cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The puzzling new class of variable stars in NGC 3766 : old friend pulsators?
Creators: name: Salmon, S. J. A. J.
name: Montalbàn, J.
name: Reese, D. R.
name: Dupret, M. -A.
name: Eggenberger, P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The recent variability survey of the NGC 3766 cluster revealed a considerable number of periodic variable stars in a region of the H-R diagram where no pulsation is expected. This region lies between the instability strips of the delta Scuti and SPB stars. Moreover the periods of the new phenomenon, P~0.1-0.7 d, do not allow to associate it a priori to either of these two types of pulsations. Stars in the NGC 3766 cluster are known as fast rotators with rotational velocities typically larger than half of their critical velocity. Rotation can affect both the geometrical properties and period domain of pulsations. It also alters the apparent stellar luminosity through gravity darkening, effect seldom taken considered in theoretical studies of the rotation-pulsation interaction. We explore if both of these effects are able to deliver a consistent interpretation for the observed properties of the "new variables" in NGC 3766: explaining their presence outside the known instability strips and their variability periods. We carry out an instability analysis of SPB models within the framework of the Traditional Approximation of Rotation and study the visibility of modes according to the angle of view and rotation. We also check how gravity darkening affects the effective temperature and luminosity of stellar models for different angles of view and rotation velocities. At the red (cold) border of the instability strip, prograde sectoral modes are preferentially excited and their visibilities are maximum when seen equator-on. Furthermore low-mass SPB models seen equator-on can appear in the gap between non-rotating SPB and delta Scuti stars due to gravity darkening. In that case, periods of these most visible modes are shifted to the 0.2-0.5 d range due to the effects of the Coriolis force. We hence suggest that the new variable stars observed in NGC 3766 are actually fast rotating SPB pulsators.
description: 8 pages, 4 figures, accepted for publication in A&A (this version does not include language editor corrections and abstract is shortened)
A model of anisotropic winds from rotating stars for evolutionary calculations
Creators: name: Hastings, Ben
name: Langer, Norbert
name: Puls, Joachim
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Context: The surface properties of rotating stars can vary from pole to equator, resulting in anisotropic stellar winds which are not included in the currently available evolutionary models. Aims: We develop a formalism to describe the mass and angular momentum loss of rotating stars which takes into account both the varying surface properties and distortion due to rotation. Methods: Adopting the mass-loss recipe for non-rotating stars, we assigned to each point on the surface of a rotating star an equivalent non-rotating star, for which the surface mass flux is given by the recipe. The global mass-loss and angular momentum loss rates are then given by integrating over the deformed stellar surface as appropriate. Evolutionary models were computed and our prescription is compared to the currently used simple mass-loss enhancement recipes for rotating stars. Results: We find that mass-loss rates are largely insensitive to rotation for models not affected by the bi-stability jump. For those affected by the bi-stability jump, the increase in mass-loss rates with respect to time is smoothed. As our prescription considers the variation of physical conditions over the stellar surface, the region affected by the bi-stability jump is able to grow gradually instead of the whole star suddenly being affected. Conclusion: We have provided an easy to implement and flexible, yet physically meaningful prescription for calculating mass and angular momentum loss rates of rotating stars in a one-dimensional stellar evolution code which compares favourably to more physically comprehensive models. The implementation of our scheme in the stellar evolution code MESA is available online: https://zenodo.org/record/7437006
description: Accepted for publication in A&A. 12 pages
Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity
Creators: name: Fourches, Denis
name: Alves, Vinicius M.
name: Andrade, Carolina H.
name: Muratov, Eugene
name: Braga, Rodolpho C.
name: Lião, Luciano M.
name: Silva, Meryck F. B.
name: Tropsha, Alexander
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The blockage of the hERG K(+) channels is closely associated with lethal cardiac arrhythmia. The notorious ligand promiscuity of this channel earmarked hERG as one of the most important antitargets to be considered in early stages of drug development process. Herein we report on the development of an innovative and freely accessible web server for early identification of putative hERG blockers and non-blockers in chemical libraries. We have collected the largest publicly available curated hERG dataset of 5,984 compounds. We succeed in developing robust and externally predictive binary (CCR≈0.8) and multiclass models (accuracy≈0.7). These models are available as a web-service freely available for public at http://labmol.farmacia.ufg.br/predherg/. Three following outcomes are available for the users: prediction by binary model, prediction by multi-class model, and the probability maps of atomic contribution. The Pred-hERG will be continuously updated and upgraded as new information became available.
