cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Calculation of commercial thinning volumes in 47 prefectures in Japan
Creators: name: Hiroshima, Takuya
name: Nakajima, Tohru
name: Kanomata, Hidesato
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences

description: The Forest and Forestry Basic Plan set Japan’s domestic timber supply goal of 32 million m3 by 2020. To achieve the goal, a large increase in thinned timber production will be required. The purpose of this study was to calculate and understand the current situation of commercial thinning volumes in all 47 prefectures as a basis for projecting future changes in thinned timber production. First, thinning records at prefectural level were obtained. Thinning areas by age classes and commercial thinning ratios were predicted for those prefectures without available thinning records using clustering, discriminant analysis, and logistic regression. A thinning yield table was also constructed for each prefecture, based on the mean volume of six tree species assuming certain thinning types, intensity, and timings. Finally, the commercial thinning volume was calculated for each prefecture by multiplying thinning area, thinning volume per unit area in a yield table, and commercial thinning ratio. Graphs of commercial thinning volumes suggested that Hokkaido and Kumamoto had particularly high thinning volumes, Akita, Nagano, Shizuoka, Oita, Miyazaki, and Kagoshima also had relatively high volumes. The calculation results in prefectures were considered reasonable, based on calibration and validation that reflected the regional difference in thinning trends.
Efficient backsplicing produces translatable circular mRNAs
Creators: name: Wang, Zefeng
name: Wang, Yang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: While the human transcriptome contains a large number of circular RNAs (circRNAs), the functions of most circRNAs remain unclear. Sequence annotation suggests that most circRNAs are generated from splicing in reversed orders across exons. However, the mechanisms of this backsplicing are largely unknown. Here we constructed a single exon minigene containing split GFP, and found that the pre-mRNA indeed produces circRNA through efficient backsplicing in human and Drosophila cells. The backsplicing is enhanced by complementary introns that form double-stranded RNA structure to bring splice sites in proximity, but such structure is not required. Moreover, backsplicing is regulated by general splicing factors and cis-elements, but with regulatory rules distinct from canonical splicing. The resulting circRNA can be translated to generate functional proteins. Unlike linear mRNA, poly-adenosine or poly-thymidine in 3′ UTR can inhibit circular mRNA translation. This study revealed that backsplicing can occur efficiently in diverse eukaryotes to generate circular mRNAs.
A fast GPU-based Monte Carlo simulation of proton transport with detailed modeling of non-elastic interactions
Creators: name: Tseung, H. Wan Chan
name: Ma, J.
name: Beltran, C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Medical Physics (physics.med-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Purpose: Very fast Monte Carlo (MC) simulations of proton transport have been implemented recently on GPUs. However, these usually use simplified models for non-elastic (NE) proton-nucleus interactions. Our primary goal is to build a GPU-based proton transport MC with detailed modeling of elastic and NE collisions. Methods: Using CUDA, we implemented GPU kernels for these tasks: (1) Simulation of spots from our scanning nozzle configurations, (2) Proton propagation through CT geometry, considering nuclear elastic scattering, multiple scattering, and energy loss straggling, (3) Modeling of the intranuclear cascade stage of NE interactions, (4) Nuclear evaporation simulation, and (5) Statistical error estimates on the dose. To validate our MC, we performed: (1) Secondary particle yield calculations in NE collisions, (2) Dose calculations in homogeneous phantoms, (3) Re-calculations of head and neck plans from a commercial treatment planning system (TPS), and compared with Geant4.9.6p2/TOPAS. Results: Yields, energy and angular distributions of secondaries from NE collisions on various nuclei agree well with the Geant4 Bertini and Binary cascade models. The 3D-gamma pass rate at 2\%-2 mm for treatment plan simulations is typically 98\%. The net calculation time on a NVIDIA GTX680 card, including all data transfers, is $\sim$20 s for $1\times10^7$ proton histories. Conclusions: Our GPU-based MC is the first of its kind to include a detailed nuclear model to handle NE interactions of protons with any nucleus. Dosimetric calculations are in very good agreement with Geant4/TOPAS. Our MC is being used to perform fast routine clinical QA of pencil-beam based treatment plans, and has also been adopted as the dose engine in a clinically-applicable MC-based IMPT TPS. The detailed nuclear modeling will allow us to perform very fast linear energy transfer and neutron dose estimates on the GPU.
description: 26 pages, 9 figures
EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates
Creators: name: Prins, Jan F.
name: Slevin, Michael K.
name: Duronio, Robert J.
name: Marzluff, William F.
name: Welch, Joshua D.
name: Tatomer, Deirdre C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3′ ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3′ ends contain post-transcriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3′ end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3′ ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1–2 nt at the 3′ end of mature histone mRNA maintaining the length of the histone transcripts. Histone mRNAs in fly embryos and ovaries show the same pattern, but with different tail nucleotide compositions. We increase the sensitivity of EnD-Seq by using cDNA priming to specifically enrich low-abundance tails of known sequence composition allowing identification of degradation intermediates. In addition, we show the broad applicability of our computational approach by using AppEnD to gain insight into 3′ additions from diverse types of sequencing data, including data from small capped RNA sequencing and some alternative polyadenylation protocols.
