cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Menger and consonant sets in the Sacks model
Creators: name: Haberl, Valentin
name: Szewczak, Piotr
name: Zdomskyy, Lyubomyr
Publisher: name: arXiv
Year: 2024
Subjects: subject: Logic (math.LO)
subject: General Topology (math.GN)
subject: FOS: Mathematics
subject: 54D20, 03E35

description: Using iterated Sacks forcing and topological games, we prove that the existence of a totally imperfect Menger set in the Cantor cube with cardinality continuum is independent from ZFC. We also analyze the structure of Hurewicz and consonant subsets of the Cantor cube in the Sacks model.
description: 26 pages
Supp_material – Supplemental material for Americans’ Perceptions of Transgender People’s Sex: Evidence from a National Survey Experiment
Creators: name: Doan, Long
name: Quadlin, Natasha
name: Powell, Brian
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: Sociology
subject: FOS: Sociology

description: Supplemental material, Supp_material for Americans’ Perceptions of Transgender People’s Sex: Evidence from a National Survey Experiment by Long Doan, Natasha Quadlin and Brian Powell in Socius
Boundary Time Crystals as AC sensors: enhancements and constraints
Creators: name: Gribben, Dominic
name: Sanpera, Anna
name: Fazio, Rosario
name: Marino, Jamir
name: Iemini, Fernando
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We investigate the use of a boundary time crystals (BTCs) as quantum sensors of AC fields. Boundary time crystals are non-equilibrium phases of matter in contact to an environment, for which a macroscopic fraction of the many-body system breaks the time translation symmetry. We find an enhanced sensitivity of the BTC when its spins are resonant with the applied AC field, as quantified by the quantum Fisher information (QFI). The QFI dynamics in this regime is shown to be captured by a relatively simple ansatz consisting of an initial power-law growth and late-time exponential decay. We study the scaling of the ansatz parameters with resources (encoding time and number of spins) and identify a moderate quantum enhancement in the sensor performance through comparison with classical QFI bounds. Investigating the precise source of this performance, we find that despite of its long coherence time and multipartite correlations (advantageous properties for quantum metrology), the entropic cost of the BTC (which grows indefinitely in the thermodynamic limit) hinders an optimal decoding of the AC field information. This result has implications for future candidates of quantum sensors in open system and we hope it will encourage future study into the role of entropy in quantum metrology.
description: 15 pages, 5 figures
Harmony of Spinning Conformal Blocks
Creators: name: Schomerus, Volker
name: Sobko, Evgeny
name: Isachenkov, Mikhail
Publisher: name: Deutsches Elektronen-Synchrotron, DESY, Hamburg
Year: 2016

description: Conformal blocks for correlation functions of tensor operators play an increasingly important role for the conformal bootstrap programme. We develop a universal approach to such spinning blocks through the harmonic analysis of certain bundles over a coset of the conformal group. The resulting Casimir equations are given by a matrix version of the Calogero-Sutherland Hamiltonian that describes the scattering of interacting spinning particles in a 1-dimensional external potential. The approach is illustrated in several examples including fermionic seed blocks in 3D CFT where they take a very simple form.
Intrinsic compressibility effects in near-wall turbulence
Creators: name: Hasan, Asif Manzoor
name: Costa, Pedro
name: Larsson, Johan
name: Pirozzoli, Sergio
name: Pecnik, Rene
Publisher: name: arXiv
Year: 2024
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: The impact of intrinsic compressibility effects -- changes in fluid volume due to pressure variations -- on high-speed wall-bounded turbulence has often been overlooked or incorrectly attributed to mean property variations. To unambiguously quantify these intrinsic compressibility effects, we perform direct numerical simulations of compressible turbulent channel flows with nearly uniform mean properties. Our simulations reveal that intrinsic compressibility effects yield a significant upward shift in the logarithmic mean velocity profile that can be attributed to the reduction in the turbulent shear stress. This reduction stems from the weakening of the near-wall quasi-streamwise vortices. We in turn attribute this weakening to the spontaneous opposition of sweeps and ejections from the near-wall expansions and contractions of the fluid, and provide a theoretical explanation for this mechanism. Our results also demonstrate that intrinsic compressibility effects are responsible for the increase in the inner-scaled streamwise turbulence intensity in compressible flows compared to incompressible flows, previously regarded to be an effect of mean property variations.
description: 29 pages, 17 figures
Heptagons from the Steinmann Cluster Bootstrap
Creators: name: Dixon, Lance J.
name: Drummond, James
name: Harrington, Thomas
name: McLeod, Andrew J.
name: Papathanasiou, Georgios
name: Spradlin, Marcus
Publisher: name: Deutsches Elektronen-Synchrotron, DESY, Hamburg
Year: 2017

