cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Introducing a Novel Simulation Tool for Interconnected Differential Expression Signatures and Its Application to Benchmarking
Creators: name: Gonzalez Gomez, Catalina
name: Rosa-Calatrava, Manuel
name: Fouret, Julien
Publisher: name: Zenodo
Year: 2024
Subjects: connectivity
drug repurposing
simulation
Transcriptomic signature
antiviral research

description: Pharmaceutical research has long used differential gene expression signatures to study external stimuli like pathogenic determinants or small molecule treatments. These signatures measure expression values for multiple tags and are often compared using the concept of connectivity. Despite the scientific community's efforts to produce unbiased datasets for evaluating connectivity-based methods for drug identification and repurposing, the limits of benchmarking data hinder their effectiveness.

To address this, we developed a simulation method to generate pairs of connected differential expression signatures, that is based on a three layers decomposition and relies on a statistical framework with different levels of parametrization. We benchmarked seven connectivity scores methods from the literature using our simulated signatures. We then evaluated the capacity of each method to retrieve the most connected signatures for a specific query, using the area under the precision-recall curves (AUPRC). Moreover, we introduced a novel application perspective by training a Siamese Neural Network with our simulated data to predict the connectivity score.

Overall, our method is a significant advance in pharmaceutical research, providing a reliable way to simulate connected differential expression signatures. It will help develop and evaluate algorithms for comparing signatures to find the most connected or reversed, leading to more effective drug repurposing. An open-source version of the package will be released at the end of 2023.
The French-Canadian WheelCon for manual wheelchair users: paediatric adaptation and preliminary evaluation of its measurement properties
Creators: name: Dib, Tatiana
name: Burrola-Mendez, Yohali
name: Brûlé-Ouimette, Laurence
name: Fung, Karen H. M.
name: Lecavalier, Mélissa
name: Rushton, Paula W.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Space Science
Medicine
Biotechnology
Biological Sciences not elsewhere classified
Science Policy

description: To adapt the Wheelchair Use Confidence Scale for Manual Wheelchair Users, French-Canadian Version (WheelCon-M-F) into a paediatric version (WheelCon-M-F-P) and to evaluate its validity. A three-phase process was conducted: (1) item adaptation using secondary analysis of focus group data; (2) item refinement using a think-aloud process; and (3) preliminary validation of the WheelCon-M-F-P (i.e. internal consistency, test-retest reliability, standard error of measurement, smallest real difference, ceiling and floor effects, limits of agreement, and relations with other variables). Phase 1: The sample consisted of occupational therapists (n = 9), paediatric manual wheelchair users (PMWUs) (n = 12), and parents of PMWUs (n = 2). Of the 65 WheelCon-M-F items, 35 were removed, 25 modified and 6 were added for the WheelCon-M-F-P. Phase 2: 4 PMWUs helped refine 14 and remove 3 items. Phase 3: 22 PMWUs participated. Cronbach’s alpha, test-retest reliability, standard error of measurement, and smallest real difference were 0.846, 0.818, 3.05, and 8.45 respectively. No ceiling or floor effects were demonstrated. Pearson correlations between the WheelCon-M-F-P and the Wheelchair Skills Test Questionnaire (capacity, confidence, and performance), and the Child Occupational Self-Assessment were 0.688, 0.711, 0.584, and 0.687 respectively. This study provides preliminary evidence of a valid and reliable WheelCon-M-F-P.IMPLICATIONS FOR REHABILITATIONThe Wheelchair Use Confidence Scale for Manual Wheelchair Users, French-Canadian Version (WheelCon-M-F-P) is an outcome measure that can be used clinically with pediatric manual wheelchair users.The WheelCon-M-F-P can help identify modifiable factors associated with wheelchair confidence.Identifying modifiable factors associated with wheelchair confidence can help guide clinicians in establishing a targeted intervention for their pediatric clients.Establishing a targeted intervention can help improve self-efficacy for wheelchair use and social participation of pediatric wheelchair users. The Wheelchair Use Confidence Scale for Manual Wheelchair Users, French-Canadian Version (WheelCon-M-F-P) is an outcome measure that can be used clinically with pediatric manual wheelchair users. The WheelCon-M-F-P can help identify modifiable factors associated with wheelchair confidence. Identifying modifiable factors associated with wheelchair confidence can help guide clinicians in establishing a targeted intervention for their pediatric clients. Establishing a targeted intervention can help improve self-efficacy for wheelchair use and social participation of pediatric wheelchair users.