Schrodinger Holography for z<2
Creators: name: Andrade, Tomas
name: Keeler, Cynthia
name: Peach, Alex
name: Ross, Simon F.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We investigate holography for asymptotically Schrodinger spacetimes, using a frame formalism. Our dictionary is based on the anisotropic scaling symmetry. We consider z <2, where the holographic dictionary is cleaner; we make some comments on z=2. We propose a definition of asymptotically locally Schrodinger spacetime where the leading components of the frame fields provide suitable geometric boundary data. We show that an asymptotic expansion exists for generic boundary data satisfying our boundary conditions for z<2.
description: 34 pages, no figures. v2: corrected typos, improved explanation on some technical points, to be published in CQG
In vivo analysis of trypanosome mitochondrial RNA function by artificial site-specific RNA endonuclease-mediated knockdown
Creators: name: Szempruch, Anthony J.
name: Hajduk, Stephen L.
name: Choudhury, Rajarshi
name: Wang, Zefeng
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Trypanosomes possess a unique mitochondrial genome called the kinetoplast DNA (kDNA). Many kDNA genes encode pre-mRNAs that must undergo guide RNA-directed editing. In addition, alternative mRNA editing gives rise to diverse mRNAs and several kDNA genes encode open reading frames of unknown function. To better understand the mechanism of RNA editing and the function of mitochondrial RNAs in trypanosomes, we have developed a reverse genetic approach using artificial site-specific RNA endonucleases (ASREs) to directly silence kDNA-encoded genes. The RNA-binding domain of an ASRE can be programmed to recognize unique 8-nucleotide sequences, allowing the design of ASREs to cleave any target RNA. Utilizing an ASRE containing a mitochondrial localization signal, we targeted the extensively edited mitochondrial mRNA for the subunit A6 of the F0F1 ATP synthase (A6) in the procyclic stage of Trypanosoma brucei. This developmental stage, found in the midgut of the insect vector, relies on mitochondrial oxidative phosphorylation for ATP production with A6 forming the critical proton half channel across the inner mitochondrial membrane. Expression of an A6-targeted ASRE in procyclic trypanosomes resulted in a 50% reduction in A6 mRNA levels after 24 h, a time-dependent decrease in mitochondrial membrane potential (ΔΨm), and growth arrest. Expression of the A6-ASRE, lacking the mitochondrial localization signal, showed no significant growth defect. The development of the A6-ASRE allowed the first in vivo functional analysis of an edited mitochondrial mRNA in T. brucei and provides a critical new tool to study mitochondrial RNA biology in trypanosomes.
Influence of clouds on the parameters of images measured by IACT at very high energies
Creators: name: Sobczynska, Dorota
name: Bednarek, Wlodek
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Observations with the Cherenkov telescopes are in principle limited to the clear sky conditions due to significant absorption of Cherenkov light by clouds. If the cloud level is high enough or the atmospheric transmission of the cloud is high, then high energy showers (with TeV energies) can still produce enough Cherenkov photons allowing detection by telescopes with large sizes and cameras with large field of view (FOV). In this paper we study the possibility of observations of showers, induced by high energy particles in the atmosphere, in the presence of clouds which are completely or partially opaque for Cherenkov radiation. We show how the image parameters of the Cherenkov light distribution on the telescope camera are influenced for different opacity and altitude of the cloud. By applying the Monte Carlo simulations, we calculate the scaled LENGTH and WIDTH parameters with the purpose to separate gamma-ray and proton initiated showers in real data. We show, that the high level of the night sky background effects the selection efficiency of the gamma-ray initiated showers. However, application of the higher image cleaning level significantly improves expected quality factors. The estimated gamma-ray selection efficiency for the detector with the camera FOV limited to 8 deg. is slightly better than for the camera with unlimited FOV, although the number of identified gamma-ray events is lower. We conclude that large Cherenkov telescopes with large FOV cameras can be used for observations of very high energy gamma-rays in the presence of clouds. Consequently, the amount of useful data can be significantly enlarged.
