cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Hierarchical heuristic species delimitation under the multispecies coalescent model with migration
Creators: name: Kornai, Daniel
name: Flouris, Thomas
name: Yang, Ziheng
Publisher: name: Zenodo
Year: 2023
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 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 under the MSC model (such as population/species divergence times, population sizes, and migration rates) estimated from genomic sequence data may be used to delimit species. Here we extend the approach of species delimitation using the genealogical divergence index (𝑔𝑑𝑖) to develop hierarchical merge and split algorithms for heuristic species delimitation and implement them in a python pipeline called hhsd. Applied to data simulated under a model of isolation by distance, the approach was able to recover the correct species delimitation, whereas model comparison by bpp failed. Analyses of empirical datasets suggest that the procedure may be less prone to over-splitting. We discuss possible strategies for accommodating paraphyletic species in the procedure, as well as the challenges of species delimitation based on heuristic criteria.
description: Funding provided by: Biotechnology and Biological Sciences Research Council
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000268
Award Number: BB/T003502/1Funding provided by: Biotechnology and Biological Sciences Research Council
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000268
Award Number: BB/X007553/1Funding provided by: Biotechnology and Biological Sciences Research Council
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000268
Award Number: BB/R01356X/1
description: The data are analyzed using our new python pipeline called HHSD.
Real-time observations of microtubule dynamic instability in living cells
Creators: name: Cassimeris, L.
name: Pryer, Nancy K.
name: Salmon, E. D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1988

description: Individual microtubule dynamics were observed in real time in primary cultures of newt lung epithelium using video-enhanced differential interference contrast microscopy and digital image processing. The linear filaments observed in cells corresponded to microtubules based on three criteria: (a) small particles translocated along them; (b) the majority of them disappeared after incubation in nocodazole; (c) and the distribution observed by differential interference contrast correlated with anti-tubulin immunofluorescence staining of the same cell. Microtubules were most clearly observed at the leading edge of cells located at the periphery of the epithelial sheet. Microtubules exhibited dynamic instability behavior: individual microtubules existed in persistent phases of elongation or rapid shortening. Microtubules elongated at a velocity of 7.2 micron/min +/- 0.3 SEM (n = 42) and rapidly shortened at a velocity of 17.3 micron/min +/- 0.7 SEM (n = 35). The transitions between elongation and rapid shortening occurred abruptly and stochastically with a transition frequency of 0.014 s-1 for catastrophe and 0.044 s-1 for rescue. Approximately 70% of the rapidly shortening microtubules were rescued and resumed elongation within the 35 x 35 micron microscopic field. A portion of the microtubule population appeared differentially stable and did not display any measurable elongation or shortening during 10-15-min observations.
Dirac dark matter with a charged mediator: a comprehensive one-loop analysis of the direct detection phenomenology
Creators: name: Ibarra, Alejandro
name: Wild, Sebastian
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We analyze the direct detection signals of a toy model consisting of a Dirac dark matter particle which couples to one Standard Model fermion via a scalar mediator. For all scenarios, the dark matter particle scatters off nucleons via one loop-induced electromagnetic and electroweak moments, as well as via the one-loop exchange of a Higgs boson. Besides, and depending on the details of the model, the scattering can also be mediated at tree level via the exchange of the scalar mediator or at one loop via gluon-gluon interactions. We show that, for thermally produced dark matter particles, the current limits from the LUX experiment on these scenarios are remarkably strong, even for dark matter coupling only to leptons. We also discuss future prospects for XENON1T and DARWIN and we argue that multi-ton xenon detectors will be able to probe practically the whole parameter space of the model consistent with thermal production and perturbativity. We also discuss briefly the implications of our results for the dark matter interpretation of the Galactic GeV excess.
description: 20 pages, 5 figures. Matches published version
Functional studies of the domains of talin
Creators: name: Nuckolls, Glen H.
name: Turner, Christopher E.
name: Burridge, Keith
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1990

description: The protein talin has two domains of approximately 200 and 47 kD, which can be cleaved apart by a variety of proteases. To examine the function of these two structural domains of talin, we have digested purified talin with a calcium-dependent protease and separated the resulting fragments chromatographically. Both fragments were radioiodinated and used to probe Western blots of whole fibroblasts and chicken gizzard extracts. The large talin fragment bound to vinculin and metavinculin. The small fragment did not demonstrate any binding in this assay. The fragments were labeled fluorescently and microinjected into fibroblasts in tissue culture. The large talin fragment incorporated quickly into focal adhesions where it remained stable for at least 14 h. The small fragment associated with focal adhesions of fibroblasts but was also distributed diffusely in the cytoplasm and the nucleus. These experiments suggest that talin has at least two sites that contribute to its localization in focal adhesions. Intact talin microinjected into Madin-Darby bovine kidney epithelial cells localized to the focal adhesions but was excluded from the zonulae adherentes, despite the localization of vinculin to both of these sites. In contrast, the large talin fragment, when microinjected into these epithelial cells, incorporated into both focal adhesions and zonulae adherentes. The difference in localization between the large talin fragment and intact talin seems to be due to the removal of the small domain. This difference in localization suggests that talin binding sites in zonulae adherentes have limited accessibility.
An uncertainty principle and sampling inequalities in Besov spaces
Creators: name: Jaming, Philippe
name: Malinnikova, Eugenia
Publisher: name: arXiv
Year: 2015
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics

