cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Baryons from Quarks in the $1/N$ Expansion
Creators: name: Luty, Markus A.
name: March-Russell, John
Publisher: name: arXiv
Year: 1993
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We present a diagrammatic analysis of baryons in the $1/N$ expansion, where $N$ is the number of QCD colors. We use this method to show that there are an infinite number of degenerate baryon states in the large-$N$ limit. We also show that forward matrix elements of quark bilinear operators satisfy the static quark-model relations in this limit, and enumerate the corrections to these relations to all orders in $1/N$. These results hold for any number of light quark flavors, and the methods used can be extended to arbitrary operators. Our results imply that for two flavors, the quark-model relations for the axial currents and magnetic moments get corrections of order $1/N^2$. For three or more flavors, the results are more complicated, and corrections are generically of order $1/N$. We write an explicit effective lagrangian which can be used to carry out chiral perturbation theory calculations in the $1/N$ expansion. Finally, we compare our results to what is expected from a chiral constituent quark model.
description: 27 pages, 5 uuencoded postscript figures, plain tex. References and acknowledgements added. LBL-34778
Learning generative models of molecular dynamics.
Creators: name: Razavian, Narges Sharif
name: Hetunandan  Kamisetty
name: Langmead, Christopher J.
Publisher: name: Carnegie Mellon University
Year: 2013
Subjects: Computational Biology

description: We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 regularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories.
Hydrogen-bonded aggregates in the mixtures of piperidine with water: thermodynamic, SANS and theoretical studies
Creators: name: Marczak, Wojciech
name: Hołaj-Krzak, Jakub T.
name: Lodowski, Piotr
name: Almásy, László
name: Fadda, Giulia C.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Structures resembling semiclathrates probably arise in liquid aqueous solutions of piperidine at the amine mole fraction below 0.03. With the increasing concentration, the structures gradually decay, but the 1:1 complexes of piperidine with water remain linked one to another through the O-H...O bonds between the hydration water molecules. A periodic order of the bicontinuous microemulsion type occurs in the range of the mole fractions from 0.08 to 0.5. In the piperidine-rich mixtures, the 1:1 complexes are dispersed uniformly in the amine. Relatively low stabilization energy of these complexes probably causes that piperidine is totally miscible with water.
Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees
Creators: name: Solomon, Brad
name: Kingsford, Carl
Publisher: name: Carnegie Mellon University
Year: 2011
Subjects: Computational Biology

