cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Genome-wide differential expression profiling of lncRNAs and mRNAs in human induced pluripotent stem cell-derived endothelial cells exposed to e-cigarette extract
Creators: name: Le, Hoai Huong Thi
name: Liu, Chen-wei
name: Denaro, Philip
name: Jousma, Jordan
name: Shao, Ning-Yi
name: Rahman, Irfan
name: Lee, Won Hee
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Fig. S1. In vitro characterization of hiPSC-ECs. A Schematic illustration of endothelial differentiation protocol of iPSCs. B Flow cytometry analysis of iPSC-ECs was utilized to assess EC differentiation efficiency. iPSC-ECs were stained with endothelial markers, such as VE-cadherin (CD144) and PECAM1 (CD31), a hematopoietic marker (CD45), and a progenitor marker (CD34). C Immunofluorescence staining of endothelial markers, such as acetylated low-density lipoprotein (Ac-LDL) and VE-cadherin (VE-CAD), was performed on iPSC-ECs. Scale bars = 100 μm. Fig. S2. Box plots showing normalized intensity of each sample for A lncRNAs and B mRNAs probed by microarray. Fig. S3. The Go terms were divided into three categories, including biological process (BP, yellow), molecular function (MF, purple), and cellular component (CC, green). Top 10 significantly up- and downregulated GO terms for differentially expressed mRNAs. Fig. S4. Expression of fatty acid oxidation-related genes. Expression of acetyl-CoA acyltransferase 1 (Acaa1), acyl-CoA synthetase long-chain family member 3 (Acsl3), and hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha (Hadha) following EAE exposure (6.5 TPE) was quantified using qPCR. Data are represented as mean ± SD. Table S1. PCR primers used for validation studies. Primers are indicated as forward (F) or reverse (R). Table S2. Top 50 differentially expressed lncRNAs regulated by e-cig. Table S3. Top 50 differentially expressed mRNAs regulated by e-cig. Table S4. mRNA–lncRNA pairs identified in the expression network for upregulated lncRNAs. Table S5. mRNA–lncRNA pairs identified in the expression network for downregulated lncRNAs.
Mixed sums of squares and triangular numbers (III)
Creators: name: Oh, Byeong-Kweon
name: Sun, Zhi-Wei
Publisher: name: arXiv
Year: 2008
Subjects: subject: Number Theory (math.NT)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 11E25; 05A05; 11D85; 11P99; 11Y11

description: In this paper we confirm a conjecture of Sun which states that each positive integer is a sum of a square, an odd square and a triangular number. Given any positive integer m, we show that p=2m+1 is a prime congruent to 3 modulo 4 if and only if T_m=m(m+1)/2 cannot be expressed as a sum of two odd squares and a triangular number, i.e., p^2=x^2+8(y^2+z^2) for no odd integers x,y,z. We also show that a positive integer cannot be written as a sum of an odd square and two triangular numbers if and only if it is of the form 2T_m (m>0) with 2m+1 having no prime divisor congruent to 3 modulo 4.
Re-examination of the Time Structure of the SN1987A Neutrino Burst Data in Kamiokande-II
Creators: name: Oyama, Yuichi
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The seven seconds' gap in the Kamiokande-II SN1987A neutrino data is reexamined.
description: 2 pages, 1 figure
Feasibility of Searches for a Higgs Boson using H->WW->ll+MET and High PT Jets at the Tevatron
Creators: name: Mellado, B.
name: Quayle, W.
name: Wu, Sau Lan
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The sensitivity of Standard Model Higgs boson searches at the Tevatron experiments with a mass 135WW->ll+MET (l=e,mu) is discussed. Three new event selections involving Higgs in association with one or two high PT hadronic jets are discussed. Using Leading Order Matrix Elements and a conservative cut-based analysis a 95% confidence level exclusion on sigmaxBR(H->WW), 1.6 times larger than that predicted by the Standard Model for MH=165 GeV, may be achieved with 5fb-1 of integrated luminosity. By combining these three event selections with the existing analysis, the sensitivity of CDF and D0 could improve significantly.
Floer homology and singular knots
Creators: name: Ozsvath, Peter
name: Stipsicz, Andras I.
name: Szabo, Zoltan
Publisher: name: arXiv
Year: 2007
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics

description: We define Floer homology theories for oriented, singular knots in S^3 and show that one of these theories can be defined combinatorially for planar singular knots.
description: Minor revisions
Evidence of High-Energy Neutrinos from SN1987A by Kamiokande-II and IMB
Creators: name: Oyama, Yuichi
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: High-energy neutrinos from SN1987A were searched for using upward-going muons recorded by the Kamiokande-II experiment and the IMB experiment. Between 1987 August 11 and October 20, and from an angular window of 10 degree radius, two upward-going muon events were recorded by Kamiokande-II, and also two events were recorded by IMB. The probability that these upward-going muons were explained by a chance coincidence of atmospheric neutrinos was calculated to be 0.27%. This shows possible evidence of high-energy neutrinos from SN1987A.