The stellar populations of local dwarfs
Creators: name: Held, Enrico V.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Recent progress in our knowledge of stellar populations in local dwarf spheroidal galaxies is briefly discussed. A few results are summarized including wide field observations of stellar populations and their spatial variations, studies of AGB and variable stars, extension to near-infrared wavelengths, and the interpretation effort based on synthetic color-magnitude diagrams and chemical evolution models.
description: 6 pages, 1 figure, invited talk to appear in the proceedings of the IAUC198 Coll. "Near-Field Cosmology with Dwarf Elliptical Galaxies", H. Jerjen & B. Binggeli (eds.)
Plant responses to auxin signals: an operating principle for dynamical sensitivity yet high resilience
Creators: name: Grigolon, Silvia
name: Bravi, Barbara
name: Martin, Olivier C.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Biological sciences

description: Plants depend on the signaling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signaling network involves a negative feedback at the level of the Aux/IAA proteins which mediate the influence of auxin (the signal) on the ARF transcription factors (the drivers of the response). To probe the role of this feedback, we consider alternative in silico signaling networks implementing different operating principles. By a comparative analysis, we find that the presence of a negative regulatory feedback loop allows the system to have a far larger sensitivity in its dynamical response to auxin. At the same time, this sensitivity does not prevent the system from being highly resilient. Given this insight, we reconsider previously published models and build a new quantitative and calibrated biomolecular model of auxin signaling.
description: 10 pages of Main Text, 5 Main Figures and Supplementary Material
Estimation of linear energy transfer distribution for broad-beam carbon-ion radiotherapy at the National Institute of Radiological Sciences, Japan
Creators: name: Kanematsu, Nobuyuki
name: Matsufuji, Naruhiro
name: Inaniwa, Taku
Publisher: name: arXiv
Year: 2017
Subjects: subject: Medical Physics (physics.med-ph)
subject: FOS: Physical sciences

description: Carbon-ion radiotherapy (CIRT) is generally evaluated with the dose weighted by relative biological effectiveness (RBE), while the radiation quality varying in the body of each patient is ignored for lack of such distribution. In this study, we attempted to develop a method to estimate linear energy transfer (LET) for a treatment planning system that only handled physical and RBE-weighted doses. The LET taken from a database of clinical broad beams was related to the RBE per energy with two polyline fitting functions for spread-out Bragg peak (SOBP) and for entrance depths, which would be selected by RBE threshold per energy per modulation. The LET estimation was consistent with the original calculation typically within a few keV/μm except for the overkill at the distal end of SOBP. The CIRT treatments can thus be related to the knowledge obtained in radiobiology experiments that used LET to represent radiation quality.
description: 6 pages, 2 tables, 5 figures
Additional file 6: of A phylogenetic analysis of the Primnoidae (Anthozoa: Octocorallia: Calcaxonia) with analyses of character evolution and a key to the genera and subgenera
Creators: name: Cairns, Stephen
name: Wirshing, Herman
Publisher: name: figshare
Year: 2018
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Figure S1a-i. Phylogenies with mapped ancestral state reconstructions using maximum parsimony and select maximum likelihoods (see text) for each morphological character. (PDF 1095Â kb)
Polarization of Lambda and Anti-Lambda in 920 GeV Fixed-Target Proton-Nucleus Collisions
Creators: name: B Collaboration
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: A measurement of the polarization of Lambda and Anti-Lambda baryons produced in pC and pW collisions at sqrt(s)=41.6 GeV has been performed with the HERA-B spectrometer. The measurements cover the kinematic range of 0.6 GeV/c < p_T<1.2 GeV/c in transverse momentum and -0.15
description: 11 pages, 3 figures
Tasks performed by parents to enable telepractice for children with communication disorders: an interview study with clinicians and parents
Creators: name: Pozniak, Kinga
name: Rosenbaum, Peter
name: Kwok, Elaine Yuen Ling
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: Current service models in childhood rehabilitation promote the active participation of parents/caregivers in their children’s therapies. The existing literature provides a limited understanding of the tasks and responsibilities parents undertake in their children’s therapies, especially over telepractice. This study describes the tasks undertaken by parents in their children’s speech therapy delivered virtually during the COVID-19 pandemic. A qualitative descriptive study was conducted with parents and speech-language pathologists, using open-ended interviews. Interviews were analyzed using a combination qualitative content analysis and thematic analysis. Parents performed many tasks to enable telepractice. These tasks happened before (e.g., setting up both physical and virtual space for therapy), during (e.g., managing child’s