cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
: Classifying and Generating Repetitive Elements in the Genome Using Deep Learning
Creators: name: Czejdo, Conrad
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description: Repetitive elements are sequence patterns in the genome which are duplicated in large quantity. They serve important functions both in genomic preservation and evolution, leading to the need for their fast and accurate classification. The current gold standard for repeat identification can be achieved by establishing correspondences between a well-annotated library of repetitive elements and a given query sequence. However, annotation quality is highly variable across species. Therefore, for genomes whose repeats are poorly annotated, de novo methods must be used. A common approach of de novo methods is to first check the sequence for protein domain conservation. The presence and order of these protein domains are used as features for an expert-crafted rule-based system or an optimized machine learning classifier. Although de novo  approaches have achieved modest success, two problems remain. Firstly, they require lengthy consensus sequences which take time to assemble, and may not be representative of the true diversity of repetitive elements in the sample. Secondly, these approaches are heavily reliant on hand-picking a comprehensive set of protein domains, which may need to be constantly adjusted as new repetitive elements are discovered. In this thesis I show that deep learning models are competitive with pattern matching based approaches at the level of a shotgun sequencing strand for de novo classification of repeat elements. I also explore ways of embedding sequences using deep learning models. Finally, I made these tools available through a web-based interface.
Variation and Series Approach to the Thomas-Fermi Equation
Creators: name: Oulne, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The Thomas - Fermi equation describing the screening of the Coulomb potential inside heavy neutral atoms is reconsidered. An accurate representation for its numerical solution was obtained by means of the variational principle. The proposed new solution has more precise asymptotic behaviour at large distances from the origin and allows us to obtain the exact value of the initial slope. The obtained new variational solution can also be developed in power series similar to the Baker's ones but more precise even than some series solutions that have been recently obtained within the homotopy analysis method and a modified variational method.
description: 7 pages, 4 tables, 2 figures
FAIR National Roadshow - Slovenia: IDs, Metadata, Interoperability: Open Science and Research Data Management Policies in Slovenia
Creators: name: Dillo, Ingrid
name: Skubic, Ivan
name: Wolmar Nyberg Åkerström
name: Ojsteršek, Milan
name: Sophie Aubin, Engineer
name: Nordling, Josefine
name: Priddy, Mike
name: Davidson, Joy
Publisher: name: Zenodo
Year: 2023
Subjects: PID, Metadata, Interoperability, Open Science, Research Data Management

description: These slides were presented during the FAIR National Roadshow Slovenia, on 28th September 2023, to showcase existing recommendations, good practices, and assessment tools that can help the Research community members start (or continue) their journey to becoming more FAIR-enabling and actively contribute to the European Open Science Cloud. Registration for this webinar was free and open to all. The event page is available at https://fair-impact.eu/events/national-roadshows/pids-metadata-interoperability-open-science-and-research-data-management
The Association of Auditory Threatful Stimuli and Neutral Images: Involuntary Adaptive Memory
Creators: name: Ergen, Irem
name: Akçay, Çağlar
name: Gulgoz, Sami
Publisher: name: Open Science Framework
Year: 2022

description: Human memory encodes and retrieves survival-related information more readily than other types of information. In the current study, we ask whether survival-related auditory stimuli lead to more involuntary visual memories than neutral auditory stimuli. We hypothesize that survival-related sounds will give an encoding and retrieval advantage to neutral pictures compared to the neutral sounds.
ENTRE A INDIFERENÇA E A CUMPLICIDADE
Creators: name: Pavao Santana, Jose Claudio
Publisher: name: Zenodo
Year: 2025

description: Ano 11 – n. 01/2023 – https://doi.org/10.5281/zenodo.8332756

Quando a Constituição da República foi escrita (com todas as

imperfeições contingentes) foi feito o que era o possível. Previa-se

vida longa a ela inobstante tenha sido alertado que com ela

ninguém conseguiria governar. Foi mais ou menos o que disse um

dos mais experientes políticos do Brasil – o ex-presidente José

Sarney.
title: Evaluation of sonically enhanced AGMD for industrial scale water treatment
Creators: name: Naji, Osamah Allawi
Publisher: name: University of Southern Queensland
Year: 2019
Subjects: subject: 090703 Environmental Technologies

description: As the global supply of freshly available water becomes a scarce commodity, low energy and cost-effective schemes to reuse and rectify contaminated water sources are becoming essential. This research investigates air-gap membrane distillation (AGMD), a novel low energy technology aimed at reclamation of contaminated water sources. While previous studies have delved into the control mechanisms of AGMD, they have only been used at extremely small scales, and cannot be readily expanded to an industrial level. In this study, key parameters which affect permeate-flux production such as feedwater temperature, concentration and flow rates were compared with two membrane types on an AGMD system which was around 14 - 18 times larger than the typical systems previously studied.