description: 4 pages, 2 figures
The distribution of localization measures of chaotic eigenstates in the stadium billiard
Creators: name: Batistić, Benjamin
name: Lozej, Črt
name: Robnik, Marko
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: The localization measures $A$ (based on the information entropy) of localized chaotic eigenstates in the Poincaré-Husimi representation have a distribution on a compact interval $[0,A_0]$, which is well approximated by the {\em beta distribution}, based on our extensive numerical calculations. The system under study is the Bunimovich' stadium billiard, which is a classically ergodic system, also fully chaotic (positive Lyapunov exponent), but in the regime of a slightly distorted circle billiard (small shape parameter $\varepsilon$) the diffusion in the momentum space is very slow. The parameter $α=t_H/t_T$, where $t_H$ and $t_T$ are the Heisenberg time and the classical transport time (diffusion time), respectively, is the important control parameter of the system, as in all quantum systems with the discrete energy spectrum. The measures $A$ and their distributions have been calculated for a large number of $\varepsilon$ and eigenenergies. The dependence of the standard deviation $σ$ on $α$ is analyzed, as well as on the spectral parameter $β$ (level repulsion exponent of the relevant Brody level spacing distribution). The paper is a continuation of our recent paper (B. Batistić, Č. Lozej and M. Robnik, Nonlinear Phenomena in Complex Systems {\bf 21}, 225 (2018)), where the spectral statistics and validity of the Brody level spacing distribution has been studied for the same system, namely the dependence of $β$ and of the mean value $$ on $α$.
description: 13 pages, 13 figures, 1 table. arXiv admin note: substantial text overlap with arXiv:2104.08915
Lightweight Soft Error Resilience for In-Order Cores
Creators: name: Zeng, Jianping
name: Kim, Hongjune
name: Lee, Jaejin
name: Jung, Changhee
Publisher: name: arXiv
Year: 2022
Subjects: subject: Hardware Architecture (cs.AR)
subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: Acoustic-sensor-based soft error resilience is particularly promising, since it can verify the absence of soft errors and eliminate silent data corruptions at a low hardware cost. However, the state-of-the-art work incurs a significant performance overhead for in-order cores due to frequent structural/data hazards during the verification. To address the problem, this paper presents Turnpike, a compiler/architecture co-design scheme that can achieve lightweight yet guaranteed soft error resilience for in-order cores. The key idea is that many of the data computed in the core can bypass the soft error verification without compromising the resilience. Along with simple microarchitectural support for realizing the idea, Turnpike leverages compiler optimizations to further reduce the performance overhead. Experimental results with 36 benchmarks demonstrate that Turnpike only incurs a 0-14% run-time overhead on average while the state-of-the-art incurs a 29-84% overhead when the worst-case latency of the sensor based error detection is 10-50 cycles.
description: 13 pages and 26 figures
Model-Independent Constraints on Lepton-Flavor-Violating Decays of the Top Quark
Creators: name: Kile, Jennifer
name: Soni, Amarjit
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The imminent start of the Large Hadron Collider, which is expected to produce $\sim 10^8$ $t\bar{t}$ pairs per year, provides an unprecedented opportunity for top physics. As the top quark is widely expected to be rather sensitive to effects of new physics, a detailed study of its properties, including rare decays, is called for. A possible, experimentally distinctive decay is the case where a top decays to a light quark and a flavor-violating lepton-antilepton pair. We use an effective operator analysis to place model-independent bounds on contributions to the decays $t\to u e^{\pm} μ^{\mp}$ and $t\to c e^{\pm} μ^{\mp}$. We enumerate the dimension-six operators which contribute to these decays and which are invariant under the Standard Model gauge group. We separate these operators into two classes, one with operators where the top quark belongs to an SU(2) doublet and thus can contribute at tree level to low-energy processes, and one class with operators where the top quark is a right-handed singlet and can only contribute to low-energy processes via loop diagrams. We use $B$ and $K$ decays to place limits on the coefficients of some of these operators, but find that several remain unconstrained and could potentially make observable contributions to top decay.
description: 15 pages, 5 figures; v2: slightly revised references, small changes in wording, two results expanded to include 2nd lepton flavor case
Additional file 1 of Introduction of ultrasound-based living anatomy into the medical curriculum: a survey on medical students’ perceptions
Creators: name: Kefala-Karli, Pelagia
name: Sassis, Leandros
name: Sassi, Marina
name: Zervides, Constantinos
Publisher: name: figshare
Year: 2021
Subjects: subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: Plant Biology

description: Additional file 1. Students' Questionnaire; Appendix I.