description: Enormous databases of short-read RNA-seq sequencing experiments such as the NIH Sequence Read Archive (SRA) are now available. However, these collections remain difficult to use due to the inability to search for a particular expressed sequence. A natural question is which of these experiments contain sequences that indicate the expression of a particular sequence such as a gene isoform, lncRNA, or uORF. However, at present this is a computationally demanding question at the scale of these databases. We introduce an indexing scheme, the Sequence Bloom Tree (SBT), to support sequence-based querying of terabase-scale collections of thousands of short-read sequencing experiments. We apply SBT to the problem of finding conditions under which query transcripts are expressed. Our experiments are conducted on a set of 2652 publicly available RNA-seq experiments contained in the NIH for the breast, blood, and brain tissues, comprising 5 terabytes of sequence. SBTs of this size can be queried for a 1000 nt sequence in 19 minutes using less than 300 MB of RAM, over 100 times faster than standard usage of SRA-BLAST and 119 times faster than STAR. SBTs allow for fast identification of experiments with expressed novel isoforms, even if these isoforms were unknown at the time the SBT was built. We also provide some theoretical guidance about appropriate parameter selection in SBT and propose a sampling-based scheme for potentially scaling SBT to even larger collections of files. While SBT can handle any set of reads, we demonstrate the effectiveness of SBT by searching a large collection of blood, brain, and breast RNA-seq files for all 214,293 known human transcripts to identify tissue-specific transcripts. The implementation used in the experiments below is in C++ and is available as open source at http://www.cs.cmu.edu/~ckingsf/software/bloomtree.
Magnetic Monopoles in the Einstein-Yang-Mills-Higgs System
Creators: name: Viet, Nguyen Ai
name: Wali, Kameshwar C.
Publisher: name: arXiv
Year: 1993
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study the Yang-Mills-Higgs system within the framework of general relativity. In the static situation, using Bogomol'nyi type analysis, we derive a positive-definite energy functional which has a lower bound. Specializing to the gauge group $SU(2)$ and the t'Hooft-Polyakov ansatz for the gauge and Higgs fields, we seek static, spherically symmetric solutions to the coupled system of equations in both the isotropic and standard coordinate systems. In both cases, in the spontaneously broken symmetry situation, we find great simplications reducing the solutions of the coupled system to the solution of a single non-linear differential equation, different one in each case, but well-known in other contexts of physics. We find abelian and non-abelian monopole solutions with gravitational fields playing the role of Higgs fields in providing attraction that balances the repulsion due to the gauge fields. Numerical solutions indicate the possibility of blackhole horizons inside the monopoles enclosing the singularity at the origin. Such non-abelian monopoles are then the analogs of Reissner-Nordström blackholes with magnetic charge.
description: 25 pages, SU-4240-558 (FIGURES appended as postscript.file)
Multi-Epoch VLBA Imaging of Twenty New TeV Blazars: Apparent Jet Speeds
Creators: name: Piner, B. Glenn
name: Edwards, Philip G.
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present 88 multi-epoch Very Long Baseline Array (VLBA) images (most at an observing frequency of 8 GHz), of 20 TeV blazars, all of the HBL class, that have not been previously studied at multiple epochs on the parsec scale. From these 20 sources, we analyze the apparent speeds of 43 jet components that are all detected at four or more epochs. As has been found for other TeV HBLs, the apparent speeds of these components are relatively slow. About two-thirds of the components have an apparent speed that is consistent (within two-sigma) with no motion; and some of these components may be stationary patterns whose apparent speed does not relate to the underlying bulk flow speed. In addition, a superluminal tail to the apparent speed distribution of the TeV HBLs is detected for the first time, with eight components in seven sources having a two-sigma lower limit on the apparent speed exceeding 1c. We combine the data from these 20 sources with an additional 18 sources from the literature to analyze the complete apparent speed distribution of all 38 TeV HBLs that have been studied with VLBI at multiple epochs. The highest two-sigma apparent speed lower limit considering all sources is 3.6c. This suggests that bulk Lorentz factors of up to about 4, but probably not much higher, exist in the parsec-scale radio emitting regions of these sources, consistent with estimates obtained in the radio by other means such as brightness temperatures. This can be reconciled with the high Lorentz factors estimated from the high-energy data if the jet has velocity structures consisting of different emission regions with different Lorentz factors. In particular, we analyze the current apparent speed data for the TeV HBLs in the context of a model with a fast central spine and a slower outer layer.
description: Astrophysical Journal, in press, reference added
The Arthritis, Autoimmune and Related Knowledge (ARK) Portal
Creators: name: Vera, Jessica M
name: Adams, Tiara
name: Sanchez, Hayley
name: Tummalacherla, Meghasyam
name: Kallaher, Amelia
name: Greenwood, Anna
name: Varma, Susheel
Publisher: name: F1000 Research Limited
Year: 2025

description: Rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) are relatively common, severe autoimmune disorders that can last a lifetime, cause severe disability, greatly affect quality of life, and are associated with increased risk of death. The Arthritis and Autoimmune-Related Diseases Knowledge (ARK) Portal was created to publicly disseminate data from the Accelerating Medicines Partnership (AMP) RA/SLE program which used novel technologies to deconstruct and analyze gene expression and signaling in subsets of immune and resident tissue cells across cohorts of RA, SLE, and healthy subjects. 

Starting with ~50 TB of uncurated, structured and unstructured data, Sage Bionetworks has collaborated with AMP RA/SLE to develop a flexible and comprehensive model of metadata standards that accommodates a broad range of data types, including epigenomic, transcriptomic, proteomic, imaging, cytometry, and clinical data. These standards facilitate the discovery and reuse of AMP RA/SLE data by diverse communities of researchers through faceted data queries and data summarizations.

Development of this data model encountered many of the common challenges facing similar biomedical metadata standards efforts, including challenges specific to multimodal single-cell, spatial transcriptomics, and imaging data types. Our model design also includes mappings to standards currently in development for the AMP Autoimmune and Immune-Mediated Diseases (AMP AIM) program, a successor of AMP RA/SLE, which will host data on the ARK Portal. 

