cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 2 of PAM50 breast cancer subtypes and survival of patients in rural Ethiopia without adjuvant treatment: a prospective observational study
Creators: name: Ballé, Judith Katharina
name: Vetter, Martina
name: Kenea, Tariku Wakuma
name: Eber-Schulz, Pia
name: Reibold, Christian
name: Ziegenhorn, Hannes-Viktor
name: Stückrath, Kathrin
name: Wickenhauser, Claudia
name: Addissie, Adamu
name: Santos, Pablo
name: Kantelhardt, Eva Johanna
name: Getachew, Sefonias
name: Bauer, Marcus
Publisher: name: figshare
Year: 2024
Subjects: Cell Biology
Biotechnology
Environmental Sciences not elsewhere classified
Cancer

description: Supplementary Material 2
An improved procedure for colouring graphs of bounded local density
Creators: name: Hurley, Eoin
name: de Verclos, Rémi de Joannis
name: Kang, Ross J.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Combinatorics (math.CO)
subject: Discrete Mathematics (cs.DM)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 05C15 (primary), 05C35, 05D40 (secondary)

description: We develop an improved bound for the chromatic number of graphs of maximum degree $Δ$ under the assumption that the number of edges spanning any neighbourhood is at most $(1-σ)\binomΔ{2}$ for some fixed $0<σ<1$. The leading term in the reduction of colours achieved through this bound is best possible as $σ\to0$. As two consequences, we advance the state of the art in two longstanding and well-studied graph colouring conjectures, the Erdős-Nešetřil conjecture and Reed's conjecture. We prove that the strong chromatic index is at most $1.772Δ^2$ for any graph $G$ with sufficiently large maximum degree $Δ$. We prove that the chromatic number is at most $\lceil 0.881(Δ+1)+0.119ω\rceil$ for any graph $G$ with clique number $ω$ and sufficiently large maximum degree $Δ$. Additionally, we show how our methods can be adapted under the additional assumption that the codegree is at most $(1-σ)Δ$, and establish what may be considered first progress towards a conjecture of Vu.
description: 33 pages; in v2 corrected the Reed's conjecture bound, added appendix on Talagrand's, added adaptation towards Vu's conjecture; v3 final published version
Universal K-matrices for quantum Kac-Moody algebras
Creators: name: Appel, Andrea
name: Vlaar, Bart
Publisher: name: arXiv
Year: 2020
Subjects: subject: Representation Theory (math.RT)
subject: Mathematical Physics (math-ph)
subject: Quantum Algebra (math.QA)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We introduce the notion of a cylindrical bialgebra, which is a quasitriangular bialgebra $H$ endowed with a universal K-matrix, i.e., a universal solution of a generalized reflection equation, yielding an action of cylindrical braid groups on tensor products of its representations. We prove that new examples of such universal K-matrices arise from quantum symmetric pairs of Kac-Moody type and depend upon the choice of a pair of generalized Satake diagrams. In finite type, this yields a refinement of a result obtained by Balagović and Kolb, producing a family of non-equivalent solutions interpolating between the quasi-K-matrix originally due to Bao and Wang and the full universal K-matrix. Finally, we prove that this construction yields formal solutions of the generalized reflection equation with a spectral parameter in the case of finite-dimensional representations over the quantum affine algebra $U_qL\mathfrak{sl}_2$.
description: Minor edits. 57 pages
Integrated Pest Management of Mustard aphid
Creators: name: Vijay Kumar* and Hemant Swami**
Publisher: name: trends in Agriculture Science
Year: 2023

description: Mustard aphid, Lipaphis erysimi (Kalt.) is considered one of the devastating insect pests of mustard in India. Aphids also act as vector and transmit plant viral diseases, i.e. turnip mosaic virus. Farmers used to apply different type of chemicals with repeated frequency in high dose. The use of chemicals for pest control leads to such problems as environmental pollution, development of resistance to insecticides, harmful effects on non-target organisms including pollinators, pest resurgence, upsetting the balance of nature and threat to the health of man.
Additional file 3 of Genomic amplification of chromosome 20q13.33 is the early biomarker for the development of sporadic colorectal carcinoma
Creators: name: Vo-Minh-Hoang Bui
name: Mettling, Clément
name: Jou, Jonathan
name: H. Sunny Sun
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 3: Table S2. Frequencies of copy number alterations in 4 target regions.