behavior), and after the virtual therapy session (e.g., carrying out home practice). While parents were willing to perform these tasks in order to help their children, some expressed the toll that it can take on them. Compared to what is known from in-person visits, some of these tasks were novel and unique to telepractice. We recommend that clinicians and parents collaboratively decide on tasks and responsibilities to avoid burdening parents, and that they weigh the costs associated with performing these tasks against the benefits of teletherapy.IMPLICATIONS FOR REHABILITATIONParents perform many tasks to support their children’s therapies, both during and outside of therapy sessionsTherapies delivered virtually require parents to assume additional tasks to support their childrenFor services to be Family-Centered, tasks and responsibilities need to be decided collaboratively between parents and clinicians Parents perform many tasks to support their children’s therapies, both during and outside of therapy sessions Therapies delivered virtually require parents to assume additional tasks to support their children For services to be Family-Centered, tasks and responsibilities need to be decided collaboratively between parents and clinicians
Linear Polarimetry with $γ\rightarrow e^+e^-$ conversions
Creators: name: Bernard, Denis
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: $γ$ rays are emitted by cosmic sources by non-thermal processes that yield either non-polarized photons, such as those from $π^0$ decay in hadronic interactions, or linearly polarized photons from synchrotron radiation and the inverse-Compton up-shifting of these on high-energy charged particles. Polarimetry in the MeV energy range would provide a powerful tool to discriminate among "leptonic" and "hadronic" emission models of blazars, for example, but no polarimeter sensitive above 1\,MeV has ever been flown into space. Low-$Z$ converter telescopes such as silicon detectors are developed to improve the angular resolution and the point-like sensitivity below 100 MeV. We have shown that in the case of a homogeneous, low-density active target such as a gas time-projection chamber (TPC), the single-track angular resolution is even better and is so good that in addition the linear polarimetry of the incoming radiation can be performed. We actually characterized the performance of a prototype of such a telescope on beam. Track momentum measurement in the tracker would enable calorimeter-free, large effective area telescopes on low-mass space missions. An optimal unbiased momentum estimate can be obtained, in the tracker alone, based on the momentum dependence of multiple scattering, from a Bayesian analysis of the innovations of Kalman filters applied to the tracks.
description: Presented at the Polarised Emission from Astrophysical Jets Conference, June 12-16, 2017, Ierapetra, Greece
Decoherence-free subspaces and subsystems for a collectively depolarizing bosonic channel
Creators: name: Ball, Jonathan L.
name: Banaszek, Konrad
Publisher: name: arXiv
Year: 2005
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We discuss the structure of decoherence-free subsystems for a bosonic channel affected by collective depolarization. A single use of the channel is defined as a transmission of a pair of bosonic modes. Collective depolarization consists in a random linear U(2) transformation of the respective mode operators, which is assumed to be identical for $N$ consecutive uses of the channel. We derive a recursion formula that characterizes the dimensionality of available decoherence-free subsystems in such a setting.
description: 13 pages, osid.sty
Perfect subspaces of quadratic laminations
Creators: name: Blokh, Alexander
name: Oversteegen, Lex
name: Timorin, Vladlen
Publisher: name: arXiv
Year: 2017
Subjects: subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 37F20 (Primary), 37F10, 37F50 (Secondary)

description: The combinatorial Mandelbrot set is a continuum in the plane, whose boundary can be defined, up to a homeomorphism, as the quotient space of the unit circle by an explicit equivalence relation. This equivalence relation was described by Douady and, in different terms, by Thurston. Thurston used quadratic invariant laminations as a major tool. As has been previously shown by the authors, the combinatorial Mandelbrot set can be interpreted as a quotient of the space of all limit quadratic invariant laminations. The topology in the space of laminations is defined by the Hausdorff distance. In this paper, we describe two similar quotients. In the first case, the identifications are the same but the space is smaller than that taken for the Mandelbrot set. The result (the quotient space) is obtained from the Mandelbrot set by "unpinching" the transitions between adjacent hyperbolic components. In the second case, we do not identify non-renormalizable laminations while identifying renormalizable laminations according to which hyperbolic lamination they can be "unrenormalised" to.
description: 29 pages, 4 figures
Psychometrically validated questionnaires to measure the effects and benefits/barriers to physical exercise in hemodialysis patients: a systematic review
Creators: name: Martins, Marcieli A.
name: Ghisi, Gabriela L. M.
name: da Silva, Kenia B.
