cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
ALMA Observation of 158 micron [CII] Line and Dust Continuum of a z=7 Normally Star-forming Galaxy in the Epoch of Reionization
Creators: name: Ota, Kazuaki
name: Walter, Fabian
name: Ohta, Kouji
name: Hatsukade, Bunyo
name: Carilli, Chris L.
name: da Cunha, Elisabete
name: González-López, Jorge
name: Decarli, Roberto
name: Hodge, Jacqueline A.
name: Nagai, Hiroshi
name: Egami, Eiichi
name: Jiang, Linhua
name: Iye, Masanori
name: Kashikawa, Nobunari
name: Riechers, Dominik A.
name: Bertoldi, Frank
name: Cox, Pierre
name: Neri, Roberto
name: Weiss, Axel
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present ALMA observations of the [CII] line and far-infrared (FIR) continuum of a normally star-forming galaxy in the reionization epoch, the z=6.96 Ly-alpha emitter (LAE) IOK-1. Probing to sensitivities of sigma_line = 240 micro-Jy/beam (40 km/s channel) and sigma_cont = 21 micro-Jy/beam, we found the galaxy undetected in both [CII] and continuum. Comparison of UV - FIR spectral energy distribution (SED) of IOK-1, including our ALMA limit, with those of several types of local galaxies (including the effects of the cosmic microwave background, CMB, on the FIR continuum) suggests that IOK-1 is similar to local dwarf/irregular galaxies in SED shape rather than highly dusty/obscured galaxies. Moreover, our 3 sigma FIR continuum limit, corrected for CMB effects, implies intrinsic dust mass M_dust < 6.4 x 10^7 M_sun, FIR luminosity L_FIR < 3.7 x 10^{10} L_sun (42.5 - 122.5 micron), total IR luminosity L_IR < 5.7 x 10^{10} L_sun (8 - 1000 micron) and dust-obscured star formation rate (SFR) < 10 M_sun/yr, if we assume that IOK-1 has a dust temperature and emissivity index typical of local dwarf galaxies. This SFR is 2.4 times lower than one estimated from the UV continuum, suggesting that < 29% of the star formation is obscured by dust. Meanwhile, our 3 sigma [CII] flux limit translates into [CII] luminosity, L_[CII] < 3.4 x 10^7 L_sun. Locations of IOK-1 and previously observed LAEs on the L_[CII] vs. SFR and L_[CII]/L_FIR vs. L_FIR diagrams imply that LAEs in the reionization epoch have significantly lower gas and dust enrichment than AGN-powered systems and starbursts at similar/lower redshifts, as well as local star-forming galaxies.
description: 15 pages, 8 figures, 1 table, accepted for publication in The Astrophysical Journal (Updates since last version: text shortened; Figures 7 & 8 updated (a new data point added, IMF unified for SFRs); references updated)
title: Pilot Project Funding Opportunities
Creators: name: Hafer, Nathaniel
name: Thomas, William D.
name: Babcock, Gregory J.
Publisher: name: eScholarship@UMMS
Year: 2012

description: Learn about funding opportunities offered through the UMCCTS in the 2012-2013 academic year. Bill Thomas and Greg Babcock describe the resources available at MassBiologics and the new Next Hundred Million Pilot Program funding opportunity.
title: Pilot Project Funding Opportunities
Creators: name: Hafer, Nathaniel
name: Deligiannidis, Kristina M.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Learn about funding opportunities offered through the UMCCTS in the 2013-2014 academic year. A previously-funded researcher (Kristina Deligiannidis) also describes her project, "Neuroendocrine & neuroimaging endophenotypes in perinatal depression."
Consistency in the Naturally Vertex-Signed Line Graph of a Signed Graph
Creators: name: Zaslavsky, Thomas
Publisher: name: arXiv
Year: 2014
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C22

description: A signed graph is a graph whose edges are signed. In a vertex-signed graph the vertices are signed. The latter is called consistent if the product of signs in every circle is positive. The line graph of a signed graph is naturally vertex-signed. Based on a characterization by Acharya, Acharya, and Sinha in 2009, we give constructions for the signed simple graphs whose naturally vertex-signed line graph is consistent.
description: 7 pp. V2: minor errors corrected
Non-Convergence and Limit Cycles in the Adam optimizer
Creators: name: Bock, Sebastian
name: Weiß, Martin Georg
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Numerical Analysis (math.NA)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: One of the most popular training algorithms for deep neural networks is the Adaptive Moment Estimation (Adam) introduced by Kingma and Ba. Despite its success in many applications there is no satisfactory convergence analysis: only local convergence can be shown for batch mode under some restrictions on the hyperparameters, counterexamples exist for incremental mode. Recent results show that for simple quadratic objective functions limit cycles of period 2 exist in batch mode, but only for atypical hyperparameters, and only for the algorithm without bias correction. %More general there are several more adaptive gradient methods which try to estimate a fitting learning rate and / or search direction from the training data to improve the learning process compared to pure gradient descent with fixed learningrate. We extend the convergence analysis for Adam in the batch mode with bias correction and show that even for quadratic objective functions as the simplest case of convex functions 2-limit-cycles exist, for all choices of the hyperparameters. We analyze the stability of these limit cycles and relate our analysis to other results where approximate convergence was shown, but under the additional assumption of bounded gradients which does not apply to quadratic functions. The investigation heavily relies on the use of computer algebra due to the complexity of the equations.
Focus Point Supersymmetry in Extended Gauge Mediation
Creators: name: Ding, Ran
name: Li, Tianjun
name: Staub, Florian
name: Zhu, Bin
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose a small extenion of the minimal gauge mediation through the combination of extended gauge mediation and conformal sequestering. We show that the focus point supersymmetry can be realized naturally, and the fine-tuning is signifcantly reduced compared to the minimal gauge mediation and extended gauge mediation without focus point. The Higgs boson mass is around 125 GeV, the gauginos remain light, and the gluino is likely to be detected at the next run of the LHC. However, the multi-TeV squarks is out of the reach of the LHC. The numerical calculation for finetuning shows that this model remains natural.
description: 23 pages, 7 figures, references added
A Preliminary Ecological Study of Areas to be Impounded in the Salt River Basin of Kentucky
Creators: name: Krumholz, Louis A.
Publisher: name: Kentucky Water Resources Research Institute, University of Kentucky
Year: 1971