The IC1396N proto-cluster at a scale of 250 AU
Creators: name: Neri, R.
name: Fuente, A.
name: Ceccarelli, C.
name: Caselli, P.
name: Johnstone, D.
name: van Dishoeck, E. F.
name: Wyrowski, F.
name: Tafalla, M.
name: Lefloch, B.
name: Plume, R.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We investigate the mm-morphology of IC1396N with unprecedented spatial resolution to analyze its dust and molecular gas properties, and draw comparisons with objects of similar mass. We have carried out sensitive observations in the most extended configurations of the IRAM Plateau de Bure interferometer, to map the thermal dust emission at 3.3 and 1.3mm, and the emission from the $J$=13$_k\to12_k$ hyperfine transitions of methyl cyanide (CH$_3$CN). We unveil the existence of a sub-cluster of hot cores in IC1396N, distributed in a direction perpendicular to the emanating outflow. The cores are embedded in a common envelope of extended and diffuse dust emission. We find striking differences in the dust properties of the cores ($β\simeq$ 0) and the surrounding envelope ($β\simeq$ 1), very likely testifying to differences in the formation and processing of dust material. The CH$_3$CN emission peaks towards the most massive hot core and is marginally extended in the outflow direction.
A Higher Order Perturbative Parton Evolution Toolkit (HOPPET)
Creators: name: Salam, Gavin P.
name: Rojo, Juan
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: This document describes a Fortran 95 package for carrying out DGLAP evolution and other common manipulations of parton distribution functions (PDFs). The PDFs are represented on a grid in x-space so as to avoid limitations on the functional form of input distributions. Good speed and accuracy are obtained through the representation of splitting functions in terms of their convolution with a set of piecewise polynomial basis functions, and Runge-Kutta techniques are used for the evolution in Q. Unpolarised evolution is provided to NNLO, including heavy-quark thresholds in the MSbar scheme, and longitudinally polarised evolution to NLO. The code is structured so as to provide simple access to the objects representing splitting functions and PDFs, making it possible for a user to extend the facilities already provided. A streamlined interface is also available, facilitating use of the evolution part of the code from F77 and C/C++.
description: 60 pages, 5 figures. Code available from http://projects.hepforge.org/hoppet/
Identifying the Adoption or Rejection of Misinformation Targeting COVID-19 Vaccines in Twitter Discourse
Creators: name: Weinzierl, Maxwell
name: Harabagiu, Sanda
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computation and Language (cs.CL)
subject: Social and Information Networks (cs.SI)
subject: FOS: Computer and information sciences

description: Although billions of COVID-19 vaccines have been administered, too many people remain hesitant. Misinformation about the COVID-19 vaccines, propagating on social media, is believed to drive hesitancy towards vaccination. However, exposure to misinformation does not necessarily indicate misinformation adoption. In this paper we describe a novel framework for identifying the stance towards misinformation, relying on attitude consistency and its properties. The interactions between attitude consistency, adoption or rejection of misinformation and the content of microblogs are exploited in a novel neural architecture, where the stance towards misinformation is organized in a knowledge graph. This new neural framework is enabling the identification of stance towards misinformation about COVID-19 vaccines with state-of-the-art results. The experiments are performed on a new dataset of misinformation towards COVID-19 vaccines, called CoVaxLies, collected from recent Twitter discourse. Because CoVaxLies provides a taxonomy of the misinformation about COVID-19 vaccines, we are able to show which type of misinformation is mostly adopted and which is mostly rejected.
description: To appear in TheWebConf 2022
Competing order, Fermi surface reconstruction, and quantum oscillations in underdoped high temperature superconductors
Creators: name: Dimov, Ivailo
name: Goswami, Pallab
name: Jia, Xun
name: Chakravarty, Sudip
Publisher: name: arXiv
Year: 2008
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We consider incommensurate $d$-density wave order in underdoped high temperature superconductors. We find that Fermi surface reconstruction can correctly capture the phenomenology of the recent quantum oscillation experiments that suggest incommensurate order. The predicted frequencies are a frequency around 530 T arising from the electron pocket, a hole frequency at around 1650 T, and a new low frequency from a smaller hole pocket at 250 T for which there are some indications that require further investigation. The oscillation corresponding to the electron pocket will be further split due to bilayer coupling but the splitting is sufficiently small to require more refined measurements. The truly incommensurate $d$-density wave breaks both time reversal and inversion but the product of these two symmetry operations is preserved. There is some similarity of our results with the spiral spin density wave order, which, as pointed out by Overhauser, also breaks time reversal and inversion. Calculations corresponding to higher order commensuration produces results similar to anti-phase spin stripes, but appear to us to be an unlikely explanation of the experiments. The analysis of the Gorkov equation in the mixed state shows that the oscillation frequencies are unshifted from the putative normal state and the additional Dingle factor arising from the presence of the mixed state can provide a subtle distinction between the spiral spin density wave and the $d$-density wave.