description: 17 pages, 7 figures, accepted for publication in Journal of Physics G: Nuclear and Particle Physics
Soft photon production from real-time dynamics of jet fragmentation
Creators: name: Loshaj, Frasher
name: Kharzeev, Dmitri E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Soft photons produced in heavy ion collisions are an important tool for probing the properties of the quark-gluon plasma. It is therefore crucial to understand the background - soft photons produced in elementary collisions. Low theorem states that soft photon production in hadron collisions is dominated by Bremsstrahlung off charged initial and final state hadrons. Surprisingly, almost every experiment observed an enhancement (by a factor of $2÷5$) above Low theorem's prediction. This is the longstanding puzzle of "anomalous soft photon production." The phenomenon is not observed in processes with leptonic final states, which suggests that the mechanism is due to nonperturbative QCD evolution. We study this phenomenon using an exactly soluble, massless, Abelian model in $1+1$ dimensions which shares with QCD many important properties: confinement, chiral symmetry breaking, axial anomaly and $θ$-vacuum. We then apply this model to the soft photon production in the fragmentation of jets produced in $Z^0$ decays and find a qualitative agreement with the data.
description: Talk presented at Quark Matter 2014 by FL
title: Quantifying flow regimes in pipelines using rock-flow cell
Creators: name: Carmosino, Catherine J.
Publisher: name: Colorado School of Mines. Arthur Lakes Library
Year: 2023

description: For multiphase system under flow, as in oil and gas production, flow regime in flow lines are of great importance to efficiently and safely transport fluids. In this research, the flow regime and mixing of the phases that occur in these flow lines are experimentally studied by using a novel device called rock-flow cell, which is a benchtop tool that simulates multiphase flow conditions by controlling temperate, pressure, liquid volume, and rocking conditions (rate and tilt angle). Through the manipulation of these conditions, every type of flow regime can be replicated and analyzed. This research aims to quantify and correlate the flow conditions in the rock-flow cell to those in flow lines by using video images with image analysis, coded in Python, to quantify the flow elements, which will later be used to match with other experiments and simulations of actual flow lines.
A supersymmetric black lens
Creators: name: Kunduri, Hari K.
name: Lucietti, James
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We present a new supersymmetric, asymptotically flat, black hole solution to five-dimensional supergravity. It is regular on and outside an event horizon of lens space topology L(2,1). It is the first example of an asymptotically flat black hole with lens space topology. The solution is characterised by a charge, two angular momenta and a magnetic flux through a non-contractible disc region ending on the horizon, with one constraint relating these.
description: 4 pages. v2: minor changes, title of published version differs
First-person experiences of endometriosis in Catalonia: recommendations of women with endometriosis for improving health care services and public policies. TRANSFORM Policy Brief 2022
Creators: name: Salas Seoane, Nora
name: Reinoso Botsho, Diana
name: Perucca Iannitelli, Carla
Publisher: name: Zenodo
Year: 2022
Subjects: endometriosis
citizen science
women's health
health
cocreation

description: This Policy Brief is the result of a participatory research using citizen science methodologies where women have acted as co-researchers talking in first person about endometriosis in Catalonia. The research aims to explain and raise awareness about how endometriosis is experienced and how it affects people's overall health, as well as for the women themselves to generate first-person recommendations to improve diagnostic and care services. This Policy Brief is aimed at policy makers and health professionals. This research has been made possible thanks to the active participation, motivation and enthusiasm of 20 women co-researchers who have been involved in the different phases of the scientific process. We are very grateful for their support, dedication and effort throughout the research, and we hope to achieve, as they wish, an impact on public health policies that will result in an improved approach to endometriosis at the health level that will improve the quality of life of present and future patients. This citizen science pilot is part of the European TRANSFORM project (grant agreement N.872687). This document reflects the views only of the authors, and neither the European Commission nor the Research Executive Agency can be held responsible for any use which may be made of the information contained therein.
All-fermion electrodynamics and fermion number anomaly inflow
Creators: name: Kravec, S. M.
name: McGreevy, John
name: Swingle, Brian
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We demonstrate that 3+1-dimensional quantum electrodynamics with fermionic charges, fermionic monopoles, and fermionic dyons arises at the edge of a 4+1-dimensional gapped state with short-range entanglement. This state cannot be adiabatically connected to a product state, even in the absence of any symmetry. This provides independent evidence for the obstruction found by arXiv:1306.3238 to a 3+1-dimensional short-distance completion of all-fermion electrodynamics. The non-triviality of the bulk is demonstrated by a novel fermion number anomaly.