A novel remediation method has been developed to tackle membrane fouling which is the most commonly encountered problem in membrane technologies. Without cleaning, membrane fouling decreased permeate-flux by approximately 25% after 70 hrs of running with feedwater of 4000 - 12 000 μS/cm. In stark contrast, the external application of ultrasonic energy with a low power range of 40 - 120 W/m2, resulted in a consistently high permeate-flux production (200 - 300 % compared to non-sonicated AGMD) with no signs of fouling evident after a 70 hrs of operation. With this low level of ultrasonic power, the occurrence of cavitational effects is highly unlikely. Hence, the observed permeate-flux improvement was attributed mainly to cleaning effects, along with mass and heat transfer enhancements. This was confirmed by microscopic examination of the membrane surface, which showed no signs of fouling or damage afterwards.
Sex differences in anxiety and fear learning behavior following genetic manipulation of the 5-HT1A receptor in the bed nucleus of the stria terminalis (BNST)
Creators: name: Dorrier, Cayce
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The bed nucleus of the stria terminalis (BNST) is a critical node in the fear and anxiety circuitry of the brain that plays a key role in an organism’s ability to respond to stress. Serotonin 1A (5-HT1A) receptor signaling in the BNST has been implicated in anxiety and fear-related behavior using acute pharmacological manipulations that target pre- and post-synaptic receptors (Levita et al., 2004; Gomes et al., 2012). The goal of this project is to elucidate the role of post-synaptic 5-HT1A receptors within the BNST in anxiety, fear, and depressive-like behavior using a genetic deletion approach that selectively targets postsynaptic 5-HT1A receptors. Viral vectors containing the gene for Cre recombinase and a fluorescent tag (AAV5-Cre-GFP) or a control vector (AAV5-GFP) were infused into the BNST of genetically modified male and female 5-HT1A receptor flox mice. One month later, behavior on the elevated plus maze (EPM), open field, forced swim, novelty-suppressed feeding and fear conditioning assays were assessed. The results of this project indicate that the genetic deletion of 5-HT1ARs in the BNST has an anxiolytic-like effect in the EPM but enhances fear consolidation and contextual fear following a tone-shock protocol in male mice. These seemingly discrepant results may reflect the fact that under low stress conditions (e.g. the EPM), deletion of the 5-HT1A receptor disinhibits BNST output neurons which are anxiolytic (Kim et al., 2013; Jennings et al., 2013). In high stress (e.g. footshock) conditions, local neurons are recruited which are both anxiogenic and fear-enhancing (Levita et al, 2004). Deletion of 5-HT1A receptors from these neurons potentiates their fear enhancing actions, resulting in an increase in fear consolidation and contextual fear. The behavioral phenotypes of the female mice following this genetic manipulation were less pronounced, which could be due to the anatomical differences of the BNST between male and female mice.
Enzyme Kinetics: How Quickly Can Acetylcholinesterase Break Up Your Thoughts?
Creators: name: Pie, Hannah
name: Starz-Gaiano, Michelle
Publisher: name: QUBES Educational Resources
Year: 2023

description: This module contains exercises designed to help upper-level cell biology students understand the common graphical methods used to evaluate enzyme activity and to see the impact of inhibitors on this activity.
Accurate determination of the Boltzmann constant by Doppler spectroscopy: Towards a new definition of the kelvin
Creators: name: Darquié, Benoît
name: Mejri, Sinda
name: Sow, Papa Lat Tabara
name: Lemarchand, Cyril
name: Triki, Meriam
name: Tokunaga, Sean
name: Bordé, Christian J.
name: Chardonnet, Christian
name: Daussy, Christophe
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Accurate molecular spectroscopy in the mid-infrared region allows precision measurements of fundamental constants. For instance, measuring the linewidth of an isolated Doppler-broadened absorption line of ammonia around 10 $μ$m enables a determination of the Boltzmann constant k B. We report on our latest measurements. By fitting this lineshape to several models which include Dicke narrowing or speed-dependent collisional effects, we find that a determination of k B with an uncertainty of a few ppm is reachable. This is comparable to the best current uncertainty obtained using acoustic methods and would make a significant contribution to any new value of k B determined by the CODATA. Furthermore, having multiple independent measurements at these accuracies opens the possibility of defining the kelvin by fixing k B, an exciting prospect considering the upcoming redefinition of the International System of Units.
description: proceedings of the ICAP 2012 conference (23rd International Conference on Atomic Physics). arXiv admin note: text overlap with arXiv:1309.4549
title: Art after atrocity: post-Holocaust representation and affect
Creators: name: Elborne, Dan
Publisher: name: University of Southern Queensland
Year: 2019
Subjects: subject: 190599 Visual Arts and Crafts not elsewhere classified
subject: 220299 History and Philosophy of Specific Fields not elsewhere classified