description: 16 pages and 8 figures
Abstract kinetic equations with positive collision operators
Creators: name: Karabash, I. M.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Spectral Theory (math.SP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 47N55, 35K70, 47B50 (Primary) 35M10, 35K90 (Secondary)

description: We consider "forward-backward" parabolic equations in the abstract form $Jd ψ/ d x + L ψ= 0$, $ 0< x < τ\leq \infty$, where $J$ and $L$ are operators in a Hilbert space $H$ such that $J=J^*=J^{-1}$, $L=L^* \geq 0$, and $\ker L = 0$. The following theorem is proved: if the operator $B=JL$ is similar to a self-adjoint operator, then associated half-range boundary problems have unique solutions. We apply this theorem to corresponding nonhomogeneous equations, to the time-independent Fokker-Plank equation $ μ\frac {\partial ψ}{\partial x} (x,μ) = b(μ) \frac {\partial^2 ψ}{\partial μ^2} (x, μ)$, $ 0
description: 20 pages, LaTeX2e, version 2, references have been added, changes in the introduction
The weight filtration for real algebraic varieties
Creators: name: McCrory, Clint
name: Parusinski, Adam
Publisher: name: arXiv
Year: 2008
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14PXX, 14A15

description: Using the work of Guillen and Navarro Aznar we associate to each real algebraic variety a filtered chain complex, the weight complex, which is well-defined up to filtered quasi-isomorphism, and which induces on Borel-Moore homology with Z/2 coefficients an analog of the weight filtration for complex algebraic varieties.
description: 29 pages. Improved discussions: weight spectral sequence (Proposition 1.8), Nash constructible functions (Theorem 3.4). New section on virtual Poincare polynomial (section 4.1)
Ultrafast electronic line width broadening in the C 1s core level of graphene
Creators: name: Curcio, Davide
name: Pakdel, Sahar
name: Volckaert, Klara
name: Miwa, Jill A.
name: Ulstrup, Søren
name: Lanatà, Nicola
name: Bianchi, Marco
name: Kutnyakhov, Dmytro
name: Pressacco, Federico
name: Brenner, Günter
name: Dziarzhytski, Siarhei
name: Redlin, Harald
name: Agustsson, Steinn
name: Medjanik, Katerina
name: Vasilyev, Dmitry
name: Elmers, Hans-Joachim
name: Schönhense, Gerd
name: Tusche, Christian
name: Chen, Ying-Jiun
name: Speck, Florian
name: Seyller, Thomas
name: Bühlmann, Kevin
name: Gort, Rafael
name: Diekmann, Florian
name: Rossnagel, Kai
name: Acremann, Yves
name: Demsar, Jure
name: Wurth, Wilfried
name: Lizzit, Daniel
name: Bignardi, Luca
name: Lacovig, Paolo
name: Lizzit, Silvano
name: Sanders, Charlotte E.
name: Hofmann, Philip
Publisher: name: arXiv
Year: 2021
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Core level binding energies and absorption edges are at the heart of many experimental techniques concerned with element-specific structure, electronic structure, chemical reactivity, elementary excitations and magnetism. X-ray photoemission spectroscopy (XPS) in particular, can provide information about the electronic and vibrational many-body interactions in a solid as these are reflected in the detailed energy distribution of the photoelectrons. Ultrafast pump-probe techniques add a new dimension to such studies, introducing the ability to probe a transient state of the many-body system. Here we use a free electron laser to investigate the effect of a transiently excited electron gas on the core level spectrum of graphene, showing that it leads to a large broadening of the C 1s peak. Confirming a decade-old prediction, the broadening is found to be caused by an exchange of energy and momentum between the photoemitted core electron and the hot electron system, rather than by vibrational excitations. This interpretation is supported by a line shape analysis that accounts for the presence of the excited electrons. Fitting the spectra to this model directly yields the electronic temperature of the system, in agreement with electronic temperature values obtained from valence band data. Furthermore, making use of time- and momentum-resolved C 1s spectra, we illustrate how the momentum change of the outgoing core electrons leads to a small but detectable change in the time-resolved photoelectron diffraction pattern and to a nearly complete elimination of the core level binding energy variation associated with the narrow $σ$-band in the C 1s state. The results demonstrate that the XPS line shape can be used as an element-specific and local probe of the excited electron system and that X-ray photoelectron diffraction investigations remain feasible at very high electronic temperatures.
description: 16 pages, 12 figures
Multiqubit entanglement witness
Creators: name: Chen, Lin
name: Chen, Yi-Xin
Publisher: name: arXiv
Year: 2007
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We introduce a feasible method of constructing the entanglement witness that detects the genuine entanglement of a given pure multiqubit state. We illustrate our method in the scenario of constructing the witnesses for the multiqubit states that are broadly theoretically and experimentally investigated. It is shown that our method can construct the effective witnesses for experiments. We also investigate the entanglement detection of symmetric states and mixed states.
description: Revtex, 11 pages
Additional file 1 of Capsule-dependent impact of MAPK signalling on host cell invasion and immune response during infection of the choroid plexus epithelium by Neisseria meningitidis
Creators: name: Herold, Rosanna
name: Scholtysik, René
name: Moroniak, Selina
name: Weiss, Christel
name: Ishikawa, Hiroshi
name: Schroten, Horst
name: Schwerk, Christian
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Inhibition of the Erk1/2 and p38 signalling pathways by specific inhibitors. HIBCPP cells grown in the inverted culture system and infected for 4 h with the NmB strain MC58siaD- (Nm). Untreated cells were used as controls. The activation of Erk1/2 was inhibited by adding 25 μM of the inhibitor U0126 (U) and detected using an immunoblot (A). The cells treated with PMA served as positive controls. Phosphorylation of p38 was inhibited by SB203580 (SB) at a concentration of 25 μM. The functionality of the inhibitor was examined using an immunoblot of the p38 target protein MAPKAPK-2 (B). Treatment with anisomycin (Aniso) was used as positive control.