description: 37 pages, 5 figures
Critical Behavior in a Massless Scalar Field Collapse with Self-interaction Potential
Creators: name: Zhang, Xuefeng
name: Lu, H.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We examine a one-parameter family of analytical solutions representing spherically symmetric collapse of a nonlinear massless scalar field with self-interaction in an asymptotically flat spacetime. The time evolution exhibits a type of critical behavior. Depending on the scalar charge parameter $q$ as compared to a critical value $q^*$, the incoming scalar wave collapses either to a globally naked central singularity if $qq^*$ (strong field), both having finite asymptotic masses. Near the critical evolution, the black hole mass follows a product-logarithmic scaling law: $-M^2\ln M \sim q-q^*$ with $0q^*$. The solution admits no self-similarity and satisfies the null and the strong energy conditions.
description: 19 pages, 6 figures
Appendix to BEH 3781
Creators: name: Grieco, Fabrizio
Publisher: name: Brill Online
Year: 2022
Subjects: Animal behaviour

description: Table A1. Table of P values and Q values. Figure A1. Histogram of raw P-values. False Discovery Rate: P-values below 0.05 = 7; P-values above 0.5 = 4 (including value P=0.466); estimated below 0.5 = 4; estimated true null hypothesis: 8; Estimated P-values below 0.05: 4/10 = 0.4; FDR = 0.4/7 = 5.71%. Figure A2. Scheme of the design of this study. (A) The main response variable was the peak frequency of the vocalizations of the focal male during countersinging interactions with either of two neighbours. (B): Each data point represents the average peak frequency of the focal male in a single interaction with a neighbour. The difference between the overall averages f determines which individual is labelled NL and which NH (see Methods). (C) Layout of the within-subject contrasts. Squares: focal males. Dots, neighbouring males. Colours represent identities. (D) Variation in the overlap of call posts of focal male (grey dots) and a neighbour (red or blue dots). The polygons represent the familiar space used by each individual during interactions. The arrows represent the signal sent by the focal male during an interaction, which is the focus if this study. Figure A3. Patterns of movement of focal males when two neighbouring males were vocally active simultaneously. Small squares in dimmed colour indicate all the call posts of the focal male, including that of solitary singing. Larger squares indicate the call posts during a specific interaction. Squares: focal subject. Dots: neighbour NL. Triangles: neighbour NH. Arrows indicate the movement of the focal male inferred from the temporal sequence of the recorded call posts. S: The starting position of the focal male. (A–E) Focal male moving towards neighbour NL (dot) once the latter began calling, while the other neighbour (NH, triangles) was already calling near or within the focal male’s territory. Multiple symbols indicate multiple positions during one interaction. A-C refer to the same focal male. Note that in A and C the focal male was initially near NH. (F, G) Focal male moving back to the centre of its territory after the neighbour NL (dot) ended the vocal display, while the other neighbour NH (triangle) continued calling at a short distance. S, starting position of the focal male; St, position of the focal male when NL ended calling.
Market Making with Decreasing Utility for Information
Creators: name: Dudík, Miroslav
name: Frongillo, Rafael
name: Vaughan, Jennifer Wortman
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: We study information elicitation in cost-function-based combinatorial prediction markets when the market maker's utility for information decreases over time. In the sudden revelation setting, it is known that some piece of information will be revealed to traders, and the market maker wishes to prevent guaranteed profits for trading on the sure information. In the gradual decrease setting, the market maker's utility for (partial) information decreases continuously over time. We design adaptive cost functions for both settings which: (1) preserve the information previously gathered in the market; (2) eliminate (or diminish) rewards to traders for the publicly revealed information; (3) leave the reward structure unaffected for other information; and (4) maintain the market maker's worst-case loss. Our constructions utilize mixed Bregman divergence, which matches our notion of utility for information.
Origin of the Moon and Lunar Water
Creators: name: Gorkavyi, Nick
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: FOS: Physical sciences

description: Three principal concepts regarding lunar formation have been examined: the accretion hypothesis, the mega-impact theory, and the multi-impact model. The multi-impact model amalgamates the salient facets of the mega-impact theory and the accretion hypothesis. As per this model, fragments of the terrestrial crust are ejected into space during collisions with numerous planetesimals (proto-asteroids) with diameters around 10-100 kilometers. This ejecta interacts with the accretion disk, augmenting its mass. Different models of lunar formation yield varied conclusions regarding the quantity of lunar water, its subsurface distribution, and isotopic composition. Geomorphological structures in the lunar polar regions (smoothed craters, landslides, regular patterns) suggest the presence of a substantial permafrost layer with an approximate thickness of a kilometer.
description: Review article, published in "Earth and Planetary Science", 2023, 2(2)
Metazoan tRNA introns generate stable circular RNAs in vivo
Creators: name: Wen, Ying
name: Matera, A. Gregory
name: Jaffrey, Samie R.
name: Lu, Zhipeng
name: Noto, John J.
name: Schmidt, Casey A.
name: Filonov, Grigory S.