name: Leopoldino, Gabriela
name: Pakosh, Maureen
name: Bundchen, Daiana C.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: To provide a critical assessment, summarize, and synthesize the evidence from studies using psychometrically validated questionnaires to assess the effects and benefits/barriers of physical exercise in hemodialysis patients. The search was performed on six electronic databases. It was conducted following the PRISMA statement and the PICO framework. The methodological quality was assessed using the MMAT. Were used the quality criteria for psychometric properties developed by Terwee et al. Overall, 70 studies were included, and 39 questionnaires identified, evaluating 13 outcomes. The quality of the psychometric properties of the questionnaires was not always described; only 13 presented positive ratings on > =6/9 properties. The most assessed measure was criterion validity, and the least assessed criteria was responsiveness. The most outcome measured by these questionnaires was quality of life using SF-36, followed by psychological health using the BDI. The DPEBBS was the only instrument identified that assessed the benefits and barriers of exercise. Quality of life and depression were the most frequent outcomes. Other measures contemplating physical, mental, cognitive performance, and especially of the perceptions benefits and barriers to exercise should be further investigated. We have clearly identified the need for more studies evaluating psychometric measures that have not been tested satisfactorily or hardly been tested at all. Reliable instruments, valid and structurally adequate were identified to support clinicians and researchers in measuring important outcomes in hemodialysis patients.Quality of life and depression were the most frequent outcomes with good research instruments.A gap was identified related to instruments that assess physical, mental, cognitive performance, and perceptions of benefits and barriers to exercise in hemodialysis patients. Reliable instruments, valid and structurally adequate were identified to support clinicians and researchers in measuring important outcomes in hemodialysis patients. Quality of life and depression were the most frequent outcomes with good research instruments. A gap was identified related to instruments that assess physical, mental, cognitive performance, and perceptions of benefits and barriers to exercise in hemodialysis patients.
Two and a half years of GRB localizations with the INTEGRAL Burst Alert System
Creators: name: Mereghetti, S.
name: Gotz, D.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We review the results on Gamma-ray Bursts obtained during the first two and a half years of operations of the INTEGRAL Burst Alert System (IBAS). In many cases GRB coordinates have been distributed with an unprecedented combination of accuracy (3 arcmin) and speed (20-30 s). The resulting rapid follow-ups at other wavelengths, including sensitive XMM-Newton and Swift observations, have led to several interesting results.
description: A shorter version of this paper will be published in the Proceedings of the 4th Workshop "Gamma-Ray Bursts in the Afterglow Era", Roma, 2004 October 18-22, eds. L. Piro, L. Amati, S. Covino, and B. Gendre. Il Nuovo Cimento, in press
Unified approach to the entropy of an extremal rotating BTZ black hole: Thin shells and horizon limits
Creators: name: Lemos, José P. S.
name: Minamitsuji, Masato
name: Zaslavskii, Oleg B.
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Using a thin shell, the first law of thermodynamics, and a unified approach, we study the thermodymanics and find the entropy of a (2+1)-dimensional extremal rotating Bañados-Teitelbom-Zanelli (BTZ) black hole. The shell in (2+1) dimensions, i.e., a ring, is taken to be circularly symmetric and rotating, with the inner region being a ground state of the anti-de Sitter (AdS) spacetime and the outer region being the rotating BTZ spacetime. The extremal BTZ rotating black hole can be obtained in three different ways depending on the way the shell approaches its own gravitational or horizon radius. These ways are explicitly worked out. The resulting three cases give that the BTZ black hole entropy is either the Bekenstein-Hawking entropy, $S=\frac{A_+}{4G}$, or it is an arbitrary function of $A_+$, $S=S(A_+)$, where $A_+=2πr_+$ is the area, i.e., the perimeter, of the event horizon in (2+1) dimensions. We speculate that the entropy of an extremal black hole should obey $0\leq S(A_+)\leq\frac{A_+}{4G}$. We also show that the contributions from the various thermodynamic quantities, namely, the mass, the circular velocity, and the temperature, for the entropy in all three cases are distinct. This study complements the previous studies in thin shell thermodynamics and entropy for BTZ black holes. It also corroborates the results found for a (3+1)-dimensional extremal electrically charged Reissner-Nordström black hole.
description: 8 pages, 1 table, no figure
Making Large Transfers Fast for in-Memory Databases in Modern Networks
Creators: name: Kesavan, Aniraj
Publisher: name: University of Utah
Year: 2019
Subjects: Computer science

description: Efficient movement of massive amounts of data over high-speed networks at high throughput is essential for a modern-day in-memory storage system. In response to the growing needs of throughput and latency demands at scale, a new class of database systems was developed in recent years. The development of these systems was guided by increased access to high throughput, low latency network fabrics, and declining cost of Dynamic Random Access Memory (DRAM). These systems were designed with On-Line Transactional Processing (OLTP) workloads in mind, and, as a result, are optimized for fast dispatch and perform well under small request-response scenarios. However, massive server responses such as those for range queries and data migration for load balancing poses challenges for this design. This thesis analyzes the effects of large transfers on scale-out systems through the lens of a modern Network Interface Card (NIC). The present-day NIC offers new and exciting opportunities and challenges for large transfers, but using them efficiently requires smart data layout and concurrency control. We evaluated the impact of modern NICs in designing data layout by measuring transmit performance and full system impact by observing the effects of Direct Memory Access (DMA), Remote Direct Memory Access (RDMA), and caching improvements such as Intel® Data Direct I/O (DDIO). We discovered that use of techniques such as Zero Copy yield around 25% savings in CPU cycles and a 50% reduction in the memory bandwidth utilization on a server by using a client-assisted design with records that are not updated in place. We also set up experiments that underlined the bottlenecks in the current approach to data migration in RAMCloud and propose guidelines for a fast and efficient migration protocol for RAMCloud.