Future ARK Portal work includes creating a structured AMP RA/SLE publications database and implementing natural language processing and large language model-based pipelines to extract key findings, experimental details, and major scientific impacts from these papers. This database will be an annotated knowledge layer that directly links impactful research findings to the underlying data hosted in the portal and is an important step towards creating a significant resource for the autoimmune research community supported by state-of-the-art biocuration and annotation efforts.
Wigner Surmise For Domain Systems
Creators: name: Gonzalez, Diego Luis
name: Tellez, Gabriel
Publisher: name: arXiv
Year: 2007
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: In random matrix theory, the spacing distribution functions $p^{(n)}(s)$ are well fitted by the Wigner surmise and its generalizations. In this approximation the spacing functions are completely described by the behavior of the exact functions in the limits s->0 and s->infinity. Most non equilibrium systems do not have analytical solutions for the spacing distribution and correlation functions. Because of that, we explore the possibility to use the Wigner surmise approximation in these systems. We found that this approximation provides a first approach to the statistical behavior of complex systems, in particular we use it to find an analytical approximation to the nearest neighbor distribution of the annihilation random walk.
Label-free detection of neuronal differentiation in cell populations using high-throughput live-cell imaging of PC12 cells.
Creators: name: Weber, Sebastian
name: Fernández-Cachón, María L.
name: Nascimento, Juliana M.
name: Knauer, Steffen
name: Offermann, Barbara
name: Murphy, Robert
name: Boerries, Melanie
name: Busch, Hauke
Publisher: name: Carnegie Mellon University
Year: 2015
Subjects: Computational Biology

description: Detection of neuronal cell differentiation is essential to study cell fate decisions under various stimuli and/or environmental conditions. Many tools exist that quantify differentiation by neurite length measurements of single cells. However, quantification of differentiation in whole cell populations remains elusive so far. Because such populations can consist of both proliferating and differentiating cells, the task to assess the overall differentiation status is not trivial and requires a high-throughput, fully automated approach to analyze sufficient data for a statistically significant discrimination to determine cell differentiation. We address the problem of detecting differentiation in a mixed population of proliferating and differentiating cells over time by supervised classification. Using nerve growth factor induced differentiation of PC12 cells, we monitor the changes in cell morphology over 6 days by phase-contrast live-cell imaging. For general applicability, the classification procedure starts out with many features to identify those that maximize discrimination of differentiated and undifferentiated cells and to eliminate features sensitive to systematic measurement artifacts. The resulting image analysis determines the optimal post treatment day for training and achieves a near perfect classification of differentiation, which we confirmed in technically and biologically independent as well as differently designed experiments. Our approach allows to monitor neuronal cell populations repeatedly over days without any interference. It requires only an initial calibration and training step and is thereafter capable to discriminate further experiments. In conclusion, this enables long-term, large-scale studies of cell populations with minimized costs and efforts for detecting effects of external manipulation of neuronal cell differentiation.
Electronic States of Magnetic Quantum Dots
Creators: name: Abolfath, Ramin M.
name: Hawrylak, Pawel
name: Zutic, Igor
Publisher: name: arXiv
Year: 2007
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We study quantum states of electrons in magnetically doped quantum dots as a function of exchange coupling between electron and impurity spins, the strength of Coulomb interaction, confining potential, and the number of electrons. The magnetic phase diagram of quantum dots, doped with a large number of magnetic Mn impurities, can be described by the energy gap in the spectrum of electrons and the mean field electron-Mn exchange coupling. A competition between these two parameters leads to a transition between spin-unpolarized and spin-polarized states, in the absence of applied magnetic field. Tuning the energy gap by electrostatic control of nonparabolicity of the confining potential can enable control of magnetization even at the fixed number of electrons. We illustrate our findings by directly comparing Mn-doped quantum dots with parabolic and Gaussian confining potential.
description: 5 pages, 5 figures, Part of Focus on Spintronics in Reduced Dimensions
Controlling systematic frequency uncertainties at the $10^{-19}$ level in linear Coulomb crystals
Creators: name: Keller, J.
name: Burgermeister, T.
name: Kalincev, D.
name: Didier, A.
name: Kulosa, A. P.
name: Nordmann, T.
name: Kiethe, J.
name: Mehlstäubler, T. E.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Trapped ions are ideally suited for precision spectroscopy, as is evident from the remarkably low systematic uncertainties of single-ion clocks. The major weakness of these clocks is the long averaging time, necessitated by the low signal of a single atom. An increased number of ions can overcome this limitation and allow for the implementation of novel clock schemes. However, this presents the challenge to maintain the excellent control over systematic shifts of a single particle in spatially extended and strongly coupled many-body systems. We measure and deduce systematic frequency uncertainties related to spectroscopy with ion chains in a newly developed rf trap array designed for precision spectroscopy on simultaneously trapped ion ensembles. For the example of an In${}^+$ clock, sympathetically cooled with Yb${}^+$ ions, we show in our system that the expected systematic frequency uncertainties related to multi-ion operation can be below $1\times10^{-19}$. Our results pave the way to advanced spectroscopy schemes such as entangled clock spectroscopy and cascaded clock operation.
description: 11 + 3 pages, 8 figures
Even shorter quantum circuit for phase estimation on early fault-tolerant quantum computers with applications to ground-state energy estimation
Creators: name: Ding, Zhiyan
name: Lin, Lin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We develop a phase estimation method with a distinct feature: its maximal runtime (which determines the circuit depth) is $δ/ε$, where $ε$ is the target precision, and the preconstant $δ$ can be arbitrarily close to $0$ as the initial state approaches the target eigenstate. The total cost of the algorithm satisfies the Heisenberg-limited scaling $\widetilde{\mathcal{O}}(ε^{-1})$. As a result, our algorithm may significantly reduce the circuit depth for performing phase estimation tasks on early fault-tolerant quantum computers. The key technique is a simple subroutine called quantum complex exponential least squares (QCELS). Our algorithm can be readily applied to reduce the circuit depth for estimating the ground-state energy of a quantum Hamiltonian, when the overlap between the initial state and the ground state is large. If this initial overlap is small, we can combine our method with the Fourier filtering method developed in [Lin, Tong, PRX Quantum 3, 010318, 2022], and the resulting algorithm provably reduces the circuit depth in the presence of a large relative overlap compared to $ε$. The relative overlap condition is similar to a spectral gap assumption, but it is aware of the information in the initial state and is therefore applicable to certain Hamiltonians with small spectral gaps. We observe that the circuit depth can be reduced by around two orders of magnitude in numerical experiments under various settings.
Natural Doublet-Triplet Splitting in Supersymmetric SO(10) Model
Creators: name: Lee, Dae Gyu
name: Mohapatra, R. N.
Publisher: name: arXiv
Year: 1993
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We construct a supersymmetric SO(10) model, where natural doublet-triplet splitting implemented via the Dimopoulos-Wilczek mechanism is stable under the addition of 126+\bar{126} Higgs superfields needed to generate the small neutrino masses via the see-saw mechanism and where both the charged fermion and neutrino masses arise from just one set of 10 and \bar{126} multiplets.
description: UMD-PP-94-50, Latex,9 pages
Inter-firm marketing collaboration in family businesses: The role of risk aversion
Creators: name: Ibáñez, María José
Publisher: name: figshare
Year: 2021
Subjects: subject: 150303 Corporate Governance and Stakeholder Engagement
subject: FOS: Economics and business