Strictification theorems for the homotopy time-slice axiom
Creators: name: Benini, Marco
name: Carmona, Victor
name: Schenkel, Alexander
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Algebraic Topology (math.AT)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 81T05, 81T70, 18N40, 18N55

description: It is proven that the homotopy time-slice axiom for many types of algebraic quantum field theories (AQFTs) taking values in chain complexes can be strictified. This includes the cases of Haag-Kastler-type AQFTs on a fixed globally hyperbolic Lorentzian manifold (with or without time-like boundary), locally covariant conformal AQFTs in two spacetime dimensions, locally covariant AQFTs in one spacetime dimension, and the relative Cauchy evolution. The strictification theorems established in this paper prove that, under suitable hypotheses that hold true for the examples listed above, there exists a Quillen equivalence between the model category of AQFTs satisfying the homotopy time-slice axiom and the model category of AQFTs satisfying the usual strict time-slice axiom.
description: v2: 22 pages. Final version accepted for publication in Letters in Mathematical Physics
Agonist-Dependent Downregulation of Progesterone Receptors in Human Cervical Stromal Fibroblasts
Creators: name: Ackerman, William
name: Summerfield, Taryn L
name: Mesiano, Sam
name: Schatz, Frederick
name: Lockwood, Charles J
name: Kniss, Douglas A
Publisher: name: University of Illinois at Chicago
Year: 2022
Subjects: Uncategorized

description: Progesterone (P(4)) maintains uterine quiescence during the majority of pregnancy, whereas diminished progesterone receptor (PR) expression and/or activity (ie, functional P(4) withdrawal) promotes parturition. To investigate the regulation of PR expression in cervical stroma, fibroblasts from premenopausal hysterectomy specimens were prepared. Greater than 99% of the cultures were vimentin positive (mesenchymal cell marker) with only occasional cytokeratin-8 positivity (epithelial cell marker) and no evidence of CD31-positive (endothelial cell marker) cells. Cells were immunolabeled with antibodies directed against PRs (PR-A and PR-B), estrogen receptor α (ER-α), and glucocorticoid receptor-α/β (GR-α/β). All cells were uniformly immunopositive for ER-α and GR-α/β but did not express PRs. Incubation of cells with 10(-8) mol/L 17β-estradiol induced a time-dependent increase in PR-A and PR-B messenger RNAs (mRNAs) by quantitative real-time polymerase chain reactions and proteins by immunoblotting and immunofluorescence. Incubation of cervical fibroblasts with PR ligands (medroxyprogesterone acetate or Org-2058) downregulated PR-A and PR-B levels. Coincubation of cells with PR ligands plus RU-486, a PR antagonist, partially abrogated agonist-induced receptor downregulation. Dexamethasone, a pure glucocorticoid, had no inhibitory effect on PR expression. These results indicate that progestins and estrogens regulate PR expression in cervical fibroblasts. We postulate that hormonal regulation of PR expression in the cervical stroma may contribute to functional P(4) withdrawal in preparation for parturition.
Electronic Structures of Hybrid Graphene/Phosphorene Nanocomposite
Creators: name: Hu, Wei
name: Wang, Tian
name: Yang, Jinlong
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Combining the electronic structures of two-dimensional monolayers in ultrathin hybrid nanocomposites is expected to display new properties beyond their simplex components. Here, first-principles calculations are performed to study the structural, electronic and optical properties of hybrid graphene and phosphorene nanocomposite. It turns out that weak van der Waals interactions dominate between graphene and phosphorene with their intrinsic electronic properties preserved. Hybrid graphene and phosphorene nanocomposite shows tunable band gaps at graphene's Dirac point and a transition from hole doing to electron doing for graphene as the interfacial distance decreases. Charge transfer between graphene to phosphorene induces interfacial electron-hole pairs in hybrid graphene and phosphorene nanocomposite with enhanced visible light response.
description: 12 pages, 5 figures
Living a Kulango Life:   Examples of Socialization under the Shadow of the Laasagyo
Creators: name: Micheli, Ilaria
Publisher: name: Università degli Studi di Torino
Year: 2016

description: The Kulango of Nassian, a Gur people living mainly in the North-Eastern territory of modern Ivory Coast, with a few villages scattered along the border in Ghana, are sedentary horticulturalists, whose relationships with the plant-kingdom they live in, share many characteristics with those typical of the Abron-Akan groups, but also of some Gur/Voltaic communities they live in contact with. Aim of this paper is to provide some examples of how these bi-dimensional cultural influences melted together giving life to the present day Kulango cultural identity.
The discussion is divided into three different parts.
Paragraph 2. contains an overview of the two most important ceremonial events of the Kulango agricultural calendar: a) the typically Akan yam feast and b) the typically Gur pearl-millet feast.
In paragraph 3. the focus moves towards the peculiar role of a tree, which the Kulango call the laasagyo and of two other vegetal elements which are still very important in the modern Kulango social world: a) palm wine, or taŋa in Kulango, and b) the kola nut, or pɛsɛ in Kulango.