Monopole deformations of 3d Seiberg-like dualities with adjoint matters
Creators: name: Hwang, Chiung
name: Kim, Sungjoon
name: Park, Jaemo
Publisher: name: Apollo - University of Cambridge Repository
Year: 2022
Subjects: Regular Article - Theoretical Physics
Duality in Gauge Field Theories
Supersymmetric Gauge Theory
Supersymmetry and Duality

description: We propose new 3d N = 2 Seiberg-like dualities by considering various monopole superpotential deformations on 3d N = 2 U(Nc) SQCDs with fundamental and adjoint matter fields. We provide nontrivial evidence of these new dualities by comparing the superconformal indices, from which we analyze the change of the moduli space due to the monopole deformation. In addition, we perform the F-maximization to check the relevance of the monopole deformation for some examples, one of which is found to exhibit nontrivial symmetry enhancement in the IR. We prove such enhancement of the global symmetry using the superconformal index.
Le radici filosofiche della professione medica
Creators: name: (:Unkn) Unknown
Publisher: name: Universita' degli Studi di Salerno
Year: 2024

description: Troppo spesso per lo sguardo del medico la malattia è solo un decorso, un esito, quasi mai ha un senso, ed il corpo diventa mero organismo. Tuttavia, la scelta professionale del medico ha alla base una vocazione squisitamente filosofica, come afferma Luigi Vero Tarca, in quanto presuppone uno sguardo che ascolta e che parla, rispetto a uno sguardo che si limita ad osservare. La vocazione filosofica del medico va ricondotta alle sue radici esistenziali ed antropologiche della cura o, per meglio dire, del voler aiutare a trovare il “bene-essere”, il vivere bene, e il pensiero filosofico di Tarca restituisce alla luce l’essenza di tale vocazione. I saggi pubblicati in questo volume sono il frutto delle suggestioni ricavate dall’analisi e dalla discussione di uno scritto di Tarca, dal titolo “La vocazione filosofica della professione medica”, in occasione di un seminario organizzato nell’ambito delle attività scientifiche del laboratorio di Antropologia “Annabella Rossi” nel dicembre 2019, presso il Dipartimento di Scienze del patrimonio culturale dell’Università degli Studi di Salerno. Il volume raccoglie i contributi di filosofi, medici, psicologi, sociologi e antropologi.
Finite size scaling of the 5D Ising model with free boundary conditions
Creators: name: Lundow, P. H.
name: Markström, K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: There has been a long running debate on the finite size scaling for the Ising model with free boundary conditions above the upper critical dimension, where the standard picture gives a $L^2$ scaling for the susceptibility and an alternative theory has promoted a $L^{5/2}$ scaling, as would be the case for cyclic boundary. In this paper we present results from simulation of the far largest systems used so far, up to side $L=160$ and find that this data clearly supports the standard scaling. Further we present a discussion of why rigorous results for the random-cluster model provides both supports the standard scaling picture and provides a clear explanation of why the scalings for free and cyclic boundary should be different.
description: 7 pages, 11 figures
Loop corrections in a solvable UV-finite model and its effective field theory
Creators: name: Brandt, F. T.
name: Frenkel, J.
name: McKeon, D. G. C.
name: Sakoda, G. S. S.
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We examine some features of the non-renormalizability induced through the use of low-energy effective Lagrangians in loop diagrams, in the context of a scalar model which is ultraviolet finite and partially soluble. In this framework, one can directly demonstrate the mechanism leading to the non-renormalizability of the effective theory. This behavior is generated by approximations that are applicable at low energies but are generally inappropriate for evaluating loop diagrams that contain virtual high-energy particles. However, it is explicitly shown that one can match the results obtained in the renormalized effective theory with those found in the full theory at low energy. We argue that the infrared sectors of these theories are inherently similar, independently of the matching procedure. A closed-form expression is obtained, to leading order in the energy expansion, for the complete effective Lagrangian at all orders in perturbation theory. The model may be useful to clarify certain aspects of realistic, but more complex, effective field theories.
description: 8 pages, 4 figures
Proteases Display Biased Agonism at Protease-Activated Receptors: Location matters!
Creators: name: Soh, U. J. K.
name: Russo, A.
name: Trejo, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Protease-activated receptors (PARs) are G protein–coupled receptors (GPCRs) that transmit cellular responses begun by the actions of extracellular proteases. The activation of a PAR occurs by a unique mechanism whereby the extracellular N-terminal segment of the inactive receptor undergoes proteolytic cleavage, resulting in irreversible activation––unlike most GPCRs that are reversibly activated. PARs mediate cellular responses to coagulant proteases in various cell types localized within the vasculature. Additionally, PARs are expressed in other cell types and respond to a plethora of proteases. Recent studies have revealed that different proteases elicit distinct responses through the activation of the same PAR. This phenomenon appears to involve stabilization of distinct active PAR conformations that facilitates selectively coupling to different effectors and is localized to caveolae, a subtype of lipid rafts.