description: The thesis investigates how to effectively address (through visual art) events of war and traumatic memory, with particular focus on the Holocaust and its subsequent visual representation. Through critical analysis and interviews with artists, theorists, historians, philosophers, writers and curators as well as the studio-based outcomes: the research creates a detailed analysis of traumatic, memory based visual representation and effective memorialization, and its purpose in contemporary society. The PhD advances the role, positioning and association of memory within the representation of horrific experience, and how this affects the creation, presentation and affecting qualities of art based on perpetrated atrocities and near incomprehensible human experience (Art After Atrocity). Accompanying the written research is a single, large-scale artwork produced in parallel to the written research. This artwork, Deathgate, consists of an individually handmade ceramic ‘stone’ for each of the 1.3 million people detained in the Auschwitz network of concentration camps creating an immersive installation environment.

The thesis involves the examination of memorialization, remembrance and traumatic memory in the context of visual art. The written research responds to 3 distinct research areas: firstly, German philosopher, Theodor Adorno’s suggestion that there can be ‘no poetry [art] after Auschwitz’, which opens discussion into the problematics of post-Holocaust representation. Secondly, ideas established by French philosopher, Jean- Francois Lyotard regarding the sublime as a way of visually and physically ‘presenting the unpresentable’, and lastly, German Jewish philosopher, Walter Benjamin’s theory concerning the transcendental qualities or ‘affective dimension’ of art (‘aura theory’) in order to establish and position the new term ‘aura of atrocity’ within the field of art theory. This term is directly associated to art with implications of traumatic memory and extreme, seemingly incomprehensible human capability and experience. The investigation of these three research areas will demonstrate the historical, and continually changing function, necessity for, and ongoing role of memorialization and the importance of visual art in relation to the continued representation, legacy and relevance of historical events such as the Holocaust.
Student Perception of Educational Best Practice Utilization in Introductory Computer Science Classes
Creators: name: Troftgruben, Jillian
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description: Lecture-based approaches to teaching introductory computer science classes have been proven to not be as effective as many other pedagogical approaches. Active learning, however, has been shown to be very effective but often is difficult to scale and takes professors a substantial amount of time to prepare for each class. This study focuses on five active learning techniques that can all be integrated into any lecture-style classroom in order to improve student engagement, increase inclusivity and community, and improve long-term learning. The techniques include quizzes, active coding, peer learning, relatable examples, and interactive activities. Other changes in activity during lecture that are not explicitly one of the five mentioned above are also tracked. This study monitors two introductory programming classes taught at the University of North Carolina at Chapel Hill to determine how commonly these active learning techniques are currently being included in lecture-style classrooms. To monitor classroom activity, the students used a web tool that assists in determining which active learning techniques the students perceive to be most helpful and in providing professors with better insight on how to improve their lectures. The results were ultimately inconclusive.
Predictions for squeezed back-to-back correlations of $ϕϕ$ and $K^+K^-$ in high-energy heavy-ion collisions by event-by-event hydrodynamics
Creators: name: Zhang, Yong
name: Zhang, Wei-Ning
Publisher: name: arXiv
Year: 2015
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We calculate the squeezed back-to-back correlation (BBC) functions of $ϕϕ$ and $K^+K^-$ for heavy-ion collisions at RHIC and LHC energies, using ($2+1$)-dimensional hydrodynamics with fluctuating initial conditions. The BBC functions averaged over event-by-event calculations for many events for the hydrodynamic sources are smoothed as a function of the particle momentum. For heavy-ion collisions of Au+Au at $\sqrt{s_{NN}}=200$ GeV, the BBC functions are larger than those for collisions of Pb+Pb at $\sqrt{s_{NN}}=2.76$ TeV. The BBC of $ϕϕ$ may possibly be observed in peripheral collisions at the RHIC and LHC energies. It is large for the smaller sources of Cu+Cu collisions at $\sqrt{s_{NN}}=200$ GeV.
description: 16 pages, 11 figures
Range-separated double-hybrid density-functional theory applied to periodic systems
Creators: name: Sansone, Giuseppe
name: Civalleri, Bartolomeo
name: Usvyat, Denis
name: Toulouse, Julien
name: Sharkas, Kamal
name: Maschio, Lorenzo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Other Condensed Matter (cond-mat.other)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Quantum chemistry methods exploiting density-functional approximations for short-range electron-electron interactions and second-order M{ø}ller-Plesset (MP2) perturbation theory for long-range electron-electron interactions have been implemented for periodic systems using Gaussian-type basis functions and the local correlation framework. The performance of these range-separated double hybrids has been benchmarked on a significant set of systems including rare-gas, molecular, ionic, and covalent crystals. The use of spin-component-scaled MP2 for the long-range part has been tested as well. The results show that the value of $μ$ = 0.5 bohr^{--1} for the range-separation parameter usually used for molecular systems is also a reasonable choice for solids. Overall, these range-separated double hybrids provide a good accuracy for binding energies using basis sets of moderate sizes such as cc-pVDZ and aug-cc-pVDZ.
Understanding Quantum Tunneling through Quantum Monte Carlo Simulations
Creators: name: Isakov, Sergei V.
name: Mazzola, Guglielmo
name: Smelyanskiy, Vadim N.
name: Jiang, Zhang
name: Boixo, Sergio
name: Neven, Hartmut
name: Troyer, Matthias
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The tunneling between the two ground states of an Ising ferromagnet is a typical example of many-body tunneling processes between two local minima, as they occur during quantum annealing. Performing quantum Monte Carlo (QMC) simulations we find that the QMC tunneling rate displays the same scaling with system size, as the rate of incoherent tunneling. The scaling in both cases is $O(Δ^2)$, where $Δ$ is the tunneling splitting. An important consequence is that QMC simulations can be used to predict the performance of a quantum annealer for tunneling through a barrier. Furthermore, by using open instead of periodic boundary conditions in imaginary time, equivalent to a projector QMC algorithm, we obtain a quadratic speedup for QMC, and achieve linear scaling in $Δ$. We provide a physical understanding of these results and their range of applicability based on an instanton picture.
description: 5 pages, 4 figures, 10 pages of supplemental material
Making Sense of Modeling in Elementary Literacy Instruction
Creators: name: Schutz, Kristine
name: Rainey, Emily
Publisher: name: University of Illinois at Chicago
Year: 2023
Subjects: Uncategorized