Paragraph 4. will be devoted to an ethnolinguistic study of the conceptualizations of what is a plant and what is a mushroom according to the Kulango Weltanschaauung.
description: Kervan. International Journal of Afro-Asiatic Studies, N. 20 (2016)
Temporal Localization of Fine-Grained Actions in Videos by Domain Transfer from Web Images
Creators: name: Sun, Chen
name: Shetty, Sanketh
name: Sukthankar, Rahul
name: Nevatia, Ram
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Multimedia (cs.MM)
subject: FOS: Computer and information sciences
subject: I.2.10

description: We address the problem of fine-grained action localization from temporally untrimmed web videos. We assume that only weak video-level annotations are available for training. The goal is to use these weak labels to identify temporal segments corresponding to the actions, and learn models that generalize to unconstrained web videos. We find that web images queried by action names serve as well-localized highlights for many actions, but are noisily labeled. To solve this problem, we propose a simple yet effective method that takes weak video labels and noisy image labels as input, and generates localized action frames as output. This is achieved by cross-domain transfer between video frames and web images, using pre-trained deep convolutional neural networks. We then use the localized action frames to train action recognition models with long short-term memory networks. We collect a fine-grained sports action data set FGA-240 of more than 130,000 YouTube videos. It has 240 fine-grained actions under 85 sports activities. Convincing results are shown on the FGA-240 data set, as well as the THUMOS 2014 localization data set with untrimmed training videos.
description: Camera ready version for ACM Multimedia 2015
Additional file 5 of Genomic amplification of chromosome 20q13.33 is the early biomarker for the development of sporadic colorectal carcinoma
Creators: name: Vo-Minh-Hoang Bui
name: Mettling, Clément
name: Jou, Jonathan
name: H. Sunny Sun
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 5: Table S4. Primers used in this study.
Spatial entanglement and state engineering via four-photon Hong-Ou-Mandel interference
Creators: name: Ferreri, A.
name: Ansari, V.
name: Brecht, B.
name: Silberhorn, C.
name: Sharapova, P. R.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The phenomenon of entanglement is the basis of quantum information and quantum communication processes. Entangled systems with a large number of photons are of great interest at present because they provide a platform for streaming technologies based on photonics. In this paper we present a device which operates with four-photons and based on the Hong-Ou-Mandel (HOM) interference. The presented device allows to maximize the degree of spatial entanglement and generate the highly entangled four-dimensional Bell states. Furthermore, the use of the interferometer in different regimes leads to fast interference fringes in the coincidence probability with period of oscillations twice smaller than the pump wavelength. We have a good agreement between theoretical simulations and experimental results.
description: 20 pages, 7 figure
The holographic quantum
Creators: name: de Cordoba, P. Fernandez
name: Isidro, J. M.
name: Molina, J. Vazquez
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We present a map of standard quantum mechanics onto a dual theory, that of the classical thermodynamics of irreversible processes. While no gravity is present in our construction, our map exhibits features that are reminiscent of the holographic principle of quantum gravity.
description: 17 pages; major revision
Unsupervised domain adaptation semantic segmentation of high-resolution remote sensing imagery with invariant domain-level prototype memory
Creators: name: Zhu, Jingru
name: Guo, Ya
name: Sun, Geng
name: Yang, Libo
name: Deng, Min
name: Chen, Jie
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Semantic segmentation is a key technique involved in automatic interpretation of high-resolution remote sensing (HRS) imagery and has drawn much attention in the remote sensing community. Deep convolutional neural networks (DCNNs) have been successfully applied to the HRS imagery semantic segmentation task due to their hierarchical representation ability. However, the heavy dependency on a large number of training data with dense annotation and the sensitiveness to the variation of data distribution severely restrict the potential application of DCNNs for the semantic segmentation of HRS imagery. This study proposes a novel unsupervised domain adaptation semantic segmentation network (MemoryAdaptNet) for the semantic segmentation of HRS imagery. MemoryAdaptNet constructs an output space adversarial learning scheme to bridge the domain distribution discrepancy between source domain and target domain and to narrow the influence of domain shift. Specifically, we embed an invariant feature memory module to store invariant domain-level context information because the features obtained from adversarial learning only tend to represent the variant feature of current limited inputs. This module is integrated by a category attention-driven invariant domain-level context aggregation module to current pseudo invariant feature for further augmenting the pixel representations. An entropy-based pseudo label filtering strategy is used to update the memory module with high-confident pseudo invariant feature of current target images. Extensive experiments under three cross-domain tasks indicate that our proposed MemoryAdaptNet is remarkably superior to the state-of-the-art methods.
description: 17 pages, 12 figures and 8 tables
Nonlinear redistribution of wealth from a stochastic approach
Creators: name: Lima, Hugo
name: Vieira, Allan R.
