cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The Biological and Biochemical Characterization of KRAS4B Q61 Mutants
Creators: name: Cooke, Adelaide
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2018

description: Nearly 30% of human cancers have mutations in one of the three RAS genes. Despite over 30 years of dedicated research, no effective therapies against cancers caused by RAS oncogene mutations have reached clinical application. Striking differences in the frequencies of missense mutations seen in RAS-mutant cancers suggest that RAS mutations previously assumed to equally result in activation have distinct consequences on protein structure and function. We hypothesized that different point mutations at the hotspot residue Q61 will have distinct consequences on RAS structure and function, resulting in unique biological activities. We evaluated the effects on biochemical and biological properties of the common mutants KRAS Q61H, KRAS Q61L, and KRAS Q61R and the rare KRAS Q61E and KRAS Q61P. We found that these KRAS Q61 mutants exhibited varying trends of guanine nucleotide exchange as well as binding to RAS effector domains in vitro. KRAS Q61L exhibited increased GEF-stimulated nucleotide exchange, whereas the Q61R and Q61P mutants were poorly responsive to GEFs. Ectopic expression of KRAS Q61 mutants in NIH 3T3 and RIE-1 cells revealed variable mutation-dependent effector signal activation, morphologic transformation and anchorage-independent growth. Unlike the other mutants, KRAS Q61E and KRAS Q61P did not appear to be activated based on morphological traits. Analysis of signaling through RAS effectors indicated these mutants were still activated; however, it still suggested that they are biologically different from each other. Q61 mutants do not equally induce actin stress fiber formation, cell migration and KRAS-dependent macropinocytosis. Our studies suggest that determination of RAS mutation-specific effects will allow for identification of mutation-selective vulnerabilities and therapies for KRAS Q61 mutants.
Artifact for "Coverage Guided Fault Injection for Cloud Systems", accepted at ICSE 2023
Creators: name: Gao, Yu
name: Dou, Wensheng
name: Wang, Dong
name: Feng, Wenhan
name: Wei, Jun
name: Zhong, Hua
name: Huang, Tao
Publisher: name: figshare
Year: 2023
Subjects: Software testing, verification and validation

description: This artifact bundles all evaluation resources related to the paper: Yu Gao, Wensheng Dou, Dong Wang, Wenhan Feng, Jun Wei, Hua Zhong, Tao Huang. 2023. Coverage Guided Fault Injection for Cloud Systems. In 45th International Conference on Software Engineering (ICSE '23).
 The full package contains: source code of our tool, tool used to run the experiments, scripts used in our experiments. Moreover, we provide .md files with guides on how to set up and run the experiments.
 In order to run the experiments, you will need Java 8 and Docker installed. More details can be found in "REQUIREMENTS.md".
 More information can be found in the "README.md" file included in this package.
Brief Follow-up on Recent Studies of Theia's Accretion
Creators: name: Kaib, Nathan A.
name: Cowan, Nicolas B.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Kaib & Cowan (2015) recently used terrestrial planet formation simulations to conclude that the moon-forming impactor (Theia) had only a ~5% or less chance of having the same oxygen isotope composition as Earth, while Mastrobuono-Battisti et al. (2015) used seemingly similar simulations and methods to arrive at a higher value of ~20% or more. Here we derive the results of both papers from a single set of simulations. Compared to Kaib & Cowan (2015), the analysis of Mastrobuono-Battisti et al. (2015) systematically yields more massive Theia analogs and imposes flatter isotopic gradients across the original protoplanetary disk. Both of these effects diminish isotopic differences between Earth and Theia analogs. While it is notoriously difficult to produce systems resembling our actual terrestrial planets, the analysis of Kaib & Cowan (2015) more often selects and analyzes Earth and Mars analogs at orbital locations near the real planets. Given this, we conclude that the greater isotopic differences between Earth and Theia found in Kaib & Cowan (2015) better reflect the predictions of terrestrial planet formation models. Finally, although simulation uncertainties and a terrestrial contribution to Moon formation enhance the fraction of Theia analogs consistent with the canonical giant impact hypothesis, this fraction still remains in the 5-8% range.