description: We extend Strichartz's uncertainty principle [18] from the setting of the Sobolov space W 1,2 (R) to more general Besov spaces B 1/p p,1 (R). The main result gives an estimate from below of the trace of a function from the Besov space on a uniformly distributed discrete subset. We also prove the corresponding result in the multivariate case and discuss some applications to irregular approximate sampling in critical Besov spaces.
Galaxy And Mass Assembly (GAMA) Blended Spectra Catalog: Strong Galaxy-Galaxy Lens and Occulting Galaxy Pair Candidates
Creators: name: Holwerda, B. W.
name: Baldry, I. K.
name: Alpaslan, M.
name: Bauer, A.
name: Bland-Hawthorn, J.
name: Brough, S.
name: Brown, M. J. I.
name: Cluver, M. E.
name: Conselice, C.
name: Driver, S. P.
name: Hopkins, A. M.
name: Jones, D. H.
name: Lopez-Sanchez, A. R.
name: Loveday, J.
name: Meyer, M. J.
name: Moffett, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present the catalogue of blended galaxy spectra from the Galaxy And Mass Assembly (GAMA) survey. These are cases where light from two galaxies are significantly detected in a single GAMA fibre. Galaxy pairs identified from their blended spectrum fall into two principal classes: they are either strong lenses, a passive galaxy lensing an emission-line galaxy; or occulting galaxies, serendipitous overlaps of two galaxies, of any type. Blended spectra can thus be used to reliably identify strong lenses for follow-up observations (high resolution imaging) and occulting pairs, especially those that are a late-type partly obscuring an early-type galaxy which are of interest for the study of dust content of spiral and irregular galaxies. The GAMA survey setup and its autoz automated redshift determination were used to identify candidate blended galaxy spectra from the cross-correlation peaks. We identify 280 blended spectra with a minimum velocity separation of 600 km/s, of which 104 are lens pair candidates, 71 emission-line-passive pairs, 78 are pairs of emission-line galaxies and and 27 are pairs of galaxies with passive spectra. We have visually inspected the candidates in the Sloan Digital Sky Survey (SDSS) and Kilo Degree Survey (KiDS) images. Many blended objects are ellipticals with blue fuzz (Ef in our classification). These latter "Ef" classifications are candidates for possible strong lenses, massive ellipticals with an emission-line galaxy in one or more lensed images. The GAMA lens and occulting galaxy candidate samples are similar in size to those identified in the entire SDSS. This blended spectrum sample stands as a testament of the power of this highly complete, second-largest spectroscopic survey in existence and offers the possibility to expand e.g., strong gravitational lens surveys.
description: 12 pages, 10 figures, 3 tables. Table 3 full length version is in the appendix. Accepted for publication by MNRAS, typo fixed so Figure 2 is included properly
Supplemental material description from Bioapatite in shark centra studied by wide-angle and by small-angle X-ray scattering
Creators: name: Park, J.S.
name: Almer, J. D.
name: James, K. C.
name: Natanson, L. J.
name: Stock, S. R.
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: 90301 Biomaterials
subject: FOS: Medical engineering

description: information on block cutting
Structure and dynamics of water at the Pt(111) interface: Molecular dynamics study
Creators: name: Motakabbir, K.
name: Raghavan, K.
name: Berkowitz, M.
name: Foster, K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1991

description: We prescribe an analytical form of the interaction potential between rigid water and a rigid platinum metal surface, which takes into account the surface symmetry and corrugation. Using this potential we perform a molecular dynamics computer simulation on water lamina restricted by two PtC 111) surfaces and investigate the structure and dynamics of water at the Pt interface. At 300 K the water layer adjacent to the metal surface displays solid-like properties. Patches of ice-like structure embedded in this layer are observed in the simulation. The next two layers of water display ordering similar to ice-I. Beyond these three layers the structure and dynamics of water are bulk-like.
Additional file 1 of Regulation of intracellular transition metal ion level with a pH-sensitive inorganic nanocluster to improve therapeutic angiogenesis by enriching conditioned medium retrieved from human adipose derived stem cells
Creators: name: Kim, Yeong Hwan
name: Euiyoung Jung
name: Gwang-Bum Im
name: Kim, Yu-Jin
name: Kim, Sung-Won
name: Gun-Jae Jeong
name: Jang, Young Charles
name: Park, Kyung Min
name: Dong-Ik Kim
name: Taekyung Yu
name: Bhang, Suk Ho
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Additional file 1: Additional experiment.
Dynamics of ion solvation in a Stockmayer fluid
Creators: name: Perera, Lalith
name: Berkowitz, Max L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1992

