-field theory (EMFT) in the linear-scaling DFT software package ONETEP, enabling hybrid functionals to be used on selected subsystems within a cheaper DFT environment. This approach is validated for several types of molecular systems, including a crystalline structure containing several thousand atoms, demonstrating the potential of the EMFT approach when combined with linear-scaling and verifying the importance of using a large explicit host environment for accurate calculations.
Additional file 1 of Can disability accommodation needs stored in electronic health records help providers prepare for patient visits? A qualitative study
Creators: name: Mudrick, Nancy R.
name: Breslin, Mary Lou
name: Kyrian A. Nielsen
name: LeeAnn C. Swager
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Science Policy

description: Additional file 1: Understanding the Role of Functional Limitation Measures in Electronic Health Records Focus Group Questions – 4.2017
Proto–Planetary Nebulae as Explosions: Bullets versus Jets and Nebular Shaping
Creators: name: Mitran, Sorin
name: Dennis, Timothy
name: Blackman, Eric
name: Cunningham, Andrew
name: Balick, Bruce
name: Frank, Adam
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Many proto-planetary nebulae (PPNs) appear as narrow collimated structures sometimes showing multiple, roughly aligned lobes. In addition, many PPN flows have been shown to have short acceleration times. In this paper we explore whether jet or "bullet" (a massive clump) models fit the observations of individual collimated lobes adequately by comparing simulations of both radiatively cooled (stable) jets and bullets. We find that the clump model is favored over jets because (1) it leads to greater collimation of outflows, (2) it accounts better and more naturally for ringlike structures observed in the PPN CRL 618, and (3) it is more successful in reproducing the Hubble-flow character of observed kinematics in some PPNs. In addition, bullets naturally account for observed multipolar flows, since the likely MHD launch mechanisms required to drive outflows make multiple nonaligned jets unlikely. We also find that the bow shock heads of bullets take on a -shaped configuration, whereas bow shock heads of jets are more -shaped. The differences in these configurations occur on a linear scale corresponding to an angular size of the order of ~3''—sufficiently large to suggest a viable means of distinguishing bullets from jets in observations. We argue that PPN outflows may be driven by explosive MHD launch mechanisms such as those discussed in the context of supernovae (SNe) and gamma-ray bursts (GRBs).
Molecular signatures associated with diuron exposure on rat urothelial mitochondria
Creators: name: Lima, Thania Rios Rossi
name: de Oliveira Lima, Estela
name: Delafiori, Jeany
name: Catharino, Rodrigo Ramos
name: de Camargo, João Lauro Viana
name: Pereira, Lílian Cristina
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Diuron, 3-(3,4-dichlorophenyl)-1,1-dimethylurea, is a worldwide used herbicide whose biotransformation gives rise to the metabolites, 3-(3,4-dichlorophenyl)-1-methylurea (DCPMU) and 3,4-dichloroaniline (DCA). Previous studies indicate that diuron and/or its metabolites are toxic to the bladder urothelium of the Wistar rats where, under certain conditions of exposure, they may induce successively urothelial cell degeneration, necrosis, hyperplasia and eventually tumors. The hypothesis was raised that the molecular initiating event (MIE) of this Adverse Outcome Pathway is the mitochondrial toxicity of those compounds. Therefore, this study aimed to investigate in vitro the metabolic alterations resulting from urothelial mitochondria isolated from male Wistar rats exposure to diuron, DCPMU and DCA at 10 and 100 µM. A non-targeted metabolomic analysis using mass spectrometry showed discriminative clustering among groups and alterations in the intensity abundance of membrane-associated molecules phosphatidylcholine, phosphatidylinositol and phosphatidylserine, in addition to methylhexanoyl-CoA and, particularly for diuron 100 µM, dehydro-L-gulonate, all of them involved in critical mitochondrial metabolism. Collectively, these data indicate the mitochondrial dysfunction as an MIE that triggers cellular damage and death observed in previous studies.
Changepoint analysis using Gaussian process regression: a Bayesian statistical model for the identification of lithological strata in geotechnical engineering
Creators: name: Bendel, Jens
Publisher: name: Imperial College London
Year: 2019