description: Abstract:
This report covers work that is an extension of Project No. A-019-KY. A series of 25 sampling stations was established in the mainstream and tributaries of the Salt River that extend from the source of the stream in Boyle County to a few miles below the site of Taylorsville Darn in Spencer County. Sampling for water chemistry and biota was carried out semimonthly. Data on temperature, oxygen, depth, and discharge, along with analyses for cations (Ca, Mg, Fe, Mn) and anions (PO4, NO3, NO2, CO3, HCO3) have been accumulated and analyzed. Bottom fauna, fishes, and plants have been sampled at each station and relative abundance and species composition of the biota have been made.
Physical and chemical data, along with flora and fauna taken from the stream present the characteristics of a relatively healthy ecosystem. Water temperatures reflect air temperatures closely and dissolved oxygen values are near saturation. Turbidity increased with runoff, the stream flow increasing rapidly during rainy periods and falling to a minimum during dry periods. Total alkalinities ranged from 135 to 210 mg/1 as CaCO3 with ranges in pH from 6.3 to 8.2. Nitrate nitrogen ranged from 2.0 to 11.3 mg/1 and orthophosphate from 0.25 to 2.78 mg/1. Iron and manganese ranged from 0.07 to 0.46 and 0.09 to 0.39 mg/1, respectively.
A total of 74 species of algae referable to 35 families were collected and identified. Green algae (Chlorophyta) were represented by 38 species, reflecting the contention that the Salt River is a relatively clean, oligosaprobic stream. More than 200 species of vascular plants referable to 50 families have been collected from the riparian vegetation. Bottom fauna includes 98 species of insects representing 8 orders and 42 families. Prominent among these are the 23 species of chironomids that have been identified to date, The most common crustaceans are Orconectes rusticus and Lirceus lineatus along with several species of Gammarus. Molluscs include gastropods, fingernail clams, and unionids. More than 50 species of fishes have been collected and will provide data for a preliminary report to be published in the open literature.
Plans include a further inventory of the fish population and continued study of the physiochemical and biological aspects of the stream ecosystem, The study of economic aspects of the area will continue at an accelerated pace.
Funding information: The work on which this report is based was supported in part by funds provided by the Office of Water Resources Research, United States Department of the Interior, as authorized under the Water Resources Research Act of 1964.
DooML: A new Database & Object-Oriented Modeling Language for database-driven web application design and development
Creators: name: Otter, Thijs
Publisher: name: arXiv
Year: 2022
Subjects: subject: Software Engineering (cs.SE)
subject: Databases (cs.DB)
subject: FOS: Computer and information sciences

description: A database driven web application is a very common software solution to rising business problems. Modeling the database and the software architecture can be challenging, hence there not being one combined modeling language for database and software architecture, specifically suited for web application development. In this paper we present Database object-oriented Modeling Language (DooML) and its primary Archetype Diagram: a notation for specifying the design of a database schema and corresponding object-oriented software architecture. It combines the syntax for drawing Entity Relationship Diagrams, the Relational Model and Universal Modeling Language Class Diagrams as well to create a mixed diagram, stating database design as well as software design specifications. By default, DooML ensures that the approach of advanced web application development is model-driven and both database-oriented as well as object-oriented.
description: 9 pages. International Journal of Software Engineering & Applications (IJSEA), Chennai, India (2022)
title: Medical Device Innovation in Massachusetts -- M2D2: Massachusetts Medical Device Development Center
Creators: name: McCarthy, Stephen P.
name: Tello, Steven
name: Hafer, Nathaniel
Publisher: name: eScholarship@UMMS
Year: 2013