description: Molecular dynamics computer simulations were performed to study the dynamics of the ionic solvation in a Stockmayer fluid. The simulations show that the solvent relaxation proceeds in two time regimes. Most of the relaxation occurs in a short time period during which the relaxation process can be described by a gaussian function. The long time regime can be described by an exponential relaxation. The decay exponent of the relaxation function in this regime is the same as the exponent describing the decay of the single dipole correlation function. In addition, the contribution of the rotational and translational modes of the solvent to the energy relaxation was investigated. It was found that when the rotational mode is the dominant mode of the solvent motion the relaxation occurs from the outside-in, in accordance with the Onsager snowball picture. When the influence of the translational mode is increased the Onsager picture breaks down.
Non-universal BBN bounds on electromagnetically decaying particles
Creators: name: Poulin, Vivian
name: Serpico, Pasquale Dario
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: In Poulin and Serpico [Phys. Rev. Lett. 114, 091101 (2015)] we have recently argued that when the energy of a photon injected in the primordial plasma falls below the pair-production threshold, the universality of the non-thermal photon spectrum from the standard theory of electromagnetic cascades onto a photon background breaks down. We showed that this could reopen or widen the parameter space for an exotic solution to the 'lithium problem'. Here we discuss another application, namely the impact that this has on non-thermal big bang nucleosynthesis constraints from 4He, 3He and 2H, using the parametric example of monochromatic photon injection of different energies. Typically, we find tighter bounds than those existing in the literature, up to more than one order of magnitude. As a consequence of the non-universality of the spectrum, the energy-dependence of the photodissociation cross-sections is important. We also compare the constraints obtained with current level and future reach of cosmic microwave background spectral distortion bounds.
description: 8 pages, 7 figures. v2: minor typographical corrections, extended comments and references
The emerging concept of glycocalyx damage as the trigger of heart failureonset and progression
Creators: name: Kowacz, Magdalena
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 320101
subject: Cardiology (incl. cardiovascular diseases)

description: The suppression of adrenergic and renin-angiotensin-aldosterone system (RAAS) activity, exaggerated due to hypoperfusion-related hypoxia and/or sodium retention, is crucial for drugs’ efficacy in heart failure (HF). Both, insufficient oxygenation and excess sodium impair the glycocalyx-dependent microcroperfusion and peripheral metabolism, therefore enhancing the adrenergic and RAAS activity. The local renal and pulmonary RAAS activity and hypoxia increase sodium retention. Interstitial sodium accumulation activates interstitial inflammation and coagulation disorders that further diminish glycocalyx-supported microperfusion and peripheral metabolism. The main trigger of glycocalyx damage in reduced ejection fraction (EF) HF is hypoxia; whereas, in HF preserved EF sodium retention prevails; both stimulate left ventricular (LV) cardiac output (CO), however, impair microperfusion and metabolic heat production. Infrared-dependent, surface-induced flow (SIF) and diamagnetic properties of oxygenated haemoglobin; both improve non-Newtonian blood flow. Therefore, the temperature-driven SIF augments the deoxygenated erythrocytes' flow, while the pulmonary oxygenation of haemoglobin, by diamagnetic properties, enables frictionless erythrocytes’ flow in the oxygenated blood compartments complementing the cardiac function in HF.
On the Scalability of Cost-EffectiveMetropolitan Network Architectures for the 5G-Era Using Flexible Coherent Interfaces
Creators: name: Costa, Nelson
name: Eira, António
name: Napoli, António
name: Pedro, João
Publisher: name: Zenodo
Year: 2019
Subjects: Metropolitan Network
5G
Network architecture

description: The potential of coherent interfaces with flexible modulation formats and symbol rates is assessed for various metro network architectures. The results show that per-node throughputs in the range of multiple Tbit/s are possible even with low-complexity express and add/drop architectures.
description: Presented at 11th Conference on Telecommunications (Conftele 2019)
Structure and dynamics of Cl − (H 2 O) 20 clusters: The effect of the polarizability and the charge of the ion
Creators: name: Berkowitz, Max L.
name: Perera, Lalith
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1992