description: Around the Earth's surface it is common for the ground to be made up of layers of different soil stacked on top of each other. This composition of layers can for example be the result of marine deposition over the course of thousands or millions of years. The field of geotechnical engineering studies these lithological layers and their effect on engineering work such as tunnelling or the construction of buildings and bridges. A standard procedure to determine a segmentation of the ground into individual layers is to take a drilling core and examine slices sampled at various depths. Typical methods to distinguish soil layers are based on microfossil content or measurements of physical quantities such as the water content of the soil. Common practice is the inspection of these properties by eye using expert engineering judgement. Such approaches lack scientific rigour and fail to address the uncertainty that is inherent to any such analysis. This thesis discusses statistical methodology (changepoint analysis) in order to propose a reproducible scientific approach for the identification of soil layers based on measurements of water content. With a focus on uncertainty quantification the proposed approach combines a Bayesian changepoint method with a Gaussian process regression model for each soil layer. This Gaussian process changepoint method is applied to data from the construction site of underground railway tunnels. The method correctly identifies well-established layers while suggesting that a previously proposed subdivision of a particular layer (A3) is not supported by the dataset. Further results indicate that more research work is needed with regard to the collection of data as well as the development of statistical methodology. Overall, this thesis shows that the proposed focus on mathematical rigour and uncertainty quantification is very much needed.
Cosmological consequences of classical flavor-space locked gauge field radiation
Creators: name: Bielefeld, Jannis
name: Caldwell, Robert R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We propose a classical SU(2) gauge field in a flavor-space locked configuration as a species of radiation in the early universe, and show that it would have a significant imprint on a primordial stochastic gravitational wave spectrum. In the flavor-space locked configuration, the electric and magnetic fields of each flavor are parallel and mutually orthogonal to other flavors, with isotropic and homogeneous stress-energy. Due to the non-Abelian coupling, the gauge field breaks the symmetry between left- and right-circularly polarized gravitational waves. This broken chiral symmetry results in a unique signal: non-zero cross correlation of the cosmic microwave background temperature and polarization, $TB$ and $EB$, both of which should be zero in the standard, chiral symmetric case. We forecast the ability of current and future CMB experiments to constrain this model. Furthermore, a wide range of behavior is shown to emerge, depending on the gauge field coupling, abundance, and allocation into electric and magnetic field energy density. The fluctuation power of primordial gravitational waves oscillates back and forth into fluctuations of the gauge field. In certain cases, the gravitational wave spectrum is shown to be suppressed or amplified by up to an order of magnitude depending on the initial conditions of the gauge field.
description: 20 pages, 11 figures
Task-based fMRI investigation of the newborn brain: sensorimotor development and learning
Creators: name: Dall'Orso, Sofia
Publisher: name: Imperial College London
Year: 2019