Copy number variants in pharmacogenetic genes
Creators: name: He, Yijing
name: Hoskins, Janelle M.
name: McLeod, Howard L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Variation in drug efficacy and toxicity remains an important clinical concern. Presently, single nucleotide polymorphisms (SNP) only explain a portion of this problem, even in situations where the pharmacological trait is clearly heritable. The Human CNV Project identified copy number variations (CNVs) across approximately 12% of the human genome, and these CNVs were considered causes of diseases. Although the contribution of CNVs to the pathogenesis of many common diseases is questionable, CNVs play a clear role in drug related genes by altering drug metabolizing and drug response. Here we provide a comprehensive review of the clinical relevance of CNVs to drug efficacy, toxicity, disease prevalence in world populations and discuss the implication of using CNVs as diagnosis in clinical intervention.
Fractional revivals through Rényi uncertainty relations
Creators: name: Romera, Elvira
name: Santos, Francisco de los
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We show that the Rényi uncertainty relations give a good description of the dynamical behavior of wave packets and constitute a sound approach to revival phenomena by analyzing three model systems: the simple harmonic oscillator, the infinite square well, and the quantum bouncer. We prove the usefulness of entropic uncertainty relations as a tool for identifying fractional revivals by providing a comparison in different contexts with the usual Heisenberg uncertainty relation and with the common approach in terms of the autocorrelation function.
description: 6 pages, 4 figures
Supplementary document for A simple approach for spectral beam combination of narrowband laser sources for spectroscopic applications - 6574299.pdf
Creators: name: Moser, Harald
name: Waclawek, Johannes
name: Pölz, Walter
name: Lendl, Bernhard
Publisher: name: Optica Publishing Group
Year: 2023
Subjects: Uncategorized

description: M2 Measurements, transmission and reflectivity data
Periphytic rotifer communities of an Australian seasonal floodplain pool
Creators: name: Pontin, Rosalind M
name: Shiel, R. J
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

A seasonal, rainfill pool (Ryans 3) on the floodplain of the River Murray, near Albury, Australia was sampled in 1991 and 1993 for periphytic rotifer species and other microfauna. The main macrophytes present were species of Myriophyllum, Pseudoraphis and Triglochin, and, in 1993, there was an extensive covering of Azolla. Sampling methods included quantitative samples taken using a simple syringe. Rotifers numbered from about 10 to 150 per 100 ml and formed about 2 to 20% of the microfaunal community. Numbers of rotifers, and numbers of rotifer species, varied with different macrophytes (chi(2) tests, P<0.001 in each case), with the greatest numbers under Azolla. The two years showed marked differences in the macrophytes present and over half the rotifer species were also different (chi(2) test, P<0.001).
Pain-relieving prospects for adenosine receptors and ectonucleotidases
Creators: name: Zylka, Mark J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Adenosine receptor agonists have potent antinociceptive effects in diverse preclinical models of chronic pain. In contrast, the efficacy of adenosine or adenosine receptor agonists at treating pain in humans is unclear. Two ectonucleotidases that generate adenosine in nociceptive neurons were recently identified. When injected spinally, these enzymes have long-lasting adenosine A1 receptor (A1R)-dependent antinociceptive effects in inflammatory and neuropathic pain models. Furthermore, recent findings indicate that spinal adenosine A2A receptor activation can enduringly inhibit neuropathic pain symptoms. Collectively, these studies suggest the possibility of treating chronic pain in humans by targeting specific adenosine receptor subtypes in anatomically defined regions with agonists or with ectonucleotidases that generate adenosine.
BRST symmetry and the convolutional double copy
Creators: name: Godazgar, M
name: Pope, CN
name: Saha, A
name: Zhang, H
Publisher: name: Apollo - University of Cambridge Repository
Year: 2022
Subjects: Regular Article - Theoretical Physics
Black Holes
BRST Quantization
Scattering Amplitudes
Supergravity Models

description: Abstract Motivated by the results of Anastasiou et al., we consider the convolutional double copy for BRST and anti-BRST covariant formulations of gravitational and gauge theories in more detail. We give a general BRST and anti-BRST invariant formulation of linearised $$ \mathcal{N} $$ N = 0 supergravity using superspace methods and show how this may be obtained from the square of linearised Yang-Mills theories. We demonstrate this relation for the Schwarzschild black hole and the ten-dimensional black string solution as two concrete examples.
Defining the toxicology of aging
Creators: name: Sharpless, Norman E.
name: Sanoff, Hanna K.
name: Sorrentino, Jessica A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Mammalian aging is complex and incompletely understood. While significant effort has been spent addressing the genetics or, more recently, the pharmacology of aging, the toxicology of aging has been relatively understudied. Just as an understanding of `carcinogens' has proven critical to modern cancer biology, an understanding of environmental toxicants that accelerate aging (`gerontogens') will inform gerontology. In this review, we discuss the evidence for the existence of mammalian gerontogens, as well as describe biomarkers needed to measure the age-promoting activity of a given toxicant. We focus on the effects of putative gerontogens on the in vivo accumulation of senescent cells, a characteristic feature of aging that plays a causal role in some age-associated phenotypes.