Partial wave analyses of J/psi to gamma pi^+ pi^- and gamma pi^0 pi^0
Creators: name: Ablikim, M.
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Results are presented on J/psi radiative decays to pi^+pi^- and pi^0pi^0 based on a sample of 58M J/psi events taken with the BESII detector. Partial wave analyses are carried out using the relativistic covariant tensor amplitude method in the 1.0 to 2.3 GeV/c^2 pipi mass range. There are conspicuous peaks due to the f_2(1270) and two 0^++ states in the 1.45 and 1.75 GeV/c^2 mass regions. The first 0^++ state has a mass of 1466\pm 6\pm 20 MeV/c^2, a width of 108^{+14}_{-11}\pm 25 MeV/c^2, and a branching fraction B(J/psi \to γf_0(1500) \toγπ^+π^-) = (0.67\pm0.02\pm0.30) \times 10^{-4}. Spin 0 is strongly preferred over spin 2. The second 0^++ state peaks at 1765^{+4}_{-3}\pm 13 MeV/c^2 with a width of 145\pm8\pm69 MeV/c^2. If this 0^++ is interpreted as coming from f_0(1710), the ratio of its branching fractions to pipi and K\bar K is 0.41^{+0.11}_{-0.17}.
description: 9 pages, 6 figures
title: ADCO, Grènetier de Cîteaux : comptes (1499-1503) (11 H 1173), f. 00615
Creators: name: de la Côte-d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CBMA/CG21/F.PETOT/2019
name: Petot, Frédéric
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: comptes
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge

description: Grènetier de Cîteaux : comptes (1499-1503), Archives départementales de la Côte-d'Or, (11 H 1173). Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Grènetier de Cîteaux : comptes (1499-1503), Archives départementales de la Côte-d'Or, (11 H 1173), f. 00615, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
Condition and capability of quantum state separation
Creators: name: Feng, Yuan
name: Duan, Runyao
name: Ji, Zhengfeng
Publisher: name: arXiv
Year: 2005
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The linearity of quantum operations puts many fundamental constraints on the information processing tasks we can achieve on a quantum system whose state is not exactly known, just as we observe in quantum cloning and quantum discrimination. In this paper we show that in probabilistic manner, linearity is in fact the only one that restricts the physically realizable tasks. To be specific, if a system is prepared in a state secretly chosen from a linearly independent pure state set, then any quantum state separation can be physically realized with a positive probability. Furthermore, we derive a lower bound on the average failure probability of any quantum state separation.
description: 6 pages, journal version
Macrophage-Stimulating Protein / Ron is a Novel Mediator of Osteoclast Activation Promoting Breast Cancer-Induced Bone Destruction andOsteoporosis
Creators: name: Andrade, Kelsi Lynn
Publisher: name: University of Utah
Year: 2019

description: The purpose of this dissertation is to define how the macrophage- stimulating protein (MSP) / Ron receptor tyrosine kinase pathway is involved in breast cancer-induced bone destruction and osteoclast activation. These studies employed in vitro osteoclast cultures and in vivo animal tumor models as systems to explore the ability of MSP to stimulate osteoclast activity and the ability of MSP-expressing tumor cells to cause bone destruction. I have also explored signaling downstream of Ron in osteoclasts and the requirement for Ron in bone destruction. I have utilized both genetic and pharmacological methods to target this pathway, thereby rigorously testing the ability of this pathway to activate osteoclasts. Included in the first part of this dissertation are two reviews. The first describes the MSP/Ron pathway, its function in cancer and inflammation, and the potential for targeting this pathway pharmacologically. The second review describes various mouse models used to study bone metastasis and bone destruction in vivo. The second part of this dissertation is focused on the ability of MSP/Ron to regulate osteoclast activation. Tumors overexpressing MSP spontaneously metastasize to bone and are osteolytic in an animal model of breast cancer. Here, I explore the function of MSP/Ron in aiding cancer cells to manipulate the iv bone microenvironment, allowing for tumor growth and bone destruction. This study reveals the MSP/Ron pathway as a novel mediator of osteoclast activity, independent of previously established pathways such as RANKL and TGFβ. Additionally, I have demonstrated that the loss or inhibition of the MSP/Ron pathway can protect from bone loss due to both breast cancer and osteoporosis. This evidence establishes the importance of this pathway in osteoclast regulation and the potential for use of Ron inhibitors in preventing bone loss.
Is the Bursting Radio-source GCRT J1745-3009 a Double Neutron Star Binary ?