description: We reformulate the heptagon cluster bootstrap to take advantage of the Steinmann relations, which require certain double discontinuities of any amplitude to vanish. These constraints vastly reduce the number of functions needed to bootstrap seven-point amplitudes in planar $\mathcal{N} = 4$ supersymmetric Yang-Mills theory, making higher-loop contributions to these amplitudes more computationally accessible. In particular, dual superconformal symmetry and well-defined collinear limits suffice to determine uniquely the symbols of the three-loop NMHV and four-loop MHV seven-point amplitudes. We also show that at three loops, relaxing the dual superconformal ($\bar{Q}$) relations and imposing dihedral symmetry (and for NMHV the absence of spurious poles) leaves only a single ambiguity in the heptagon amplitudes. These results point to a strong tension between the collinear properties of the amplitudes and the Steinmann relations.
Efficient Hardware Accelerator Based on Medium Granularity Dataflow for SpTRSV
Creators: name: Chen, Qian
name: Yang, Xiaofeng
name: Lu, Shengli
Publisher: name: arXiv
Year: 2024
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Hardware Architecture (cs.AR)
subject: Numerical Analysis (math.NA)
subject: Performance (cs.PF)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Sparse triangular solve (SpTRSV) is widely used in various domains. Numerous studies have been conducted using CPUs, GPUs, and specific hardware accelerators, where dataflows can be categorized into coarse and fine granularity. Coarse dataflows offer good spatial locality but suffer from low parallelism, while fine dataflows provide high parallelism but disrupt the spatial structure, leading to increased nodes and poor data reuse. This paper proposes a novel hardware accelerator for SpTRSV or SpTRSV-like DAGs. The accelerator implements a medium granularity dataflow through hardware-software codesign and achieves both excellent spatial locality and high parallelism. Additionally, a partial sum caching mechanism is introduced to reduce the blocking frequency of processing elements (PEs), and a reordering algorithm of intra-node edges computation is developed to enhance data reuse. Experimental results on 245 benchmarks with node counts reaching up to 85,392 demonstrate that this work achieves average performance improvements of 7.0$\times$ (up to 27.8$\times$) over CPUs and 5.8$\times$ (up to 98.8$\times$) over GPUs. Compared to the state-of-the-art technique (DPU-v2), this work shows a 2.5$\times$ (up to 5.9$\times$) average performance improvement and 1.7$\times$ (up to 4.1$\times$) average energy efficiency enhancement.
Information-theoretic evaluation of covariate distributions models
Creators: name: Hartung, Niklas
name: Khatova, Aleksandra
Publisher: name: arXiv
Year: 2024
Subjects: subject: Applications (stat.AP)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Statistical modelling of covariate distributions allows to generate virtual populations or to impute missing values in a covariate dataset. Covariate distributions typically have non-Gaussian margins and show nonlinear correlation structures, which simple multivariate Gaussian distributions fail to represent. Prominent non-Gaussian frameworks for covariate distribution modelling are copula-based models and models based on multiple imputation by chained equations (MICE). While both frameworks have already found applications in the life sciences, a systematic investigation of their goodness-of-fit to the theoretical underlying distribution, indicating strengths and weaknesses under different conditions, is still lacking. To bridge this gap, we thoroughly evaluated covariate distribution models in terms of Kullback-Leibler divergence (KL-D), a scale-invariant information-theoretic goodness-of-fit criterion for distributions. Methodologically, we proposed a new approach to construct confidence intervals for KL-D by combining nearest neighbour-based KL-D estimators with subsampling-based uncertainty quantification. In relevant data sets of different sizes and dimensionalities with both continuous and discrete covariates, non-Gaussian models showed consistent improvements in KL-D, compared to simpler Gaussian or scale transform approximations. KL-D estimates were also robust to the inclusion of latent variables and large fractions of missing values. While good generalization behaviour to new data could be seen in copula-based models, MICE shows a trend for overfitting and its performance should always be evaluated on separate test data. Parametric copula models and MICE were found to scale much better with the dataset dimension than nonparametric copula models. These findings corroborate the potential of non-Gaussian models for modelling realistic life science covariate distributions.
AUT900594_Supplemental_material_Appendix_B – Supplemental material for Looking or talking: Visual attention and verbal engagement during shared book reading of preschool children on the autism spectrum
Creators: name: Wicks, Rachelle
name: Paynter, Jessica
name: Westerveld, Marleen F
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: 170199 Psychology not elsewhere classified
subject: FOS: Psychology
subject: 110319 Psychiatry (incl. Psychotherapy)
subject: FOS: Clinical medicine
subject: 111799 Public Health and Health Services not elsewhere classified
subject: FOS: Health sciences
subject: Education
subject: 130312 Special Education and Disability
subject: FOS: Educational sciences

description: Supplemental material, AUT900594_Supplemental_material_Appendix_B for Looking or talking: Visual attention and verbal engagement during shared book reading of preschool children on the autism spectrum by Rachelle Wicks, Jessica Paynter and Marleen F Westerveld in Autism
Supplemental Material1 - Supplemental material for Correcting for non-participation bias in health surveys using record-linkage, synthetic observations and pattern mixture modelling
Creators: name: Linsay Gray
name: Gorman, Emma
name: White, Ian R
name: S Vittal Katikireddi
name: McCartney, Gerry
name: Rutherford, Lisa
name: Leyland, Alastair H
Publisher: name: SAGE Journals
Year: 2019
Subjects: subject: 111708 Health and Community Services
subject: FOS: Health sciences
subject: 111099 Nursing not elsewhere classified
subject: 160807 Sociological Methodology and Research Methods
subject: FOS: Sociology