2d Gauge Theories and Generalized Geometry
Creators: name: Kotov, Alexei
name: Salnikov, Vladimir
name: Strobl, Thomas
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Differential Geometry (math.DG)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We show that in the context of two-dimensional sigma models minimal coupling of an ordinary rigid symmetry Lie algebra $\mathfrak{g}$ leads naturally to the appearance of the "generalized tangent bundle" $\mathbb{T}M \equiv TM \oplus T^*M$ by means of composite fields. Gauge transformations of the composite fields follow the Courant bracket, closing upon the choice of a Dirac structure $D \subset \mathbb{T}M$ (or, more generally, the choide of a "small Dirac-Rinehart sheaf" $\cal{D}$), in which the fields as well as the symmetry parameters are to take values. In these new variables, the gauge theory takes the form of a (non-topological) Dirac sigma model, which is applicable in a more general context and proves to be universal in two space-time dimensions: A gauging of $\mathfrak{g}$ of a standard sigma model with Wess-Zumino term exists, \emph{iff} there is a prolongation of the rigid symmetry to a Lie algebroid morphism from the action Lie algebroid $M \times \mathfrak{g}\to M$ into $D\to M$ (or the algebraic analogue of the morphism in the case of $\cal{D}$). The gauged sigma model results from a pullback by this morphism from the Dirac sigma model, which proves to be universal in two-spacetime dimensions in this sense.
description: 22 pages, 2 figures; To appear in Journal of High Energy Physics
fCAT: Assessing gene set completeness using domain-architecture aware targeted ortholog searches
Creators: name: Tran, Vinh
name: Ebersberger, Ingo
Publisher: name: F1000 Research Limited
Year: 2022

description: The assessment of gene set completeness is a routine task in genome analysis. The standard workflows start with the identification of a set of single copy core genes for the taxonomic group the newly sequenced species, the target, is part of. The fraction of missing core genes serves then as a proxy of the target gene set completeness. Genes that are represented but differ significantly in length from the expectation provide information about the fragmentation status of the predicted gene models, and ultimately gene duplication levels can be assessed. Though well established, this approach comes along with a number of restrictions of which the focus on single copy genes, the use of an error-prone unidirectional ortholog search, and the application of a simple length cutoff criterion are the most prominent ones. Here we present fCAT, a novel algorithm for assessing gene set completeness using a targeted and domain architecture-aware ortholog search. As a consequence, fCAT's core sets are not limited to single-copy orthologs by that providing a comprehensive overview of the core gene set. Next to the conventional length difference assessment, fCAT identifies target genes that significantly differ in their domain architectures from the core genes allowing an alternative view on the accuracy of target gene models. Phylogenetic profiles resulting from the analysis can be visualized and explored in the context of the entire orthologous groups which provides the necessary information to identify and ultimately correct erroneous gene annotations.
Vortex-penetration field at a groove with a depth smaller than the penetration depth
Creators: name: Kubo, Takayuki
Publisher: name: arXiv
Year: 2014
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Analytical formula to evaluate the vortex-penetration field at a groove with a depth smaller than penetration depth is derived, which can be applied to surfaces of cavities or test pieces made from extreme type II superconductors such as nitrogen-doped Nb or alternative materials like Nb3Sn or NbN.
description: 3 pages, 1 figure, the 27th Linear Accelerator Conference, LINAC14, Geneva, Switzerland, 31 August - 5 September, 2014
Identifying Active Galactic Nuclei at $z\sim3$ from the HETDEX Survey Using Machine Learning
Creators: name: Poleo, Valentina Tardugno
name: Finkelstein, Steven
name: Leung, Gene C. K.
name: Cooper, Erin Mentuch
name: Gebhardt, Karl
name: Farrow, Daniel
name: Gawiser, Eric
name: Zeimann, Gregory
name: Schneider, Donald
name: Morabito, Leah
name: Mock, Daniel
name: Liu, Chenxu
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We used data from the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX) to study the incidence of AGN in continuum-selected galaxies at $z\sim3$. From optical and infrared imaging in the 24 deg$^{2}$ Spitzer HETDEX Exploratory Large Area (SHELA) survey, we constructed a sample of photometric-redshift selected $z\sim3$ galaxies. We extracted HETDEX spectra at the position of 716 of these sources and used machine learning methods to identify those which exhibited AGN-like features. The dimensionality of the spectra was reduced using an autoencoder, and the latent space was visualized through t-distributed stochastic neighbor embedding (t-SNE). Gaussian mixture models were employed to cluster the encoded data and a labeled dataset was used to label each cluster as either AGN, stars, high-redshift galaxies, or low-redshift galaxies. Our photometric redshift (photo-z) sample was labeled with an estimated $92\%$ overall accuracy, an AGN accuracy of $83\%$, and an AGN contamination of $5\%$. The number of identified AGN was used to measure an AGN fraction for different magnitude bins. The UV absolute magnitude where the AGN fraction reaches $50\%$ is $M_{UV} = -23.8$. When combined with results in the literature, our measurements of AGN fraction imply that the bright end of the galaxy luminosity function exhibits a power-law rather than exponential decline, with a relatively shallow faint-end slope for the $z\sim3$ AGN luminosity function.