description: This presentation describes the role of the medical device industry in the economy of Massachusetts and how the Massachusetts Medical Device Development (M2D2) Center can assist entrepreneurs and new companies working in this space.
Electric-Field-Modulated Nonvolatile Resistance Switching in VO2/PMN-PT(111) Heterostructures
Creators: name: Zhi, Bowen
name: Gao, Guanyin
name: Xu, Haoran
name: Chen, Feng
name: Tan, Xuelian
name: Chen, Pingfan
name: Wang, Lingfei
name: Wu, Wenbin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The electric-field-modulated resistance switching in VO2 thin films grown on piezoelectric (111)-0.68Pb(Mg1/3Nb2/3)O3-0.32PbTiO3 (PMN-PT) substrates has been investigated. Large relative change in resistance (10.7%) was observed in VO2/PMN-PT(111) hererostructures at room temperature. For a substrate with a given polarization direction, stable resistive states of VO2 films can be realized even when the applied electric fields are removed from the heterostructures. By sweeping electric fields across the heterostructure appropriately, multiple resistive states can be achieved. These stable resistive states result from the different stable remnant strain states of substrate, which is related to the rearrangements of ferroelectric domain structures in PMN-PT(111) substrate. The resistance switching tuned by electric field in our work may have potential applications for novel electronic devices.
description: 20 pages, 5 figures
Analysis of Global Published Literature on Library and Information Science: an Empirical Study through Big Data Approach (1920-2020)
Creators: name: Panda, Subhajit
name: Sinhababu, Atasi
name: Chakravarty, Dr. Rupak
Publisher: name: figshare
Year: 2023
Subjects: Library studies
Library and information studies not elsewhere classified

description: The purpose of this paper is to investigate the extent of LIS (Library and Information Science) literature referring to and being referred by patents in the form of scholarly citations they attribute and/or receive. The analysis of the present study was done based on a total data-set of 237820 research publications of the LIS discipline ranging from April 1920 to April 2020 (100 years) as mined from the LENS database. LIS research corpus received 22.75 scholarly citations and 6.87 patent citations per paper while utilizing and citing 18667 patents and thus establishing the correlation between the citing-cited link in the research ecosystem. In addition, this paper also evaluates the decadal Relative Growth Rate (RGR) and Doubling Time (Dt) of LIS publications ranging from May 1920 to April 2020. The paper reflects the value of LIS research in patents and vice versa depicting the cross-disciplinary nature and decadal growth rate of LIS in general and information science in particular.
title: 2010 K12 Awardees: Overview of Research Projects
Creators: name: Cutrona, Sarah L.
name: Santry, Heena P.
Publisher: name: eScholarship@UMMS
Year: 2014

description: Two UMCCTS Clinical Research Scholars (K awardees) describe their research projects and professional growth as junior faculty:

- Sarah Cutrona on "Electronic Transmission of Health Information across Networks"

- Heena Santry on "Career Development for an Academic Acute Care Surgeon and Acute Care Surgery Practice Patterns: A Tale of Two Complexities"
title: “So You Think You Have a Drug You Want to Develop”
Creators: name: Klempner, Mark S.
Publisher: name: eScholarship@UMMS
Year: 2014

description: Mark Klempner, MD, Executive Vice Chancellor, MassBiologics of UMass Medical School and Professor of Medicine, describes MassBiologics and their process for developing a new medicine. MassBiologics is the only non-profit, FDA-licensed manufacturer of vaccines and biologics in the United States.
Asteroid spin-states of a 4 Gyr collisional family
Creators: name: Athanasopoulos, D.
name: Hanus, J.
name: Avdellidou, C.
name: Bonamico, R.
name: Delbo, M.
name: Conjat, M.
name: Ferrero, A.
name: Gazeas, K.
name: Rivet, J. P.
name: Sioulas, N.
name: van Belle, G.
name: Antonini, P.
name: Audejean, M.
name: Behrend, R.
name: Bernasconi, L.
name: Brinsfield, J. W.
name: Brouillard, S.
name: Brunetto, L.
name: Fauvaud, M.
name: Fauvaud, S.
name: González, R.
name: Higgins, D.
name: Holoien, T. W. -S.
name: Kobber, G.
name: Koff, R. A.
name: Kryszczynska, A.
name: Livet, F.
name: Marciniak, A.
name: Oey, J.
name: Pejcha, O.
name: Rives, J. J.
name: Roy, R.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Families of asteroids generated by the collisional fragmentation of a common parent body have been identified using clustering methods of asteroids in their proper orbital element space. An alternative method has been developed in order to identify collisional families from the correlation between the asteroid fragment sizes and their proper semi-major axis distance from the family centre (V-shape). This method has been shown to be effective in the cases of the very diffuse families that formed billions of years ago. We obtained photometric observations of asteroids in order to construct their rotational light curves; we combine them with the literature light curves and sparse-in-time photometry; we input these data in the light curve inversion methods to determine the shape and the spin pole of the asteroids in order to assess whether an object is prograde or retrograde. The ultimate goal is to assess whether we find an excess of retrograde asteroids on the inward side of the V-shape of a 4 Gyr asteroid family identified via the V-shape method. This excess of retrograde rotators is predicted by the theory of asteroid family evolution. We obtained the spin poles for 55 asteroids claimed to belong to a 4 Gyr collisional family of the inner main belt that consists of low-albedo asteroids. After re-evaluating the albedo and spectroscopic information, we found that nine of these asteroids are interlopers in the 4 Gyr family. Of the 46 remaining asteroids, 31 are found to be retrograde and 15 prograde. We also found that these retrograde rotators have a very low probability (1.29%) of being due to random sampling from an underlying uniform distribution of spin poles. Our results constitute corroborating evidence that the asteroids identified as members of a 4 Gyr collisional family have a common origin, thus strengthening their family membership.
description: 20 pages, 7 figures. A&A (2022)
title: RNA Therapeutics: Informational drugs as a pandemic response tool
Creators: name: Khvorova, Anastasia
Publisher: name: eScholarship@UMMS
Year: 2020