Creators: name: Turolla, R.
name: Possenti, A.
name: Treves, A.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: GCRT J1745-3009 is a peculiar transient radio-source in the direction of the Galactic Center. It was observed to emit a series of ~ 1 Jy bursts at 0.33 GHz, with typical duration ~ 10 min and at apparently regular intervals of ~ 77 min. If the source is indeed at the distance of the Galactic Center as it seems likely, we show that its observational properties are compatible with those expected from a double neutron star binary, similar to the double pulsar system J0737-3039. In the picture we propose the (coherent) radio emission comes from the shock originating in the interaction of the wind of the more energetic pulsar with the magnetosphere of the companion. The observed modulation of the radio signal is the consequence of an eccentric orbit, along which the separation between the two stars varies. This cyclically drives the shock inside the light cylinder radius of the less energetic pulsar.
description: 5 pages, 3 figures, accepted for publication in The Astrophysical Journal Letters, comment on geodetic precession added
Low-Dimensional Frustrated Quantum Magnets: A Playground for Novel Phases
Creators: name: Jin, Wen
Publisher: name: University of Utah
Year: 2019
Subjects: Physics

description: Low-dimensionality, magnetic frustration, and quantum fluctuations are three ingredients that give rise to nontrivial magnetic orders or exotic ground states, such as spin nematics and spin liquids. In this dissertation I discuss some efforts to find novel interesting magnetic phases by cooking up all these ingredients together. First, a large fraction of this dissertation is devoted to the behavior of quantum spin chains in the presence of a uniform Dzyaloshinskii-Moriya (DM) interaction. This problem is analyzed by the bosonization technique. Spin chain is the building block of many materials, such as K2CuSO4(Cl/Br)2 which strongly motivates our study. DM interaction originates from spin-orbit coupling, and is widely present in real materials. Theories of these systems are derived and described for both individual chain and weakly coupled ones at zero and finite temperature and in the presence of external magnetic field. A special geometry of DM interactions-staggered between chains, but uniform within a given chain-leads to a peculiar type of frustration that effectively cancels the transverse interchain coupling and strongly reduces the ordering temperature. By taking advantage of this special geometry of DM interaction, one can construct a chiral spin liquid, which shares some basic features of fractional quantum Hall effect, such as gapped bulk and gapless chiral edge states, in arrays of spin chains. The second part of this dissertation describes the investigation of the interplay between frustration, quantum fluctuations, and magnetic field in the phase diagram of quantum antiferromagnets on triangular lattice. For triangular antiferromagnets with spacial and/or exchange anisotropy and near the fully polarized field, the competition between classical degeneracies and quantum fluctuations leads to multiple phase transitions and highly nontrivial intermediate phases. As for a toy model of a zigzag chain, a spin chain with competing nearest and next-nearest exchange interactions, I investigate quantum fluctuations and geometric frustrations establish a 1/3 magnetization plateau and a bond-nematic state, which has a nonzero vector chirality on every lattice bond and circulating spin currents in every elementary triangle.
Bottomonium and Drell-Yan production in p-A collisions at 450 GeV
Creators: name: NA50 Collaboration
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The NA50 Collaboration has measured heavy-quarkonium production in p-A collisions at 450 GeV incident energy (sqrt(s) = 29.1 GeV). We report here results on the production of the Upsilon states and of high-mass Drell-Yan muon pairs (m > 6 GeV). The cross-section at midrapidity and the A-dependence of the measured yields are determined and compared with the results of other fixed-target experiments and with the available theoretical estimates. Finally, we also address some issues concerning the transverse momentum distributions of the measured dimuons.