description: Family businesses show low participation in inter-organizational collaborations. Inter-firm collaborations are activities in which companies seek to access resources and develop capabilities that they cannot achieve on their own. While there is empirical evidence that family businesses show a high level of risk aversion, some studies have shown the opposite. Further, research on this topic has focused mainly on economic and financial decisions, but few studies explore family business attitudes toward risk in non-financial decisions, such as marketing collaborations. Using a bivariate probit model in a sample of 1,118 Chilean family firms, we analyzed the extent to which the degree of risk aversion influences the probability of family firms participating in marketing collaborations with other firms and on the probability of cooperating with firms with which the family firm has had previous business experience. We found that although most conservative family firms are reluctant to take risks when entering a collaborative relationship, they are willing to take risks when engaging with partners with whom they have not had a previous relationship. The findings expand on research regarding family businesses’ attitudes toward risk, relative to strategic non-financial decisions, and the theoretical development of their collaborative marketing visions.
SoK: Secure Human-centered Wireless Sensing
Creators: name: Sun, Wei
name: Chen, Tingjun
name: Gong, Neil
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cryptography and Security (cs.CR)
subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: Human-centered wireless sensing (HCWS) aims to understand the fine-grained environment and activities of a human using the diverse wireless signals around him/her. While the sensed information about a human can be used for many good purposes such as enhancing life quality, an adversary can also abuse it to steal private information about the human (e.g., location and person's identity). However, the literature lacks a systematic understanding of the privacy vulnerabilities of wireless sensing and the defenses against them, resulting in the privacy-compromising HCWS design.
 In this work, we aim to bridge this gap to achieve the vision of secure human-centered wireless sensing. First, we propose a signal processing pipeline to identify private information leakage and further understand the benefits and tradeoffs of wireless sensing-based inference attacks and defenses. Based on this framework, we present the taxonomy of existing inference attacks and defenses. As a result, we can identify the open challenges and gaps in achieving privacy-preserving human-centered wireless sensing in the era of machine learning and further propose directions for future research in this field.
Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap
Creators: name: Wang, Hao
name: C. Joel McManus
name: Kingsford, Carl
Publisher: name: Carnegie Mellon University
Year: 2012
Subjects: Computational Biology