description: This presentation, hosted by the University of Massachusetts Medical School, describes the development of siRNA-based approaches for modulation of COVID-19 in the lung in a three-month time frame. It was the second in a webinar series called the COVID-19 Research Community Forum. Researchers from the four federally-funded Clinical and Translational Science (CTSA) programs in Massachusetts -- the UMass Center for Clinical and Translational Science, Tufts Clinical and Translational Science Institute, Harvard Catalyst, and Boston University Clinical and Translational Science Institute -- present about COVID-19 research happening here in Massachusetts.
The resonant dynamics of arbitrarily-shaped meta-atoms
Creators: name: Powell, David A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Meta-atoms, nano-antennas, plasmonic particles and other small scatterers are commonly modeled in terms of their modes. However these modal solutions are seldom determined explicitly, due to the conceptual and numerical difficulties in solving eigenvalue problems for open systems with strong radiative losses. Here these modes are directly calculated from Maxwell's equations expressed in integral operator form, by finding the complex frequencies which yield a homogenous solution. This gives a clear physical interpretation of the modes, and enables their conduction or polarization current distribution to be calculated numerically for particles of arbitrary shape. By combining the modal current distribution with a scalar impedance function, simple yet accurate models of scatterers are constructed which describe their response to an arbitrary incident field over a broad bandwidth. These models generalize both equivalent-dipole and and equivalent-circuit models to finite sized structures with multiple modes. They are applied here to explain the frequency-splitting for a pair of coupled split rings, and the accompanying change in radiative losses. The approach presented in this paper is made available in an open-source code.
ProxNLP: a primal-dual augmented Lagrangian solver for nonlinear programming in Robotics and beyond
Creators: name: Jallet, Wilson
name: Bambade, Antoine
name: Mansard, Nicolas
name: Carpentier, Justin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: Mathematical optimization is the workhorse behind several aspects of modern robotics and control. In these applications, the focus is on constrained optimization, and the ability to work on manifolds (such as the classical matrix Lie groups), along with a specific requirement for robustness and speed. In recent years, augmented Lagrangian methods have seen a resurgence due to their robustness and flexibility, their connections to (inexact) proximal-point methods, and their interoperability with Newton or semismooth Newton methods. In the sequel, we present primal-dual augmented Lagrangian method for inequality-constrained problems on manifolds, which we introduced in our recent work, as well as an efficient C++ implementation suitable for use in robotics applications and beyond.
description: Workshop paper at the 6th Legged Robots Workshop, at the IEEE International Conference on Robotics and Automation (ICRA) 2022
Number-Resolved Detection of Dark Ions in Coulomb Crystals
Creators: name: Schmid, Fabian
name: Weitenberg, Johannes
name: Moreno, Jorge
name: Hänsch, Theodor W.
name: Udem, Thomas
name: Ozawa, Akira
Publisher: name: arXiv
Year: 2022
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: While it is straightforward to count laser-cooled trapped ions by fluorescence imaging, detecting the number of dark ions embedded and sympathetically cooled in a mixed ion crystal is more challenging. We demonstrate a method to track the number of dark ions in real time with single-particle sensitivity. This is achieved by observing discrete steps in the amount of fluorescence emitted from the coolant ions while exciting secular motional resonances of dark ions. By counting the number of fluorescence steps, we can identify the number of dark ions without calibration and without relying on any physical model of the motional excitation. We demonstrate the scheme by detecting H$_2^+$ and H$_3^+$ ions embedded in a Be$^+$ ion Coulomb crystal in a linear radio frequency trap. Our method allows observing the generation and destruction of individual ions simultaneously for different types of ions. Besides high-resolution spectroscopy of dark ions, another application is the detection of chemical reactions in real time with single-particle sensitivity. This is demonstrated in this work.
Spatiotemporal Dynamics of Calcium-Driven Cardiac Alternans
Creators: name: Skardal, Per Sebastian
name: Karma, Alain
name: Restrepo, Juan G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Tissues and Organs (q-bio.TO)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: We investigate the dynamics of spatially discordant alternans (SDA) driven by an instability of intracellular calcium cycling using both amplitude equations [P. S. Skardal, A. Karma, and J. G. Restrepo, Phys. Rev. Lett. 108, 108103 (2012)] and ionic model simulations. We find that, close to the alternans bifurcation, SDA is manifested as a smooth wavy modulation of the amplitudes of both repolarization and calcium transient (CaT) alternans, similarly to the well-studied case of voltage-driven alternans. In contrast, further away from the bifurcation, the amplitude of CaT alternans jumps discontinuously at the nodes separating out-of-phase regions, while the amplitude of repolarization alternans remains smooth. We show that node motion of discontinuous SDA patterns is strongly hysteretic even in homogeneous tissue due to the novel phenomenon of "unidirectional pinning": node movement can only be induced towards, but not away from, the pacing site in response to a change of pacing rate or physiological parameter. In addition, we show that the wavelength of discontinuous SDA patterns scales linearly with the conduction velocity restitution length scale, in contrast to the wavelength of smooth patterns that scales sub-linearly with this length scale. Those results are also shown to be robust against cell-to-cell fluctuations owing to the property that unidirectional node motion collapses multiple jumps accumulating in nodal regions into a single jump. Amplitude equation predictions are in good overall agreement with ionic model simulations. Finally, we briefly discuss physiological implications of our findings. In particular, we suggest that due to the tendency of conduction blocks to form near nodes, the presence of unidirectional pinning makes calcium-driven alternans potentially more arrhythmogenic than voltage-driven alternans.
description: 26 pages, 26 figures
THE PHILOSOPHY OF GEORGES BATAILLE: EROTICISM AS AN OBJECT OF STUDY
Creators: name: GUERRA, Avaetê de Lunetta e Rodrigues
name: NOGUEIRA, Elce Nunes Nogueira da Costa e
name: COSTA, Michel da
Publisher: name: Editora IOLE
Year: 2023
Subjects: subject: Bataille
subject: Erocticism
subject: Philosophy
subject: FOS: Philosophy, ethics and religion