name: Hatkevich, Talia L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: We report the discovery of a class of abundant circular noncoding RNAs that are produced during metazoan tRNA splicing. These transcripts, termed tRNA intronic circular (tric)RNAs, are conserved features of animal transcriptomes. Biogenesis of tricRNAs requires anciently conserved tRNA sequence motifs and processing enzymes, and their expression is regulated in an age-dependent and tissue-specific manner. Furthermore, we exploited this biogenesis pathway to develop an in vivo expression system for generating “designer” circular RNAs in human cells. Reporter constructs expressing RNA aptamers such as Spinach and Broccoli can be used to follow the transcription and subcellular localization of tricRNAs in living cells. Owing to the superior stability of circular vs. linear RNA isoforms, this expression system has a wide range of potential applications, from basic research to pharmaceutical science.
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures
Creators: name: Westhof, Eric
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5–3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson–Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/.
CubeSat deployable origami-inspired drag sail for drag control
Creators: name: Marx, Joseph
Publisher: name: Unknown
Year: 2019

description: CubeSats are small cost-effective satellites that provide a platform for students and
researchers to perform various experiments and conduct data acquisition in space. Many CubeSats
have mission plans that require them to reach a target altitude quickly, which is commonly
accomplished by incorporating one-time deployment mechanisms to increase drag. This project
investigates a mechanism designed to dynamically adjust the drag. This was done by researching
concepts for drag rate systems such as developable mechanisms, deployable solar arrays, and
origami-based drag sails. Based on the combination of performance criteria of least moving parts,
greatest possible area to increase drag, and highest potential of reliable deployment the design
chosen was an origami-based drag sail with tape spring booms. The anticipated reduction in deorbiting
time for the proposed design is 20%, with the drag sail fitting into a lU CubeSat, and a
possible deployed area of 0.414 m^. The concept chosen shows promise for increasing the drag to
de-orbit quickly and the reducing drag to maximize time at a desired altitude.
miR-122 and the Hepatitis C RNA genome: More than just stability
Creators: name: Li, You
name: Lemon, Stanley M.
name: Masaki, Takahiro
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: MicroRNA-122 (miR-122) plays a key role in hepatitis C virus (HCV) replication, but understanding exactly how it functions in the viral lifecycle has been elusive. HCV is a positive-strand virus with a messenger-sense RNA genome, to which miR-122 binds in a non-canonical fashion at two sites near the 5′ end. Recent studies show that miR-122 recruits Ago-2 to the genomic RNA, stabilizing it and slowing its decay in infected cells. This led us to investigate decay pathways that mediate degradation of the viral RNA. We found HCV RNA is degraded primarily by the cytoplasmic 5′ exonuclease Xrn1 in infected cells. miR-122 lost its stabilizing effect when cells were depleted of Xrn1 using an RNAi strategy, providing strong evidence that miR-122 acts to protect the viral RNA from Xrn1-mediated 5′ exonucleolytic decay. However, Xrn1 depletion did not rescue replication of a viral mutant defective in miR-122 binding, indicating that there is much more to miR-122’s actions than prevention of Xrn1 decay. Here, we consider the role of miR-122 in the viral lifecycle, and explore the possibility that it might function directly in viral RNA synthesis.
The Higgs oscillator on the hyperbolic plane and Light-Front Holography
Creators: name: Pallares-Rivera, A.
name: Kirchbach, M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The Light Front Holographic (LFH) wave equation, which is the conformal scalar equation on the plane, is revisited from the perspective of the supersymmetric quantum mechanics, and attention is drawn to the fact that it naturally emerges in the small hyperbolic angle approximation to the "curved" Higgs oscillator on the hyperbolic plane, i.e. on the upper part of the two-dimensional hyperboloid of two sheets, a space of constant negative curvature. Such occurs because the particle dynamics under consideration reduces to the one dimensional Schrödinger equation with the second hyperbolic Pöschl-Teller potential, whose flat-space (small-angle) limit reduces to the conformally invariant inverse square distance plus harmonic oscillator interaction, on which LFH is based. In consequence, energies and wave functions of the LFH spectrum can be approached by the solutions of the Higgs oscillator on the hyperbolic plane in employing its curvature and the potential strength as fitting parameters. Also the proton electric charge form factor is well reproduced within this scheme by means of a Fourier-Helgason hyperbolic wave transform of the charge density. In conclusion, in the small angle approximation, the Higgs oscillator on the hyperbolic plane is demonstrated to satisfactory parallel essential outcomes of the Light Front Holographic QCD. The findings are suggestive of associating the hyperboloid curvature of the with a second scale in LFH, which then could be employed in the definition of a chemical potential.