The Globular Cluster Luminosity Function and Specific Frequency in Dwarf Elliptical Galaxies
Creators: name: Miller, Bryan W.
name: Lotz, Jennifer M.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The globular cluster luminosity function, specific globular cluster frequency, S_N, specific globular cluster mass, T_MP, and globular cluster mass fraction in dwarf elliptical galaxies are explored using the full 69 galaxy sample of the HST WFPC2 Dwarf Elliptical Galaxy Snapshot Survey. The GCLFs of the dEs are well-represented with a t_5 function with a peak at M_{V,Z}^0(dE,HST) = -7.3 +/- 0.1. This is ~0.3 magnitudes fainter than the GCLF peaks in giant spiral and elliptical galaxies, but the results are consistent within the uncertainties. The bright-end slope of the luminosity distribution has a power-law form with slope alpha = -1.9 +/- 0.1. The trend of increasing S_N or T_MP with decreasing host galaxy luminosity is confirmed. The mean value for T_MP in dE,N galaxies is about a factor of two higher than the mean value for non-nucleated galaxies and the distributions of T_MP in dE,N and dE,noN galaxies are statistically different. These data are combined with results from the literature for a wide range of galaxy types and environments. At low host galaxy masses the distribution of T_MP for dE,noN and dI galaxies are similar. This supports the idea that one pathway for forming dE,noN galaxies is by the stripping of dIs. The formation of nuclei and the larger values of T_MP in dE,N galaxies may be due to higher star formation rates and star cluster formation efficiencies due to interactions in galaxy cluster environments.
description: 53 pages, 13 figures, 12 tables, accepted by the Astrophysical Journal
Additional file 2 of Capsule-dependent impact of MAPK signalling on host cell invasion and immune response during infection of the choroid plexus epithelium by Neisseria meningitidis
Creators: name: Herold, Rosanna
name: Scholtysik, René
name: Moroniak, Selina
name: Weiss, Christel
name: Ishikawa, Hiroshi
name: Schroten, Horst
name: Schwerk, Christian
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2. Summary of DEG determined by MACE Analysis of the transcriptome of HIBCPP cells during infection with Nm. The DEG were determined by comparing the control conditions (con, con + U0126) with the corresponding treated, infected cells. The lists shown here were filtered for a FDR p-value of < 0.05 as well as a fold change of +/- 4 (log2 fold change +/- 2).
Long-term GRMHD simulation of magnetic field in isolated neutron stars
Creators: name: Sur, Ankan
name: Cook, William
name: Radice, David
name: Haskell, Brynmor
name: Bernuzzi, Sebastiano
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Strong magnetic fields play an important role in powering the emission of neutron stars. Nevertheless a full understanding of the interior configuration of the field remains elusive. In this work, we present General Relativistic MagnetoHydroDynamics simulations of the magnetic field evolution in neutron stars lasting 500 ms (5 Alfven crossing times) and up to resolutions of 0.231 km using Athena++. We explore two different initial conditions, one with purely poloidal magnetic field and the other with a dominant toroidal component, and study the poloidal and toroidal field energies, the growth times of the various instability-driven oscillation modes and turbulence. We find that the purely poloidal setup generates a toroidal field which later decays exponentially reaching 1% of the total magnetic energy, showing no evidence of reaching equilibrium. The initially stronger toroidal field setup, on the other hand, loses up to 20% of toroidal energy and maintains this state till the end of our simulation. We also explore the hypothesis, drawn from previous MHD simulations, that turbulence plays an important role in the quasi equilibrium state. An analysis of the spectra in our higher resolution setups reveal, however, that in most cases we are not observing turbulence at small scales, but rather a noisy velocity field inside the star. We also observe that the majority of the magnetic energy gets dissipated as heat increasing the internal energy of the star, while a small fraction gets radiated away as electromagnetic radiation.
description: 11 pages, 8 figures; Accepted version in MNRAS
HST PanCET Program: A Complete Near-UV to Infrared Transmission Spectrum for the Hot Jupiter WASP-79b
Creators: name: Rathcke, Alexander D.
name: MacDonald, Ryan J.
name: Barstow, Joanna K.
name: Goyal, Jayesh M.
name: Lopez-Morales, Mercedes
name: Mendonça, João M.
name: Sanz-Forcada, Jorge
name: Henry, Gregory W.