description: Bataille argued that eroticism was a primordial and essential force in human existence. In this research, we will explore how Bataille challenges social norms and invites us to rethink human nature through the lens of sexual desire. The methodology used was bibliographical research, carried out in a systematic and organized way, following some basic steps. The first stage consisted of defining the study topic and delimiting the research object, to direct the search more efficiently. After defining the theme, a bibliographic search was carried out in different sources of information, such as books, scientific articles, theses, dissertations, technical reports, among others. It is concluded that Georges Bataille's philosophy brought a deep and complex approach to eroticism as an object of study. His vision of eroticism as a primordial and transgressive force, capable of providing pleasure and transcendence, brought new perspectives to the field of philosophy. Furthermore, his emphasis on ethical responsibility and the importance of human connection makes his approach even more relevant today.
HARMONI at ELT: A Zernike wavefront sensor for the high-contrast module -- Testbed results with realistic observation conditions
Creators: name: Hours, Adrien
name: Carlotti, Alexis
name: Mouillet, David
name: Delboulbé, Alain
name: Guieu, Sylvain
name: Jocou, Laurent
name: Moulin, Thibaut
name: Pancher, Fabrice
name: Rabou, Patrick
name: Choquet, Elodie
name: Dohlen, Kjetil
name: Sauvage, Jean-François
name: N'Diaye, Mamadou
Publisher: name: arXiv
Year: 2022
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: ELT-HARMONI is the first light visible and near-IR integral field spectrograph (IFS) for the ELT. It covers a large spectral range from 450nm to 2450nm with resolving powers from 3500 to 18000 and spatial sampling from 60mas to 4mas. It can operate in two Adaptive Optics modes - SCAO (including a High Contrast capability) and LTAO - or with NOAO. The project is preparing for Final Design Reviews. The High Contrast Module (HCM) will allow HARMONI to perform direct imaging and spectral analysis of exoplanets up to one million times fainter than their host star. Quasi-static aberrations are a limiting factor and must be calibrated as close as possible to the focal plane masks to reach the specified contrast. A Zernike sensor for Extremely Low-level Differential Aberrations (ZELDA) will be used in real-time and closed-loop operation at 0.1Hz frequency for this purpose. Unlike a Shack-Hartmann, the ZELDA wavefront sensor is sensitive to Island and low-wind effects. The ZELDA sensor has already been tested on VLT-SPHERE and will be used in other instruments. Our objective is to adapt this sensor to the specific case of HARMONI. A ZELDA prototype is being both simulated and experimentally tested at IPAG. Its nanometric precision has first been checked in 2020 in the case of slowly evolving, small wavefront errors, and without dispersion nor turbulence residuals. On this experimental basis, we address the performance of the sensor under realistic operational conditions including residuals, mis-centring, dispersion, sensitivity, etc. Atmospheric refraction residuals were introduced by the use of a prism, and turbulence was introduced by a spatial light modulator which is also used to minimise wavefront residuals in a closed loop in the observing conditions expected with HARMONI.
description: 14 pages, 13 figures, SPIE Astronomical Telescopes + Instrumentation (AS22)
Open Science & Reproducibility: The Turing Way Workshop
Creators: name: Garcia, Roman
name: , Steele
Publisher: name: Zenodo
Year: 2023
Subjects: the turing way
reproducibility