description: Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a naïve mapping. Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap.
Lattice Functions for the Analysis of Analog-to-Digital Conversion
Creators: name: Martínez-Nuevo, Pablo
name: Oppenheim, Alan. V.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Signal Processing (eess.SP)
subject: Information Theory (cs.IT)
subject: Complex Variables (math.CV)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: H.1.0
subject: 30D20 (Primary) 30D15 (Secondary)

description: Analog-to-digital (A/D) converters are the common interface between analog signals and the domain of digital discrete-time signal processing. In essence, this domain simultaneously incorporates quantization both in amplitude and time, i.e. amplitude quantization and uniform time sampling. Thus, we view A/D conversion as a sampling process in both the time and amplitude domains based on the observation that the underlying continuous-time signals representing digital sequences can be sampled in a lattice---i.e. at points restricted to lie on a uniform grid both in time and amplitude. We refer to them as lattice functions. This is in contrast with the traditional approach based on the classical sampling theorem and quantization error analysis. The latter has been mainly addressed with the help of probabilistic models, or deterministic ones either confined to very particular scenarios or considering worst-case assumptions. In this paper, we provide a deterministic theoretical analysis and framework for the functions involved in digital discrete-time processing. We show that lattice functions possess a rich analytic structure in the context of integral-valued entire functions of exponential type. We derive set and spectral properties of this class of functions. This allows us to prove in a deterministic way and for general bandlimited functions a fundamental lower bound on the maximum frequency component introduced by quantization that is independent of the resolution of the quantizer.
description: 9 pages, 5 figures, journal paper
Low-temperature scanning tunneling microscopy of ring-like surface electronic structures around Co islands on InAs(110) surfaces
Creators: name: Muzychenko, D. A.
name: Schouteden, K.
name: Savinov, S. V.
name: Maslova, N. S.
name: Panov, V. I.
name: Van Haesendonck, C.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report on the experimental observation by scanning tunneling microscopy at low temperature of ring-like features that appear around Co metal clusters deposited on a clean (110) oriented surface of cleaved p-type InAs crystals. These features are visible in spectroscopic images within a certain range of negative tunneling bias voltages due to the presence of a negative differential conductance in the current-voltage dependence. A theoretical model is introduced, which takes into account non-equilibrium effects in the small tunneling junction area. In the framework of this model the appearance of the ring-like features is explained in terms of interference effects between electrons tunneling directly and indirectly (via a Co island) between the tip and the InAs surface.
description: 8 pages, 4 figures
Cosmological constraints on an exponential interaction in the dark sector
Creators: name: Yang, Weiqiang
name: Pan, Supriya
name: Paliathanasis, Andronikos
Publisher: name: arXiv
Year: 2018
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Cosmological models where dark matter (DM) and dark energy (DE) interact with each other are the general scenarios in compared to the non-interacting models. The interaction is usually motivated from the phenomenological ground and thus there is no such rule to prefer a particular interaction between DM and DE. Being motivated, in this work, allowing an exponential interaction between DM and DE in a spatially flat homogeneous and isotropic universe, we explore the dynamics of the universe through the constraints of the free parameters where the strength of the interaction is characterized by the dimensionless coupling parameter $ξ$ and the equation of state (EoS) for DE, $w_x$, is supposed to be a constant. The interaction scenario is fitted using the latest available observational data. Our analyses report that the observational data permit a non-zero value of $ξ$ but it is very small and consistent with $ξ=0$. From the constraints on $w_x$, we find that both phantom ($w_x< -1$) and quintessence ($w_x> -1$) regimes are equally allowed but $w_x$ is very close to `$-1$'. The overall results indicate that at the background level, the interaction model cannot be distinguished from the base $Λ$-cold dark matter model while from the perturbative analyses, the interaction model mildly deviates from the base model. We highlight that, even if we allow DM and DE to interact in an exponential manner, but according to the observational data, the evidence for a non-zero coupling is very small.
description: 13 pages, 7 figures, 2 tables; version published in MNRAS
Digital social entrepreneurship: the N-Helix response to stakeholders’ COVID-19 needs
Creators: name: Ibáñez, María José
Publisher: name: figshare
Year: 2021
Subjects: subject: 150304 Entrepreneurship
subject: FOS: Economics and business
subject: 150307 Innovation and Technology Management