Dust Buried Compact Sources in the Dwarf Galaxy NGC 4449
Creators: name: Calzetti, Daniela
name: Linden, Sean T.
name: McQuaid, Timothy
name: Messa, Matteo
name: Ji, Zhiyuan
name: Krumholz, Mark R.
name: Adamo, Angela
name: Elmegreen, Bruce
name: Grasha, Kathryn
name: Johnson, Kelsey E.
name: Sabbi, Elena
name: Smith, Linda
name: Bajaj, Varun
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Multi-wavelength images from the Hubble Space Telescope covering the wavelength range 0.27-1.6 $μ$m show that the central area of the nearby dwarf galaxy NGC4449 contains several tens of compact sources that are emitting in the hydrogen recombination line Pa$β$ (1.2818 $μ$m) but are only marginally detected in H$α$ (0.6563 $μ$m) and undetected at wavelengths $λ\le$0.55 $μ$m. An analysis of the spectral energy distributions (SEDs) of these sources indicates that they are likely relatively young star clusters heavily attenuated by dust. The selection function used to identify the sources prevents meaningful statistical analyses of their age, mass, and dust extinction distributions. However, these cluster candidates have ages $\sim$5-6 Myr and A$_V>$6 mag, according to their SED fits, and are extremely compact, with typical deconvolved radii of 1 pc. The dusty clusters are located at the periphery of dark clouds within the galaxy and appear to be partially embedded. Density and pressure considerations indicate that the HII regions surrounding these clusters may be stalled, and that pre-supernova feedback has not been able to clear the clusters of their natal cocoons. These findings are in potential tension with existing models that regulate star formation with pre-supernova feedback, since pre-supernova feedback acts on short timescales, $\lesssim$4 Myr, for a standard Stellar Initial Mass function. The existence of a population of dusty star clusters with ages $>$4 Myr, if confirmed by future observations, paints a more complex picture for the role of stellar feedback in controlling star formation.
description: 27 pages, 22 figures; accepted for publication in the Astrophysical Journal
Appendix 1. Use of outpatient health services by adolescents
Creators: name: Montañez, Julio
Publisher: name: figshare
Year: 2023
Subjects: Health services and systems not elsewhere classified

description: Health needs prompting the search for care by category: adolescents using outpatient services, Mexico, ENSANUT 2018-2019
CytoPipeline: building and visualizing automated pre-processing and quality control pipelines for flow cytometry data
Creators: name: Hauchamps, Philippe
name: Lin, Dan
name: Gatto, Laurent
Publisher: name: F1000 Research Limited
Year: 2022

description: With the increase of the dimensionality in conventional flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data analysis pipelines. Examples of such pipelines have been documented in the recent literature (e.g. [1],[2]). A crucial part of these pipelines consists of pre-processing and applying quality control filtering to the raw data, in order to use high quality events in the downstream statistical analysis. This part can in turn be split into a number of elementary steps : margin events removal, signal compensation, scale transformations, debris and dead cells removal, batch effect correction,… etc.

 However, as a bioinformatician who designs and builds automated flow cytometry data analysis pipelines, assembling and assessing the pre-processing part can be challenging for a number of reasons. First, each of the involved elementary steps can be implemented using various methods and R packages. Second, the order of the steps can have an impact on the downstream analysis results. Finally, each method typically comes with its specific, unstandardized diagnostic and visualizations, making objective comparison difficult for the end user.

 In this work, we present CytoPipeline, an R package to build, compare and assess pre-processing pipelines for flow cytometry data. We focus on three main aspects: explicit and centralized description of the pipeline steps, extensibility and maintainability through the use of S4 classes, and genericity and flexibility of interactive visualization utilities. To demonstrate our tool, we present the different steps involved in designing a pre-processing pipeline on publicly available data, and show the accompanying visualization utilities.
Differential colonization with segmented filamentous bacteria and Lactobacillus murinus do not drive divergent development of diet-induced obesity in C57BL/6 mice
Creators: name: Raver, Christine
name: Flick, Leah M.
name: Tschöp, Matthias H.
name: Giles, Daniel A.
name: Karp, Christopher L.
name: Divanovic, Senad
name: Stankiewicz, Traci E.
name: McAlees, Jaclyn W.
name: Wills-Karp, Marsha
name: Hembree, Jazzminn
name: Balfour Sartor, R.
name: Rewerts, Cheryl L.
name: Downey, Jordan
name: Walters, Stephanie
name: Pfluger, Paul T.
name: Burgess, Stacey L.