description: Supplemental material, Supplemental Material1 for Correcting for non-participation bias in health surveys using record-linkage, synthetic observations and pattern mixture modelling by Linsay Gray, Emma Gorman, Ian R White, S Vittal Katikireddi, Gerry McCartney, Lisa Rutherford and Alastair H Leyland in Statistical Methods in Medical Research
Additional file 1 of Exosomal HSP90 induced by remote ischemic preconditioning alleviates myocardial ischemia/reperfusion injury by inhibiting complement activation and inflammation
Creators: name: Cheng, Xiao-Fang
name: He, Shi-Tao
name: Zhong, Guo-Qiang
name: Meng, Jian-Jun
name: Wang, Min
name: Bi, Qi
name: Tu, Rong-Hui
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology

description: Additional file 1. Original images of western blots displayed in Fig. 1E, Fig. 2A, Fig. 6A and Fig. 7A.
Additional file 1 of E-cigarette product preferences of Australian adolescent and adult users: a 2022 study
Creators: name: Jongenelis, Michelle I
Publisher: name: figshare
Year: 2024
Subjects: subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Supplementary Material 1
Bayesian Circular Regression with von Mises Quasi-Processes
Creators: name: Cohen, Yarden
name: Navarro, Alexandre Khae Wu
name: Frellsen, Jes
name: Turner, Richard E.
name: Riemer, Raziel
name: Pakman, Ari
Publisher: name: arXiv
Year: 2024
Subjects: subject: Machine Learning (stat.ML)
subject: Machine Learning (cs.LG)
subject: Computation (stat.CO)
subject: FOS: Computer and information sciences

description: The need for regression models to predict circular values arises in many scientific fields. In this work we explore a family of expressive and interpretable distributions over circle-valued random functions related to Gaussian processes targeting two Euclidean dimensions conditioned on the unit circle. The probability model has connections with continuous spin models in statistical physics. Moreover, its density is very simple and has maximum-entropy, unlike previous Gaussian process-based approaches, which use wrapping or radial marginalization. For posterior inference, we introduce a new Stratonovich-like augmentation that lends itself to fast Gibbs sampling. We argue that transductive learning in these models favors a Bayesian approach to the parameters and apply our sampling scheme to the Double Metropolis-Hastings algorithm. We present experiments applying this model to the prediction of (i) wind directions and (ii) the percentage of the running gait cycle as a function of joint angles.
A large-scale multicenter breast cancer DCE-MRI benchmark dataset with expert segmentations
Creators: name: Garrucho, Lidia
name: Kushibar, Kaisar
name: Reidel, Claire-Anne
name: Joshi, Smriti
name: Osuala, Richard
name: Tsirikoglou, Apostolia
name: Bobowicz, Maciej
name: del Riego, Javier
name: Catanese, Alessandro
name: Gwoździewicz, Katarzyna
name: Cosaka, Maria-Laura
name: Abo-Elhoda, Pasant M.
name: Tantawy, Sara W.
name: Sakrana, Shorouq S.
name: Shawky-Abdelfatah, Norhan O.
name: Abdo-Salem, Amr Muhammad
name: Kozana, Androniki
name: Divjak, Eugen
name: Ivanac, Gordana
name: Nikiforaki, Katerina
name: Klontzas, Michail E.
name: García-Dosdá, Rosa
name: Gulsun-Akpinar, Meltem
name: Lafcı, Oğuz
name: Mann, Ritse
name: Martín-Isla, Carlos
name: Prior, Fred
name: Marias, Kostas
name: Starmans, Martijn P. A.
name: Strand, Fredrik
name: Díaz, Oliver
name: Igual, Laura
name: Lekadir, Karim
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: Databases (cs.DB)
subject: FOS: Computer and information sciences

description: Artificial Intelligence (AI) research in breast cancer Magnetic Resonance Imaging (MRI) faces challenges due to limited expert-labeled segmentations. To address this, we present a multicenter dataset of 1506 pre-treatment T1-weighted dynamic contrast-enhanced MRI cases, including expert annotations of primary tumors and non-mass-enhanced regions. The dataset integrates imaging data from four collections in The Cancer Imaging Archive (TCIA), where only 163 cases with expert segmentations were initially available. To facilitate the annotation process, a deep learning model was trained to produce preliminary segmentations for the remaining cases. These were subsequently corrected and verified by 16 breast cancer experts (averaging 9 years of experience), creating a fully annotated dataset. Additionally, the dataset includes 49 harmonized clinical and demographic variables, as well as pre-trained weights for a baseline nnU-Net model trained on the annotated data. This resource addresses a critical gap in publicly available breast cancer datasets, enabling the development, validation, and benchmarking of advanced deep learning models, thus driving progress in breast cancer diagnostics, treatment response prediction, and personalized care.
description: 15 paes, 7 figures, 3 tables
Sensitivity_Alm_Backman – Supplemental material for ‘When it rains, it pours’: Housing evictions and criminal convictions in Sweden
Creators: name: Alm, Susanne
name: Bäckman, Olof
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: 160299 Criminology not elsewhere classified
subject: FOS: Law
subject: 120505 Regional Analysis and Development
subject: FOS: Social and economic geography