description: Presented at Newcastle University's conference from 6-7 March 2023: "Data Science Perspectives - Multidisciplinary PhD Conference". Originally given as a workshop September 2022 with Malvika Sharan: https://zenodo.org/record/7050678#.ZAdeiOzP2qU Was accompanied by interactive HackMD: https://hackmd.io/@turingway/02-2023-newcastle
title: Analysis of Myogenic and Candidate Disease Biomarkers in FSHD Muscle Cells
Creators: name: Chen, Jennifer C. J.
name: Jones, Takako I.
name: King, Oliver D.
name: Hanger, Kendal
name: Rahimov, Fedik
name: Homma, Sachiko
name: Beermann, Mary Lou
name: Bibat, Genila M.
name: Miller, Jeffrey B.
name: Kunkel, Louise M.
name: Wagner, Kathryn R.
name: Jones, Peter L.
name: Emerson, Jr., Charles P.
Publisher: name: eScholarship@UMMS
Year: 2013

description: The UMMS Wellstone Program is a foundation and NIH-funded cooperative research center focusing on identifying biomarkers for facioscapulohumeral muscular dystrophy (FSHD) to gain insight into the molecular pathology of the disease and to develop potential therapies. FSHD is characterized by progressive wasting of skeletal muscles, with weakness often initiating in facial muscles and muscles supporting the scapula and upper arms. While the genetics associated with FSHD are complex, the major form of the disease, FSHD1, is linked to contraction of the D4Z4 repeat region located at chromosome 4q. Recently, a transcript encoded at the distal end of the repeat region, Dux4-fl, normally expressed in embryonic stem cells and germ cells, was also detected in differentiated muscle cells and biopsies from FSHD subjects, giving rise to the hypothesis that DUX4-FL function contributes to muscle weakness.

We established a repository of high quality, well-characterized primary and immortalized muscle cell strains from FSHD and control subjects in affected families to provide biomaterials for cell and molecular studies to the FSHD research community. qPCR and immunostaining analyses demonstrate similar growth and differentiation characteristics in cells from FSHD and control subjects within families. We detected Dux4-fl transcript and protein in FSHD cells as recently described; interestingly, we also detected Dux4-fl in muscle cells from a subset of control individuals, suggesting that any Dux4-fl-mediated myopathy would require additional modifying elements. Microarray analysis of FSHD and control muscle cells demonstrated that several genes were upregulated in FSHD cells, including genes that were concurrently identified as downstream targets of Dux4-fl and as candidate FSHD disease genes. Future studies will further characterize the RNA and protein expression of candidate disease genes in cells from FSHD and control subjects, including nonmanifesting subjects with the D4Z4 lesion but no muscle weakness, and utilizing whole transcriptome sequencing (RNAseq) to identify additional candidates.
title: Epigenetic variability is a modifier of facioscapulohumeral muscular dystrophy
Creators: name: Jones, Takako I.
name: Sun, Chia-Yun
name: Debarnot, Celine
name: Himeda, Charis
name: Emerson, Jr., Charles P.
name: Jones, Peter L.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Facioscapulohumeral muscular dystrophy (FSHD), the most prevalent myopathy afflicting both children and adults, is strongly associated with epigenetic changes of the 4q35-localized macrosatellite D4Z4 repeat. Recent studies propose that FSHD pathology is caused by the misexpression and missplicing of the DUX4 (double homeobox 4) gene, encoded within the repeat array, resulting in production of a pathogenic protein, DUX4-FL. We have analyzed DUX4 mRNA and protein expression in a large collection of myogenic cells and muscle biopsies derived from muscles of FSHD1 affected subjects and their unaffected first-degree relatives. We confirmed that stable DUX4-fl mRNA and protein were expressed in myogenic cells and muscle tissues derived from FSHD affected subjects, including several genetically diagnosed adults yet to show clinical manifestations of the disease; however, there was great individual and familial variation in the levels of DUX4-FL. In addition, we found DUX4-fl mRNA and protein expression in muscle biopsies and myogenic cells from genetically unaffected relatives of the FSHD subjects, although at a significantly lower frequency. These results establish that DUX4-fl expression per se is not sufficient for FSHD muscle pathology. To investigate if subtle differences in the epigenetic status of the 4q35 region could account for the wide variation in DUX4-fl expression among FSHD1 subjects and potentially the spurious expression in certain unaffected controls, family cohorts of myogenic cells from FSHD1 subjects were tested for their sensitivity to small molecules that can alter the chromatin state. We find that myogenic cells from FSHD1 subjects are overall epigenetically poised to express DUX4 compared with unaffected subjects; however, FSHD1 subjects show individual differences in their capacity to express DUX4-fl in response to DNA demethylation and blocking histone deacetylation. Therefor, individual differences in the epigenetic status likely impacts progression of disease pathology, variability in age of onset, disease severity, and asymmetry of affected muscles.
Identifying cognitive impairment with story recall (Wilson et al., 2024)
Creators: name: Wilson, Sarah C.
name: Teghipco, Alex
name: Sayers, Sara
name: Newman-Norlund, Roger
name: Newman-Norlund, Sarah
name: Fridriksson, Julius
Publisher: name: ASHA journals
Year: 2024
Subjects: classificationCode: 520405
subject: Psycholinguistics (incl. speech production and comprehension)
classificationCode: 320905
subject: Neurology and neuromuscular diseases
classificationCode: 520401
subject: Cognition