description: 5 pages, 4 figures, accepted to Icarus
title: Σχεδιασμός και ανάπτυξη μιας διαδικτυακής πλατφόρμας διδασκαλίας γλωσσών προγραμματισμού
title: Design and development of a web application for teaching programming languages
titleType: AlternativeTitle
Creators: name: Γιαννόπουλος, Παναγιώτης
Publisher: name: Πανεπιστήμιο Πειραιώς
Year: 2022
Subjects: subject: Web
subject: HTML
subject: CSS
subject: JavaScript
subject: PHP
subject: MySQL
subject: jQuery
subject: Ajax
subject: CodeMirror
subject: Linux

description: Σκοπός της μεταπτυχιακής αυτής εργασίας είναι η σχεδίαση και η δημιουργία μίας πλατφόρμας για το εργαστήριο Τεχνολογίες Διαδικτύου. Κατά τη διάρκεια της πανδημίας δημιουργήθηκε η ανάγκη της τηλεδιάσκεψης. Οι φοιτητές δε μπορούσανε να πάνε στα εργαστήρια με αποτέλεσμα οι καθηγητές να διαμορφώσουν το εκπαιδευτικό υλικό ώστε να είναι δυνατή η πρόσβαση και η καθοδήγηση από το σπίτι και από τον υπολογιστή. Αποφασίστηκε, να δημιουργηθεί μια πλατφόρμα στην οποία οι φοιτητές θα έχουν πρόσβαση απομακρυσμένα και θα μπορούν να γνωρίσουν γλώσσες σήμανσης όπως είναι η HTML και η CSS και τη γλώσσα προγραμματισμού JavaScript. Η πλατφόρμα επιπλέον παρέχει ένα εργαλείο στο οποίο ο φοιτητής θα μπορεί να γράψει κώδικα και να δει τα αποτελέσματά του καθώς και να μάθει από τα σφάλματα που προκύπτουν. Τέλος, υπάρχει η δυνατότητα διαμοιρασμού του κώδικα του με τον καθηγητή μέσω της πλατφόρμας. Το υλικό που έχει τοποθετηθεί στην πλατφόρμα προέχεται από το εγχειρίδιο του εργαστηρίου.
Cnidoscolus aurelii Fern. Casas, Fontqueria
Creators: name: Maya-Lastra, Carlos A.
name: Steinmann, Victor W.
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Malpighiales
Euphorbiaceae
Cnidoscolus
Cnidoscolus aurelii

description: 12. Cnidoscolus aurelii Fern.Casas, Fontqueria 55: 216 (2004). Type:— BRAZIL. Tocantins: Aurora do Tocantins, 12 km N, na rodovia Campos Belos–Taguatinga, 500 m, 5 October 2000, G.G. Hatschbach, E. Barbosa & A. Schinini 70848 (holotype MBM-0249332!; isotypes CTES-0000733!, U-0085365!).
 Distribution:— Brazil (microendemic).
description: Published as part of Maya-Lastra, Carlos A. & Steinmann, Victor W., 2018, A Nomenclator of Cnidoscolus (Euphorbiaceae), pp. 1-30 in Phytotaxa 346 (1) on pages 6-7, DOI: 10.11646/phytotaxa.346.1.1, http://zenodo.org/record/13708395
Salamandra salamandra merged assembly
Creators: name: Libro, Pietro
name: Chiocchio, Andrea
name: De Risky, Erika
name: Di Martino, Jessica
name: Bisconti, Roberta
name: Castrignanò, Tiziana
name: Canestrelli, Daniele
Publisher: name: figshare
Year: 2023
Subjects: Bioinformatics and computational biology not elsewhere classified

description: Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we contribute to the study of the genetic underpinnings of dispersal-related behavioral variation by assembling and annotating the first de novo transcriptome of the head tissues of Salamandra salamandra. Although dispersal occurs mostly during the post-metamorphic terrestrial life stage in this species, variation in dispersal-related personality traits is already evident at the aquatic larval stage, making it an excellent candidate species for studies of carry-over effects. We employed a structured pipeline to de-novo assemble and annotate transcripts from RNA-Seq in a set of individuals representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully de novo assembled and annotated. The high-quality assembly was confirmed by comparing BUSCO, DETONATE and TransRate with the S. salamandra dataset. By aligning the contigs against the de novo transcriptome we obtained a percentage of mapping higher than 94%. The homology annotation performed with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NCBI nr, Swiss-Prot and TrEMBL. The domain and site protein prediction made with InterProScan led to 9850 GO-annotated contigs. This de-novo transcriptome represents reliable reference for whole transcriptome and proteome studies of other amphibians, for designing primers to clone specific genes or monitor their expression, and for analyzing comparative gene expression profiles between alternative behavioral types.