description: The effect of the polarizability and the sign of the ionic charge were studied in C1(H2O)20 clusters using molecular dynamics computer simulation technique. From our simulations we concluded that the reduction in the ionic polarizability did not significantly change the
structure and dynamics of the Cl - (H20)20 cluster, but the inversion of the sign of the ionic
charge produced a large effect. The energetic considerations helped us to understand why CIis
located on the surface of the cluster. By being on the surface the anion permits the creation
of the hydrogen bonded network between water molecules and that lowers the total energy of
the cluster. Simulations with the inverted sign of the ionic charge correspond to that with a
hypothetical "Cl + " ion which is similar in size and polarizability to a Cs + ion. The dynamical
structures and the quenched structures ofCl + (H20)20 clusters are compared with the
idealized structure of the Cs + (HZO)20 cluster proposed recently [A. Selinger and A. W.
Castleman, Jr., J. Phys. Chern. 95, 8442 (1991)].
A double molecular disc in the triple-barred starburst galaxy NGC 6946: structure and stability
Creators: name: Romeo, Alessandro B.
name: Fathi, Kambiz
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Fluid Dynamics (physics.flu-dyn)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: The late-type spiral galaxy NGC 6946 is a prime example of molecular gas dynamics driven by "bars within bars". Here we use data from the BIMA SONG and HERACLES surveys to analyse the structure and stability of its molecular disc. Our radial profiles exhibit a clear transition at distance R ~ 1 kpc from the galaxy centre. In particular, the surface density profile breaks at R ~ 0.8 kpc and is well fitted by a double exponential distribution with scale lengths R_1 ~ 200 pc and R_2 ~ 3 kpc, while the 1D velocity dispersion sigma decreases steeply in the central kpc and is approximately constant at larger radii. The fact that we derive and use the full radial profile of sigma rather than a constant value is perhaps the most novel feature of our stability analysis. We show that the profile of the Q stability parameter traced by CO emission is remarkably flat and well above unity, while the characteristic instability wavelength exhibits clear signatures of the nuclear starburst and inner bar within bar. We also show that CO-dark molecular gas, stars and other factors can play a significant role in the stability scenario of NGC 6946. Our results provide strong evidence that gravitational instability, radial inflow and disc heating have driven the formation of the inner structures and the dynamics of molecular gas in the central kpc.
description: MNRAS, in press
Hands-on Demonstration of Open-Source Filterless-Aware Offline Planning and Analysis Tool for WDM Networks
Creators: name: Pavon-Marino, Pablo
name: Garrich, Miquel
name: Moreno-Muro, Francisco Javier
name: Quagliotti, Marco
name: Riccardi, Emilio
name: Rafel, Albert
name: Andrew Lord
Publisher: name: Zenodo
Year: 2020

description: This material was used as "poster" for the presentation of: https://zenodo.org/record/3895685 We demonstrate an open-source filterless-aware multilayer WDM-network planning
 tool, that allows hands-on creation of mixed filterless/ed topologies and the application of built-in
 or user-developed algorithms and analysis tools for line engineering, spectrum and cost planning.
Mobility of stretched water
Creators: name: Vaisman, Iosif I.
name: Perera, Lalith
name: Berkowitz, Max L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1993

description: To study the mobility of stretched SPC/E water and its dependence on temperature and density, five molecular dynamics computer simulation runs were performed. Three runs were performed at temperature 300 K and densities 1.0, 0.9, and 0.8 g/cc. Two more runs were performed at temperature 273 K and densities 1.0 and 0.9 g/cc. At temperature 300 K, the translational diffusion coefficient of the stretched SPC/E water increased with the stretch, at temperature 273 K the translational diffusion decreased with the stretch. This behavior is correlated with the observed changes in the hydrogen bonding pattern of water.To study the mobility of stretched SPC/E water and its dependence on temperature and density, five molecular dynamics computer simulation runs were performed. Three runs were performed at temperature 300 K and densities 1.0, 0.9, and 0.8 g/cc. Two more runs were performed at temperature 273 K and densities 1.0 and 0.9 g/cc. At temperature 300 K, the translational diffusion coefficient of the stretched SPC/E water increased with the stretch, at temperature 273 K the translational diffusion decreased with the stretch. This behavior is correlated with the observed changes in the hydrogen bonding pattern of water.
Homotopy colimits and global observables in Abelian gauge theory
Creators: name: Benini, Marco
name: Schenkel, Alexander
name: Szabo, Richard J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Algebraic Topology (math.AT)
subject: Category Theory (math.CT)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 70S15, 81T13, 55U15, 55N20

description: We study chain complexes of field configurations and observables for Abelian gauge theory on contractible manifolds, and show that they can be extended to non-contractible manifolds by using techniques from homotopy theory. The extension prescription yields functors from a category of manifolds to suitable categories of chain complexes. The extended functors properly describe the global field and observable content of Abelian gauge theory, while the original gauge field configurations and observables on contractible manifolds are recovered up to a natural weak equivalence.
description: 24 pages. v2: 25 pages, Sections 3.2 and 4.2 expanded, one reference added. Published in Letters in Mathematical Physics
Stabilization energies of Cl − , Br − , and I − ions in water clusters
Creators: name: Berkowitz, Max L.
name: Perera, Lalith
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1993