name: Anteneodo, Celia
Publisher: name: arXiv
Year: 2020
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: We investigate the effect of applying nonlinear redistributive taxes to the yard-sale dynamics of assets. An amount of money is collected from each individual (tax) and distributed back equally. We consider (i) a piecewise linear tax, exempting those with wealth below a threshold $w_0$, and taxing the excess wealth otherwise, and (ii) a power-law tax with exponent $α>0$, which allows embracing regressive, proportional and progressive rules. The distribution of wealth obtained from numerical simulations of the agent-based dynamics is compared with the solution of its associated Fokker-Planck equation for the probability density function $P(w,t)$ of wealth $w$ at time $t$, in good agreement. Based on these solutions, we analyze how the different rules modify the distribution of wealth across the population, quantifying the level of inequality through the Gini coefficient. We note that the introduction of an exemption threshold does not always diminish inequality, depending on the implementation details. Moreover, nonlinearity brings new stylized facts in the distribution of wealth compared to the linear case, e.g., negative skewness, bimodality, indicating stratification, or a flat shape meaning equality populated wealth layers.
description: 10 pages, 13 figures
Tensor-variate machine learning on graphs
Creators: name: Xu, Yao Lei
Publisher: name: Imperial College London
Year: 2023

description: Traditional machine learning algorithms are facing significant challenges as the world enters the era of big data, with a dramatic expansion in volume and range of applications and an increase in the variety of data sources. The large- and multi-dimensional nature of data often increases the computational costs associated with their processing and raises the risks of model over-fitting - a phenomenon known as the curse of dimensionality. To this end, tensors have become a subject of great interest in the data analytics community, owing to their remarkable ability to super-compress high-dimensional data into a low-rank format, while retaining the original data structure and interpretability. This leads to a significant reduction in computational costs, from an exponential complexity to a linear one in the data dimensions. An additional challenge when processing modern big data is that they often reside on irregular domains and exhibit relational structures, which violates the regular grid assumptions of traditional machine learning models. To this end, there has been an increasing amount of research in generalizing traditional learning algorithms to graph data. This allows for the processing of graph signals while accounting for the underlying relational structure, such as user interactions in social networks, vehicle flows in traffic networks, transactions in supply chains, chemical bonds in proteins, and trading data in financial networks, to name a few. Although promising results have been achieved in these fields, there is a void in literature when it comes to the conjoint treatment of tensors and graphs for data analytics. Solutions in this area are increasingly urgent, as modern big data is both large-dimensional and irregular in structure. To this end, the goal of this thesis is to explore machine learning methods that can fully exploit the advantages of both tensors and graphs. In particular, the following approaches are introduced: (i) Graph-regularized tensor regression framework for modelling high-dimensional data while accounting for the underlying graph structure; (ii) Tensor-algebraic approach for computing efficient convolution on graphs; (iii) Graph tensor network framework for designing neural learning systems which is both general enough to describe most existing neural network architectures and flexible enough to model large-dimensional data on any and many irregular domains. The considered frameworks were employed in several real-world applications, including air quality forecasting, protein classification, and financial modelling. Experimental results validate the advantages of the proposed methods, which achieved better or comparable performance against state-of-the-art models. Additionally, these methods benefit from increased interpretability and reduced computational costs, which are crucial for tackling the challenges posed by the era of big data.
Additional file 4 of Genomic amplification of chromosome 20q13.33 is the early biomarker for the development of sporadic colorectal carcinoma
Creators: name: Vo-Minh-Hoang Bui
name: Mettling, Clément
name: Jou, Jonathan
name: H. Sunny Sun
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 4: Table S3. Detailed clinical information and 20q13.33 copy number estimation of CRC sample showing 20q13.33 copy number loss in their non-tumor part.
An HHL-Based Algorithm for Computing Hitting Probabilities of Quantum Random Walks
Creators: name: Guan, Ji
name: Wang, Qisheng
name: Ying, Mingsheng
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present a novel application of the HHL (Harrow-Hassidim-Lloyd) algorithm -- a quantum algorithm solving systems of linear equations -- in solving an open problem about quantum random walks, namely computing hitting (or absorption) probabilities of a general (not only Hadamard) one-dimensional quantum random walks with two absorbing boundaries. This is achieved by a simple observation that the problem of computing hitting probabilities of quantum random walks can be reduced to inverting a matrix. Then a quantum algorithm with the HHL algorithm as a subroutine is developed for solving the problem, which is faster than the known classical algorithms by numerical experiments.