Shadow of Schwarzschild Black Hole in the Cold Dark Matter Halo
Creators: name: Ma, Shi-Jie
name: Ma, Tian-Chi
name: Deng, Jian-Bo
name: Hu, Xian-Ru
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The Schwarzschild black hole in the Cold Dark Matter (CDM) halo is studied, and the radiation laws of the thin accretion disk near the black hole are discussed and summarized. The orbits of light around the black hole are also calculated. Additionally, using the Novikov-Thorne model's light intensity function of the thin accretion disk, it is possible to solve for the shadow created by the thin accretion disk near the Schwarzschild black hole as well as the observed luminosity of the disk.
description: 23pages
Economies of Expansion: Chinese Peacekeeping Contributions Bolster "China's Peaceful Development"
Creators: name: Alderman, Morgan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description: Over the past thirty years China has shifted its approach to United Nations (UN) peacekeeping operations from determined opposition to leading supporter. During this time period, China has also become a dominant force globally. With the second largest economy and expansive global infrastructure projects, China is positioning itself as the next great power. Under China’s “peaceful development” strategy, its global engagement with UN peacekeeping and international development are key components of China’s rising power. As a part of this, China’s continued economic success is not only a central aspect of Chinese grand strategy, but also plays an integral role in its peacekeeping contribution decision-making. Particularly concerned with the preservation of Chinese resource and raw material investments across Africa, China has elected to send more troops to support its growing economic interests in the region.  I thus argue that China's peacekeeping contributions are strategically motivated by Chinese economic interests abroad, and that China's peacekeeping contributions are sent to support Chinese economic interests abroad in the broader context of China's "peaceful development".
Global Properties of Neutral Hydrogen in Compact Groups
Creators: name: Walker, Lisa May
name: Johnson, Kelsey E.
name: Gallagher, Sarah C.
name: Privon, George C.
name: Kepley, Amanda A.
name: Whelan, David G.
name: Desjardins, Tyler D.
name: Zabludoff, Ann I.
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: Compact groups of galaxies provide a unique environment to study the evolution of galaxies amid frequent gravitational encounters. These nearby groups have conditions similar to those in the earlier universe when galaxies were assembled and give us the opportunity to witness hierarchical formation in progress. To understand how the compact group environment affects galaxy evolution, we examine the gas and dust in these groups. We present new single-dish GBT neutral hydrogen (HI) observations of 30 compact groups and define a new way to quantify the group HI content as the HI-to-stellar mass ratio of the group as a whole. We compare the HI content with mid-IR indicators of star formation and optical [g-r] color to search for correlations between group gas content and star formation activity of individual group members. Quiescent galaxies tend to live in HI-poor groups, and galaxies with active star formation are more commonly found in HI-rich groups. Intriguingly, we also find "rogue" galaxies whose star formation does not correlate with group HI content. In particular, we identify three galaxies (NGC 2968 in RSCG 34, KUG 1131+202A in RSCG 42, and NGC 4613 in RSCG 64) whose mid-IR activity is discrepant with the HI. We speculate that this mismatch between mid-IR activity and HI content is a consequence of strong interactions in this environment that can strip HI from galaxies and abruptly affect star-formation. Ultimately, characterizing how and on what timescales the gas is processed in compact groups will help us understand the interstellar medium in complex, dense environments similar to the earlier Universe.
description: Accepted to AJ
Assignment 5: meta-analysis (methods)
Creators: name: Singh, Jasmine
Publisher: name: Open Science Framework
Year: 2022

description: This project will use a meta-analysis design to understand the correlation between self-esteem and extraversion and its moderation by sex. This study will use RStudio and the Psychmeta package to calculate statistical estimates. Statistical estimates that will be used in this design include: p-values, confidence intervals and credibility intervals.