description: Although modeling is an instructional approach commonly named in literacy education circles, the authors struggled to articulate the essential features of modeling to preservice teachers. This was a problem for them and for the preservice teachers with whom they worked. The problem also represents a larger one in the field, which is that educators are still building that which is the foundation of most other professions: a shared professional language. Efforts to build a shared professional language are important for literacy educators seeking to reflect on and improve their craft, literacy leaders working to make change at the school level, and mentor teachers and teacher educators tasked with preparing the next generation of teachers. The authors describe their efforts to articulate and represent modeling in elementary literacy instruction.
Dietary Restraint Scales and Their Relationship to Generalized Executive Functioning
Creators: name: Thompson, Andrew David, Jr.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Dietary restraint may be defined as the intentional restriction of caloric intake. Due to the
association between caloric intake and weight, dietary restraint may be used to reduce weight or
prevent weight gain. This is particularly important considering the prevalence of obesity and its
negative effects. However, reported dietary restraint may not be associated with actual decreases
in intake. Impulsivity may be one factor which determines whether attempts at dietary restraint
are successful. In this study, we assessed BMI, two self-report measures of dietary restraint, and
a behavioral and a self-report measure of impulsivity in a sample of twenty healthy-weight
individuals. The behavioral measure of impulsivity was negatively associated with one measure
of dietary restraint, but the self-report measure of impulsivity was not associated with dietary
restraint, and no association was observed between dietary restraint and BMI. Future studies
should utilize a larger sample with a more inclusive BMI range.
Hydrodynamical Description of the QCD Dirac Spectrum at Finite Chemical Potential
Creators: name: Liu, Yizhuang
name: Warchol, Piotr
name: Zahed, Ismail
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We present a hydrodynamical description of the QCD Dirac spectrum at finite chemical potential as an uncompressible droplet in the complex eigenvalue space. For a large droplet, the fluctuation spectrum around the hydrostatic solution is gapped by a longitudinal Coulomb plasmon, and exhibits a frictionless odd viscosity. The stochastic relaxation time for the restoration/breaking of chiral symmetry is set by twice the plasmon frequency. The leading droplet size correction to the relaxation time is fixed by a universal odd viscosity to density ratio $η_O/ρ_0=(β-2)/4$ for the three Dyson ensembles $β=1,2,4$.
description: 5 pages
Can recurrence networks show small world property?
Creators: name: Jacob, Rinku
name: Harikrishnan, K. P.
name: Misra, R.
name: Ambika, G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: Recurrence networks are complex networks, constructed from time series data, having several practical applications. Though their properties when constructed with the threshold value εchosen at or just above the percolation threshold of the network are quite well understood, what happens as the threshold increases beyond the usual operational window is still not clear from a complex network perspective. The present Letter is focused mainly on the network properties at intermediate-to-large values of the recurrence threshold, for which no systematic study has been performed so far. We argue, with numerical support, that recurrence networks constructed from chaotic attractors with εequal to the usual recurrence threshold or slightly above cannot, in general, show small-world property. However, if the threshold is further increased, the recurrence network topology initially changes to a small-worldstructure and finally to that of a classical random graph as the threshold approaches the size of the strange attractor.
description: 17 pages, 6 figures, published in Physics Letters A
Evaluation of AAV Vector Constructs to Titrate Transgene Expression
Creators: name: Peralta, Michael
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Adeno-associated virus (AAV) gene therapy vectors represent a promising method of
treating inherited disorders. Regulatory elements, such as polyadenylation sequences or introns,
combined with specific promoters, have been known to affect post-infection viral transgene
expression levels. An important component of therapy design is the engineering of precise
expression control while staying within the DNA capacity constraints of the viral capsid. Under- or
over-expression of the delivered gene can cause adverse effects in the target cell population,
such as cell death. While many regulatory elements have been characterized in isolation, the
manner in which they interact to affect expression has not been well characterized.
Midwifery Qualification in Primary Care
Creators: name: Md.Sharif, Shakirah
name: Shauki, Nor
name: SARARAKS, SONDI
name: Hong, Fun
name: Ali, Nur
name: Lin, Kong
name: Jailani, Anis
name: Sindot, Salbiah
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Family health
subject: MAera
subject: Post-data collection
subject: Protocol
subject: Rapid review