description: Human brain development relies upon the interaction between genetic and environmental factors, and the latter plays a critical role during the perinatal period. In this period, neuronal plasticity through experience-dependent activity is enhanced in the sensory systems, and drive the maturation of the brain. While plasticity is essential for maturation, it is also a source of vulnerability as altered early experiences may interact with the normal course of development. This is particularly evident in infants born preterm, who are prematurely exposed to a sensory-rich environment, and at risk or neurodevelopmental disorders. In keeping with the somatosensory system being at a critical period for development during late gestation, sensorimotor disorders, such as cerebral palsy, are more common in preterm compared with full-term born infants. It is therefore important to understand the normal trajectory of sensorimotor development and how this may be moulded by early sensory experiences. It is well acknowledged that the sensorimotor cortex is topographically organised so that different body parts map to a specific location within the cortex and this map is generally referred to as the ``homunculus". Although the somatotopy has been well characterised in the mature brain, it remains unknown when this organisation emerges during development. Animal studies hints that functional cortical maps might emerge across the equivalent period to the third trimester of human gestation, nevertheless there is currently no evidence. Therefore, I first investigated the topography of the preterm somatosensory cortex in a group of newborn infants. In this purpose I used fMRI and automated robotic tools and measured the functional responses to different sensory simulations (delivered to the mouth, wrists and ankles). The results provide evidence that it is possible to identify distinct areas in the somatosensory cortex devoted to different body parts even in the preterm brain supporting the presence of an immature \textit{homunculus}. Next, I wanted to investigate how activity and development in the sensorimotor system are influenced by experience. Experience-dependent plasticity is the basis of learning (e.g. adaptive behaviour), which is observed in newborn infants. Associative learning in particular has been widely investigated in infants, however, the underlining neuronal processes have previously been poorly understood. To study the neural correlates of associative learning in newborn infants, I developed and used a classical conditioning paradigm in combination with robot-assisted fMRI. The results confirm that associative learning can occur even at this early stage of life and with non-aversive stimuli. More importantly, I could observe learning-induced changes in brain activity within the primary sensory cortices, suggesting that such experience can shape cortical circuitry and is likely to influence early brain development.
THE EFFECTS OF THE pep NUCLEAR REACTION AND OTHER IMPROVEMENTS IN THE NUCLEAR REACTION RATE LIBRARY ON SIMULATIONS OF THE CLASSICAL NOVA OUTBURST
Creators: name: Sparks, W. M.
name: Starrfield, S.
name: Hix, W. R.
name: Timmes, F. X.
name: Iliadis, C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Nova explosions occur on the white dwarf (WD) component of a cataclysmic variable binary stellar system which is accreting matter lost by its companion. When sufficient material has been accreted by the WD, a thermonuclear runaway (TNR) occurs and ejects material in what is observed as a classical nova (CN) explosion. We have continued our studies of TNRs on 1.25 M sun and 1.35 M sun WDs (ONeMg composition) under conditions which produce mass ejection and a rapid increase in the emitted light, by examining the effects of changes in the nuclear reaction rates on both the observable features and the nucleosynthesis during the outburst. In order to improve our calculations over previous work, we have incorporated a modern nuclear reaction network into our one-dimensional, fully implicit, hydrodynamic computer code. We find that the updates in the nuclear reaction rate libraries change the amount of ejected mass, peak luminosity, and the resulting nucleosynthesis. Because the evolutionary sequences on the 1.35 M sun WD reach higher temperatures, the effects of library changes are more important for this mass. In addition, as a result of our improvements, we discovered that the pep reaction (p + e - + p {yields} d +more » ?) was not included in our previous studies of CN explosions (or to the best of our knowledge those of other investigators). Although the energy production from this reaction is not important in the Sun, the densities in WD envelopes can exceed 104 g cm-3 and the presence of this reaction increases the energy generation during the time that the p-p chain is operating. Since it is only the p-p chain that is operating during most of the accretion phase prior to the final rise to the TNR, the effect of the increased energy generation is to reduce the evolution time to the peak of the TNR and, thereby, the accreted mass as compared to the evolutionary sequences done without this reaction included. As expected from our previous work, the reduction in accreted mass has important consequences on the characteristics of the resulting TNR and is discussed in this paper.« less
On coupling resolved and unresolved physical processes in finite element discretisations of geophysical fluids
Creators: name: Bendall, Thomas Matthew
Publisher: name: Imperial College London
Year: 2019

description: At the heart of modern numerical weather forecasting and climate modelling lie simulations of two geophysical fluids: the atmosphere and the ocean. These endeavours rely on numerically solving the equations that describe these fluids. A key challenge is that the fluids contain motions spanning a range of scales. As the small-scale processes (unresolved by the numerical model) affect the resolved motions, they need to be described in the model, which is known as parametrisation. One major class of methods for numerically solving such partial differential equations is the finite element method. This thesis focuses on the coupling of such parametrised processes to the resolved flow within finite element discretisations. Four sets of research are presented, falling under two main categories. The first is the development of a compatible finite element discretisation for use in numerical weather prediction models, so as to avoid the bottleneck in computational scalability associated with the convergence at the poles of latitude-longitude grids. We present a transport scheme for use with the lowest-order function spaces in such a compatible finite element method, which is motivated by the coupling of the resolved and unresolved processes within the model. This then facilitates the use of the lower-order spaces within Gusto, a toolkit for studying such compatible finite element discretisations. Then, we present a compatible finite element discretisation of the moist compressible Euler equations, parametrising the unresolved moist processes. This is a major step in the development of Gusto, extending it to describe its first unresolved processes. The second category with which this thesis is concerned is the stochastic variational framework presented by Holm [Variational principles for stochastic fluid dynamics, P. Roy. Soc. A-Math. Phy. 471 (2176), (2015)]. In this framework, the effect of the unresolved processes and their uncertainty is expressed through a stochastic component to the advecting velocity. This framework ensures the circulation theorem is preserved by the stochastic equations. We consider the application of this formulation to two simple geophysical fluid models. First, we discuss the statistical properties of an enstrophy-preserving finite element discretisation of the stochastic quasi-geostrophic equation. We find that the choice of discretisation and the properties that it preserves affects the statistics of the solution. The final research presented is a finite element discretisation of the stochastic Camassa-Holm equation, which is used to numerically investigate the formation of ‘peakons’ within this set-up, finding that they do still always form despite the noise’s presence.
Context-aware learning for robot-assisted endovascular catheterization
Creators: name: Chi, Wenqiang
Publisher: name: Imperial College London
Year: 2019