description: This study explores the emergence of a new entrepreneurship phenomenon (digital social entrepreneurship) as a result of the collaboration among many agents (N-Helix), given the government’s limited capacity to respond to the stakeholders’ needs satisfaction related to an exogenous event (e.g., the COVID-19 pandemic). Our theory development is based on three ongoing academic debates related to (a) the unrepresentativeness of the stakeholder theory in entrepreneurship research; (b) the emergence of digital social entrepreneurship (DSE) as a bridge between stakeholders’ needs, socio-economic actors, and digital-social initiatives; and (c) the role of N-Helix collaborations to facilitate the emergence of global knowledge-intensive initiatives and the rapid adoptions of open innovations. Our results support our assumptions about the positive mediation effect of DSE in the relationship between N-Helix collaborations and stakeholders’ satisfaction. Notably, results show how pandemic has intensified these relationships and how DSE in N-Helix collaborations can generate social impacts globally. Some implications for policy-makers have emerged from our results that should be considered during/post-COVID-19 pandemic.
RE-ENTRY INTO ENTREPRENEURSHIP AFTER FAILURE: FACTORS INFLUENCING SERIAL AND SECOND CHANCE ENTREPRENEURS
Creators: name: Ibáñez, María José
Publisher: name: figshare
Year: 2021
Subjects: subject: 150304 Entrepreneurship
subject: FOS: Economics and business

description: This article investigates factors that influence the probability of re-starting after business failure, including sociodemographic and economic variables. Particularly, it examines the effect of age, educational level, the entrepreneur’s role as provider in the family, the coverage of public instruments and services for entrepreneurship and the reasons that lead the entrepreneur to close the business, on the willingness of the failed entrepreneur to start a new business. It uses a sample of 274 failed entrepreneurs from Chile, the country with the highest rate of Total early-stage Entrepreneurial Activity (TEA) in the world, according to the GEM 2019/2020 report. The results of this study indicate that the main variables have a negative influence on the probability of re-entering entrepreneurship after business failure, but only age, regional coverage of technical services for entrepreneurship, bankruptcy, preference for wage-employment and the level of regional unemployment are significant. This research contributes to broadening the empirical evidence regarding the factors that influence serial and second-chance entrepreneurs, beyond aspects related to entrepreneurial intent and elements of entrepreneurial behavior. This paper provides relevant conclusions for the design of public policies and support instruments for entrepreneurs who are willing to create a new business after business failure.
Phase transition between non-extremal and extremal Reissner-Nordström black holes
Creators: name: Myung, Yun Soo
Publisher: name: arXiv
Year: 2007
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We discuss the phase transition between non-extremal and extremal Reissner-Nordström black holes. This transition is considered as the $T \to 0$ limit of the transition between the non-extremal and near-extremal black holes. We show that an evaporating process from non-extremal black hole to extremal one is possible to occur, but its reverse process is not possible to occur because of the presence of the maximum temperature. Furthermore, it is shown that the Hawking-Page phase transition between small and large black holes unlikely occurs in the AdS Reissner-Nordström black holes.
description: 12 pages, 6 figures, version to appear in MPLA
Image-derived, three-dimensional generative models of cellular organization.
Creators: name: Peng, Tao
name: Murphy, Robert
Publisher: name: Carnegie Mellon University
Year: 2011
Subjects: Computational Biology

description: Given the importance of subcellular location to protein function, computational simulations of cell behaviors will ultimately require the ability to model the distributions of proteins within organelles and other structures. Toward this end, statistical learning methods have previously been used to build models of sets of two-dimensional microscope images, where each set contains multiple images for a single subcellular location pattern. The model learned from each set of images not only represents the pattern but also captures the variation in that pattern from cell to cell. The models consist of sub-models for nuclear shape, cell shape, organelle size and shape, and organelle distribution relative to nuclear and cell boundaries, and allow synthesis of images with the expectation that they are drawn from the same underlying statistical distribution as the images used to train them. Here we extend this generative models approach to three dimensions using a similar framework, permitting protein subcellular locations to be described more accurately. Models of different patterns can be combined to yield a synthetic multi-channel image containing as many proteins as desired, something that is difficult to obtain by direct microscope imaging for more than a few proteins. In addition, the model parameters represent a more compact and interpretable way of communicating subcellular patterns than descriptive image features and may be particularly effective for automated identification of changes in subcellular organization caused by perturbagens.
Identification of alternative topological domains in chromatin.
Creators: name: Filippova, Darya
name: Patro, Rob
name: Geet  Duggal
name: Kingsford, Carl
Publisher: name: Carnegie Mellon University
Year: 2014
Subjects: Computational Biology