Neutrino Masses from Neutral Top Partners
Creators: name: Batell, Brian
name: McCullough, Matthew
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present theories of `Natural Neutrinos' in which neutral fermionic top partner fields are simultaneously the right-handed neutrinos (RHN), linking seemingly disparate aspects of the Standard Model structure: a) The RHN top partners are responsible for the observed small neutrino masses, b) They help ameliorate the tuning in the weak scale and address the little hierarchy problem, and c) The factor of $3$ arising from $N_c$ in the top-loop Higgs mass corrections is countered by a factor $3$ from the number of vector-like generations of RHN. The RHN top partners may arise in pseudo-Nambu-Goldstone-Boson (pNGB) Higgs models such as the Twin Higgs, as well as more general Composite, Little, and Orbifold Higgs scenarios, and three simple example models are presented. This framework firmly predicts a TeV-scale seesaw, as the RHN masses are bounded to be below the TeV scale by naturalness. The generation of light neutrino masses relies on a collective breaking of lepton number, allowing for comparatively large neutrino Yukawa couplings and a rich associated phenomenology. The structure of the neutrino mass mechanism realizes in certain limits the Inverse or Linear classes of seesaw. Natural Neutrino models are testable at a variety of current and future experiments, particularly in tests of lepton universality, searches for lepton flavor violation, and precision electroweak and Higgs coupling measurements possible at high energy $e^+ e^-$ and hadron colliders.
description: 18 pages, 5 figures; v2: references added, additional discussion of proton decay
Additional file 1 of First month of the epidemic caused by COVID-19 in Italy: current status and real-time outbreak development forecast
Creators: name: Megna, Rosario
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1.
Additional file 1 of IDH2 regulates macrophage polarization and tumorigenesis by modulating mitochondrial metabolism in macrophages
Creators: name: Lee, Sung Woo
name: Kim, Soyoon
name: Kim, Bokyung
name: Seong, Jung Bae
name: Park, Young-Ho
name: Lee, Hong Jun
name: Choi, Dong Kyu
name: Yeom, Eunbyul
name: Lee, Dong-Seok
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1.
Energy-Based Molecular Orbital Localization in a Specific Spatial Region
Creators: name: Giovannini, Tommaso
name: Koch, Henrik
Publisher: name: arXiv
Year: 2020
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: We present a novel energy-based localization procedure able to localize molecular orbitals into specific spatial regions. The method is applied to several cases including both conjugated and non-conjugated systems. The obtained localized molecular orbitals are used in a multiscale framework based on the multilevel Hartree-Fock approach. An almost perfect agreement with reference values is achieved for both ground state properties, such as dipole moments, and local excitation energies calculated at the coupled cluster level. The proposed approach is useful to extend the application range of high level electron correlation methods. In fact, the reduced number of molecular orbitals can lead to a large reduction in the computational cost of correlated calculations.
description: 29 pages and 7 figures
Multilevel Density Functional Theory
Creators: name: Marrazzini, Gioia
name: Giovannini, Tommaso
name: Scavino, Marco
name: Egidi, Franco
name: Cappelli, Chiara
name: Koch, Henrik
Publisher: name: arXiv
Year: 2020
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: We introduce a novel density-based multilevel approach in density functional theory. In this multilevel density functional theory (MLDFT), the system is partitioned in an active and an inactive fragment, and all interactions are retained between the two parts. In MLDFT, the Kohn-Sham equations are solved in the MO basis for the active part only, while keeping the inactive density frozen. This results in a reduction of computational cost. We outline the theory and implementation, and discuss applications to aqueous solutions of methyloxirane and glycidol.
description: 33 pages and 9 figures
On the Occurrence Rate of Hot Jupiters in Different Stellar Environments
Creators: name: Wang, Ji
name: Fischer, Debra A.
name: Horch, Elliott P.
name: Huang, Xu
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Many Hot Jupiters (HJs) are detected by the Doppler and the transit techniques. From surveys using these two techniques, however, the measured HJ occurrence rates differ by a factor of two or more. Using the California Planet Survey sample and the Kepler sample, we investigate the causes for the difference of HJ occurrence rate. First, we find that $12.8\%\pm0.24\%$ of HJs are misidentified in the Kepler mission because of photometric dilution and subgiant contamination. Second, we explore the differences between the Doppler sample and the Kepler sample that can account for the different HJ occurrence rate. Third, we discuss how to measure the fundamental HJ occurrence rates by synthesizing the results from the Doppler and Kepler surveys. The fundamental HJ occurrence rates are a measure of HJ occurrence rate as a function of stellar multiplicity and evolutionary stage, e.g., the HJ occurrence rate for single and multiple stars or for main sequence and subgiant stars. While we find qualitative evidence that HJs occur less frequently in subgiants and multiple stellar systems, we conclude that our current knowledge of stellar properties and stellar multiplicity rate is too limited for us to reach any quantitative result for the fundamental HJ occurrence rates. This concern extends to $η_{\rm{Earth}}$, the occurrence rate of Earth-like planets.