name: Harley, Isaac T.W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Alterations in the gut microbiota have been proposed to modify the development and maintenance of obesity and its sequelae. Definition of underlying mechanisms has lagged, although the ability of commensal gut microbes to drive pathways involved in inflammation and metabolism has generated compelling, testable hypotheses. We studied C57BL/6 mice from two vendors that differ in their obesogenic response and in their colonization by specific members of the gut microbiota having well-described roles in regulating gut immune responses. We confirmed the presence of robust differences in weight gain in mice from these different vendors during high fat diet stress. However, neither specific, highly divergent members of the gut microbiota (Lactobacillus murinus, segmented filamentous bacteria) nor the horizontally transmissible gut microbiota were found to be responsible. Constitutive differences in locomotor activity were observed, however. These data underscore the importance of selecting appropriate controls in this widely used model of human obesity.
Electroweak Form Factors of the $Δ$(1232) Resonance
Creators: name: Graczyk, Krzysztof M.
name: Zmuda, Jakub
name: Sobczyk, Jan T.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Nucleon $\to Δ(1232)$ transition electroweak form factors are discussed in a single pion production model with nonresonant background terms originating from a chiral perturbation theory. Fits to electron-proton scattering $F_2$ as well as neutrino scattering bubble chamber experimental data are performed. Both $ν$-proton and $ν$-neutron channel data are discussed in a unified statistical model. A new parametrization of the $N\toΔ(1232)$ vector form factors is proposed. Fit to neutrino scattering data gives axial mass $M_{AΔ}=0.85{+0.09}{-0.08}\;$(GeV) and $C_5^A(0) = 1.10{+0.15}{-0.14}$ in accordance with Goldberger-Treiman relation as long as deuteron nuclear effects are considered.
description: 11 pages, 8 figures
Crystal structure of the Leishmania major phosphodiesterase LmjPDEB1 and insight into the design of the parasite-selective inhibitors
Creators: name: Yan, Zier
name: Wang, Huanchen
name: Geng, Jie
name: Ke, Hengming
name: Seebeck, Thomas
name: Kunz, Stefan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Human leishmaniasis is a major public health problem in many countries, but chemotherapy is in an unsatisfactory state. Leishmania major phosphodiesterases (LmjPDEs) have been shown to play important roles in cell proliferation and apoptosis of the parasite. Thus LmjPDE inhibitors may potentially represent a novel class of drugs for the treatment of leishmaniasis. Reported here are the kinetic characterization of the LmjPDEB1 catalytic domain and its crystal structure as a complex with 3-isobutyl-1-methylxanthine (IBMX) at 1.55 Å resolution. The structure of LmjPDEB1 is similar to that of human PDEs. IBMX stacks against the conserved phenylalanine and forms a hydrogen bond with the invariant glutamine, in a pattern common to most inhibitors bound to human PDEs. However, an extensive structural comparison reveals subtle but significant differences between the active sites of LmjPDEB1 and human PDEs. In addition, a pocket next to the inhibitor binding site is found to be unique to LmjPDEB1. This pocket is isolated by two gating residues in human PDE families, but constitutes a natural expansion of the inhibitor binding pocket in LmjPDEB1. The structure particularity might be useful for the development of parasite-selective inhibitors for the treatment of leishmaniasis.
Multi-point study of the energy release and impulsive CME dynamics in an eruptive C7 flare
Creators: name: Saqri, J.
name: Veronig, A. M.
name: Dickson, E. C. M.
name: Podladchikova, T.
name: Warmuth, A.
name: Xiao, H.
name: Gary, D. E.
name: Battaglia, A. F.
name: Krucker, S.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We combine observations from different vantage points to perform a detailed study of a long duration eruptive C7 class flare that occurred on 17 April 2021 and was partially occulted from Earth view. The dynamics and thermal properties of the flare-related plasma flows, the flaring arcade, and the energy releases and particle acceleration are studied together with the kinematic evolution of the associated CME in order to place this long duration event in context of previous eruptive flare studies. The flare showed hard X-ray (HXR) bursts over the duration of an hour in two phases lasting from 16:04 UT to 17:05 UT. During the first phase, a strong increase in emission from hot plasma and impulsive acceleration of the CME was observed. The CME acceleration profile shows a three-part evolution of slow rise, acceleration, and propagation in line with the first STIX HXR burst phase, which is triggered by a rising hot (14 MK) plasmoid. During the CME acceleration phase, we find signatures of ongoing magnetic reconnection behind the erupting structure, in agreement with the standard eruptive flare scenario. The subsequent HXR bursts that occur about 30 minutes after the primary CME acceleration show a spectral hardening (from $δ\approx $ 7 to $δ\approx $ 4) but do not correspond to further CME acceleration and chromospheric evaporation. Therefore, the CME-flare feedback relationship may only be of significance within the first 25 minutes of the event under study, as thereafter the flare and the CME eruption evolve independently of each other.