description: Molecular dynamics computer simulations were performed on clusters of Cl-(H20)n (n =2, ... ,15). From the simulations we calculated the stabilization energies of the anion in the cluster. These energies were compared with the values of stabilization energies obtained from the photodetachment spectra of X-(H20)n clusters (X=CI-, Br-, or 1-). The comparison confirms the hypothesis that the anion is attached to the water cluster.
Non-decaying hydrodynamic interactions along narrow channels
Creators: name: Misiunas, Karolis
name: Pagliara, Stefano
name: Lauga, Eric
name: Lister, John R.
name: Keyser, Ulrich F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Particle-particle interactions are of paramount importance in every multi-body system as they determine the collective behaviour and coupling strength. Many well-known interactions like electro-static, van der Waals or screened Coulomb, decay exponentially or with negative powers of the particle spacing r. Similarly, hydrodynamic interactions between particles undergoing Brownian motion decay as 1/r in bulk, and are assumed to decay in small channels. Such interactions are ubiquitous in biological and technological systems. Here we confine two particles undergoing Brownian motion in narrow, microfluidic channels and study their coupling through hydrodynamic interactions. Our experiments show that the hydrodynamic particle-particle interactions are distance-independent in these channels. This finding is of fundamental importance for the interpretation of experiments where dense mixtures of particles or molecules diffuse through finite length, water-filled channels or pore networks.
description: 4 figures
Active dipole clusters: from helical motion to fission
Creators: name: Kaiser, Andreas
name: Popowa, Katarina
name: Löwen, Hartmut
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The structure of a finite particle cluster is typically determined by total energy minimization. Here we consider the case where a cluster of soft sphere dipoles becomes active, i.e. when the individual particles exhibit an additional self-propulsion along their dipole moments. We numerically solve the overdamped equations of motion for soft-sphere dipoles in a solvent. Starting from an initial metastable dipolar cluster, the self-propulsion generates a complex cluster dynamics. The final cluster state has in general a structure widely different to the initial one, the details depend on the model parameters and on the protocol of how the self-propulsion is turned on. The center-of-mass of the cluster moves on a helical path, the details of which are governed by the initial cluster magnetization. An instantaneous switch to a high self-propulsion leads to fission of the cluster. However, fission does not occur if the self-propulsion is increased slowly to high strengths. Our predictions can be verified through experiments with self-phoretic colloidal Janus-particles and for macroscopic self-propelled dipoles in a highly viscous solvent.
description: 9 pages, 7 figures
Structures of Cl − (H 2 O) n and F − (H 2 O) n ( n =2,3,...,15) clusters. Molecular dynamics computer simulations
Creators: name: Perera, Lalith
name: Berkowitz, Max L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1994

description: We have performed molecular dynamics calculations on Cl−(H2O) n and F−(H2O) n (n=2,3,...,15) clusters. The calculations show that the F− ion is solvated in these clusters, while Cl− remains attached to the water in the clusters. We also obtained the minimum energy structures for the Cl−(H2O) n and F−(H2O) n (n=6,7,8) clusters. From the comparison of these structures with the dynamical structures we conclude that the solvation of the F− ion is due to the entropy effect.
Impact of the solid Earth mass adjustment by the 2011 Tohoku-Oki earthquake on the regional sea level and hydrological mass change recovery from GRACE
Creators: name: Jeon, Taehwan
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Physical Sciences and Mathematics
subject: GRACE
subject: 2011 Tohoku-Oki earthquake
subject: GRACE earthquake correction

description: The monthly gravity changes due to the 2011 Tohoku-Oki earthquake.
Additional file 1 of MR-proANP and incident cardiovascular disease in patients with type 2 diabetes with and without heart failure with preserved ejection fraction
Creators: name: Jensen, Jesper
name: Schou, Morten
name: Kistorp, Caroline
name: Faber, Jens
name: Hansen, Tine W.
name: Jensen, Magnus T.
name: Andersen, Henrik U.
name: Rossing, Peter
name: Vilsbøll, Tina
name: Jørgensen, Peter G.
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Hematology

description: Additional file 1: Table S1. Competing risk analyses with Fine-Gray method with all-cause mortality as competing risk to CV event. Table S2: Associations between MR-proANP and echocardiographic measures.
Effect of the treatment of long‐range forces on the dynamics of ions in aqueous solutions
Creators: name: Essmann, Ulrich
name: Perera, Lalith
name: Berkowitz, Max
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1995