HERpetology: Gender, Power, and Snake Transformation in Edo Period Japan
Creators: name: Petersen, Haley
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: This essay will detail, through a close examination of three specific manifestations of snakes and women in Edo period literature, art, and theater, the ways in which these creatures were presented and understood by men and women at the time. Chapter 2, “From Snakes to Women: Folklore and Fairy Tales,” will consider the various ways in which snakes are perceived in Japanese folklore, the influences and motivation in the recording and presentation of traditional Japanese folk tales, and the popularity of such otherworldly encounters with shape-shifting snakes. Chapter 3, “Snake Women: Ghosts, Goblins, and Gender,” will discuss the category of bizarre Japanese monsters known as yōkai, which were regarded with a mixture of both dread and amusement during fashionable ghost-story parties, and their metaphorical allusions to Edo period sexuality and gender roles. Chapter 4, “From Women to Snakes: Demons and Damnation,” will delve into the female snake metamorphosis trope presented in Buddhist salvation tales, as well as its often discordant representations throughout several forms of secular entertainment, with a particular emphasis on the figure of the young woman in the famous play Dōjōji. By taking into account the vast landscape of beliefs concerning snakes and women, as well as of how an array of interpretations were presented to and understood by the Japanese people of the Edo period, this essay aims to unveil the subtle intricacies of gender and power in traditional Japanese culture.
Renormalization-Group Theory of 1D quasiperiodic lattice models with commensurate approximants
Creators: name: Gonçalves, Miguel
name: Amorim, Bruno
name: Castro, Eduardo V.
name: Ribeiro, Pedro
Publisher: name: arXiv
Year: 2022
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We develop a renormalization group (RG) description of the localization properties of onedimensional (1D) quasiperiodic lattice models. The RG flow is induced by increasing the unit cell of subsequent commensurate approximants. Phases of quasiperiodic systems are characterized by RG fixed points associated with renormalized single-band models. We identify fixed-points that include many previously reported exactly solvable quasiperiodic models. By classifying relevant and irrelevant perturbations, we show that phase boundaries of more generic models can be determined with exponential accuracy in the approximant's unit cell size, and in some cases analytically. Our findings provide a unified understanding of widely different classes of 1D quasiperiodic systems.
Inequality and Development in China
Creators: name: Xi, Jin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Using a panel data of China that covers the time period from 1997 to 2011, this
research studies the impacts of four factors on inequality – income level, emigration,
public spending on education, and public spending on infrastructure. This study
contributes to the literature with seven key findings. First, there is no strong evidence
that supports the Kuznets Hypothesis. Second, the impact of emigration on inequality
in the sending area shows significant heterogeneity across municipalities. Third, the
effect of emigration depends on the definition: overall, permanent emigration has
reducing effect, whereas temporary emigration and emigration of people who sought
employment have increasing effects. Forth, the impact of temporary emigration and
emigration of people who sought employment vary with the income level: they tend
to decrease inequality when income level is low, and increase inequality when income
level is high. Fifth, I find public spending on education increases inequality within
regions. Sixth, public spending on infrastructure has reducing effect on inequality.
Lastly, by using the lagged term, I find the income level affect inequality only after a
period of time.
Polarons in Binary Bose-Einstein Condensates
Creators: name: Liu, Ning
name: Tu, Z. C.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Bose polarons are quasiparticles formed through the interaction between impurities and Bose-Einstein condensates. In this paper, we derive an effective Fröhlich Hamiltonian using the generalized Bogoliubov transformation. The effective Fröhlich Hamiltonian encompasses two types of effective interactions: impurity-density (ID) coupling and impurity-spin (IS) coupling. Furthermore, we employ the Lee-Low-Pines variational approach to investigate the relevant properties of Bose polarons induced by the ID and IS coupling. These properties include the ground state energy, effective mass, and average number of virtual phonons. Our findings reveal that the contribution resulting from IS couplings to the ground energy decreases to zero near the miscible-immiscible boundary. Additionally, the increase of the IS coupling induces a greater number of virtual phonons, impeding the movement of impurities and leading to a significant increase in the effective mass of Bose polarons.