description: Purpose: The current study used behavioral measures of discourse complexity and story recall accuracy in an expository discourse task to distinguish older adults testing within range of cognitive impairment according to a standardized cognitive screening tool in a sample of self-reported healthy older adults.Method: Seventy-three older adults who self-identified as healthy completed an expository discourse task and neuropsychological screener. Discourse data were used to classify participants testing within range of cognitive impairment using multiple machine learning algorithms and stability analysis for identifying reliably predictive features in an effort to maximize prediction accuracy. We hypothesized that a higher rate of pronoun use and lower scores on story recall would best classify older adults testing within range of cognitive impairment.Results: The highest classification accuracy exploited a single variable in a remarkably intuitive way: using 66% story recall as a cutoff for cognitive impairment. Forcing this decision tree model to use more features or increasing its complexity did not improve accuracy. Permutation testing confirmed that the 77% accuracy and 0.18 Brier skill score achieved by the model were statistically significant (p < .00001).Conclusions: These results suggest that expository discourse tasks that place demands on executive functions, such as working memory, can be used to identify aging adults who test within range of cognitive impairment. Accurate representation of story elements in working memory is critical for coherent discourse. Our simple yet highly accurate predictive model of expository discourse provides a promising assessment for easy identification of cognitive impairment in older adults.Supplemental Material S1. Individual participants’ demographics (including age, sex, race, education, ethnicity), MoCA total scores, and MoCA Memory Index Scores.Supplemental Material S2. Discourse measures and descriptions from the CLAN software (including duration, MLU, type-token ratio, etc.).Supplemental Material S3. Full Pearson’s correlation table for the CLAN discourse measures, story recall elements recalled, percent story recall accuracy, and MoCA total scores.Wilson, S. C., Teghipco, A., Sayers, S., Newman-Norlund, R., Newman-Norlund, S., & Fridriksson, J. (2024). Story recall in peer conflict resolution discourse task to identify older adults testing within range of cognitive impairment. American Journal of Speech-Language Pathology, 33(5), 2582–2598. https://doi.org/10.1044/2024_AJSLP-24-00005
title: Dux4 Target Gene Expression in Mouse Muscle Transplanted with Muscle Cells from FSHD Patients
Creators: name: Windelborn, James A.
name: Emerson, Jr., Charles P.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Facioscapulohumeral Muscular Dystrophy (FSHD) is one of the most prevalent forms of muscular dystrophy. However, because of the unique nature of the genetic abnormality underlying the disease, there is currently no widely available laboratory model. In order to gain insights into FSHD molecular pathology, we developed a xenograft model by transplanting myogenic cells from patients with FSHD (4qA contractions) as well as from their unaffected relatives into the tibialis anterior muscles of immunodeficient mice. Our findings show that muscle xenografts derived from FSHD myogenic cells express Dux4 target genes, recapitulating the expression of these disease biomarkers in muscle biopsies of FSHD patients. FSHD muscle xenografts provide an animal model for investigations of the molecular pathogenesis of FSHD muscles and for drug development.
Application of Novel Interplanetary Scintillation Visualisations using LOFAR: A Case Study of Merged CMEs from September 2017
Creators: name: Fallows, R. A.
name: Iwai, K.
name: Jackson, B. V.
name: Zhang, P.
name: Bisi, M. M.
name: Zucca, P.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: Observations of interplanetary scintillation (IPS - the scintillation of compact radio sources due to density variations in the solar wind) enable the velocity of the solar wind to be determined, and its bulk density to be estimated, throughout the inner heliosphere. A series of observations using the Low Frequency Array (LOFAR - a radio telescope centred on the Netherlands with stations across Europe) were undertaken using this technique to observe the passage of an ultra-fast CME which launched from the Sun following the X-class flare of 10 September 2017. LOFAR observed the strong radio source 3C147 at an elongation of 82 degrees from the Sun over a period of more than 30 hours and observed a strong increase in speed to 900km/s followed two hours later by a strong increase in the level of scintillation, interpreted as a strong increase in density. Both speed and density remained enhanced for a period of more than seven hours, to beyond the period of observation. Further analysis of these data demonstrates a view of magnetic-field rotation due to the passage of the CME, using advanced IPS techniques only available to a unique instrument such as LOFAR.
description: Accepted for publication in Advances in Space Research, 17 pages, 18 figures
Decay constants of the charmed vector mesons $D^*$ and $D^*_s$ from QCD sum rules
Creators: name: Lucha, Wolfgang
name: Melikhov, Dmitri
name: Simula, Silvano
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present a sum-rule calculation of the decay constants of the charmed vector mesons $D^*$ and $D^*_s$ from the two-point correlator of vector currents. First, we show that the perturbative expansion in terms of the pole mass exhibits no sign of convergence whereas the reorganization of this expansion in terms of the $\overline{\rm MS}$ mass leads to a distinct hierarchy. Second, making use of the operator product expansion in terms of the $\overline{\rm MS}$ mass, we determine the decay constants of the $D^*$ and $D^*_s$ mesons with an emphasis on the uncertainties in these theoretically predicted quantities related both to the input QCD parameters and to the limited accuracy of the method of sum rules. Our results are $f_{D^*}=(252.2 \pm 22.3_{\rm OPE}\pm 4_{\rm syst})\; {\rm MeV}$ and $f_{D_s^*}=(305.5 \pm 26.8_{\rm OPE}\pm 5_{\rm syst})\; {\rm MeV}$. For the ratios of the vector-to-pseudoscalar decay constants we report $f_{D^*}/f_D= 1.221\pm 0.080_{\rm OPE}\pm 0.008_{\rm syst}$ and $f_{D^*_s}/f_{D_s}= 1.241\pm 0.057_{\rm OPE}\pm 0.007_{\rm syst}$.
description: 9 pages, published version
Internet Service Providers' and Individuals' Attitudes, Barriers, and Incentives to Secure IoT
Creators: name: Sombatruang, Nissy
name: Caulfield, Tristan
name: Becker, Ingolf
name: Fujita, Akira
name: Kasama, Takahiro
name: Nakao, Koji
name: Inoue, Daisuke
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computers and Society (cs.CY)
subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Internet Service Providers (ISPs) and individual users of Internet of Things (IoT) play a vital role in securing IoT. However, encouraging them to do so is hard. Our study investigates ISPs' and individuals' attitudes towards the security of IoT, the obstacles they face, and their incentives to keep IoT secure, drawing evidence from Japan. Due to the complex interactions of the stakeholders, we follow an iterative methodology where we present issues and potential solutions to our stakeholders in turn. For ISPs, we survey 27 ISPs in Japan, followed by a workshop with representatives from government and 5 ISPs. Based on the findings from this, we conduct semi-structured interviews with 20 participants followed by a more quantitative survey with 328 participants. We review these results in a second workshop with representatives from government and 7 ISPs. The appreciation of challenges by each party has lead to findings that are supported by all stakeholders. Securing IoT devices is neither users' nor ISPs' priority. Individuals are keen on more interventions both from the government as part of regulation and from ISPs in terms of filtering malicious traffic. Participants are willing to pay for enhanced monitoring and filtering. While ISPs do want to help users, there appears to be a lack of effective technology to aid them. ISPs would like to see more public recognition for their efforts, but internally they struggle with executive buy-in and effective means to communicate with their customers. The majority of barriers and incentives are external to ISPs and individuals, demonstrating the complexity of keeping IoT secure and emphasizing the need for relevant stakeholders in the IoT ecosystem to work in tandem.
description: This is an extended version of our USENIX Security '23 paper
Tests of the CMB temperature-redshift relation, CMB spectral distortions and why adiabatic photon production is hard
Creators: name: Chluba, Jens
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In the expanding Universe, the average temperature of the cosmic microwave background (CMB) is expected to depend like TCMB~(1+z) on redshift z. Adiabatic photon production (or destruction) or deviations from isotropy and homogeneity could modify this scaling and several observational tests have been carried out in response. Here, we explain why `adiabatic' conditions are extremely difficult to establish in the redshift range targeted by these tests. Thus, instead of leading to a simple rescaling of the CMB temperature, a spectral distortion should be produced, which can be constrained using COBE/FIRAS. For scenarios with late photon production, tests of the temperature-redshift relation (TRR) should therefore be reinterpreted as weak spectral distortion limits, directly probing the energy dependence of the photon production process. For inhomogeneous cosmologies, an average y-type distortion is produced, but this type of distortion can be created in several other ways. Here, we briefly discuss possible effects that may help disentangling different contributions to the distortion signal, finding this to be very challenging. We furthermore argue that tests of the TRR, using the SZ effect have limited applicability and that for non-gravitational changes to the TRR the CMB anisotropy spectrum should exhibit an additional y-type dependence.
description: 8 pages, accepted by MNRAS
title: Library Web Development: A Decade in Review
Creators: name: Piorun, Mary E.
name: Vander Hart, Robert
Publisher: name: eScholarship@UMMS
Year: 2004