description: The goal of the present work is to study the dependence of the limiting ionic mobility of such anions as fluoride, chloride, and bromide in water on the way the long-range forces are treated in the computer simulations. With this in mind we have performed molecular dynamics computer simulations where the long-range electrostatic forces were treated using: (a) simple truncation procedure, (b) energy switching procedure, (c) reaction field method, and (d) Ewald summation technique. Our analysis shows that the switching procedure with the short-range switching function introduces artifacts into the simulations. These artifacts are responsible for the faster decay and oscillations in the velocity autocorrelation function of the ions and therefore for the lower value of the diffusion coefficients.
Chemical composition and nutritional value of nine wild edible mushrooms from Northwestern Tunisia
Creators: name: Ouali, Zouhour
name: Chaar, Hatem
name: Venturella, Giuseppe
name: Cirlincione, Fortunato
name: Gargano, Maria Letizia
name: Jaouani, Atef
Publisher: name: Italian Journal of Mycology
Year: 2023

description: The chemical composition evaluation and the nutritional value of nine most widespread wild edible mushroom species (Agaricus arvensis, Cantharellus cibarius, C. lutescens, Craterellus cornucopioides, Hericium erinaceus, Hydnum repandum, Lactarius deliciosus, Pleurotus pulmonarius, and Ramaria flavescens) and much collected in northwestern Tunisia, have been analyzed and determined according to standard methodologies. The chemical composition of edible mushrooms was validated by statistical PCA analyzes. Overall results showed that most of the studied species had interesting values for almost all measured variables. In particular, the species H. erinaceus had the highest quantity of carbohydrates (89.70%), oleic (24.05%), and docosahexaenoic acid (3.19%), phenolic compounds (11.25 mg g-1 dw), flavonoids (57.5 mg g-1 dw), and minerals K, Mg and Ca but also the lowest content of proteins (4.80%) and carbohydrates (3.96%). On the other hand, the species P. pulmonarius had the lowest lipid content (7.30%) and the lowest caloric value (371.76 Kcal). These promising data can be exploited by taking advantage of the high-quality nutritional value of these interesting species.
description: Italian Journal of Mycology, Vol. 52 (2023)
Itinerant ferromagnetism in the As 4$p$ conduction band of Ba$_{0.6}$K$_{0.4}$Mn$_{2}$As$_{2}$ identified by x-ray magnetic circular dichroism
Creators: name: Ueland, B. G.
name: Pandey, Abhishek
name: Lee, Y.
name: Sapkota, A.
name: Choi, Y.
name: Haskel, D.
name: Rosenberg, R. A.
name: Lang, J. C.
name: Harmon, B. N.
name: Johnston, D. C.
name: Kreyssig, A.
name: Goldman, A. I.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: X-ray magnetic circular dichroism (XMCD) measurements on single-crystal and powder samples of Ba$_{0.6}$K$_{0.4}$Mn$_{2}$As$_{2}$ show that the ferromagnetism below $T_{\textrm{C}}\approx$ 100 K arises in the As $4p$ conduction band. No XMCD signal is observed at the Mn x-ray absorption edges. Below $T_{\textrm{C}}$, however, a clear XMCD signal is found at the As $K$ edge which increases with decreasing temperature. The XMCD signal is absent in data taken with the beam directed parallel to the crystallographic $\textrm{c}$ axis indicating that the orbital magnetic moment lies in the basal plane of the tetragonal lattice. These results show that the previously reported itinerant ferromagnetism is associated with the As $4p$ conduction band and that distinct local-moment antiferromagnetism and itinerant ferromagnetism with perpendicular easy axes coexist in this compound at low temperature.
description: 6 pages; Supplemental Material Included; The text in version 2 is slightly different from the text in version 1
Transport and particle-hole asymmetry in graphene on boron nitride
Creators: name: DaSilva, Ashley M.
name: Jung, Jeil
name: Adam, Shaffique
name: MacDonald, Allan H.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: All local electronic properties of graphene on a hexagonal boron nitride (hBN) substrate exhibit spatial moiré patterns related to lattice constant and orientation differences between shared triangular Bravais lattices. We apply a previously derived effective Hamiltonian for the $π$-bands of graphene on h-BN to address the carrier-dependence of transport properties, concentrating on the conductivity features at four electrons and four holes per unit cell. These transport features measure the strength of Bragg scattering of $π$-electrons off the moiré pattern, and exhibit a striking particle-hole asymmetry that we trace to specific features of the effective Hamiltonian that we interpret physically.
Additional file 2 of Immune-related adverse events: a retrospective look into the future of oncology in the intensive care unit
Creators: name: Joseph, Adrien
name: Simonaggio, Audrey
name: Stoclin, Annabelle
name: Vieillard-Baron, Antoine
name: Geri, Guillaume
name: Oudard, Stéphane
name: Michot, Jean-Marie
name: Lambotte, Olivier
name: Azoulay, Elie
name: Lemiale, Virginie
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Cardiology