A new twist on an old pathway – accessory secretion systems
Creators: name: Rigel, Nathan W.
name: Braunstein, Miriam
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The export of proteins from their site of synthesis in the cytoplasm across the inner membrane is an important aspect of bacterial physiology. Because the location of extracytoplasmic proteins is ideal for host-pathogen interactions, protein export is also important to bacterial virulence. In bacteria there are conserved protein export systems that are responsible for the majority of protein export: the general secretion (Sec) pathway and the twin-arginine translocation (Tat) pathway. In some bacteria, there are also specialized export systems dedicated to exporting specific subsets of proteins. In this review, we discuss a specialized export system that exists in some Gram-positive bacteria and mycobacteria – the accessory Sec system. The common element to the accessory Sec system is an accessory SecA protein called SecA2. Here we present our current understanding of accessory Sec systems in Streptococcus gordonii, Streptococcus parasanguinis, Mycobacterium smegmatis, Mycobacterium tuberculosis, and Listeria monocytogenes, making an effort to highlight apparent similarities and differences between the systems. We also review the data showing that accessory Sec systems can contribute to bacterial virulence.
Rootzone dynamics in constructed wetlands receiving wastewater: a comparison of vertical and horizontal flow systems
Creators: name: Breen, Peter F
name: Chick, Alan J
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

Profile conditions were examined in both small experimental and pilot scale sub-surface flow wetlands. The study systems differed in their hydraulic design. The experimental systems had a vertical up-flow design whereas the pilot system was a horizontal flow trench design. Both systems were found to have significant physical, chemical and biological gradients within the sub-surface profile. System age and plant root density appear to be important factors in determining profile differentiation within the experimental systems. Root densities were found to be partitioned between the upper and lower layers on a 70%/30% split respectively. However, in the experimental systems as the systems aged and root densities increased beyond 112-251 g.m(-2) chemical water quality differentiation id the profile disappeared. Pilot scale systems were found to have physical gradients within the profile as evidenced by hydraulic short-circuiting. Vertical root density distribution is proposed as a major cause of this condition in horizontal flow systems.
The Problem of Two Fixed Centers: Bifurcation Diagram for Positive Energies
Creators: name: Seri, Marcello
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 37J20, 37D05

description: We give a comprehensive analysis of the Euler-Jacobi problem of motion in the field of two fixed centers with arbitrary relative strength and for positive values of the energy. These systems represent nontrivial examples of integrable dynamics and are analysed from the point of view of the energy-momentum mapping from the phase space to the space of the integration constants. In this setting we describe the structure of the scattering trajectories in phase space and derive an explicit description of the bifurcation diagram, i.e. the set of critical value of the energy-momentum map.
description: 18 pages, 8 figures, submitted
Two variable active site residues modulate response regulator phosphoryl group stability
Creators: name: Bourret, Robert B.
name: Brewster, Jocelyn A.
name: Thomas, Stephanie A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Many signal transduction networks control their output by switching regulatory elements on or off. To synchronize biological response with environmental stimulus, switching kinetics must be faster than changes in input. Two-component regulatory systems (used for signal transduction by bacteria, archaea, and eukaryotes) switch via phosphorylation or dephosphorylation of the receiver domain in response regulator proteins. Although receiver domains share conserved active site residues and similar three-dimensional structures, rates of self-catalyzed dephosphorylation span a ≥40,000-fold range in response regulators that control diverse biological processes. For example, autodephosphorylation of the chemotaxis response regulator CheY is 640-fold faster than Spo0F, which controls sporulation. Here we demonstrate that substitutions at two variable active site positions decreased CheY autodephosphorylation up to 40-fold and increased the Spo0F rate up to 110-fold. Particular amino acids had qualitatively similar effects in different response regulators. However, mutant proteins matched to other response regulators at the two key variable positions did not always exhibit similar autodephosphorylation kinetics. Therefore, unknown factors also influence absolute rates. Understanding the effects that particular active site amino acid compositions have on autodephosphorylation rate may allow manipulation of phosphoryl group stability for useful purposes, as well as prediction of signal transduction kinetics from amino acid sequence.
Rotifers of the Kalahari Gemsbok National Park, South Africa
Creators: name: Brain, C. K
name: Fourie, Ilema
name: Shiel, R. J
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

The Kalahari Gemsbok National Park in the Northern Cape Province, South Africa, is bounded by two dry river beds in which 39 artificial water sources have been provided for the use of the wild animals. The water in these sources varies from fresh to highly saline and an opportunity is thus provided to determine, not only which rotifer species are able to colonise such sources, but what their salinity tolerances are. The rotifer fauna, studied in summer and winter, is dominated by mixed populations of Brachionus calyciflorus, B. plicatilis and Hexarthra jenkinae, with only a few other monogononts and bdelloids. The most striking feature of the rotifer fauna in these troughs is the very low species diversity encountered.