description: Rapid evidence synthesis on the midwifery competency/qualification in countries with MMR <40 per 100,000 live births based on 2015 World Bank data
An X-shooter composite of bright 1 < z < 2 quasars from UV to infrared
Creators: name: Selsing, Jonatan
name: Fynbo, Johan P. U.
name: Christensen, Lise
name: Krogager, Jens-Kristian
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Quasi-stellar object (QSO) spectral templates are important both to QSO physics and for investigations that use QSOs as probes of intervening gas and dust. However, combinations of various QSO samples obtained at different times and with different instruments so as to expand a composite and to cover a wider rest frame wavelength region may create systematic effects, and the contribution from QSO hosts may contaminate the composite. We have constructed a composite spectrum from luminous blue QSOs at 1 < z < 2.1 selected from the Sloan Digital Sky Survey (SDSS). The observations with X-shooter simultaneously cover ultraviolet (UV) to near- infrared (NIR) light, which ensures that the composite spectrum covers the full rest-frame range from Ly$β$ to 11350 $Å$ without any significant host contamination. Assuming a power-law continuum for the composite we find a spectral slope of $α_λ$ = 1.70+/-0.01, which is steeper than previously found in the literature. We attribute the differences to our broader spectral wavelength coverage, which allows us to effectively avoid fitting any regions that are affected either by strong QSO emissions lines (e.g., Balmer lines and complex [Fe II] blends) or by intrinsic host galaxy emission. Finally, we demonstrate the application of the QSO composite spectrum for evaluating the reddening in other QSOs.
description: 14 pages, 8 figures, accepted for publication in A&A
An Optimal Single-Path Routing Algorithm in the Datacenter Network DPillar
Creators: name: Erickson, Alejandro
name: Kiasari, Abbas Eslami
name: Navaridas, Javier
name: Stewart, Iain A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences
subject: B.4.3; C.2.1