description: Additional file 2: Figure S2. A: Pie chart of ICI treatments (n = 112). B: Pie chart of primary tumor sites (n = 112). C: Radar chart of types of irAE according to class of ICI (n = 29). Each class of ICI is represented in a different color and the number of each type of complication is featured on an axis. D: Status at ICU discharge according to the type of irAE (n = 29). The number patients alive and dead at discharge from ICU for each type of complication is featured on axis in blue and yellow color.
Compressed sensing for ECG signal compression using DWT based sensing matrices
Creators: name: Parkale, Yuvraj V.
name: Nalbalwar, Sanjay L.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Space Science
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: In this article, we have investigated the 1-D discrete wavelet transform (DWT)-based measurement matrices for electrocardiogram (ECG) compression. Moreover, the current work examines the suitability of the diverse DWT matrices, namely Symlets, Battle, Coiflets, Vaidyanathan, and Beylkin wavelet families, for ECG compression. Furthermore, this article shows the comparative performance study of the proposed DWT matrices with conventional deterministic and random measurement matrices. Overall, the Battle1 wavelet-based measurement matrices demonstrate the enhanced performance against the db3, coif5, and sym6 based measurement matrices in terms of Percentage Root-Mean Squared Difference (PRD), Root Mean Square Error (RMSE), and Signal-to-Noise Ratio (SNR). Finally, it was seen that the proposed Battle1 matrix demonstrates the improved performance against the conventional measurement matrices such as the Karhunen–Loeve transform (KLT), Discrete Cosine Transform (DCT) matrix, and random Hadamard measurement matrix. Thus, the result shows the adequacy of DWT measurement matrices for the compression of ECG.
Collisional Penrose Process in Rotating Wormhole Spacetime
Creators: name: Tsukamoto, Naoki
name: Bambi, Cosimo
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In a collisional Penrose process, two particles coming from the asymptotically flat region collide in the ergosphere of a compact object. The collision produces two new particles, one with positive energy and one with negative energy. When the particle with positive energy escapes to infinity, the process extracts energy from the compact object. In this paper, we study the collisional Penrose process in a rotating wormhole spacetime. We consider the simple case of a head-on collision at the throat of a Teo wormhole. We find that the process of energy extraction from a Teo wormhole can be substantially more efficient than the collisional Penrose process in the Kerr black hole spacetime.
description: 8 pages, 2 figures. v2: corrected a few typos
Cube to cage transitions in (H 2 O) n ( n =12, 16, and 20)
Creators: name: Perera, Lalith
name: Sremaniak, Laura S.
name: Berkowitz, Max
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1996

description: Molecular dynamics computer simulations were performed for (H2O)n (n=12, 16, and 20) followed by systematic quenching under a polarizable and a nonpolarizable model to determine the minimum energy structures each favored. Ab initio calculations were done on several minima for (H2O)12 to determine their relative energies. The polarizable model prefers cagelike structures for all cluster sizes, whereas the nonpolarizable model predicts minima of fused cubes for (H2O)12 and (H2O)16 but makes the transition to a cagelike minimum at (H2O)20.
Fox News Poll: Coronavirus/2020 Election/Relief Package: April 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); Vice-president Joe Biden vs. President Donald Trump for President (1); economic conditions (1); economy get better or worse over next year (1); favorability of presidential candidates (2); concern about coronavirus (8); approve/disapprove of responses to coronavirus (6); United States moving in right/wrong direction on coronavirus pandemic (1); worst is over or yet to come (1); Trump reaction to coronavirus outbreak (1); federal government could have slowed spread of virus (1); Trump's handling of coronavirus outbreak (4); federal government response to coronavirus (2); coronavirus relief package passed by Congress (1); changed everyday life in response to coronavirus (1); friendly interactions with other people since coronavirus (1); silver linings of coronavirus outbreak (1); know anyone who has coronavirus (1); household lost job or had hours reduced (1); vote in 2016 presidential election (1).
Majorana Entanglement Bridge
Creators: name: Plugge, S.
name: Zazunov, A.
name: Sodano, P.
name: Egger, R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study the concurrence of entanglement between two quantum dots in contact to Majorana bound states on a floating superconducting island. The distance between the Majorana states, the charging energy of the island, and the average island charge are shown to be decisive parameters for the efficiency of entanglement generation. We find that long-range entanglement with basically distance-independent concurrence is possible over wide parameter regions, where the proposed setup realizes a "Majorana entanglement bridge". We also study the time-dependent concurrence obtained after one of the tunnel couplings is suddenly switched on, which reveals the timescales for generating entanglement. Accurate analytical expressions for the concurrence are derived both for the static and the time-dependent case. Our results indicate that entanglement formation in interacting Majorana devices can be fully understood in terms of an interplay of elastic cotunneling (also referred to as "teleportation") and crossed Andreev reflection processes.
description: 16 pages, 8 figures, version to appear in PRB
CENTRE: A Bioconductor package for cell- type specific enhancer-target prediction
Creators: name: De Vargas, Sara Lopez Ruiz
name: Rapakoulia, Trisevgeni
name: Persia Akbari-Omgba
name: Laupert, Verena
name: Vingron, Martin
Publisher: name: F1000 Research Limited
Year: 2024