description: 10 pages, 3 figures, 1 table, submitted to ApJ
Modeling the electronic structure of organic materials: A solid-state physicist's perspective
Creators: name: Cocchi, Caterina
name: Guerrini, Michele
name: Krumland, Jannis
name: Nguyen, Ngoc Trung
name: Valencia, Ana M.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Modeling the electronic and optical properties of organic semiconductors remains a challenge for theory, despite the remarkable progress achieved in the last three decades. The complexity of these systems, including structural (dis)order and the still debated doping mechanisms, has been engaging theorists with different backgrounds. Regardless of the common interest across the various communities active in this field, these efforts have not led so far to a truly interdisciplinary research area. In the attempt to move further in this direction, we present our perspective as solid-state theorists for the study of molecular materials in different states of matter. Considering exemplary systems belonging to well-known families of oligo-acenes and -thiophenes, we provide a quantitative description of electronic properties and optical excitations obtained with state-of-the-art first-principles methods such as density-functional theory and many-body perturbation theory. Simulating the systems as gas-phase molecules, clusters, and periodic lattices, we are able to identify short- and long-range effects in their electronic structure. While the latter are usually dominant in organic crystals, the former play an important role, too, especially in the case of donor/acceptor complexes. Furthermore, we demonstrate the viability of implicit schemes to evaluate band gaps of molecules embedded in isotropic and even anisotropic environments, in quantitative agreement with experiments. In the context of doped organic semiconductors, we show how the crystalline packing enhances the favorable characteristics of these systems for opto-electronic applications. The counter-intuitive behavior predicted for their electronic and optical properties is deciphered with the aid of a tight-binding model, which represents a connection to the most common approaches to evaluate transport properties in these materials.
Analysis of a mixed discontinuous Galerkin method for the time-harmonic Maxwell equations with minimal smoothness requirements
Creators: name: Liu, Kaifang
name: Gallistl, Dietmar
name: Schlottbom, Matthias
name: van der Vegt, J. J. W.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 35R05, 35Q61, 65N12, 65N15, 65N30

description: An error analysis of a mixed discontinuous Galerkin (DG) method with Brezzi numerical flux for the time-harmonic Maxwell equations with minimal smoothness requirements is presented. The key difficulty in the error analysis for the DG method is that the tangential or normal trace of the exact solution is not well-defined on the mesh faces of the computational mesh. We overcome this difficulty by two steps. First, we employ a lifting operator to replace the integrals of the tangential/normal traces on mesh faces by volume integrals. Second, optimal convergence rates are proven by using smoothed interpolations that are well-defined for merely integrable functions. As a byproduct of our analysis, an explicit and easily computable stabilization parameter is given.
A Comprehensive Study of Real-Time Object Detection Networks Across Multiple Domains: A Survey
Creators: name: Arani, Elahe
name: Gowda, Shruthi
name: Mukherjee, Ratnajit
name: Magdy, Omar
name: Kathiresan, Senthilkumar
name: Zonooz, Bahram
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Deep neural network based object detectors are continuously evolving and are used in a multitude of applications, each having its own set of requirements. While safety-critical applications need high accuracy and reliability, low-latency tasks need resource and energy-efficient networks. Real-time detectors, which are a necessity in high-impact real-world applications, are continuously proposed, but they overemphasize the improvements in accuracy and speed while other capabilities such as versatility, robustness, resource and energy efficiency are omitted. A reference benchmark for existing networks does not exist, nor does a standard evaluation guideline for designing new networks, which results in ambiguous and inconsistent comparisons. We, thus, conduct a comprehensive study on multiple real-time detectors (anchor-, keypoint-, and transformer-based) on a wide range of datasets and report results on an extensive set of metrics. We also study the impact of variables such as image size, anchor dimensions, confidence thresholds, and architecture layers on the overall performance. We analyze the robustness of detection networks against distribution shifts, natural corruptions, and adversarial attacks. Also, we provide a calibration analysis to gauge the reliability of the predictions. Finally, to highlight the real-world impact, we conduct two unique case studies, on autonomous driving and healthcare applications. To further gauge the capability of networks in critical real-time applications, we report the performance after deploying the detection networks on edge devices. Our extensive empirical study can act as a guideline for the industrial community to make an informed choice on the existing networks. We also hope to inspire the research community towards a new direction in the design and evaluation of networks that focuses on a bigger and holistic overview for a far-reaching impact.
description: Published in Transactions on Machine Learning Research (TMLR) with Survey Certification
The supersymmetric Higgs boson with flavoured A-terms
Creators: name: Brignole, Andrea
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider a supersymmetric scenario with large flavour violating A-terms in the stop/scharm sector and study their impact on the Higgs mass, the electroweak rho parameter and the effective Higgs couplings to gluons, photons and charm quarks. For each observable we present explicit analytical expressions which exhibit the relevant parametric dependences, both in the general case and in specific limits. We find significant effects and comment on phenomenological implications for the LHC and future colliders.