description: DPillar has recently been proposed as a server-centric datacenter network and is combinatorially related to (but distinct from) the well-known wrapped butterfly network. We explain the relationship between DPillar and the wrapped butterfly network before proving that the underlying graph of DPillar is a Cayley graph; hence, the datacenter network DPillar is node-symmetric. We use this symmetry property to establish a single-path routing algorithm for DPillar that computes a shortest path and has time complexity $O(k)$, where $k$ parameterizes the dimension of DPillar (we refer to the number of ports in its switches as $n$). Our analysis also enables us to calculate the diameter of DPillar exactly. Moreover, our algorithm is trivial to implement, being essentially a conditional clause of numeric tests, and improves significantly upon a routing algorithm earlier employed for DPillar. Furthermore, we provide empirical data in order to demonstrate this improvement. In particular, we empirically show that our routing algorithm improves the average length of paths found, the aggregate bottleneck throughput, and the communication latency. A secondary, yet important, effect of our work is that it emphasises that datacenter networks are amenable to a closer combinatorial scrutiny that can significantly improve their computational efficiency and performance.
description: Accepted in IEEE Transactions on Parallel & Distributed Systems, July 2016
Perturbations of vortex ring pairs
Creators: name: Gubser, Steven S.
name: Horn, Bart
name: Parikh, Sarthak
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study pairs of co-axial vortex rings starting from the action for a classical bosonic string in a three-form background. We complete earlier work on the phase diagram of classical orbits by explicitly considering the case where the circulations of the two vortex rings are equal and opposite. We then go on to study perturbations, focusing on cases where the relevant four-dimensional transfer matrix splits into two-dimensional blocks. When the circulations of the rings have the same sign, instabilities are mostly limited to wavelengths smaller than a dynamically generated length scale at which single-ring instabilities occur. When the circulations have the opposite sign, larger wavelength instabilities can occur.
description: 62 pages, 21 figures
MP.2018.895.Witt
Creators: name: Schönbrodt, Felix
name: Carlsson, Rickard
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Meta-Psychology
subject: Submission

description: Submission to Meta-Psychology. Contains the full history, including all correspondence, decisions, reviews, revisions etc. Anyone can participate in peer review directly at this OSF project page, by sending the editor an email, or through discussion on social media. The preferred way of open commenting, however, is to use the hypothes.is integration at PsyArxiv and directly comment on the PDF there.
Dysregulation of Phospholipase C gamma1 in Adult T-cell Leukemia/Lymphoma
Creators: name: Keith, Nicholas
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2018