description: Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The ensemble of domains we identify allows us to quantify the degree to which the domain structure is hierarchical as opposed to overlapping, and our analysis reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone marks at the boundaries.
IFU spectroscopy of southern PN VI: The extraordinary chemo-dynamics of Hen 2-111
Creators: name: Dopita, M. A.
name: Ali, A.
name: Karakas, A. I.
name: Goldman, D.
name: Amer, M. A.
name: Sutherland, R. S.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: In this paper we present integral field spectroscopy of the extraordinary Type I bipolar planetary nebula Hen 2-111. In the lobes we map fast moving knots of material with [N II]$λ6584$/H$α$ ratios up to 12, and with radial velocities relative to systemic from -340 km/s up to +390 km/s. We find evidence of a bipolar ejection event at a velocity $\sim 600$ km/s from the central star (assumed to be a binary), which occurred about 8000yr ago. The fast moving material is chemically quite distinct from the lower velocity gas in the bipolar lobes., and displays very high N abundances. We show that the fast moving N-rich knots are not photoionised by the central star, and have constructed detailed shock models for the brightest knot. We find a pre-shock density $\sim 6$cm$^{-3}$, and a shock velocity $\sim150$ km/s. The shock is not fully radiative, being only $\sim 600$yr old. This shocked gas is partially H-burnt, with a helium abundance by mass exceeding that of hydrogen, and is interacting with partially H-burnt material ejected in an earlier episode of mass loss. We conclude that the high-velocity material and the bipolar shell must have originated during the late stages of evolution of a common-envelope phase in a close binary system.
description: 15 pages, 14 figures, 2 tables. Accepted for publication in MNRAS
WEBINAR: Getting started with deep learning
Creators: name: Tang, Titus
Publisher: name: Zenodo
Year: 2021
Subjects: subject: Deep learning
subject: Neural networks
subject: Machine learning
subject: http://edamontology.org/topic_3474

description: This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with deep learning’. This webinar took place on 21 July 2021. Are you wondering what deep learning is and how it might be useful in your research? This high level overview introduces deep learning ‘in a nutshell’ and provides tips on which concepts and skills you will need to know to build a deep learning application. The presentation also provides pointers to various resources you can use to get started in deep learning. The webinar is followed by a short Q&A session. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Getting Started with Deep Learning - Slides (PDF): Slides used in the presentation
Genuine multipartite entanglement measures based on multi-party teleportation capability
Creators: name: Choi, Minjin
name: Bae, Eunok
name: Lee, Soojoon
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantifying entanglement is vital to understand entanglement as a resource in quantum information processing, and many entanglement measures have been suggested for this purpose. When mathematically defining an entanglement measure, we should consider the distinguishability between entangled and separable states, the invariance under local transformation, the monotonicity under local operations and classical communication, and the convexity. These are reasonable requirements but may be insufficient, in particular when taking into account the usefulness of quantum states in multi-party quantum information processing. Therefore, if we want to investigate multipartite entanglement as a resource, then it can be necessary to consider the usefulness of quantum states in multi-party quantum information processing when we define a multipartite entanglement measure. In this paper, we define new multipartite entanglement measures for three-qubit systems based on the three-party teleportation capability, and show that these entanglement measures satisfy the requirements for being genuine multipartite entanglement measures. We also generalize our entanglement measures for $N$-qubit systems, where $N \ge 4$, and discuss that these quantities may be good candidates to measure genuine multipartite entanglement.
description: 14 pages, 2 figures
Curating gene alias relationships to resolve gene symbol ambiguity
Creators: name: Bratulin, Anastasia
name: Stevenson, James S.
name: Kuzma, Kori
name: Cannon, Matthew
name: Goar, Wesley
name: Wagner, Alex
Publisher: name: F1000 Research Limited
Year: 2025

description: Gene nomenclature supports clear and consistent communication about genomic knowledge. What happens when the tool used to clarify, leads to ambiguity? We see this occur in gene symbols when one gene is represented by multiple gene symbols or the same symbol is used to represent multiple genes. Defining the relationships between genes and the symbols that are used to represent them will help resolve ambiguities that can arise in applications that organize data by gene symbol and in manual literature review.
On the Higher Order Corrections to Heavy Quark Effective Theory
Creators: name: Das, Ashok
Publisher: name: arXiv
Year: 1993
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We show that the different ways of deriving the Heavy Quark Effective Theory (HQET) lead to equivalent theories. The equivalence can be established through a careful redefinition of the field variables. We demonstrate the equivalence to order ${1 \over m^5}$ in the presence of a constant electric field.
description: 17 pages, UR-1325, ER-40685-775
Variations on a Hypergeometric Theme
Creators: name: Milgram, Michael
Publisher: name: arXiv
Year: 2018
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 33B15, 33C20, 30-02, 30B99, 33-02, 40-02, 40C99