description: 24 pages, 8 figures
Light Stops and Observation of Supersymmetry at LHC RUN-II
Creators: name: Kaufman, Bryan
name: Nath, Pran
name: Nelson, Brent D
name: Spisak, Andrew
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Light stops consistent with the Higgs boson mass of $\sim126\,{\rm GeV}$ are investigated within the framework of minimal supergravity. It is shown that models with light stops which are also consistent with the thermal relic density constraints require stop coannihilation with the neutralino LSP. The analysis shows that the residual set of parameter points with light stops satisfying both the Higgs mass and the relic density constraints lie within a series of thin strips in the $m_0-m_{1/2}$ plane for different values of $A_0/m_0$. Consequently, this region of minimal supergravity parameter space makes a number of very precise predictions. It is found that light stops of mass down to 400~GeV or lower can exist consistent with all constraints. A signal analysis for this class of models at LHC RUN-II is carried out and the dominant signals for their detection identified. Also computed is the minimum integrated luminosity for $5σ$ discovery of the models analyzed. If supersymmetry is realized in this manner, the stop masses can be as low as 400~GeV or lower, and the mass gap between the lightest neutralino and lightest stop will be approximately 30-40~GeV. We have optimized the ATLAS signal regions specifically for stop searches in the parameter space and find that a stop with mass $\sim 375\,{\rm GeV}$ can be discovered with as little as $\sim$ 60~fb$^{-1}$ of integrated luminosity at RUN-II of the LHC; the integrated luminosity needed for discovery could be further reduced with more efficient signature analyses. The direct detection of dark matter in this class of models is also discussed. It is found that dark matter cross sections lie close to, but above, coherent neutrino scattering and would require multi-ton detectors such as LZ to see a signal of dark matter for this class of models.
description: 21pages, 8 figures. Version published in PRD
Cnidoscolus autlanensis Breckon, Contr. Univ.
Creators: name: Maya-Lastra, Carlos A.
name: Steinmann, Victor W.
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Malpighiales
Euphorbiaceae
Cnidoscolus
Cnidoscolus autlanensis

description: 13. Cnidoscolus autlanensis Breckon, Contr. Univ. Michigan Herb. 20: 201 (1995). Type:— MEXICO. Jalisco: Oak-dominated slopes facing the Pacific, 10 mi S of Autlán, 4600 ft, 8 August 1949, R.L. Wilbur & C.R. Wilbur 2185 (holotype MICH-1000124! [mounted on two sheets]; isotypes CAS-0002040!, DS, DUKE-10000392!, MEXU-00058931!, US-00170372!, US-00170373!, WIS-V0255772 WIS!,).
 Distribution:— Mexico (regional endemic).
description: Published as part of Maya-Lastra, Carlos A. & Steinmann, Victor W., 2018, A Nomenclator of Cnidoscolus (Euphorbiaceae), pp. 1-30 in Phytotaxa 346 (1) on page 7, DOI: 10.11646/phytotaxa.346.1.1, http://zenodo.org/record/13708395
Pore-Scale Visualization of Hydrogen Storage in a Sandstone at Subsurface Pressure and Temperature Conditions: Trapping, Dissolution and Wettability
Creators: name: Jangda, Zaid
name: Menke, Hannah
name: Busch, Andreas
name: Geiger, Sebastian
name: Bultreys, Tom
name: Lewis, Helen
name: Singh, Kamaljit
Publisher: name: arXiv
Year: 2022
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: The global commitment to achieve net-zero has led to increasing investment towards the production and usage of green hydrogen (H2).However, the massive quantity needed to match future demand will require new storage facilities. Underground storage of H2 is a potentially viable solution, but poses unique challenges due to the distinctive physical and chemical properties of H2, that have yet to be studied quantitatively in the subsurface environment. We have performed in situ X-ray flow experiments to investigate the fundamentals of pore-scale fluid displacement processes during H2 injection into an initially brine saturated Bentheimer sandstone sample. Two different injection schemes were followed, the displacement of H2 with H2-equilibrated brine and non-H2-equilibrated brine both at temperature and pressure conditions representative of deep underground reservoirs. H2 was found to be non-wetting to brine after both displacement cycles, with average contact angles between 53.72 and 52.72, respectively. We also found a higher recovery of H2 (43.1%) for non-H2-equilibrated brine compared to that of H2-equilibrated brine (31.6%), indicating potential dissolution of H2 in unequilibrated brine at reservoir conditions. Our results suggest that H2 storage may indeed be a suitable strategy for energy storage, but considerable further research is needed to fully comprehend the pore-scale interactions at reservoir conditions.