description: Phospholipase C gamma1 (PLCg1) hydrolyzes membrane-bound phosphatidylinositol 4,5-bisphosphate into the classical second messengers inositol 1,4,5-trisphosphate and diacylglycerol, both of which participate in various downstream signal transduction cascades. These signaling cascades help control various cellular functions, from embryonic development to cell migration. Interestingly, PLCg1 was recently reported to be mutated with a frequency of ~40% in a cohort of patients with adult T-cell leukemia/lymphoma (ATL), making it the most frequently mutated gene in this cancer. However, it is not known how these mutations affect the catalytic activity of PLCg1, and we hypothesized that mutant forms of PLCg1 found in ATL have elevated phospholipase activity. The accumulation of inositol phosphates, a readout of PLCg1 activity, was quantified after transient over-expression of mutant forms of PLCg1 in human embryonic kidney (HEK293) cells. In addition, the activity of these PLCg1 mutants was also quantified separately after receptor-dependent activation. All 20 mutations found in ATL constitutively activated PLCg1, increasing basal activity 8- to 1700-fold relative to wild-type. Furthermore, all mutants also had further enhanced activity in the context of epidermal growth factor receptor activation. These results corroborate other findings suggesting that PLCg1 is an oncogene and may be a viable drug target for treatment of ATL and other cancers.
"Dangerous & Moving: posthuman desire in the fleeting wilderness of content"
Creators: name: Johnson, Rachel
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The Animal’s Song: music as the ocean of meaning from which the named and numbered rivers of human language have channeled and carved out words. (Meaning is never held solely within the signifier of the word, especially when the word is intoned, or musical.) Even more than the capacity for language, a narrative understanding of the world has traditionally been viewed as an essential part of the human experience. Through narrative, the chaos of stimuli we encounter becomes building blocks that shifting into place to build expectations and understandings that give us a sense of place, time, and identity. It is through narrative that we organize life and understand beginnings and ends. Narratives are related to the biological in that they originate in experience and observation of life; however, narratives, passed down through culture, also color how we interpret experience. Our actions, guided by cultural morals and norms, then map these guiding narratives back onto the world. In this way the loop between the narrative that is a distillation of Life and the Life that lies outside the narrative is connected through human action.
Linked and knotted chimera filaments in oscillatory systems
Creators: name: Lau, Hon Wai
name: Davidsen, Jörn
Publisher: name: arXiv
Year: 2015
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a novel topological superstructure combining knotted filaments and synchronization defect sheets.
description: 5 figures, supplemental pdf (supplementary video at the publication website)
On the persistence of two small-scale problems in ΛCDM
Creators: name: Pawlowski, Marcel S.
name: Famaey, Benoit
name: Merritt, David
name: Kroupa, Pavel
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We investigate the degree to which the inclusion of baryonic physics can overcome two long-standing problems of the standard cosmological model on galaxy scales: (i) the problem of satellite planes around Local Group galaxies, and (ii) the "too big to fail" problem. By comparing dissipational and dissipationless simulations, we find no indication that the addition of baryonic physics results in more flattened satellite distributions around Milky-Way-like systems. Recent claims to the contrary are shown to derive in part from a non-standard metric for the degree of flattening, which ignores the satellites' radial positions. If the full 3D positions of the satellite galaxies are considered, none of the simulations we analyse reproduce the observed flattening nor the observed degree of kinematic coherence of the Milky Way satellite system. Our results are consistent with the expectation that baryonic physics should have little or no influence on the structure of satellite systems on scales of hundreds of kiloparsecs. Claims that the "too big to fail" problem can be resolved by the addition of baryonic physics are also shown to be problematic.
description: 13 pages, 5 figures. Accepted for publication in ApJ. Partially written in response to arXiv:1412.2748
Friends of Hot Jupiters III: An Infrared Spectroscopic Search for Low-Mass Stellar Companions
Creators: name: Piskorz, Danielle
name: Knutson, Heather A.
name: Ngo, Henry
name: Muirhead, Philip S.
name: Batygin, Konstantin
name: Crepp, Justin R.
name: Hinkley, Sasha
name: Morton, Timothy D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Surveys of nearby field stars indicate that stellar binaries are common, yet little is known about the effects that these companions may have on planet formation and evolution. The Friends of Hot Jupiters project uses three complementary techniques to search for stellar companions to known planet-hosting stars: radial velocity monitoring, adaptive optics imaging, and near-infrared spectroscopy. In this paper, we examine high-resolution K band infrared spectra of fifty stars hosting gas giant planets on short-period orbits. We use spectral fitting to search for blended lines due to the presence of cool stellar companions in the spectra of our target stars, where we are sensitive to companions with temperatures between 3500-5000 K and projected separations less than 100 AU in most systems. We identify eight systems with candidate low-mass companions, including one companion that was independently detected in our AO imaging survey. For systems with radial velocity accelerations, a spectroscopic non-detection rules out scenarios involving a stellar companion in a high inclination orbit. We use these data to place an upper limit on the stellar binary fraction at small projected separations, and show that the observed population of candidate companions is consistent with that of field stars and also with the population of wide-separation companions detected in our previous AO survey. We find no evidence that spectroscopic stellar companions are preferentially located in systems with short-period gas giant planets on eccentric and/or misaligned orbits.
description: 15 pages, 5 figures, accepted to ApJ
Newly Determined Explosion Center of Tycho's Supernova and the Implications for Proposed Ex-Companion Stars of the Progenitor
Creators: name: Xue, Zhichao
name: Schaefer, Bradley E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: `Star G', near the center of the supernova remnant of Tycho's SN1572, has been claimed to be the ex-companion star of the exploding white dwarf, thus pointing to the progenitor being like a recurrent nova. This claim has been controversial, but there have been no confident proofs or disproofs. Previously, no has seriously addressed the question as to the exact explosion site in 1572. We now provide accurate measures of the supernova position by two radically different methods. Our first method is to use the 42 measured angular distances between the supernova in 1572 and bright nearby stars, with individual measures being as good as 84 arc-seconds, and all resulting in a position with a 1-$σ$ error radius of 39 arc-seconds (including systematic uncertainties). Our second method is to use a detailed and realistic expansion model for 19 positions around the edge of the remnant, where the swept-up material has measured densities, and we determine the center of expansion with a chi-square fit to the 19 measured radii and velocities. This method has a 1-$σ$ error radius of 7.5 arc-seconds. Both measures are substantially offset from the geometric center, and both agree closely, proving that neither has any significant systematic errors. Our final combined position for the site of the 1572 explosion is J2000 $α$=0h 25m 15.36s, $δ=64^{\circ} 8' 40.2"$, with a 7.3 arc-second 1-sigma uncertainty. Star G is rejected at the 8.2-$σ$ confidence level. Our new position lies mostly outside the region previously searched for ex-companion stars.
description: to be published in ApJ
Possessive Constructions in P’urépecha
Creators: name: Zhu, Yining
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2018

description: In this paper, my objective is to present the possessive constructions of P’urépecha and to discuss these constructions under the current findings of possessive constructions cross-linguistically.Some of the findings are different from the current literature on P’urépecha: i) genitive case marker functioning as a clitic instead of a suffix; ii) more restrictive distribution of inalienable possessive marking. Others have rarely been discussed: four possessive verbs; ii) the integration of locative and possessive expressions. P’urépecha has four verbs that cover different types of predicative possession. The distribution of the four verbs exhibits split possession and unity of possessive and locative structure.
Maurizio Vaudagna
Creators: name: VV., AA.
Publisher: name: RSAJournal
Year: 2023