description: Objective: This poster examines how academic medical libraries have presented their web sites over the past decade:

1) How have advances in web technologies influenced the “look and feel” of the web site?

2) What other developments contributed to the evolution of medical library web sites?

3) How has the librarian's role in web development changed in the last ten years?

Method: Reviewing the history of the web and developments in new technology, we will note significant turning points in the design of our own library web site and that of other institutions of a similar size and mission. Using data and images from the Way Back Machine at www.archive.org we will plot how changes in technology effect: what information is presented, page layout and usability. We will examine how changes in librarianship and the “information explosion” have helped the medical library web site progress.

Results: From examining our own web site history we have determined that we were slow to implement new design technologies. Many of the technologies that were initially incorporated into the web page design improved on graphical elements at first. Improvements on layout, searching and form design soon followed. In 2000 a new underlining database structure (Cold Fusion) was added to the web site that allowed staff to better manage the large number of e-resources the Library provided. Once a full time position dedicated to web management was created our web site was able to focus on layout and usability.

Conclusion: From looking at other web sites of similar size we have determined that many Libraries web sites progressed first as an “online directory” providing basic information, to a page that started to offer services such as request forms and links to an OPAC and/or Medline, to finally a dynamic page with electronic books, journals and databases. Many institutions offer customized pages for individual users. Additional research is recommended.