description: 21 pages, 6 figures; v2: minor changes, references added (journal version)
Quantum reflection and Liouville transformations from wells to walls
Creators: name: Dufour, Gabriel
name: Guérout, Romain
name: Lambrecht, Astrid
name: Reynaud, Serge
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Liouville transformations map in a rigorous manner one Schrödinger equation into another, with a changed scattering potential. They are used here to transform quantum reflection of an atom on an attractive well into reflection of the atom on a repulsive wall. While the scattering properties are preserved, the corresponding semiclassical descriptions are completely different. A quantitative evaluation of quantum reflection probabilities is deduced from this method.
On the impact of galaxy bias uncertainties on primordial non-Gaussianity constraints
Creators: name: Barreira, Alexandre
Publisher: name: arXiv
Year: 2020
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We study the impact that uncertainties on assumed relations between galaxy bias parameters have on constraints of the local PNG $f_{\rm NL}$ parameter. We focus on the relation between the linear density galaxy bias $b_1$ and local PNG bias $b_ϕ$ in an idealized forecast setup with multitracer galaxy power spectrum and bispectrum data. We consider two parametrizations of galaxy bias: 1) one inspired by the universality relation where $b_ϕ= 2δ_c\left(b_1 - p\right)$ and $p$ is a free parameter; and 2) another in which the product of bias parameters and $f_{\rm NL}$, like $f_{\rm NL} b_ϕ$, is directly fitted for. The constraints on the $f_{\rm NL}-p$ plane are markedly bimodal, and both the central value and width of marginalized constraints on $f_{\rm NL}$ depend sensitively on the priors on $p$. Assuming fixed $p=1$ in the constraints with a fiducial value of $p=0.55$ can bias the inferred $f_{\rm NL}$ by $0.5σ$ to $1σ$; priors $Δp \approx 0.5$ around this fiducial value are however sufficient in our setup to return unbiased constraints. In power spectrum analyses, parametrization 2, that makes no assumptions on $b_ϕ$, can distinguish $f_{\rm NL} \neq 0$ with the same significance as parametrization 1 assuming perfect knowledge of $b_ϕ$ (the value of $f_{\rm NL}$ is however left unknown). A drawback of parametrization 2 is that the addition of the bispectrum information is not as beneficial as in parametrization 1. Our results motivate strongly the incorporation of mitigation strategies for bias uncertainties in PNG constraint analyses, as well as further theoretical studies on the relations between bias parameters to better inform those strategies.
description: 16 pages + 2 appendices; 7 figures; comments welcomed!
The kinetics, mechanisms, and consequences of HTLV-1 plus-strand expression in naturally-infected T-cell clones
Creators: name: Ramanayake, Saumya
Publisher: name: Imperial College London
Year: 2023

description: HTLV-1 replication requires the expression of plus-strand-encoded transcriptional transactivator protein Tax. However, Tax protein, a surrogate for HTLV-1 plus-strand expression is seldom detected in freshly isolated infected blood. The kinetics and consequences of plus-strand expression remain poorly understood. I used two fluorescent protein-based Tax reporter systems to study the dynamics and consequences of plus-strand expression and the changes to the host gene expression during plus-strand expression in naturally HTLV-1-infected, non-malignant T-cell clones. Time-lapse live-cell imaging followed by single-cell analysis of two T-cell clones stably transduced with a short-lived enhanced green fluorescent protein Tax reporter system identified five patterns of Tax expression in both clones and the distribution of these patterns was different between the two clones. Mathematical modelling of the experimental data revealed that the mean duration of Tax expression differed between the two clones – 94 and 417 hours, respectively. Host cell transcriptome analysis during successive stages of plus-strand strand expression using a fluorescent timer protein-based Tax reporter system in naturally-infected T-cell clones identified dysregulation in the expression of genes related to multiple cellular processes, including cell cycle, DNA damage response, and apoptosis at the initiation of the plus-strand transcriptional burst. The plus-strand expression showed immediate but transient adverse effects, including reduced proliferation, increased apoptosis, upregulation of a DNA damage marker, and impaired cell cycle progression. In the longer term, the immediate negative consequences of Tax expression were offset by reduced apoptosis and increased proliferation as cells terminated plus-strand expression. Plus-strand expression was also associated with cell-to-cell adhesion and reduced motility. These findings show within and between clone variability in the patterns and duration of HTLV-1 plus-strand expression, changes to the host gene expression during successive stages of the plus-strand expression, and the balance between the beneficial and adverse effects on the host cell associated with the plus-strand expression.