description: revised version, presentation restructured, discussion improved, no statement changes
Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts
Creators: name: Baric, Ralph S
name: Eisfeld, Amie J
name: Thomas, Matthew J
name: Kawaoka, Yoshihiro
name: Josset, Laurence
name: Katze, Michael G
name: Peng, Xinxia
name: Green, Richard R
name: Gralinski, Lisa E
name: Heise, Mark T
name: Ferris, Martin T
name: Tchitchek, Nicolas
name: Schroth, Gary P
name: Pardo-Manuel de Villena, Fernando
name: Tisoncik-Go, Jennifer
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The outcome of respiratory virus infection is determined by a complex interplay of viral and host factors. Some potentially important host factors for the antiviral response, whose functions remain largely unexplored, are long non-coding RNAs (lncRNAs). Here we systematically inferred the regulatory functions of host lncRNAs in response to influenza A virus and severe acute respiratory syndrome coronavirus (SARS-CoV) based on their similarity in expression with genes of known function. We performed total RNA-Seq on viral-infected lungs from eight mouse strains, yielding a large data set of transcriptional responses. Overall 5,329 lncRNAs were differentially expressed after infection. Most of the lncRNAs were co-expressed with coding genes in modules enriched in genes associated with lung homeostasis pathways or immune response processes. Each lncRNA was further individually annotated using a rank-based method, enabling us to associate 5,295 lncRNAs to at least one gene set and to predict their potential cis effects. We validated the lncRNAs predicted to be interferon-stimulated by profiling mouse responses after interferon-α treatment. Altogether, these results provide a broad categorization of potential lncRNA functions and identify subsets of lncRNAs with likely key roles in respiratory virus pathogenesis. These data are fully accessible through the MOuse NOn-Code Lung interactive database (MONOCLdb).
Multicomponent Activity Cycles using Hilbert-Huang Analysis
Creators: name: Velloso, E. N.
name: Anthony, F.
name: Nascimento, J. D. do
name: Silveira, L. F. Q.
name: Hall, J.
name: Saar, S. H.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The temporal analysis of stellar activity evolution is usually dominated by a complex trade-off between model complexity and interpretability, often by neglecting the non-stationary nature of the process. Recent studies appear to indicate that the presence of multiple coexisting cycles in a single star is more common than previously thought. The correct identification of physically meaningful cyclic components in spectroscopic time series is therefore a crucial task, which cannot overlook local behaviors. Here we propose a decomposition technique which adaptively recovers amplitude- and frequency-varying components. We present our results for the solar activity as measured both by the sunspot number and the $K$-line emission index, and we consistently recover the Schwabe and Gleissberg cycles as well as the Gnevyshev-Ohl pattern probably related to the Hale cycle. We also recover the known 8-year cycle for 61 Cygni A, in addition to evidence of a three-cycles long pattern reminiscent of the Gnevyshev-Ohl rule. This is particularly interesting as we cannot discard the possibility of a relationship between the measured field polarity reversals and this Hale-like periodicity.
description: 8 pages, 3 figures
Array of biodegradable microrafts for isolation and implantation of living, adherent cells
Creators: name: Yeh, Jen Jen
name: Wang, Yuli
name: Herrera, Gabriela S.
name: Sims, Christopher E.
name: Allbritton, Nancy L.
name: Phillips, Colleen N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: A new strategy for efficient sorting and implantation of viable adherent cells into animals is described. An array of biodegradable micro-structures (microrafts) was fabricated using a polydimethylsiloxane substrate for micromolding poly(lactic-co-glycolic acid) (PLGA). Screening various forms of PLGA determined that the suitability of PLGA for microraft manufacture, biocompatibility and in vitro degradation was dependent on molecular weight and lactic/glycolic ratio. Cells plated on the array selectively attached to the microrafts and could be identified by their fluorescence, morphology or other criteria. The cells were efficiently dislodged and collected from the array using a microneedle device. The platform was used to isolate specific cells from a mixed population establishing the ability to sort target cells for direct implantation. As a proof of concept, fluorescently conjugated microrafts carrying tumor cells stably expressing luciferase were isolated from an array and implanted subcutaneously into mice. In vivo bio-luminescence imaging confirmed the growth of a tumor in the recipient animals. Imaging of tissue sections from the tumors demonstrated in vivo degradation of the implanted microrafts. The process is a new strategy for isolating and delivering a small number of adherent cells for animal implantation with potential applications in tissue repair, tumor induction, in vivo differentiation of stem cells and other biomedical research.