description: Endovascular intervention has become a mainstream treatment of cardiovascular diseases. However, multiple challenges remain such as unwanted radiation exposures, limited two-dimensional image guidance, insufficient force perception and haptic cues. Fast evolving robot-assisted platforms improve the stability and accuracy of instrument manipulation. The master-slave system also removes radiation to the operator. However, the integration of robotic systems into the current surgical workflow is still debatable since repetitive, easy tasks have little value to be executed by the robotic teleoperation. Current systems offer very low autonomy, potential autonomous features could bring more benefits such as reduced cognitive workloads and human error, safer and more consistent instrument manipulation, ability to incorporate various medical imaging and sensing modalities. This research proposes frameworks for automated catheterisation with different machine learning-based algorithms, includes Learning-from-Demonstration, Reinforcement Learning, and Imitation Learning. Those frameworks focused on integrating context for tasks in the process of skill learning, hence achieving better adaptation to different situations and safer tool-tissue interactions. Furthermore, the autonomous feature was applied to next-generation, MR-safe robotic catheterisation platform. The results provide important insights into improving catheter navigation in the form of autonomous task planning, self-optimization with clinical relevant factors, and motivate the design of intelligent, intuitive, and collaborative robots under non-ionizing image modalities.
Three dimensional correlative imaging for measurement of strain in cartilage and cartilage replacement materials
Creators: name: Clark, Jeffrey Nicholas
Publisher: name: Imperial College London
Year: 2020

description: Articular cartilage injuries are debilitating and often lead to osteoarthritis: a foremost cause of disability worldwide. Currently no interventions provide satisfactory long-term outcomes. Successful regeneration of articular cartilage through early stage intervention would be life-changing for millions of individuals. Providing suitable mechanical stimulation to promote articular cartilage regrowth is a crucial element to achieve success. Articular cartilage is complex with in-homogenous mechanical properties which have not been not well characterised: a clear barrier to designing suitable orthopaedic implants for this application. Furthermore, it is necessary to interrogate intended implants to ensure they are providing appropriate loading to cells throughout the entire volumetric device. Digital volume correlation (DVC) offers the potential for non-destructive three-dimensional visualisation of deformation. The technique relies upon tracking the displacement of features within a sample across three-dimensional scans with successive in-situ loading applied. Analysis provides quantification of displacement and strain components within the three-dimensional volume. A method was developed to utilise the cells within articular cartilage as natural features for DVC and was validated against established 2D histological analysis. DVC of human articular cartilage provided 3D strain measurements with sufficient spatial resolution to inform implant design, with measurements compared against manually-calculated values (R2 = 0.93). Subsequently DVC of novel hybrid materials implants enabled strain to be visualised within individual struts of the scaffolds (R2 = 0.98): providing the necessary intra-device resolution for successful matching of mechanical properties. Finally the complete tissue-biomaterial system was assessed using DVC with an explant analysed after six weeks of implantation within an ovine model, enabling measurement of implant micromotion and strain fields across the system components. In conclusion, DVC was successfully utilised to characterise strain within articular cartilage, novel biomaterials and tissue-biomaterial systems. Incorporating the technique as part of the device development pathway could be an effective tool to regenerate articular cartilage.
Exchange interaction between $J$-multiplets
Creators: name: Iwahara, Naoya
name: Chibotaru, Liviu F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Analytical expressions for the exchange interaction between $J$-multiplets of interacting metallic centers are derived on the basis of a complete electronic model. A common belief that this interaction can be approximated by an isotropic form $\propto {\mathbf{J}}_1\cdot{\mathbf{J}}_2$ (or $\propto {\mathbf{J}}_1\cdot{\mathbf{S}}_2$ in the case of interaction with an isotropic spin) is found to be ungrounded. It is also shown that the often used "1/U approximation" for the description of the kinetic contribution of the exchange interaction is not valid in the case of $J$-multiplets. The developed theory can be used for microscopic description of exchange interaction in materials containing lanthanides, actinides and some transition metal ions.
description: 20 pages, 3 figures
Additional file 3 of Overexpression of an ethylene-forming ACC oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max
Creators: name: Zabala, Gracia
name: Anupreet Kour
name: Vodkin, Lila O.
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Plant Biology