Salamandra salamandra merged assembly.fa
Creators: name: Libro, Pietro
name: Chiocchio, Andrea
name: De Risky, Erika
name: Di Martino, Jessica
name: Bisconti, Roberta
name: Castrignanò, Tiziana
name: Canestrelli, Daniele
Publisher: name: figshare
Year: 2023
Subjects: Bioinformatics and computational biology not elsewhere classified

description: Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we contribute to the study of the genetic underpinnings of dispersal-related behavioral variation by assembling and annotating the first de novo transcriptome of the head tissues of Salamandra salamandra. Although dispersal occurs mostly during the post-metamorphic terrestrial life stage in this species, variation in dispersal-related personality traits is already evident at the aquatic larval stage, making it an excellent candidate species for studies of carry-over effects. We employed a structured pipeline to de-novo assemble and annotate transcripts from RNA-Seq in a set of individuals representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully de novo assembled and annotated. The high-quality assembly was confirmed by comparing BUSCO, DETONATE and TransRate with the S. salamandra dataset. By aligning the contigs against the de novo transcriptome we obtained a percentage of mapping higher than 94%. The homology annotation performed with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NCBI nr, Swiss-Prot and TrEMBL. The domain and site protein prediction made with InterProScan led to 9850 GO-annotated contigs. This de-novo transcriptome represents reliable reference for whole transcriptome and proteome studies of other amphibians, for designing primers to clone specific genes or monitor their expression, and for analyzing comparative gene expression profiles between alternative behavioral types.
Isolation of the p53 Portable Degron to Incorporate into and MDM2 Reporter
Creators: name: Dumberger, Lukas
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The tumor suppressor p53 plays a significant role in a variety of cellular functions including DNA
repair, cell cycle modulation, and programmed cell death, also called apoptosis. Mutations or
functional inactivation of p53 is a hallmark in many cancer types, such as breast and colorectal cancer,
affecting greater than 22 million people. Approximately half of these patients display mutant p53 that
has lost its tumor suppressor function, while the other half exhibit decreased p53 levels due to
overexpression of the E3 ubiquitin ligases murine double minute 2 (MDM2) and MDMX. MDM2
decreases p53 levels by acting as a transcriptional inhibitor and as an E3 ligase facilitating degradation
of p53 via the proteasome. In fact, there is overwhelming molecular and genetic evidence that the
major role of MDM2, and its related complexes, is the targeting of p53 for proteasomal degradation.
Conversely, overexpression of p53 has been linked to the up-regulation of genes involved in cellular
growth and apoptosis. Due to this, p53 has become an attractive therapeutic target by being the most
frequently mutated gene in human cancer that not only plays a vital role in cellular function, but also
has been proven to rescue apoptotic pathways in cancer cells.
Bayesian models and methods to estimate age-specific infectious disease transmission dynamics: integrating disease surveillance time series, mobility, and vaccination data
Creators: name: Monod, Melodie
Publisher: name: Imperial College London
Year: 2022

description: As of 2022, the coronavirus disease 2019 (COVID-19) pandemic is an ongoing global public health issue. To mount efficient public health control programs, it is essential to understand infection patterns involving, for example, the demographics of vulnerable populations or populations driving transmissions and how these vary over time. In this thesis, we make contributions to the use of Bayesian models and methods to capture fine-scale transmission dynamics of infectious diseases, with applications to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). From a statistical point of view, transmission dynamics may be informed by various data, and we make additional contributions by extracting and using novel data types. We aim to push the complexity of the model as much as the stratification of the data and computational power allow us to, and we perform inference on these complex models using appropriate Bayesian methods. The thesis is structured around two parts. In the first part, we build on age-specific renewal models and develop a Bayesian framework for estimating age-specific transmission dynamics in the context of time-varying social contacts using daily, age-specific human mobility, and mortality data. The model is applied to reconstruct and evaluate the resurgence of COVID-19 between March to October 2020 in the United States (US). We identified the population age groups driving SARS-CoV-2 spread across the US through October 29, 2020 and projected the changes in transmission dynamics after school reopening. This work was published in the Science journal. In the second part, we develop and characterise a computationally efficient, non-parametric smoothing prior, a low-rank Gaussian process projected by regularised B-splines, as an approximation to a standard Gaussian process. We embed this prior into a Bayesian hierarchical model to estimate the evolution of age-specific COVID-19 deaths by 1-year age bands across 50 US states from May 2020 to January 2022. We uncover longitudinal trends in the age profile of COVID-19 deaths, identified states with unusually high mortality in older age groups, explored associations with deaths in carehomes, and showed that strong resurgences in deaths during the summer of 2021 are associated with low vaccination coverage. This work was published in the Bayesian Analysis journal.