HaloTag pseudotyped lentivirus: Quantifying uptake and internalisation in vitro using a fluorescent click sensor
Creators: name: KUAH, JIA YI
Publisher: name: Monash University
Year: 2023
Subjects: Pharmaceutical sciences

description: Observing how viruses work and enter a cell is very challenging, especially when it comes to labelling and tracking small amounts of viruses. A portable platform using an established system was developed and tested to help look at viral entry. This would help material scientists and virologists to assist them in better understanding how they enter cells and develop better drug delivery systems.
Lipid-coated nanoscale coordination polymers for targeted cisplatin delivery
Creators: name: Liu, Demin
name: Huxford-Phillips, Rachel C.
name: Lin, Wenbin
name: Russell, Shane R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Nanoscale coordination polymers (NCPs) containing a Pt(IV) cisplatin prodrug, disuccinatocisplatin, were formed by a surfactant-templated synthesis and were shown to have a prodrug loading of 8.2 wt% and a diameter of ~133 nm by dynamic light scattering. These NCPs were stabilized by coating with a DOPC/cholesterol/DSPE-Peg2K lipid layer; a release profile in phosphate buffered saline showed an initial drug release of ~25% within the first hour and no more release observed up to 192 h. The NCP was rendered target-specific for sigma receptors by addition of an AA-DSPE-Peg2K conjugate (AA = anisamide) in the lipid formulation. The AA-containing NCP showed a statistically significant decrease in IC50 (inhibitory concentration, 50%) compared to the non-targeted NCP. Enhanced uptake of the AA-containing NCP was further supported by confocal microscopy and competitive binding assays.
Anomalous Magneto Response and the Stückelberg Axion in Holography
Creators: name: Jimenez-Alba, Amadeo
name: Landsteiner, Karl
name: Melgar, Luis
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the magneto response with non-conserved currents in Holography. Non-conserved currents are dual to massive vector fields in AdS. We introduce the mass in a gauge invariant way via the Stückelberg mechanism. In particular we find generalizations of the Chiral Magnetic Effect, the Chiral Separation Effect and the Chiral Magnetic Wave. Since the associated charge is not conserved we need to source it explicitly by a coupling, the generalization of the chemical potential. In this setup we find that in general the anomalous transport phenomena are still realized. The values we find for non-zero mass connect however continuously to the values of the anomalous conductivities of the consistent currents. i.e. the proper chiral magnetic effect vanishes for all masses (as it does for the consistent current in the zero mass case) whereas the chiral separation effect is fully present. The generalization of the chiral magnetic wave shows that for small momenta there is no propagating wave but two purely absorptive modes (one of them diffusive). At higher momenta we recover the chiral magnetic wave as a combination of the two absorptive modes. We also study the negative magneto resistivity and find that it grows quadratically with the magnetic field. Since the (classical) $U(1)_A$ symmetry of QCD is not at all a symmetry at the quantum level we also argue that using massive vectors in AdS to model the axial singlet current might result in a more realistic holographic model of QCD and should be a good starting point to investigate the dynamics of anomalous transport in the strongly coupled quark gluon plasma.
description: 27 pages + 4 appendices, 14 figures
Proliferation of preosteoblasts on TiO 2 nanotubes is FAK/RhoA related
Creators: name: Masako, Nagasawa
name: Lee, Dong Joon
name: Cooper, Lyndon F.
name: Zhang, He
name: Yang, Sheng
name: Ko, Ching-Chang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Model for FAK/RhoA modulation of topography-regulated proliferation.
Quantum Optimization of Fully-Connected Spin Glasses
Creators: name: Venturelli, Davide
name: Mandrà, Salvatore
name: Knysh, Sergey
name: O'Gorman, Bryan
name: Biswas, Rupak
name: Smelyanskiy, Vadim
Publisher: name: arXiv
Year: 2014
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The Sherrington-Kirkpatrick model with random $\pm1$ couplings is programmed on the D-Wave Two annealer featuring 509 qubits interacting on a Chimera-type graph. The performance of the optimizer compares and correlates to simulated annealing. When considering the effect of the static noise, which degrades the performance of the annealer, one can estimate an improvement on the comparative scaling of the two methods in favor of the D-Wave machine. The optimal choice of parameters of the embedding on the Chimera graph is shown to be associated to the emergence of the spin-glass critical temperature of the embedded problem.
description: includes supplemental material
title: Daniel Gauchat, geboren am 12. Okt. 1869, gestorben am 13. Mai 1930
title: Abschiedsworte bei der Bestattung von Herrn Daniel Gauchat am 16. Mai 1930 im Krematorium Zürich
titleType: Subtitle
Creators: name: Zimmermann, Karl
name: Schirmer, Hermann
Publisher: name: Orell Füssli
Year: 1930
Subjects: subject: 920 Biografien, Genealogie, Insignien
subject: Nachruf
subject: Gauchat, Daniel
subject: Zürich
subject: Bern

description: Inhalt: Ansprache des Herrn Pfarrer Karl Zimmermann ; Ansprache des Herrn Professor Dr. Hermann Schirmer
Holography as a Gauge Phenomenon in Higher Spin Duality
Creators: name: Koch, Robert de Mello
name: Jevicki, Antal
name: Rodrigues, Joao P.