description: Enhancers are non-coding DNA regions ranging from 100bp to 1000bp in size. They serve as a landing space for Transcription Factors and interact with

promoter regions to regulate gene expression dynamically. The configuration of active enhancer-promoter interactions is cell-type and condition-specific.

Identifying active enhancer-promoter pairs is crucial to understanding gene regulation, phenotypes, and diseases. Up to now, several computational methods

have been developed to predict enhancer gene interactions, but they require many epigenomic and transcriptomic experimental assays to generate cell-type-

specific predictions. Thus, inferring enhancer gene interactions becomes laborious and costly, especially when looking for cell type (CT) specific contacts.



Recently, we introduced the workflow of CENTRE[1], aimed at predicting CT-specific enhancer-target interactions with minimal experimental input. CENTRE

uses an XGBoost[2] classifier to predict enhancer target interactions in a CT-specific manner, relying solely on gene expression and ChIP-seq data for three

histone modifications pertinent to the CT of interest. Leveraging available datasets, CENTRE combines cell-type-agnostic statistics with CT-specific features.

For enhanced software accessibility, we now implement the CENTRE workflow as a Bioconductor package and introduce a novel Hi-C module, enabling users

to incorporate Hi-C data seamlessly without needing to provide it themselves. CENTRE has undergone extensive validation across diverse datasets and cell

types, consistently demonstrating comparable or superior performance to existing algorithms reliant on extensive experimental data.
The solvation of Cl − , Br − , and I − in acetonitrile clusters: Photoelectron spectroscopy and molecular dynamics simulations
Creators: name: Markovich, Gil
name: Berkowitz, Max
name: Perera, Lalith
name: Cheshnovsky, Ori
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1996

description: We present the photoelectron spectra of Cl−, Br−, and I− solvated in acetonitrile clusters (CH3CN) n with n=1–33, 1–40, and 1–55, respectively, taken with 7.9 eV photon energy. Anion–solvent electrostatic stabilization energies are extracted from the measured vertical electron binding energies. The leveling of stabilization energies beyond n=10–12 for the three halides signifies the completion of the first solvation layer. This is different from the behavior of anion–water clusters which probably do not fill the first solvation layer, but rather form surface solvation states. Classical molecular dynamics simulations of halide–acetonitrile clusters reproduce the measured stabilization energies and generate full solvation shells of 11–12, 12, and 12–13 solvent molecules for Cl−, Br−, and I−, respectively. Ordered shell structures with high stability were found for the clusters of Cl−, Br−, and I− with n=9, 9, and 12. This special stability is reflected in the intensity distribution of the clusters in the mass spectra. Larger anion–acetonitrile clusters have the molecules beyond the first solvation layer packed in a small droplet which is attached to the first layer. It is suggested that in general, anions solvated in large clusters of polar solvents, might be located close to their surface.
Urban Magnetism Through The Lens of Geo-tagged Photography
Creators: name: Paldino, Silvia
name: Bojic, Iva
name: Sobolevsky, Stanislav
name: Ratti, Carlo
name: Gonzalez, Marta C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences
subject: 91D30

description: There is an increasing trend of people leaving digital traces through social media. This reality opens new horizons for urban studies. With this kind of data, researchers and urban planners can detect many aspects of how people live in cities and can also suggest how to transform cities into more efficient and smarter places to live in. In particular, their digital trails can be used to investigate tastes of individuals, and what attracts them to live in a particular city or to spend their vacation there. In this paper we propose an unconventional way to study how people experience the city, using information from geotagged photographs that people take at different locations. We compare the spatial behavior of residents and tourists in 10 most photographed cities all around the world. The study was conducted on both a global and local level. On the global scale we analyze the 10 most photographed cities and measure how attractive each city is for people visiting it from other cities within the same country or from abroad. For the purpose of our analysis we construct the users mobility network and measure the strength of the links between each pair of cities as a level of attraction of people living in one city (i.e., origin) to the other city (i.e., destination). On the local level we study the spatial distribution of user activity and identify the photographed hotspots inside each city. The proposed methodology and the results of our study are a low cost mean to characterize a touristic activity within a certain location and can help in urban organization to strengthen their touristic potential.
description: 17 pages, 10 figures, 6 tables