Cnidoscolus beckii Fern. Casas, Fontqueria
Creators: name: Maya-Lastra, Carlos A.
name: Steinmann, Victor W.
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Malpighiales
Euphorbiaceae
Cnidoscolus
Cnidoscolus beckii

description: 16. Cnidoscolus beckii Fern.Casas, Fontqueria 55: 277 (2005). Type:— BOLIVIA. Chuquisaca: Luis Calvo: Al pie de la Serranía de Aguarague, Villamontes: 70 km hacia Camiri, 20°42 ′ 36 ″ S, 64°43 ′ 48 ″ W, 430 m, 26 October 1983, S.G. Beck & M. Liberman 9778 (holotype LPB-0000628!; isotypes DAV, M-0233239!, MO-1267349, NY).
 Distribution:— Bolivia (regional endemic).
description: Published as part of Maya-Lastra, Carlos A. & Steinmann, Victor W., 2018, A Nomenclator of Cnidoscolus (Euphorbiaceae), pp. 1-30 in Phytotaxa 346 (1) on page 7, DOI: 10.11646/phytotaxa.346.1.1, http://zenodo.org/record/13708395
Hardware-in-the-Loop Simulation for Evaluating Communication Impacts on the Wireless-Network-Controlled Robots
Creators: name: Lv, Honghao
name: Pang, Zhibo
name: Xiao, Ming
name: Yang, Geng
Publisher: name: arXiv
Year: 2022
Subjects: subject: Robotics (cs.RO)
subject: Hardware Architecture (cs.AR)
subject: FOS: Computer and information sciences

description: More and more robot automation applications have changed to wireless communication, and network performance has a growing impact on robotic systems. This study proposes a hardware-in-the-loop (HiL) simulation methodology for connecting the simulated robot platform to real network devices. This project seeks to provide robotic engineers and researchers with the capability to experiment without heavily modifying the original controller and get more realistic test results that correlate with actual network conditions. We deployed this HiL simulation system in two common cases for wireless-network-controlled robotic applications: (1) safe multi-robot coordination for mobile robots, and (2) human-motion-based teleoperation for manipulators. The HiL simulation system is deployed and tested under various network conditions in all circumstances. The experiment results are analyzed and compared with the previous simulation methods, demonstrating that the proposed HiL simulation methodology can identify a more reliable communication impact on robot systems.
description: 6 pages, 11 figures, to appear in 48th Annual Conference of the Industrial Electronics Society IECON 2022 Conference
Probing flavor models with Ge-76-based experiments on neutrinoless double-beta decay
Creators: name: Agostini, Matteo
name: Merle, Alexander
name: Zuber, Kai
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: The physics impact of a staged approach for double-beta decay experiments based on Ge-76 is studied. The scenario considered relies on realistic time schedules envisioned by the GERDA and the MAJORANA collaborations, which are jointly working towards the realization of a future larger scale Ge-76 experiment. Intermediate stages of the experiments are conceived to perform quasi background-free measurements, and different data sets can be reliably combined to maximize the physics outcome. The sensitivity for such a global analysis is presented, with focus on how neutrino flavor models can be probed already with preliminary phases of the experiments. The synergy between theory and experiment yields strong benefits for both sides: the model predictions can be used to sensibly plan the experimental stages, and results from intermediate stages can be used to constrain whole groups of theoretical scenarios. This strategy clearly generates added value to the experimental efforts, while at the same time it allows to achieve valuable physics results as early as possible.
Sparse least squares solutions of multilinear equations
Creators: name: Li, Xin
name: Luo, Ziyan
name: Chen, Yang
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: In this paper, we propose a sparse least squares (SLS) optimization model for solving multilinear equations, in which the sparsity constraint on the solutions can effectively reduce storage and computation costs. By employing variational properties of the sparsity set, along with differentiation properties of the objective function in the SLS model, the first-order optimality conditions are analyzed in terms of the stationary points. Based on the equivalent characterization of the stationary points, we propose the Newton Hard-Threshold Pursuit (NHTP) algorithm and establish its locally quadratic convergence under some regularity conditions. Numerical experiments conducted on simulated datasets including cases of Completely Positive(CP)-tensors and symmetric strong M-tensors illustrate the efficacy of our proposed NHTP method.