name: Yoon, Junggi
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Employing the world line spinning particle picture we discuss the appearance of several different `gauges' which we use to gain a deeper explanation of the Collective/Gravity identification. We discuss transformations and algebraic equivalences between them. For a bulk identification we develop a `gauge independent' representation where all gauge constraints are eliminated. This `gauge reduction' of Higher Spin Gravity demonstrates that the physical content of 4D AdS HS theory is represented by the dynamics of an unconstrained scalar field in 6d. It is in this gauge reduced form that HS Theory can be seen to be equivalent to a 3+3 dimensional bi-local collective representation of CFT3.
description: 22 pages, v2: references updated; v3: minor corrections
Understanding the In Vivo Behaviour of Nanoparticle Therapies
Creators: name: ONG, YIH RUE
Publisher: name: Monash University
Year: 2023
Subjects: Nanomedicine
Pharmaceutical sciences

description: The main impediment to efficient delivery of nanoparticles is the immune system, as it readily identifies nanoparticles as foreign and removes them before they can reach their target. This project developed and used a murine model to understand and quantify nanoparticle-immune cell interactions in various tissues. The model identified that substantial improvement in delivery efficiency can be achieved by reducing nanoparticle associations with immune cells. This work advances the field of knowledge on the cellular interactions of nanoparticles in the body, and contributes towards advancing drug delivery efficiencies of future therapeutics.
The Role of Social Capital in Educational Aspirations of Rural Youth*: Educational Aspirations of Rural Youth
Creators: name: Meece, Judith L.
name: Irvin, Matthew J.
name: Byun, Soo-yong
name: Hutchins, Bryan C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Drawing on a recent national survey of rural high school students, this study investigated the relationship between social capital and educational aspirations of rural youth. Results showed that various process features of family and school social capital were important to predict rural youth's educational aspirations beyond sociodemographic background. In particular, parents' and teachers' educational expectations for their child and student respectively were positively related to educational aspirations of rural youth. In addition, discussion with parents about college was positively related to educational aspirations of rural youth. On the other hand, there was little evidence to suggest that number of siblings and school proportions of students on free lunch and minority students are related to educational aspirations of rural youth, after controlling for the other variables. The authors highlight unique features of rural families, schools, and communities that may combine to explain the complexity of the role of social capital in shaping educational aspirations of rural youth.
title: Zum Andenken an Frau Frida Stahel-Hüssy
title: 4. Juni 1874 - 21. Juni 1949
titleType: Subtitle
Creators: name: Schaufelberger, Max
Publisher: name: [Verlag nicht ermittelbar]
Year: 1949
Subjects: subject: 920 Biografien, Genealogie, Insignien
subject: Nachruf
subject: Stahel-Hüssy, Frida
subject: Safenwil
subject: Küsnacht (Kanton Zürich)

description: Inhalt: Ansprache von Herrn Dekan Dr. M. Schaufelberger, Küsnacht im Krematorium Zürich, am 24. Juni 1949 ; Abdankung von Herrn Dekan Dr. M. Schaufelberger, Küsnacht in der Kirche Küsnacht, am 24. Juni1949
Understanding the large shift photocurrent of WS$_{2}$ nanotubes: A comparative analysis with monolayers
Creators: name: Krishna, Jyoti
name: Garcia-Goiricelaya, Peio
name: de Juan, Fernando
name: Ibañez-Azpiroz, Julen
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study the similarities and differences in the shift photocurrent contribution to the bulk photovoltaic effect between transition-metal dichalcogenide monolayers and nanotubes. Our analysis is based on density functional theory in combination with the Wannier interpolation technique for the calculation of the shift photoconductivity tensor. Our results show that for nanotube radii of practical interest $r>60$~Å, the shift photoconductivity of a single-wall nanotube is well described by that of the monolayer. Additionally, we quantify the shift photocurrent generated under realistic experimental conditions like device geometry and absorption capabilities. We show that a typical nanotube can generate a photocurrent of around 10 nA, while the monolayer only attains a maximum of 1 nA. This enhancement is mainly due to the larger conducting cross section of a nanotube in comparison to a monolayer. Finally, we discuss our results in the context of recent experimental measurements on WS$_{2}$ monolayer and nanotubes[Zhang et al., Nature 570, 349 (2019)].
description: 11 pages, 9 figures