description: Additional file 3 Expression levels of ethylene forming enzyme gene (ACO) family members based on RNA-Seq reads aligning to the transcript sequence of Williams 82.
Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation
Creators: name: Ralph, Duncan K.
name: Matsen, Frederick A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Genomics (q-bio.GN)
subject: FOS: Biological sciences

description: VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.
THE EFFECTS OF FLOW-INHOMOGENEITIES ON MOLECULAR CLOUD FORMATION: LOCAL VERSUS GLOBAL COLLAPSE
Creators: name: Frank, Adam
name: Carroll-Nellenback, Jonathan
name: Heitsch, Fabian
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Observational evidence from local star-forming regions mandates that star formation occurs shortly after, or even during, molecular cloud formation. Models of molecular cloud formation in large-scale converging flows have identified the physical mechanisms driving the necessary rapid fragmentation. They also point to global gravitational collapse driving supersonic turbulence in molecular clouds. Previous cloud formation models have focused on turbulence generation, gravitational collapse, magnetic fields, and feedback. Here, we explore the effect of structure in the flow on the resulting clouds and the ensuing gravitational collapse. We compare two extreme cases, one with a collision between two smooth streams, and one with streams containing small clumps. We find that structured converging flows lead to a delay of local gravitational collapse ("core formation"). Hence, the cloud has more time to accumulate mass, eventually leading to a strong global collapse, and thus to a high core formation rate. Uniform converging flows fragment hydrodynamically early on, leading to the rapid onset of local gravitational collapse and an overall low core formation rate. This is also mirrored in the core mass distribution: the uniform initial conditions lead to more low-mass cores than the clumpy initial conditions. Kinetic (Ek) and gravitational energy (Eg) budgets suggest that collapse is only prevented for Ek Eg, which occurs for large scales in the smooth flow, and for small scales for the clumpy flow. Whenever Ek ≈ Eg, we observe gravitational collapse on those scales. Signatures of chemical abundance variations evolve differently for the gas phase and for the stellar population. For smooth flows, the forming cloud is well mixed, while its stellar population retains more information about the initial metallicities. For clumpy flows, the gas phase is less well mixed, while the stellar population has lost most of the information about its origin.
Proton‐induced Thermonuclear Reaction Rates for A = 20–40 Nuclei
Creators: name: Iliadis, Christian
name: Starrfield, Sumner
name: Wiescher, Michael
name: Thompson, William
name: D'Auria, John
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2001

description: Proton-induced reaction rates on 26 stable and 29 unstable target nuclei in the mass A = 20–40 region have been evaluated and compiled. Recommended reaction rates, assuming that all interacting nuclei are in the ground state, are presented in tabular form on a temperature grid in the range T = 0.01–10.0 GK. Most reaction rates involving stable targets were normalized to a set of measured standard resonance strengths in the sd shell. For the majority of reaction rates, experimental information from transfer reaction studies has been used consistently. Our results are compared with recent statistical model (Hauser-Feshbach) calculations. Reaction rate uncertainties are presented and amount to several orders of magnitude for many of the reactions. Several of these reaction rates and/or their corresponding uncertainties deviate from results of previous compilations. In most cases, the deviations are explained by the fact that new experimental information became available recently. Examples are given for calculating reaction rates and reverse reaction rates for thermally excited nuclei from the present results. The survey of literature for this review was concluded in 2000 August.
Fox News Poll: Coronavirus/Biden VP Pick/Economy: March 2020
Creators: name: Fox News
Publisher: name: Roper Center for Public Opinion Research
Year: 2020