description: Supplemental material, Sensitivity_Alm_Backman for ‘When it rains, it pours’: Housing evictions and criminal convictions in Sweden by Susanne Alm and Olof Bäckman in European Journal of Criminology
Additional file 1 of Elevated free interleukin-18 associated with severity and mortality in prospective cohort study of 206 hospitalised COVID-19 patients
Creators: name: Nasser, Syed M. T.
name: Rana, Anas A.
name: Doffinger, Rainer
name: Kafizas, Andreas
name: Khan, Tauseef A.
name: Nasser, Shuaib
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: Additional file 1. Supplementary Methods. Supplementary Results.
Efficient Design and Implementation of Fast-Convolution-Based Variable-Bandwidth Filters
Creators: name: Moryakova, Oksana
name: Johansson, Håkan
Publisher: name: arXiv
Year: 2024
Subjects: subject: Signal Processing (eess.SP)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: This paper introduces an efficient design approach for a fast-convolution-based variable-bandwidth (VBW) filter. The proposed approach is based on a hybrid of frequency sampling and optimization (HFSO), that offers significant computational complexity reduction compared to existing solutions for a given performance. The paper provides a design procedure based on minimax optimization to obtain the minimum complexity of the overall filter. A design example includes a comparison of the proposed design-based VBW filter and time-domain designed VBW filters implemented in the time domain and in the frequency domain. It is shown that not only the implementation complexity can be reduced but also the design complexity by excluding any computations when the bandwidth of the filter is adjusted. Moreover, memory requirements are also decreased compared to the existing frequency-domain implementations.
Inhomogeneity-induced wavenumber diffusion
Creators: name: Cox, Michael R.
name: Kafiabad, Hossein A.
name: Vanneste, Jacques
Publisher: name: arXiv
Year: 2024
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: FOS: Physical sciences

description: Inertia-gravity waves are scattered by background flows as a result of Doppler shift by a non-uniform velocity. In the WKB regime, the scattering process reduces to a diffusion in spectral space. Other inhomogeneities the waves encounter, such as density variations, also cause scattering and spectral diffusion. We generalise the spectral diffusion equation to account for these inhomogeneities. We apply the result to the rotating shallow water system, for which height inhomogeneities arise from velocity inhomogeneities through geostrophy, and to the Boussinesq system for which buoyancy inhomogeneities arise similarly. We compare the contributions that height and buoyancy variations make to the spectral diffusion with the contribution of the Doppler shift. In both systems, we find regimes where all contributions are significant. We support our findings with exact solutions of the diffusion equation and with ray tracing simulations in the shallow water case.
Propagating Instability for Wave Dark Matter
Creators: name: Zhang, Ui-Han
name: Woo, Tak-Pong
name: Chiueh, Tzihong
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In the early Universe, large-scale flows were omnipresent, and the flow collisions produced sheets and filaments. This phenomenon occurs for both particle and wave dark matter. But for the latter, these sheets and filaments are the modulations of even finer-scale, large-amplitude interference fringes. This work aims to investigate the instability of the interference fringes arising from colliding waves. Two colliding streams in classical collisionless fluid systems can produce small-scale unstable oscillations with a finite complex frequency, identified as propagating instabilities. In fact, propagating unstable oscillations have never been observed in the conventional quantum system due to its being Sturm-Liouville property. For example, quantum fluid equations with Madelung variables only exhibit either Jeans instability, a purely growing unstable mode, or stable oscillations, for which the squared frequency is real. Despite that, this work discovers that quantum interference fringes can indeed generate propagating unstable oscillations with a complex squared frequency when the gravitational feedback perturbation is included. The presence of local density nulls in the background density is shown to be the necessary condition for such an instability. We establish a phase diagram separating the propagating instability, Jeans instability, and stable oscillation regions, and is verified by computer simulations. Generally speaking, Jeans instabilities tend to occur for long-wave density perturbations as expected; propagating instabilities on the other hand tend to occur for short density waves with wavelengths comparable to the fringe size, i.e., near the center of the Bloch zone; lastly, both instabilities diminish for very low density fringes. The propagating unstable fluctuation may possibly collapse into halos of small sizes, potentially seeding the formation of proto-globular clusters.
description: 33 pages, 6 figures, 1 table
Additional file 9 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Creators: name: Leonard, Alexander S.
name: Crysnanto, Danang
name: Mapel, Xena M.
name: Bhati, Meenu
name: Pausch, Hubert
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified

description: Additional file 9: Table S8. Minigraph pangenomes constructed with different “minimum variant length” parameter (L) values. CPU hours required for pangenome construction increased dramatically for L smaller than 10 bp. Warnings refer to the number of “impossible insert” warnings issued during pangenome construction, relating to unsuitable graph topology. Bubbles and Nodes respectively refer to the number of top-level bubbles and nodes present across the autosomes. VNTR overlaps is the number of VNTRs (in total 9,568) that overlap with a graph bubble.
Tayler-Spruit dynamo in stably stratified rotating fluids: Application to proto-magnetars
Creators: name: Barrère, Paul
name: Guilet, Jérôme
name: Raynaud, Raphaël
name: Reboul-Salze, Alexis
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: The formation of highly magnetized young neutron stars, called magnetars, is still a strongly debated question. A promising scenario invokes the amplification of the magnetic field by the Tayler-Spruit dynamo in a proto-neutron star (PNS) spun up by fallback. Barrère et al. 2023 supports this scenario by demonstrating that this dynamo can generate magnetar-like magnetic fields in stably stratified Boussinesq models of a PNS interior. To further investigate the Tayler-Spruit dynamo, we perform 3D-MHD numerical simulations with the MagIC code varying the ratio between the Brunt-Väisälä frequency and the rotation rate. We first demonstrate that a self-sustained dynamo process can be maintained for a Brunt-Väisälä frequency about 4 times higher than the angular rotation frequency. The generated magnetic fields and angular momentum transport follow the analytical scaling laws of Fuller et al. 2019, which confirms our previous results. We also report for the first time the existence of an intermittent Tayler-Spruit dynamo. For a typical PNS Brunt-Väisälä frequency of $10^{3}\,{\rm s}^{-1}$, the axisymmetric toroidal and dipolar magnetic fields range between $1.2\times 10^{15}-2\times 10^{16}\,{\rm G}$ and $1.4\times 10^{13}-3\times 10^{15}\,{\rm G}$, for rotation periods of $1-10\,{\rm ms}$. Thus, our results provide numerical evidence that our scenario can explain the formation of magnetars. As the Tayler-Spruit dynamo is often invoked for the angular momentum transport in stellar radiative zones, our results are also of particular importance in this field and we provide a calibration of the Fuller et al.'s prescription based on our simulations, with a dimensionless normalisation factor of the order of $10^{-2}$.
description: 14 pages, 13 figures (2 pages, 1 figure for the appendix), submitted to A&A
Additional file 8 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Creators: name: Leonard, Alexander S.
name: Crysnanto, Danang
name: Mapel, Xena M.
name: Bhati, Meenu
name: Pausch, Hubert
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified

description: Additional file 8: Table S7. Several obvious misalignments found in different pangenomes which affects TR count genotyping. Part of the size difference may be true if there is variation in the number of tandem repeats, but the obvious majority of the large mis-translated regions are due to repetitive regions or spurious graph cycles. Δ bp is the size difference for the lifted-over sample TR coordinates from the original reference TR coordinates.
Jetted subgalactic-size radio sources in merging galaxies -- A jet redirection scenario
Creators: name: Stanghellini, C.
name: Orienti, M.
name: Spingola, C.
name: Zanichelli, A.
name: Dallacasa, D.
name: Cassaro, P.
name: O'Dea, C. P.
name: Baum, S. A.
name: Pérez-Torres, M.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Context: The long-standing question concerning jetted subgalactic-size (JSS) radio sources is whether they will evolve into large radio galaxies, die before escaping the host galaxy, or remain indefinitely confined to their compact size. Aims: Our main goal is to propose a scenario that explains the relative number of JSS radio sources and their general properties. Methods: We studied the parsec-scale radio morphology of a complete sample of 21 objects using Very Long Baseline Array (VLBA) observations at various frequencies and analyzed the morphological characteristics of their optical hosts. Results: Many of these radio sources exhibit radio morphologies consistent with transverse motions of their bright edges and are found in dynamically disturbed galaxies. VLBA images suggest the possible presence of large-angle, short-period precessing jets, and an orbital motion of the radio-loud active galactic nucleus (AGN) in a dual or binary system. The majority of JSS radio sources appear to be in systems in different stages of their merging evolution. Conclusions: We propose a scenario where rapid jet redirection, through precession or orbital motion, prevents the jet from penetrating the interstellar medium (ISM) sufficiently to escape the host galaxy. Most JSS radio sources remain compact due to their occurrence in merging galaxies.
description: 35 pages, 24 figures, 4 tables, accepted for publication in Astronomy & Astrophysics
Additional file 10 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Creators: name: Leonard, Alexander S.
name: Crysnanto, Danang
name: Mapel, Xena M.
name: Bhati, Meenu
name: Pausch, Hubert
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified

description: Additional file 10. Review History.
Additional file 4 of A genetic tool to express long fungal biosynthetic genes
Creators: name: Kirchgaessner, Leo
name: Wurlitzer, Jacob M.
name: Seibold, Paula S.
name: Rakhmanov, Malik
name: Gressler, Markus
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4: Table S3. Oligonucleotides used in this study.
Improving Computer Vision Interpretability: Transparent Two-level Classification for Complex Scenes
Creators: name: Scholz, Stefan
name: Weidmann, Nils B.
name: Steinert-Threlkeld, Zachary C.
name: Keremoğlu, Eda
name: Goldlücke, Bastian
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Treating images as data has become increasingly popular in political science. While existing classifiers for images reach high levels of accuracy, it is difficult to systematically assess the visual features on which they base their classification. This paper presents a two-level classification method that addresses this transparency problem. At the first stage, an image segmenter detects the objects present in the image and a feature vector is created from those objects. In the second stage, this feature vector is used as input for standard machine learning classifiers to discriminate between images. We apply this method to a new dataset of more than 140,000 images to detect which ones display political protest. This analysis demonstrates three advantages to this paper's approach. First, identifying objects in images improves transparency by providing human-understandable labels for the objects shown on an image. Second, knowing these objects enables analysis of which distinguish protest images from non-protest ones. Third, comparing the importance of objects across countries reveals how protest behavior varies. These insights are not available using conventional computer vision classifiers and provide new opportunities for comparative research.
Additional file 6 of A genetic tool to express long fungal biosynthetic genes
Creators: name: Kirchgaessner, Leo
name: Wurlitzer, Jacob M.
name: Seibold, Paula S.
name: Rakhmanov, Malik
name: Gressler, Markus
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 6: Figure S2. Plasmid maps of the expression vectors. The plasmids pLK04 (A), pLK05 (B), pMG56 (C) and pMG58 (D) are based on the pSMX2-URA plasmid [1]. The gene fragments are: bla; β-lactamase (confers ampicillin resistance); calA1/5; 1 kb of the 5′or 3′ end of the calA gene; fwnAup and fwnAdown, 1 kb up- and downstream the A. niger fwnA polyketide synthase gene; URA-blaster (dark blue, contains several genes; see below); PterA, promoter of the terA terrein polyketide synthase gene of Aspergillus terreus; Tag, encodes the hexahistidin tag (and includes an SpeI and PacI site for insertion of the GOI); TtrpC, terminator of the trpC anthranilatsynthase component 2 gene of A. terreus; rep origin, origin of plasmid replication. The URA-blaster contains: PpyrG, promoter of the pyrG gene from Aspergillus nidulans; pyrG, orotidine 5′-phosphate decarboxylase gene from A. nidulans (confers uracil prototrophy); TpyrG, terminator of the pyrG gene from A. nidulans; and two prpB flanks that encode the methylcitrate synthase gene from Escherichia coli that facilitate a subsequent removal of the URA blaster cassette from the A. niger genome via a homologous recombination event (counter selection) by addition of 5-fluoroorotic acid [2].
Magic spreading in random quantum circuits
Creators: name: Turkeshi, Xhek
name: Tirrito, Emanuele
name: Sierant, Piotr
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Magic is the resource that quantifies the amount of beyond-Clifford operations necessary for universal quantum computing. It bounds the cost of classically simulating quantum systems via stabilizer circuits central to quantum error correction and computation. How rapidly do generic many-body dynamics generate magic resources under the constraints of locality and unitarity? We address this central question by exploring magic spreading in brick-wall random unitary circuits. We explore scalable magic measures intimately connected to the algebraic structure of the Clifford group. These metrics enable the investigation of the spreading of magic for system sizes of up to $N=1024$ qudits, surpassing the previous state-of-the-art, which was restricted to about a dozen qudits. We demonstrate that magic resources equilibrate on timescales logarithmic in the system size, akin to anti-concentration and Hilbert space delocalization phenomena, but qualitatively different from the spreading of entanglement entropy. As random circuits are minimal models for chaotic dynamics, we conjecture that our findings describe the phenomenology of magic resources growth in a broad class of chaotic many-body systems.
description: Updated version, comments are welcome!
Science Using Single-Pulse Exploration with Combined Telescopes. I. The mode switching, flaring, and single-pulse morphology of PSR B1822-09
Creators: name: Jankowski, F.
name: Griessmeier, J. -M.
name: Surnis, M.
name: Theureau, G.
name: Petri, J.
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Aims. We aim to elucidate the pulsar radio emission by studying several single-pulse phenomena, how they relate, and how they evolve with observing frequency. We intend to inspire models for the pulsar radio emission and fast radio bursts. Methods. We set up an observing programme called the SUSPECT project running at the Nancay Radio Observatory telescopes in France (10-85 MHz, 110-240 MHz, and 1.1-3.5GHz) and the upgraded Giant Metrewave Radio Telescope (uGMRT) in India. This first paper focuses on high sensitivity data of PSR B1822-09 obtained with the uGMRT between 550 and 750 MHz. The pulsar has precursor (PC), main pulse (MP), and interpulse (IP) emission and exhibits mode switching. We present its single-pulse stacks, investigate its mode switching using a hidden Markov switching model, and analyse its single-pulse morphology. Results. PSR B1822-09's pulse profile decomposes into seven components. We show that its mode switching is well described using a hidden Markov switching model operating on single-pulse profile features. The pulsar exhibits at least three stable emission modes, one of which is a newly discovered bright flaring Bf-mode. We confirm that the PC and MP switch synchronously to each other and both asynchronously to the IP, indicating information transfer between the polar caps. Additionally, we performed a fluctuation spectral analysis and discovered three fluctuation features in its quiescent Q-mode emission, one of which is well known. We conclude that the latter feature is due to longitude-stationary amplitude modulation. Finally, we visually classified the single pulses into four categories. We found extensive microstructure in the PC with a typical duration of 0.2-0.4 ms and a quasi-periodicity of 0.8 ms. There is clear evidence of mode mixing. We discovered low-intensity square-like pulses and extremely bright pulses in the MP, which suggest bursting.
description: 22 pages, 19 figures, 3 tables. Accepted for publication in A&A. Abstract shortened to fit the arXiv limit
Supplemental_Material_McCarthy_et_al – Supplemental material for The Impact of Variable Selection Coverage on Detection of Ligands from a DNA-Encoded Library Screen
Creators: name: McCarthy, Kelly A.
name: G. Joseph Franklin
name: Lancia, David R.
name: Olbrot, Martin
name: Pardo, Eneida
name: O’Connell, Jonathan C.
name: Kollmann, Christopher S.
Publisher: name: SAGE Journals
Year: 2020
Subjects: subject: 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
subject: FOS: Clinical medicine