description: Andrea Carosso, Simone Cinotto, Ferdinando Fasce, Cristina Iuli, Marco Mariano and Elisabetta Vezzosi remember Maurizio Vaudagna
description: RSAJournal, Vol. 34 (2023): Memories
The clustering of dark matter halos: scale-dependent bias on quasi-linear scales
Creators: name: Jose, Charles
name: Lacey, Cedric G.
name: Baugh, Carlton M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We investigate the spatial clustering of dark matter halos, collapsing from $1-4 σ$ fluctuations, in the redshift range $0 - 5$ using N-body simulations. The halo bias of high redshift halos ($z \geq 2$) is found to be strongly non-linear and scale-dependent on quasi-linear scales that are larger than their virial radii ($0.5-10$ Mpc/h). However, at lower redshifts, the scale-dependence of non-linear bias is weaker and and is of the order of a few percent on quasi-linear scales at $z \sim 0$. We find that the redshift evolution of the scale dependent bias of dark matter halos can be expressed as a function of four physical parameters: the peak height of halos, the non-linear matter correlation function at the scale of interest, an effective power law index of the {\it rms} linear density fluctuations and the matter density of the universe at the given redshift. This suggests that the scale-dependence of halo bias is not a universal function of the dark matter power spectrum, which is commonly assumed. We provide a fitting function for the scale dependent halo bias as a function of these four parameters. Our fit reproduces the simulation results to an accuracy of better than 4 % over the redshift range $0\leq z \leq 5$. We also extend our model by expressing the non-linear bias as a function of the linear matter correlation function. It is important to incorporate our results into the clustering models of dark matter halos at any redshift, including those hosting early generations of stars and galaxies before reionization.
description: Accepted for publication in MNRAS
The Secondary and Tertiary Structure of the Satellite Tobacco Mosaic Virus RNA Genome
Creators: name: Larman, Bridget
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Satellite tobacco mosaic virus (STMV) is a small plant virus that is a member of the
icosahedral plus-strand RNA virus family. A large portion of known viruses fall into this family
including larger more complex viruses such as poliovirus. STMV is one of the most basic viruses
in this family and was thus chosen as a model system on which to study plus-strand icosahedral
RNA viruses. Many biological processes in these viruses are RNA-mediated but very little is
known about the higher order structures of the RNA. This makes it difficult to determine how
RNA structure governs function. Two structures have been proposed for the structure of STMV
RNA. However, there is little consensus between the models and very few models of the RNA
within the virion exist. We investigated the secondary and tertiary structure of the STMV RNA
genome both within and isolated from the virion.
Here we show that the STMV ex virio and in virio RNA structures are dominated by
long-range interactions. In general, both structures form a well-defined central T-shaped domain
that is flanked on either side by regions of local stem loops. We observed significant differences
between the ex virio and in virio predicted structures in one region of the central T-shaped
domain. We found that neither of the structures displayed many tertiary interactions. We propose
that the difference between ex virio and in virio structure indicates that the STMV RNA adopts
multiple conformations depending on the functional state.
Microwave Boson Sampling
Creators: name: Peropadre, Borja
name: Guerreschi, Gian Giacomo
name: Huh, Joonsuk
name: Aspuru-Guzik, Alán
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The first post-classical computation will most probably be performed not on a universal quantum computer, but rather on a dedicated quantum hardware. A strong candidate for achieving this is represented by the task of sampling from the output distribution of linear quantum optical networks. This problem, known as boson sampling, has recently been shown to be intractable for any classical computer, but it is naturally carried out by running the corresponding experiment. However, only small scale realizations of boson sampling experiments have been demonstrated to date. Their main limitation is related to the non-deterministic state preparation and inefficient measurement step. Here, we propose an alternative setup to implement boson sampling that is based on microwave photons and not on optical photons. The certified scalability of superconducting devices indicates that this direction is promising for a large-scale implementation of boson sampling and allows for more flexible features like arbitrary state preparation and efficient photon-number measurements.
Parikh matrices and Parikh Rewriting Systems
Creators: name: Teh, Wen Chean
Publisher: name: arXiv
Year: 2015
Subjects: subject: Formal Languages and Automata Theory (cs.FL)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Since the introduction of the Parikh matrix mapping, its injectivity problem is on top of the list of open problems in this topic. In 2010 Salomaa provided a solution for the ternary alphabet in terms of a Thue system with an additional feature called counter. This paper proposes the notion of a Parikh rewriting system as a generalization and systematization of Salomaa's result. It will be shown that every Parikh rewriting system induces a Thue system without counters that serves as a feasible solution to the injectivity problem.
description: 15 pages, preprint