The operator product expansion converges in massless $φ_4^4$-theory
Creators: name: Holland, Jan
name: Hollands, Stefan
name: Kopper, Christoph
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: It has been shown recently that the mathematical status of the operator product expansion (OPE) is better than was expected before: namely considering massive Euclidean $φ^4$-theory in the perturbative loop expansion, the OPE converges at any loop order when considering (as is usually done) composite operator insertions into correlation functions. In the present paper we prove the same result for the massless theory. While the short-distance properties of massive and massless theories may be expected to be similar on physical grounds, the proof in the massless case requires entirely new techniques. In our inductive construction we have to control with sufficient precision the exceptional momentum singularities of the massless correlation functions. In fact the bounds we state are expressed in terms of weight factors associated to certain tree graphs. Our proof is again based on the flow equations of the renormalisation group.
description: 57 pages, 10 figures
Characterisation of Aquifer Thermal Energy Storage for applications in the UK
Creators: name: Regnier, Geraldine
Publisher: name: Imperial College London
Year: 2023

description: Aquifer Thermal Energy Storage (ATES) is a proven technology to provide low carbon space heating and cooling. Counting more than 3000 deployments, the Netherlands is the current market leader. Other countries, such as the UK, despite a large potential, only comprise a handful of installations. This thesis provides an overview of the current state of ATES in the UK, reviewing active installations, encountered challenges and opportunities for growth. To illustrate the potential for ATES in the UK, a case study of an ATES system is reported: the Wandsworth Riverside Quarter ATES which targets the Chalk aquifer. Monitoring data is used to assess the performance of the system, demonstrating the feasibility of ATES systems in geologically complex aquifers, such as the Chalk. Uncertainty in subsurface response is an important challenge when designing ATES deployments. Target aquifers for ATES in the UK, such as the Sherwood Sandstone or Chalk aquifers, comprise important geological heterogeneity, rendering predicting the subsurface response challenging. Therefore, a numerical modelling approach for ATES with dynamic mesh optimisation and surface-based modelling is introduced. The use of dynamic mesh optimisation is demonstrated to speed up simulations compared to using a fixed mesh by up to a factor of 15. Numerical modelling can also be an important tool to derisk deployments, for example ensuring that groundwater quality is not compromised during ATES operation. The modelling approach that was previously introduced is applied to investigate the risk of contamination during ATES operation in aquifers where a shallow freshwater/saltwater interface is present. Two non-dimensional parameters are introduced to allow for rapid assessment of contamination risk at the well heads and downstream, for a given ATES system operating in a homogeneous aquifer. This thesis provides learnings and tools for key stakeholders to support the sustainable development of ATES systems in the UK.
Moduli rolling to a natural MSSM with gravitino dark matter
Creators: name: Otsuka, Hajime
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We propose the gravitino dark matter in the gravity mediated supersymmetry breaking scenario. The mass hierarchies between the gravitino and other superparticles can be achieved by the nontrivial Kähler metric of the supersymmetry breaking field. As a concrete model, we consider the five-dimensional supergravity model in which moduli are stabilized, and then one of the moduli induces the slow-roll inflation. It is found that the relic abundance of the gravitino and the Higgs boson mass reside in the allowed range without a severe fine-tuning.
description: 35 pages, 3 figures, Typos corrected, and Title is changed in PRD
Refined pointwise estimates for solutions to the 1D barotropic compressible Navier--Stokes equations: An application to the long-time behavior of a point mass
Creators: name: Koike, Kai
Publisher: name: arXiv
Year: 2020
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We study the long-time behavior of a point mass moving in a one-dimensional viscous compressible fluid. Previously, we showed that the velocity of the point mass $V(t)$ satisfies a decay estimate $V(t)=O(t^{-3/2})$~[K. Koike, J. Differential Equations \textbf{271} (2021) 356--413]. This result was obtained as a corollary to pointwise estimates of solutions to a free boundary problem of barotropic compressible Navier--Stokes equations. In this paper, we give a simple necessary and sufficient condition on the initial data for the decay estimate $V(t)=O(t^{-3/2})$ to be optimal. This is achieved by refining the pointwise estimates previously obtained: we make use of \textit{inter-diffusion waves} that, together with the classical \textit{diffusion waves}, give an improved approximation of the fluid behavior around the point mass; this then leads to a sharper understanding of the long-time behavior of the point mass.
description: Ver 1: 54 pages. Any comments on the paper (reports of typos or logical errors, suggestions to increase readability) are welcome. Ver 2: 59 pages, 1 figure. NOTE: The title of the paper is slightly changed. We largely rewritten the introduction and changed the organization of the proof. The mathematical content of the paper is essentially unchanged. Some minor errors are fixed