description: Supplemental material, Supplemental_Material_McCarthy_et_al for The Impact of Variable Selection Coverage on Detection of Ligands from a DNA-Encoded Library Screen by Kelly A. McCarthy, G. Joseph Franklin, David R. Lancia, Martin Olbrot, Eneida Pardo, Jonathan C. O’Connell and Christopher S. Kollmann in SLAS Discovery
Additional file 6 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Creators: name: Leonard, Alexander S.
name: Crysnanto, Danang
name: Mapel, Xena M.
name: Bhati, Meenu
name: Pausch, Hubert
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified

description: Additional file 6: Table S5. Compute resources for alignment of additional assemblies. Compute resources for aligning the 12 assemblies included in pangenome construction and the 8 held out for analysis. CPU hours are averaged per assembly for both the bulk and centro-/telomeric regions, and memory is the peak RAM usage across all assemblies.
Additional file 1 of High prevalence of mental disorder symptoms among medical and other health specialties residents during the COVID-19 pandemic
Creators: name: Silva, Nayane Miranda
name: da Nobrega Lucena Pinho, Rebeca
name: Costa, Thais Ferreira
name: Areal, Adriana Ferreira Barros
name: De Mattos Salles, André
name: Ribeiro Alves Oliveira, Andrea Pedrosa
name: Esselin Rassi, Carlos Henrique Reis
name: Valero, Caroline Elizabeth Brero
name: Gomes, Ciro Martins
name: da Silva, Dayde Lane Mendonça
name: de Oliveira, Fernando Araujo Rodrigues
name: Jochims, Isadora
name: Vaz Filho, Ivan Henrique Ranulfo
name: De Brito Seixas Neves, Juliana
name: de Brito Oliveira, Lucas Alves
name: Dantas, Maria Luisa Nogueira
name: Rosal, Marta Alves
name: Soares, Mayra Veloso Ayrimoraes
name: Kurizky, Patrícia Shu
name: Peterle, Viviane Cristina Uliana
name: Faro, Yasmin Furtado
name: Gomides, Ana Paula Monteiro
name: da Mota, Licia Maria Henrique
name: de Albuquerque, Cleandro Pires
name: Simaan, Cezar Kozak
name: Amado, Veronica Moreira
Publisher: name: figshare
Year: 2024
Subjects: Biological Sciences not elsewhere classified
Science Policy
Mental Health

description: Supplementary Material 1
Resonant leptogenesis in minimal $U(1)_X$ extensions of the Standard Model
Creators: name: Das, Arindam
name: Orikasa, Yuta
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We investigate a general $U(1)_X$ scenario where we introduce three generations of Standard Model (SM) singlet Right Handed Neutrinos (RHNs) to generate the light neutrino mass through the seesaw mechanism after the breaking of $U(1)_X$ and electroweak symmetries. In addition to that, a general $U(1)_X$ scenario involves an SM-singlet scalar field and due to the $U(1)_X$ symmetry breaking the mass of a neutral beyond the SM (BSM) gauge boson $Z^\prime$ is evolved. The RHNs, being charged under $U(1)_X$ scenario, can explain the origin of observed baryon asymmetry through the resonant leptogenesis process. Applying observed neutrino oscillation data we study $Z^\prime$ and BSM scalar induced processes to reproduce the observed baryon asymmetry. Hence we estimate bounds on the $U(1)_X$ gauge coupling $(g_X)$ and the mass of the $Z^\prime$ $(M_{Z^\prime})$ for different $U(1)_X$ charges and benchmark masses of RHN and SM-singlet scalar. Finally we compare our results with limits obtained from the existing limits from LEP-II and LHC. We find that depending on the $U(1)_X$ charges, the masses of RHNs and SM-singlet scalar resonant leptogenesis could provide stronger limit on $g_X$ for $M_{Z^\prime} > 5.8$ TeV which could be probed by high energy scattering experiment in future.
description: 13 pages, two figures
Flavour mixings in flux compactifications
Creators: name: Buchmuller, Wilfried
name: Schweizer, Julian
Publisher: name: Deutsches Elektronen-Synchrotron, DESY, Hamburg
Year: 2017