description: Registered to vote (1); President Donald Trump job approval (1); Congress job approval (1); interest in presidential election (1); importance of outcome of November election (1); Democratic vs. Republican presidential and vice-presidential candidates (4); Biden promising to pick a woman as his running mate (1); economic conditions (1); family better or worse off than 4 years ago (1); economy get better or worse over next year (1); nervous or confident about nation's economy (1); concern about health care and economy (5); news about coronavirus outbreak (1); concern about coronavirus (6); approve/disapprove of responses to coronavirus (6); federal government response to coronavirus (8); prepared to deal with coronavirus outbreak (3): reactions to coronavirus outbreak (2); federal government could have slowed spread of virus (1); changed everyday life in response to coronavirus (1); actions in past week (6); know anyone who has coronavirus (1); household lost job or had hours reduced (1); vote in 2016 presidential election (1); work situation (1); how often do you attend religious services (1).
Canonical Trees, Compact Prefix-free Codes and Sums of Unit Fractions: A Probabilistic Analysis
Creators: name: Heuberger, Clemens
name: Krenn, Daniel
name: Wagner, Stephan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: Combinatorics (math.CO)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60C05, 05A16

description: For fixed $t\ge 2$, we consider the class of representations of $1$ as sum of unit fractions whose denominators are powers of $t$ or equivalently the class of canonical compact $t$-ary Huffman codes or equivalently rooted $t$-ary plane "canonical" trees. We study the probabilistic behaviour of the height (limit distribution is shown to be normal), the number of distinct summands (normal distribution), the path length (normal distribution), the width (main term of the expectation and concentration property) and the number of leaves at maximum distance from the root (discrete distribution).
Estimation of Distance of Singing Conspecifics by the Carolina Wren
Creators: name: Richards, Douglas G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1981

description: Measurements of the propagation of sound in a forest have shown that signal degradation is unavoidable but to some degree predictable. Carolina Wrens (Thryothorus ludovicianus) have a song structure suited for the estimation of distance by a comparison of the relative degradation of the components of the signal. Playback experiments using song recorded at two distances from a singing wren demonstrated that wrens can use cues other than the absolute attentuation of the sound for the estimation of the distance of the singer. The wrens responded to the near-sounding song by attack and to the far-sounding song by countersinging. The ability of the wrens to use the distance information in the song serves the same purpose as the recognition of familiar neighbors: conservation of time and energy used in territorial defense.
Further Holographic Investigations of Big Bang Singularities
Creators: name: Engelhardt, Netta
name: Hertog, Thomas
name: Horowitz, Gary T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We further explore the quantum dynamics near past cosmological singularities in anisotropic Kasner-AdS solutions using gauge/gravity duality. The dual description of the bulk evolution involves N=4 super Yang-Mills on the contracting branch of an anisotropic de Sitter space and is well defined. We compute two-point correlators of Yang-Mills operators of large dimensions using spacelike geodesics anchored on the boundary. The correlator between two points separated in a direction with negative Kasner exponent p always exhibits a pole at horizon scales, in any dimension, which we interpret as a dual signature of the classical bulk singularity. We find evidence that the pole is absent at finite coupling in the dual field theory, indicating the singularity is resolved.
description: 26 pages, 3 figures. Version 3: added discussion on the validity of the geodesic approximation
Maximally coherent mixed states: Complementarity between maximal coherence and mixedness
Creators: name: Singh, Uttam
name: Bera, Manabendra Nath
name: Dhar, Himadri Shekhar
name: Pati, Arun Kumar
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum coherence is a key element in topical research on quantum resource theories and a primary facilitator for design and implementation of quantum technologies. However, the resourcefulness of quantum coherence is severely restricted by environmental noise, which is indicated by the loss of information in a quantum system, measured in terms of its purity. In this work, we derive the limits imposed by the mixedness of a quantum system on the amount of quantum coherence that it can possess. We obtain an analytical trade-off between the two quantities that upperbound the maximum quantum coherence for fixed mixedness in a system. This gives rise to a class of quantum states, "maximally coherent mixed states," whose coherence cannot be increased further under any purity-preserving operation. For the above class of states, quantum coherence and mixedness satisfy a complementarity relation, which is crucial to understand the interplay between a resource and noise in open quantum systems.
description: 8 pages, 1 figure, REVTex 4.1, close to published version
A Light-Independent Magnetic Compass in the Leatherback Sea Turtle
Creators: name: Lohmann, Catherine M. Fittinghoff
name: Lohmann, Kenneth J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1993