description: 18 pages, 9 figures, to be published in Phys. Lett. B
Long-term, Adverse Cardiovascular, Genitourinary, and Gastrointestinal Outcomes Among Endometrial Cancer Survivors in a Population-based Cohort Study
Creators: name: Soisson, Sean Patrick
Publisher: name: University of Utah
Year: 2019
Subjects: Public health

description: Endometrial cancer is the second most common cancer among female cancer survivors in the United States. A variety of long-term, adverse health effects have been observed among endometrial cancer survivors but the relationship between endometrial cancer diagnosis and treatment and these outcomes among survivors, years after diagnosis remains poorly understood. Because of the high survival rate and the increasing rate at which new cases are being diagnosed, examining the risk for long-term, adverse health effects among endometrial cancer survivors is essential. Cohorts of 2,648 endometrial cancer survivors diagnosed in Utah between 1997 and 2012 and 10,503 age-matched, cancer-free women from the general population were identified. Electronic medical record data including all International Classification of Diseases , 9th revision (ICD-9) diagnosis codes from Utah's two largest healthcare providers as well as statewide ambulatory surgery and inpatient records were used to capture all available cardiovascular, genitourinary, and gastrointestinal outcomes. Cox regression models were used to estimate risk for outcomes between survivors and individuals in the general population at 1-5 and >5-10 years after diagnosis. Cox regression models were also used to examine potential risk factors for various conditions among endometrial cancer survivors. Endometrial cancer survivors were at elevated risk for cardiovascular, genitourinary, and gastrointestinal disorders overall and for dozens of more specific outcomes within these broader categories compared to the general population. Between 1-5 years after diagnosis, endometrial cancer survivors treated with surgery in conjunction with chemotherapy and/or radiation were at elevated risk for heart, circulatory system, urinary system, genital organ, upper gastrointestinal, lower gastrointestinal, abdominal hernia, and liver disorders compared to those treated with surgery alone. Elevated risk for abdominal hernias and lower gastrointestinal disorders persisted between >5-10 years after diagnosis. These results present sufficient evidence that endometrial cancer survivors experience a greater burden of adverse cardiovascular, genitourinary, and gastrointestinal outcomes many years after diagnosis compared to the general population and that these outcomes may be related to cancer treatment. Many of these conditions contribute to increased morbidity and mortality and adversely affect quality of life. For these reasons, greater attention should be focused both on long-term surveillance and prevention of these conditions among endometrial cancer survivors.
Additional file 3: of Validating an algorithm to identify metastatic gastric cancer in the absence of routinely collected TNM staging data
Creators: name: Mahar, Alyson
name: Yunni Jeong
name: Zagorski, Brandon
name: Coburn, Natalie
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Table S3. Number of patients in each cell, by algorithm, The breakdown of the number of true positive, true negatives, false positives and false negatives for each algorithm. (DOCX 19Â kb)
Quasi-semisimple elements
Creators: name: Digne, François
name: Michel, Jean
Publisher: name: arXiv
Year: 2017
Subjects: subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 20G15

description: We study quasi-semisimple elements of disconnected reductive algebraic groups over an algebraically closed field. We describe their centralizers, define isolated and quasi-isolated quasi-semisimple elements and classify their conjugacy classes.
description: This version: some corrections; index added
Entanglement of bosonic modes in symmetric graphs
Creators: name: Asoudeh, M.
name: Karimipour, V.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The ground and thermal states of a quadratic hamiltonian representing the interaction of bosonic modes or particles are always Gaussian states. We investigate the entanglement properties of these states for the case where the interactions are represented by harmonic forces acting along the edges of symmetric graphs, i.e. 1, 2, and 3 dimensional rectangular lattices, mean field clusters and platonic solids. We determine the Entanglement of Formation (EoF) as a function of the interaction strength, calculate the maximum EoF in each case and compare these values with the bounds found in \cite{wolf} which are valid for any quadratic hamiltonian.
description: 15 pages, 8 figures, 3 tables, Latex, Accepted for publication in Physical Review A
Limits on Brane-World and Particle Dark Radiation from Big Bang Nucleosynthesis and the CMB
Creators: name: Sasankan, Nishanth
name: Gangopadhyay, Mayukh. R.
name: Mathews, Grant. J.
name: Kusakabe, Motohiko
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The term dark radiation is used both to describe a noninteracting neutrino species and as a correction to the Friedmann Equation in the simplest five-dimensional RS-II brane-world cosmology. In this paper we consider the constraints on both meanings of dark radiation based upon the newest results for light-element nuclear reaction rates, observed light-element abundances and the power spectrum of the Cosmic Microwave Background (CMB). Adding dark radiation during big bang nucleosynthesis (BBN) alters the Friedmann expansion rate causing the nuclear reactions to freeze out at a different temperature. This changes the final light element abundances at the end of BBN. Its influence on the CMB is to change the effective expansion rate at the surface of last scattering. We find that the BBN constraint reduces the allowed range for both types of dark radiation at 10 Mev to between $-12.1\%$ and $+6.2\%$ of the {\bf total} background energy density at 10 Mev. Combining this result with fits to the CMB power spectrum, produces different results for particle vs. brane-world dark radiation. In the brane-world, the range decreases to $-6.0\%$ to $+6.2\%$. Thus, we find, that the ratio of dark radiation to the background total relativistic mass energy density $ρ_{\rm DR}/ρ$ is consistent with zero although there remains a very slight preference for a positive (rather than negative) contribution.
description: arXiv admin note: substantial text overlap with arXiv:1607.06858
Dynamical quintessence fields Press-Schechter mass function: detectability and effect on dark haloes
Creators: name: Delliou, Morgan Le
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We present an investigations on the influence of dynamical quintessence field models on the formation of non-linear structures. In particular, we focus on the structure traced by the mass function. Our contribution builds on previous studies by considering two potentials not treated previousy and investigating the impact of the free parameters of two other models. Our approach emphasises the physical insight into the key role of the evolution of the equation of state. We use the variations in the spherical non-linear collapse caused by quintessence as a function of the model's potential in a Press Schechter scheme to obtain the differences in halo mass functions. The comparison is also done with the more usual scenario $Λ$CDM. We conclude the method should be promissing for discrimination using cluster mass determination and that the key role lies within the evolution of the equation of state.
description: submitted to JCAP, 22pp, corrected typo in eq.(3.3)
Observation of B0 Meson Decay to a1(1260)+- pi-+
Creators: name: The BABAR Collaboration
name: Aubert, B.