description: A multiplicity of quark-lepton families can naturally arise as zero-modes in flux compactifications. The flavour structure of quark and lepton mass matrices is then determined by the wave function profiles of the zero-modes. We consider a supersymmetric $SO(10)\times U(1)$ model in six dimensions compactified on the orbifold $T^2/{\mathbb Z_2}$ with Abelian magnetic flux. A bulk $\mathbf{16}$-plet charged under the $U(1)$ provides the quark-lepton generations whereas two uncharged $\mathbf{10}$-plets yield two Higgs doublets. Bulk anomaly cancellation requires the presence of additional $\mathbf{16}$- and $\mathbf{10}$-plets. The corresponding zero-modes form vectorlike split multiplets that are needed to obtain a successful flavour phenomenology. We analyze the pattern of flavour mixings for the two heaviest families of the Standard Model and discuss possible generalizations to three and more generations.
Einasto profile as the halo model solution coupled to the depletion radius
Creators: name: Zhou, Yifeng
name: Han, Jiaxin
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We constrain the halo profiles outside the halo boundaries by solving for the matching profiles required by the halo model. In the halo model framework, the matter distribution in the universe can be decomposed into the spatial distribution of halos convolved with their internal structures. This leads to a set of linear equations in Fourier space which uniquely determines the matching halo profiles for any given halo catalog. In this work, we construct three halo catalogs with different boundary definitions, and solve for the matching profiles in each case using measurements of halo-matter and halo-halo power spectra. Our results show that for a given halo field, there is always a set of matching profiles to accurately reconstruct the input statistics of the matter field, even though it might be complex to model the profiles analytically. Comparing the solutions from different halo catalogs, we find their mass distributions inside the inner depletion radii are nearly identical, while they deviate from each other on larger scales, with a larger boundary resulting in a more extended profile. For the depletion radius based catalog, the numerical solution agrees well with the Einasto profile. Coupling the Einasto profile with the depletion catalog, the resulting halo model can simultaneously predict the halo-matter power spectra to $10\%$ and matter-matter power spectrum to $5\%$, improving over conventional models in both the interpretability and versatility. The conditions and limitation of using the Navarro-Frenk-White profile in the halo model are also discussed.
description: 15 pages, 10 figures
Strings as particle arrays
Creators: name: Jusinskas, Renann Lipinski
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: These notes discuss the emergence of the Polyakov action from the low-energy limit of an array of relativistic particles with harmonic interactions, which is suggestive of a ``microscopic'' description of string theory.
description: 10 pages. v2: small improvements, references added. v3: streamlined presentation of the physical constraints, matches published version
Enhanced quantum state transfer via feedforward cancellation of optical phase noise
Creators: name: Maddox, Benjamin P.
name: Mortlock, Jonathan M.
name: Hepworth, Tom R.
name: Raghuram, Adarsh P.
name: Gregory, Philip D.
name: Guttridge, Alexander
name: Cornish, Simon L.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Many experimental platforms for quantum science depend on state control via laser fields. Frequently, however, the control fidelity is limited by optical phase noise. This is exacerbated in stabilized laser systems where high-frequency phase noise is an unavoidable consequence of feedback. Here we implement an optical feedforward technique to suppress laser phase noise in the STIRAP state transfer of ultracold RbCs molecules, across 114 THz, from a weakly bound Feshbach state to the rovibrational ground state. By performing over 100 state transfers on single molecules, we measure a significantly enhanced transfer efficiency of 98.7(1)% limited only by available laser intensity.
Additional file 8 of A genetic tool to express long fungal biosynthetic genes
Creators: name: Kirchgaessner, Leo
name: Wurlitzer, Jacob M.
name: Seibold, Paula S.
name: Rakhmanov, Malik
name: Gressler, Markus
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 8: Figure S4. Determination of the homologous integration of the PterA:TtrpC construct into the fwnA locus of recipient strains ATNT and tLK01. A. Schematic representation of the genomic fwnA locus of the parental strain ATNT and tLK01 (ATNT∆akuB) (upper lane) and the deletion mutants ATNT∆fwnA (tLK06) and tLK07 (ATNT∆akuB∆fwnA). B. Agarose gel of two diagnostic PCRs targeting the fwnA gene (upper lane) and the PterA promoter (lower lane). In contrast to the parental strains ATNT and tLK01, the non-pigmented ∆fwnA mutants (tLK06 and tLK07) lack the signal of the fwnA gene (upper panel). In lieu thereof, the homologous integration of PterA:TtrpC could be determined in the mutants (lower panel).