name: Sing, David K.
name: Alam, Munazza K.
name: Lewis, Nikole K.
name: Chubb, Katy L.
name: Taylor, Jake
name: Nikolov, Nikolay
name: Buchhave, Lars A.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present a new optical transmission spectrum of the hot Jupiter WASP-79b. We observed three transits with the STIS instrument mounted on HST, spanning 0.3 - 1.0 um. Combining these transits with previous observations, we construct a complete 0.3 - 5.0 um transmission spectrum of WASP-79b. Both HST and ground-based observations show decreasing transit depths towards blue wavelengths, contrary to expectations from Rayleigh scattering or hazes. We infer atmospheric and stellar properties from the full near-UV to infrared transmission spectrum of WASP-79b using three independent retrieval codes, all of which yield consistent results. Our retrievals confirm previous detections of H$_{2}$O (at 4.0$σ$ confidence), while providing moderate evidence of H$^{-}$ bound-free opacity (3.3$σ$) and strong evidence of stellar contamination from unocculted faculae (4.7$σ$). The retrieved H$_{2}$O abundance ($\sim$ 1$\%$) suggests a super-stellar atmospheric metallicity, though stellar or sub-stellar abundances remain consistent with present observations (O/H = 0.3 - 34$\times$ stellar). All three retrieval codes obtain a precise H$^{-}$ abundance constraint: log(X$_{\rm{H^{-}}}$) $\approx$ -8.0 $\pm$ 0.7. The potential presence of H$^{-}$ suggests that JWST observations may be sensitive to ionic chemistry in the atmosphere of WASP-79b. The inferred faculae are $\sim$ 500 K hotter than the stellar photosphere, covering $\sim$ 15$\%$ of the stellar surface. Our analysis underscores the importance of observing UV - optical transmission spectra in order to disentangle the influence of unocculted stellar heterogeneities from planetary transmission spectra.
description: 27 pages, 10 figures. Resubmitted to AJ after referee report
Molecular pathways in the development of HPV-induced cervical cancer
Creators: name: Rasi Bonab, Farnaz
name: Baghbanzadeh, Amir
name: Ghaseminia, Moslem
name: Bolandi, Nadia
name: Mokhtarzadeh, Ahad
name: Amini, Mohammad
name: Dadashzadeh, Kianoosh
name: Hajiasgharzadeh, Khalil
name: Baradaran, Behzad
name: Bannazadeh Baghi, Hossein
Publisher: name: IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund
Year: 2021
Subjects: cervical cancer
HPV
oncoprotein
E6 and E7
signaling pathway

description: Recently, human papillomavirus (HPV) has gained considerable attention in cervical cancer research studies. It is one of the most important sexually transmitted diseases that can affect 160 to 289 out of 10000 persons every year. Due to the infectious nature of this virus, HPV can be considered a serious threat. The knowledge of viral structure, especially for viral oncoproteins like E6, E7, and their role in causing cancer is very important. This virus has different paths (PI3K/Akt, Wnt/β-catenin, ERK/MAPK, and JAK/STA) that are involved in the transmission of signaling paths through active molecules like MEK (pMEK), ERK (pERK), and Akt (pAkt). It’s eventually through these paths that cancer is developed. Precise knowledge of these paths and their signals give us the prognosis to adopt appropriate goals for prevention and control of these series of cancer.
description: EXCLI Journal; 20:Doc320; ISSN 1611-2156
Whole Brain Vessel Graphs: A Dataset and Benchmark for Graph Learning and Neuroscience (VesselGraph)
Creators: name: Paetzold, Johannes C.
name: McGinnis, Julian
name: Shit, Suprosanna
name: Ezhov, Ivan
name: Büschl, Paul
name: Prabhakar, Chinmay
name: Todorov, Mihail I.
name: Sekuboyina, Anjany
name: Kaissis, Georgios
name: Ertürk, Ali
name: Günnemann, Stephan
name: Menze, Bjoern H.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .
description: Thirty-fifth Conference on Neural Information Processing Systems Datasets and Benchmarks Track
Eta' gluonic content and J/psi->VP decays
Creators: name: Escribano, R.
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The $η$-$η^\prime$ pseudoscalar mixing angle and the gluonium content of the $η^\prime$ meson are deduced from an updated phenomenological analysis of $J/ψ$ decays into a vector and a pseudoscalar meson. The values for the mixing angle and the gluonic content of the $η^\prime$ wave function are $ϕ_P=(44.5\pm 4.3)^\circ$ and $Z^2_{η^\prime}=0.28\pm 0.21$, respectively.