description: The question was asked: Is it possible to express the function \begin{equation} \tag{1.1} h(a)\equiv\,{_4F_3}(a,a,a,a;2a,a+1,a+1;1) \label{question} \end{equation} in closed form? After considerable analysis, the answer appears to be "no", but during the attempt to answer this question, a number of interesting (and unexpected) related results were obtained, either as specialized transformations, or as closed-form expressions for several related functions. The purpose of this paper is to record and review both the methods attempted and the related identities obtained (specifically new $_4F_3(1)$, $_5F_6(1)$ and (generalized Euler) sums containing digamma functions) - the former for their educational merit, since they appear to be not-very-well-known, the latter because they do not appear to exist in the literature.
description: In this (second) revision, Appendix C is corrected. This paper has been accepted for publication in the (Open Access) Journal of Classical Analysis
Higher-order chromatin domains link eQTLs with the expression of far-away genes.
Creators: name: Geet  Duggal
name: Wang, Hao
name: Kingsford, Carl
Publisher: name: Carnegie Mellon University
Year: 2011
Subjects: Computational Biology

description: Distal expression quantitative trait loci (distal eQTLs) are genetic mutations that affect the expression of genes genomically far away. However, the mechanisms that cause a distal eQTL to modulate gene expression are not yet clear. Recent high-resolution chromosome conformation capture experiments along with a growing database of eQTLs provide an opportunity to understand the spatial mechanisms influencing distal eQTL associations on a genome-wide scale. We test the hypothesis that spatial proximity contributes to eQTL-gene regulation in the context of the higher-order domain structure of chromatin as determined from recent Hi-C chromosome conformation experiments. This analysis suggests that the large-scale topology of chromatin is coupled with eQTL associations by providing evidence that eQTLs are in general spatially close to their target genes, occur often around topological domain boundaries and preferentially associate with genes across domains. We also find that within-domain eQTLs that overlap with regulatory elements such as promoters and enhancers are spatially more close than the overall set of within-domain eQTLs, suggesting that spatial proximity derived from the domain structure in chromatin plays an important role in the regulation of gene expression.
Pegcetacoplan: First Approval
Creators: name: Hoy, Sheridan M.
Publisher: name: Adis Journals
Year: 2021
Subjects: Medicine

description: DeclarationsFunding The preparation of this review was not supported by any external funding.Authorship and Conflict of interest During the peer review process the manufacturer of the agent under review was offered an opportunity to comment on the article. Changes resulting from any comments received were made by the authors on the basis of scientific completeness and accuracy. Sheridan Hoy is a salaried employee of Adis International Ltd/Springer Nature, and declares no relevant conflicts of interest. All authors contributed to the review and are responsible for the article content.Ethics approval, Consent to participate, Consent to publish, Availability of data and material, Code availability Not applicable.

Additional information about this Adis Drug Review can be found here.

AbstractPegcetacoplan (Empaveli™) is a PEGylated pentadecapeptide developed by Apellis Pharmaceuticals for the treatment of complement-mediated diseases. It binds to complement component 3 (C3) and its activation fragment C3b, controlling the cleavage of C3 and the generation of the downstream effectors of complement activation and thus both C3b-mediated extravascular haemolysis and terminal complement-mediated intravascular haemolysis. Pegcetacoplan is the first C3-targeted paroxysmal nocturnal haemoglobinuria (PNH) therapy to be approved (in May 2021) in the USA, where it is indicated for the treatment of adults with PNH, including those switching from C5 inhibitor therapy with eculizumab and ravulizumab. A regulatory assessment of pegcetacoplan for the treatment of PNH is currently underway in the EU and Australia. Pegcetacoplan is also being investigated as a therapeutic option in other complement-mediated diseases, including age-related macular degeneration, C3 glomerulopathy and autoimmune haemolytic anaemia. The recommended dosage regimen of pegcetacoplan is 1080 mg twice weekly, administered as a subcutaneous infusion via an infusion pump with a ≥ 20 mL reservoir. This article summarizes the milestones in the development of pegcetacoplan leading to this first approval for the treatment of adults with PNH.

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