The diet of Anisopteran larvae from two streams in north-eastern Victoria, Australia
Creators: name: Hawking, J. H
name: New, T. R
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

The diets of larvae of 7 spp. from the Kiewa River and Middle Creek, Victoria were examined and compared from faecal pellet examination. Differences between spp. instars and season reflect a high degree of opportunism among these polyphagous predators, with differences in prey spectrum reflecting habitat and feeding method.
Non-thermal Gamma-ray Emission from Delayed Pair Breakdown in a Magnetized and Photon-rich Outflow
Creators: name: Gill, Ramandeep
name: Thompson, Christopher
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We consider delayed, volumetric heating in a magnetized outflow that has broken out of a confining medium and expanded to a high Lorentz factor ($Γ\sim 10^2-10^3$) and low optical depth to scattering ($τ_{\rm T} \sim 10^{-3}-10^{-2}$). The energy flux at breakout is dominated by the magnetic field, with a modest contribution from quasi-thermal gamma rays whose spectrum was calculated in Paper I. We focus on the case of extreme baryon depletion in the magnetized material, but allow for a separate baryonic component that is entrained from a confining medium. Dissipation is driven by relativistic motion between these two components, which develops once the photon compactness drops below $ 4\times 10^3(Y_e/0.5)^{-1}$. We first calculate the acceleration of the magnetized component following breakout, showing that embedded MHD turbulence provides significant inertia, the neglect of which leads to unrealistically high estimates of flow Lorentz factor. After re-heating begins, the pair and photon distributions are evolved self-consistently using a one-zone kinetic code that incorporates an exact treatment of Compton scattering, pair production and annihilation, and Coulomb scattering. Heating leads to a surge in pair creation, and the scattering depth saturates at $τ_{\rm T} \sim$ 1-4. The plasma maintains a very low ratio of particle to magnetic pressure, and can support strong anisotropy in the charged particle distribution, with cooling dominated by Compton scattering. High-energy power-law spectra with photon indices in the range observed in GRBs ($-3 < β< -3/2$) are obtained by varying the ratio of heat input to the seed energy in quasi-thermal photons. We contrast our results with those for continuous heating across an expanding photosphere, and show that the latter model produces soft-hard evolution that is inconsistent with observations of GRBs.
description: Submitted to the ApJ, 27 pages, 19 figures
Revisiting the Parameter Space of Binary Neutron Star Merger Event GW170817
Creators: name: McDowell, Austin
name: MacFadyen, Andrew
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Since the gravitational wave event GW170817 and gamma-ray burst GW170817A there have been numerous studies constraining the burst properties through analysis of the afterglow light curves. Most agree that the burst was viewed off-axis with a ratio of the observer angle to the jet angle ($θ_{obs}/θ_j$) between 4 - 6. We use a parameterized model and broadband synchrotron data up to $\sim 800$ days post-merger to constrain parameters of the burst. To reproduce the hydrodynamics of a gamma-ray burst outflow we use a two-parameter "boosted fireball" model. The structure of a boosted fireball is determined by the specific internal energy, $η_0$, and the bulk Lorentz factor, $γ_B(\sim 1/θ_j)$ with shapes varying smoothly from a quasi-spherical outflow for low values of $γ_B$ to a highly collimated jet for high values. We run simulations with $γ_B$ in the range $1-20$ and $η_0$ in the range $2-15$. To calculate light curves we use a synchrotron radiation model characterized by $F_{peak}$, $ν_m$, and $ν_c$ and calculate millions of spectra at different times and $θ_{obs}$ values using the \texttt{boxfit} radiation code. We can tabulate the spectral parameter values from our spectra and rapidly generate arbitrary light curves for comparison to data in MCMC analysis. We find that our model prefers a gamma-ray burst with jet energy $E_j\sim10^{50}$ ergs and with an observer angle of $θ_{obs}=0.65^{+0.13}_{-0.14}$ radians and ratio to jet opening angle of ($θ_{obs}/θ_j$) = 5.4$^{+0.53}_{-0.38}$.
NMR structure of a fungal virulence factor reveals structural homology with mammalian saposin B
Creators: name: Cistola, David P.
name: Goldman, William E.
name: Beck, Moriah R.
name: DeKoster, Gregory T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The fungal protein CBP (calcium binding protein) is a known virulence factor with an unknown virulence mechanism. The protein was identified based on its ability to bind calcium and its prevalence as Histoplasma capsulatum’s most abundant secreted protein. However, CBP has no sequence homology with other calcium binding proteins and contains no known calcium-binding motifs. Here, the NMR structure of CBP reveals a highly intertwined homodimer and represents the first atomic level NMR model of any fungal virulence factor. Each CBP monomer is comprised of four α-helices that adopt the saposin fold, characteristic of a protein family that binds to membranes and lipids. This structural homology suggests that CBP functions as a lipid-binding protein, potentially interacting with host glycolipids in the phagolysosome of host cells.