description: 5 pages, uses espcrc2 style. Talk presented at the International Workshop on e+e- collisions from Phi to Psi (PHIPSI08), Laboratori Nazionali di Frascati (Rome), Italy, 7-10 April 2008
Hamiltonian truncation in Anti-de Sitter spacetime
Creators: name: Hogervorst, Matthijs
name: Meineri, Marco
name: Penedones, Joao
name: Vaziri, Kamran Salehi
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Quantum Field Theories (QFTs) in Anti-de Sitter (AdS) spacetime are often strongly coupled when the radius of AdS is large, and few methods are available to study them. In this work, we develop a Hamiltonian truncation method to compute the energy spectrum of QFTs in two-dimensional AdS. The infinite volume of constant timeslices of AdS leads to divergences in the energy levels. We propose a simple prescription to obtain finite physical energies and test it with numerical diagonalization in several models: the free massive scalar field, $ϕ^4$ theory, Lee-Yang and Ising field theory. Along the way, we discuss spontaneous symmetry breaking in AdS and derive a compact formula for perturbation theory in quantum mechanics at arbitrary order. Our results suggest that all conformal boundary conditions for a given theory are connected via bulk renormalization group flows in AdS.
description: 63 pages + appendices, 44 figures
Mass spectrum of diquarks and mesons in the color--flavor locked phase of dense quark matter
Creators: name: Ebert, D.
name: Klimenko, K. G.
name: Yudichev, V. L.
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The spectrum of meson and diquark excitations of dense quark matter is considered in the framework of the Nambu -- Jona-Lasinio model with three types of massless quarks in the presense of a quark number chemical potential $μ$. We investigate the effective action of meson- and diquark fields both at sufficiently large values of $μ>μ_c\approx 330$ MeV, where the color--flavor locked (CFL) phase is realized, and in the chirally broken phase of quark matter ($μμ_c$.
description: 14 pages; references added; multiplet structure of diquark excitations of the CFL phase is revised
Characterization of cbg : a cloned gene encoding an extracellular [beta]-glucosidase from Cellulomonas fimi
Creators: name: Bates, Nancy Carol
Publisher: name: University of British Columbia
Year: 2010

description: A group of Escherichia coli clones harbouring recombinant pBR322 plasmid, containing Cellulomonas fimi DNA inserts, that reacted with antiserum to C.fimi culture supernatant, was screened for their ability to hydrolyze carboxymethyl cellulose (CMC) and 4-methylumbeliferyll-β-D-cellobioside (MUC). A clone, pEC62, hydrolyzed MUC but did not hydrolyze CMC. The recombinant enzyme encoded by pEC62 was shown to be a β-glucosidase (cellobiase). C.fimii itself was shown to encode an extracellular β-glucosidase in C.fimi. This is the first report of an extracellular β-glucosidase from a bacterium. Deletion analysis localized the cloned gene (cbg)to the tet promoter proximal region of the 7.0 kilobase insert of pEC62. Further analysis and sequence data showed a highly active derivative of pEC62 contained a translational gene fusion between lacZ of pUC13 and cbg. From this data, a location for the cbg start site was proposed.
On the weak lensing masses of a new sample of galaxy groups
Creators: name: Gonzalez, Elizabeth J.
name: Rodriguez, Facundo
name: Merchán, Manuel
name: Lambas, Diego García
name: Makler, Martín
name: Chalela, Martín
name: Pereira, Maria E. S.
name: Moraes, Bruno
name: Shan, HuanYuan
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Galaxy group masses are important to relate these systems with the dark matter halo hosts. However, deriving accurate mass estimates is particularly challenging for low-mass galaxy groups. Moreover, calibration of bservational mass-proxies using weak-lensing estimates have been mainly focused on massive clusters. We present here a study of halo masses for a sample of galaxy groups identified according to a spectroscopic catalogue, spanning a wide mass range. The main motivation of our analysis is to assess mass estimates provided by the galaxy group catalogue derived through an abundance matching luminosity technique. We derive total halo mass estimates according to a stacking weak-lensing analysis. Our study allows to test the accuracy of mass estimates based on this technique as a proxy for the halo masses of large group samples. Lensing profiles are computed combining the groups in different bins of abundance matching mass, richness and redshift. Fitted lensing masses correlate with the masses obtained from abundance matching. However, when considering groups in the low- and intermediate-mass ranges, masses computed according to the characteristic group luminosity tend to predict higher values than the determined by the weak-lensing analysis. The agreement improves for the low-mass range if the groups selected have a central early-type galaxy. Presented results validate the use of mass estimates based on abundance matching techniques which provide good proxies to the halo host mass in a wide mass range.
description: 13 pages, 8 figures, plus appendices. Accepted in MNRAS
Bistability and mode interaction in microlasers
Creators: name: Zhukovsky, Sergei V.
name: Chigrin, Dmitry N.
name: Kroha, Johann
Publisher: name: arXiv
Year: 2008
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We investigate the possibility of bistable lasing in microcavity lasers as opposed to bulk lasers. To that end, the dynamic behavior of a microlaser featuring two coupled, interacting modes is analytically investigated within the framework of a semiclassical laser model, suitable for a wide range of cavity shapes and mode geometries. Closed-form coupled mode equations are obtained for all classes of laser dynamics. We show that bistable operation is possible in all of these classes. In the simplest case (class-A lasers) bistability is shown to result from an interplay between coherent (population-pulsation) and incoherent (hole-burning) processes of mode interaction. We find that microcavities offer better conditions to achieve bistable lasing than bulk cavities, especially if the modes are not degenerate in frequency. This results from better matching of the spatial intensity distribution of microcavity modes. In more complicated laser models (class-B and class-C) bistability is shown to persist for modes even further apart in frequency than in the class-A case. The predictions of the coupled mode theory have been confirmed using numerical finite-difference time-domain calculations.
description: accepted to PRA, now 18 pages in the revised version
The running fine structure constant alpha(E) via the Adler function
Creators: name: Jegerlehner, F.