description: Diverse animals can orient to the earth's magnetic field (1-6), but the mechanism or mechanisms undrlying magnetic field detection have not been determined. Behavioral (7-9) amd neurophysiological (10-12) results suggest that the transduction process underlying magnetic compass orientation in vertebrates is light-dependent, a finding consistent with theoretical models proposing that magnetoreception involves a modulation of the response of retinal photoreceptors to light (13, 14). We report, however, that leatherback sea turtle (Dermochelys coriacea) hatchlings orient to the geomagnetic field in complete darkness. Thus, light-dependence is not a universal feature of vertebrate magnetic compasses.
Additional file 1 of The greater use of flavoured snus among ever-smokers versus never-smokers in Norway
Creators: name: Vedoy, Tord Finne
name: Lund, Karl Erik
Publisher: name: figshare
Year: 2020
Subjects: subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1. Beta coefficients and model fit for Model 1 and Model 2. Adjusted probabilities of using snus with flavour and 95% confidence intervals (CI) in all groups from Model 2. Bonferroni corrected tests of differences.
Additional file 1 of Signaling pathways have an inherent need for noise to acquire information
Creators: name: Azpeitia, Eugenio
name: Balanzario, Eugenio P.
name: Wagner, Andreas
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Supplementary figures 1 to 9, supplementary tables 1 to 5, and supplementary texts 1 and 2.
The effectiveness of a technologically facilitated classroom-based early reading intervention: The targeted Reading Intervention
Creators: name: Vernon-Feagans, Lynne
name: Amendum, Steven J.
name: Ginsberg, Marnie C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The purpose of this study was to evaluate the efficacy of a classroom-teacher-delivered reading intervention for struggling readers called the Targeted Reading Intervention (TRI), designed particularly for kindergarten and first-grade teachers and their struggling students in rural, low-wealth communities. The TRI was delivered via an innovative Web-conferencing system using laptop computers and webcam technology. Seven schools from the southwestern United States were randomly assigned to experimental and control conditions in a cluster randomized design. All children in the study (n = 364) were administered a battery of standardized reading skill tests in the fall and spring of the school year. Intent-to-treat analyses were conducted to estimate mixed models of children’s 1-year growth in Word Attack, Letter/Word Identification, Passage Comprehension, and Spelling of Sounds. Results showed that struggling readers from experimental schools outperformed those from control schools on all spring reading outcomes, controlling for fall scores.
Protein-tyrosine Kinase Pyk2 Mediates Endothelin-induced p38 MAPK Activation in Glomerular Mesangial Cells
Creators: name: Sorokin, Andrey
name: Kozlowski, Piotr
name: Philip, Andrew
name: Graves, Lee
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2001

description: Endothelin-1 (ET-1), a member of a family of 21 amino acid peptides possessing vasoconstrictor properties, is known to stimulate mesangial cell proliferation. In this study, ET-1 (100 nm) induced a rapid activation of p21(ras) in human glomerular mesangial cells (HMC). Inhibition of Src family tyrosine kinase activation with [4-Amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine] or chelation of intracellular free calcium with 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid acetoxymethyl ester significantly decreased ET-1dependent p21(ras) activation and suggested the involvement of the cytoplasmic proline-rich tyrosine kinase Pyk2. We have observed that Pyk2 was expressed in HMC and was tyrosine-phosphorylated within 5 min of ET-1 treatment. ET-1-induced activation of Pyk2 was further confirmed using phospho-specific anti-Pyk2 antibodies. Surprisingly, Src kinase activity was required upstream of ET-1-induced autophosphorylation of Pyk2. To determine whether Pyk2 autophosphorylation mediated ET-1-dependent p21(ras) activation, adenovirus-mediated transfer was employed to express a dominant-negative form of Pyk2 (CRNK). CRNK expression inhibited ET-1-induced endogenous Pyk2 autophosphorylation, but did not abolish ET-1-mediated increases in GTP-bound p21(ras) levels. ET-1-induced activation of the p38 MAPK (but not ERK) pathway was inhibited in HMC and in rat glomerular mesangial cells expressing the dominant-negative form of Pyk2. These findings suggest that the engagement of Pyk2 is important for ET-1-mediated p38 MAPK activation and hence the biological effect of this peptide in mesangial cells.
Hierarchical heuristic species delimitation under the multispecies coalescent model with migration
Creators: name: Kornai, Daniel
name: Jiao, Xiyun
name: Ji, Jiayi
name: Flouris, Thomas
name: Yang, Ziheng
Publisher: name: Zenodo
Year: 2024
Subjects: BPP
genealogical divergence index
Gene flow
multispecies coalescent |
Species delimitation
giraffes
milksnakes
sunfish