Publisher: name: arXiv
Year: 2006
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We present a measurement of the branching fraction of the decay B0 --> a1(1260)^{+-} pi^{-+} with a1(1260)^{+-} --> pi^{-+} pi^{+-} pi^{+-}. The data sample consists of 218 million B B-bar pairs collected at the Y(4S) resonance and recorded by the BaBar detector at the PEP-II asymmetric-energy e+e- collider at SLAC. The analysis is based on unbinned multivariate maximum likelihood fit. The measured branching fraction is: (16.6 +/- 1.9 +/- 1.5) 10^{-6}. The decay mode, observed for the first time, is seen with a significance of 9.2 sigma (systematic uncertainties included).
description: 7 pages, 2 postscript figures. Submitted to Phys. Rev. Lett
Management of Nutrients at Central Valley Water Reclamation Facility
Creators: name: Chahal, Simran
Publisher: name: University of Utah
Year: 2019
Subjects: Water Resource Management

description: Activated sludge process (ASP) is the most common method for wastewater treatment of domestic wastewater. In ASP, a consortium of microbes is used to consume different contaminants of concern using redox chemistry in which case, microbes gain energy through substrate partitioning. The main contaminants of concern are carbon, nitrogen (N) and phosphorus (P) in municipal wastewater with the latter two collectively known as nutrients. ASP is a robust process with proven performance metrics. Between nitrogen and phosphorus, phosphorus is the main nutrient of concern because it is often cited as a limiting nutrient for biota. Furthermore, as a useful fertilizer, phosphorus is essential for plants and as a result, there is a global demand for P. Unfortunately, P is limited in nature with only five countries in the world supplying the total P demands. Hence, the focus of wastewater treatment management is changing from the removal of P to the recovery of P. A study was conducted at Central Valley Water Reclamation Facility (CVWRF) to evaluate the P recovery potential at different segments of the treatment train. A P mass balance was also conducted under a hypothetical scenario, where enhanced biological P removal was assumed at CVWRF. Results show that while aluminum was the superior chemical at removing phosphorus, all chemicals were successful at a rate of over 80% P removal at the optimum pH value. Magnesium, on the other hand, was superior at nitrogen removal. The sludge and filtrate have higher dissolved P loads, making them ideal areas for phosphorus removal and recovery. The installation of a Biological Nutrient Recovery (BNR) system with Enhanced Biological Phosphorus Removal (EBPR) would also release up to 7 times the amount of phosphorus and make it available for recovery in the sludge handling phase compared to a classic ASP. Based on these results, the ideal system for recovery of phosphorus and nitrogen would be a BNR process combined with a struvite recovery system. The overall evaluation of a combination of analyses concluded that shifting to a form of recovery that includes a combination of EBPR on the liquids stream followed by precipitation on the solids stream could recover a vast amount of the phosphorus coming into the treatment plant. This would not only make Central Valley Water Reclamation Facility more sustainable and efficient, but could imply an economic value as well, if phosphorus was sold to other industries.
Operator Quantum Error Correcting Subsystems for Self-Correcting Quantum Memories
Creators: name: Bacon, Dave
Publisher: name: arXiv
Year: 2005
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The most general method for encoding quantum information is not to encode the information into a subspace of a Hilbert space, but to encode information into a subsystem of a Hilbert space. Recently this notion has led to a more general notion of quantum error correction known as operator quantum error correction. In standard quantum error correcting codes, one requires the ability to apply a procedure which exactly reverses on the error correcting subspace any correctable error. In contrast, for operator error correcting subsystems, the correction procedure need not undo the error which has occurred, but instead one must perform correction only modulo the subsystem structure. This does not lead to codes which differ from subspace codes, but does lead to recovery routines which explicitly make use of the subsystem structure. Here we present two examples of such operator error correcting subsystems. These examples are motivated by simple spatially local Hamiltonians on square and cubic lattices. In three dimensions we provide evidence, in the form a simple mean field theory, that our Hamiltonian gives rise to a system which is self-correcting. Such a system will be a natural high-temperature quantum memory, robust to noise without external intervening quantum error correction procedures.
description: 17 pages, 3 figures, typos fixed, references added