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present an up-to-date analysis for a precise determination of the effective fine structure constant and discuss the prospects for future improvements. We advocate to use a determination monitored by the Adler function which allows us to exploit perturbative QCD in an optimal well controlled way. Together with a long term program of hadronic cross section measurements at energies up to a few GeV, a determination of alpha(M_Z) at a precision comparable to the one of the Z mass M_Z should be feasible. Presently alpha(E) at E>1 GeV is the least precisely known of the fundamental parameters of the SM. Since, in spite of substantial progress due to new BaBar exclusive data, the region 1.4 to 2.4 GeV remains the most problematic one a major step in the reduction of the uncertainties are expected from VEPP-2000 and from a possible ``high-energy'' option DAFNE-2 at Frascati. The up-to-date evaluation reads Delta alpha^{(5)}_{had}(M_Z^2) = 0.027515 +/- 0.000149 or alpha^{-1}(M_Z)=128.957 +/- 0.020.
description: 7 pages, 6 figures
A novel stellar spectrum denoising method based on deep Bayesian modeling
Creators: name: Kang, Xin
name: He, Shiyuan
name: Zhang, Yanxia
Publisher: name: arXiv
Year: 2021
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Spectrum denoising is an important procedure for large-scale spectroscopical surveys. This work proposes a novel stellar spectrum denoising method based on deep Bayesian modeling. The construction of our model includes a prior distribution for each stellar subclass, a spectrum generator and a flow-based noise model. Our method takes into account the noise correlation structure, and it is not susceptible to strong sky emission lines and cosmic rays. Moreover, it is able to naturally handle spectra with missing flux values without ad-hoc imputation. The proposed method is evaluated on real stellar spectra from the Sloan Digital Sky Survey (SDSS) with a comprehensive list of common stellar subclasses and compared to the standard denoising auto-encoder. Our denoising method demonstrates superior performance to the standard denoising auto-encoder, in respect of denoising quality and missing flux imputation. It may be potentially helpful in improving the accuracy of the classification and physical parameter measurement of stars when applying our method during data preprocessing.
description: 20 pages, 15 Figures, accepted by Research in Astronomy and Astrophysics
21 cm Forest Constraints on Primordial Black Holes
Creators: name: Villanueva-Domingo, Pablo
name: Ichiki, Kiyotomo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Primordial black holes (PBHs) as part of the Dark Matter (DM) would modify the evolution of large-scale structures and the thermal history of the universe. Future 21 cm forest observations, sensitive to small scales and the thermal state of the Inter Galactic Medium (IGM), could probe the existence of such PBHs. In this article, we show that the shot noise isocurvature mode on small scales induced by the presence of PBHs can enhance the amount of low mass halos, or minihalos, and thus, the number of 21 cm absorption lines. However, if the mass of PBHs is as large as $M_{\rm PBH}\gtrsim 10 \, M_\odot$, with an abundant enough fraction of PBHs as DM, $f_{\rm PBH}$, the IGM heating due to accretion onto the PBHs counteracts the enhancement due to the isocurvature mode, reducing the number of absorption lines instead. The concurrence of both effects imprints distinctive signatures in the number of absorbers, allowing to bound the abundance of PBHs. We compute the prospects for constraining PBHs with future 21 cm forest observations, finding achievable competitive upper limits on the abundance as low as $f_{\rm PBH} \sim 10^{-3}$ at $M_{\rm PBH}= 100 \, M_\odot$, or even lower at larger masses, in unexplored regions of the parameter space by current probes. The impact of astrophysical X-ray sources on the IGM temperature is also studied, which could potentially weaken the bounds.
description: 18 pages, 8 figures
Violation of the Wiedemann-Franz law in the Topological Kondo model
Creators: name: Buccheri, Francesco
name: Nava, Andrea
name: Egger, Reinhold
name: Sodano, Pasquale
name: Giuliano, Domenico
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We study the thermal transport through a Majorana island connected to multiple external quantum wires. In the presence of a large charging energy, we find that the Wiedemann-Franz law is nontrivially violated at low temperature, contrarily to what happens for the overscreened Kondo effect and for nontopological junctions. For three wires, we find that the Lorenz ratio is rescaled by a universal factor 2/3 and we show that this behavior is due to the presence of localized Majorana modes on the island.
description: 6 pages, 2 figures. Published version