description: The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species phylogeny) may be formulated as instances of MSC models (e.g., MSC for one species versus MSC for two species) and compared using Bayesian model selection. This approach, implemented in the program bpp, has been found to be prone to over-splitting. Alternatively heuristic criteria based on population parameters (such as population split times, population sizes, and migration rates) estimated from genomic data may be used to delimit species. Here we develop hierarchical merge and split algorithms for heuristic species delimitation based on the genealogical divergence index (𝑔𝑑𝑖) and implement them in a python pipeline called hhsd. We characterize the behavior of the 𝑔𝑑𝑖 under a few simple scenarios of gene flow. We apply the new approaches to a dataset simulated under a model of isolation by distance as well as three empirical datasets. Our tests suggest that the new approaches produced sensible results and were less prone to over-splitting. We discuss possible strategies for accommodating paraphyletic species in the hierarchical algorithm, as well as the challenges of species delimitation based on heuristic criteria.
description: Funding provided by: Biotechnology and Biological Sciences Research CouncilROR ID: https://ror.org/00cwqg982Award Number: BB/T003502/1
Funding provided by: Biotechnology and Biological Sciences Research CouncilROR ID: https://ror.org/00cwqg982Award Number: BB/X007553/1
Funding provided by: Biotechnology and Biological Sciences Research CouncilROR ID: https://ror.org/00cwqg982Award Number: BB/R01356X/1
Funding provided by: Natural Science Foundation of China (NSFC)*Crossref Funder Registry ID: Award Number: 12101295
description: The data are analyzed using our new python pipeline called HHSD.
Additional file 1 of The absolute risk of gout by clusters of gout-associated comorbidities and lifestyle factors—30 years follow-up of the Malmö Preventive Project
Creators: name: Fatima, Tahzeeb
name: Nilsson, Peter M.
name: Turesson, Carl
name: Dehlin, Mats
name: Dalbeth, Nicola
name: Jacobsson, Lennart T. H.
name: Kapetanovic, Meliha C.
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Marine Biology
subject: Computational Biology

description: Additional file 1. Supplemental material. Figure S1 to S2 and Tables S1 to S4.
Are Firms Successful at Selective Hedging?
Creators: name: Crabb, Peter R.
name: Haushalter, David
name: Brown, Gregory W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: We analyze the corporate risk management policies of 44 companies in the gold mining industry. Firms tend to decrease hedging as prices move against them—behavior contrary to that predicted by risk management theory. These results, along with new survey evidence, suggest that firms attempt to time market prices, so-called selective hedging. Although estimates show a statistically significant ability of producers to favorably adjust hedge ratios, this can be attributed to sample-specific negative autocorrelation in gold prices. Economic gains to selective hedging are small, and no evidence suggests that selective hedging leads to superior operating or financial performance.
N=2 supersymmetric Pais-Uhlenbeck oscillator
Creators: name: Masterov, Ivan
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We construct an N=2 supersymmetric extension of the Pais-Uhlenbeck oscillator for distinct frequencies of oscillation. A link to a set of decoupled N=2 supersymmetric harmonic oscillators with alternating sign in the Hamiltonian is introduced. Symmetries of the model are discussed in detail. The investigation of a quantum counterpart of the constructed model shows that the corresponding Fock space contains negative norm states and the energy spectrum of the system is unbounded from below.
description: Published version