Cnidoscolus byssinus Fern. Casas, Fontqueria
Creators: name: Maya-Lastra, Carlos A.
name: Steinmann, Victor W.
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Malpighiales
Euphorbiaceae
Cnidoscolus
Cnidoscolus byssinus

description: 18. Cnidoscolus byssinus Fern.Casas, Fontqueria 55: 81 (2003). Type:— BRAZIL. Bahia: São Inácio, area muito pedregosa e muito seca, 11°7 ′ 48 ″ S, 42°48 ′ 0 ″ W, 500 m, 6 October 1990, A. Freire Fierro 1801 (holotype SPF-104901!; isotype MAF).
 Distribution:— Brazil (microendemic).
 Notes:— Fernández Casas (2006e) compared this species with C. obtusifolius (as C. pubescens). It was distinguished by having an androecium with six whorls instead of the four verticiles characteristic of C. obtusifolius. He also mentions the similarities between C. byssinus and C. rupestris, suggesting that the latter could be a hybrid of C. obtusifolius and C. byssinus. More study of the relationships among these three species would be beneficial.
description: Published as part of Maya-Lastra, Carlos A. & Steinmann, Victor W., 2018, A Nomenclator of Cnidoscolus (Euphorbiaceae), pp. 1-30 in Phytotaxa 346 (1) on page 7, DOI: 10.11646/phytotaxa.346.1.1, http://zenodo.org/record/13708395
Supplementary material to Modelling Data-Aware Stochastic Processes - Discovery and Conformance Checking
Creators: name: Mannhardt, Felix
name: Leemans, Sander J.J.
name: Schwanen, Christopher T.
name: De Leoni, Massimiliano
Publisher: name: Zenodo
Year: 2023
Subjects: process mining

description: This package contains the source code and experimental results underlying the
 paper "Modelling Data-Aware Stochastic Processes - Discovery and Conformance Checking"
 by Felix Mannhardt, Sander J.J. Leemans, Christopher T. Schwanen, and Massimiliano de Leoni.
Metabolism And Adverse Effects of Arsenic In Genetically Diverse Mouse Strains
Creators: name: Ji, Jinglin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description: Through drinking water and food, millions of people worldwide are exposed to arsenic (As), which is a naturally occurring diabetogenic metalloid 13. Inorganic arsenic (iAs) exposure may disrupt glucose homeostasis leading to type 2 diabetes (T2D), including: (i) insulin resistance due to inhibition of insulin signaling, (ii) inhibition of insulin secretion, and (iii) aberrant micro RNA expression and activity 1, 2, 13. Arsenic methyltransferase (AS3MT) is the key enzyme in iAs detoxification pathway that determines disease outcome 3. Polymorphisms in AS3MT is the single most important genetic factor affecting iAs metabolism and susceptibility to adverse effects of iAs exposure, including diabetes. This study aims to examine the relationship between As3mt polymorphism and the adverse outcomes of iAs exposure in two Collaborative Cross (CC) mouse strains, CC021/Unc (CC021) and CC027/TauUnc (CC027), with different genetic backgrounds. Metabolic phenotype and susceptibility to adverse effects of iAs exposure are hypothesized to differ in CC021 and CC027 due to the differences in their hepatic As3mt expression and iAs metabolism (in liver). The metabolic/diabetic phenotype and iAs metabolism were assessed in both strains after 12 weeks of exposure to 100 ppb or 50 ppm iAs (sodium arsenite) in drinking water. The differences we observed between phenotypes of CC021 and CC027 mice were determined mainly by the genetic backgrounds of these strains and only to smaller extent by iAs exposure. Differences due to iAs exposure were found in weight gain, glycemia and insulin response to i.p. glucose injection, as well as in total As level in urine and in the percentage of total As represented by iAs. In future studies, we aim to identify other genes that underlie the susceptibility to iAs-associated T2D and establish a better mouse model in which As3mt expression and iAs metabolism resemble those in humans.
Investigating the contribution of author- and publication-specific features to scholars' h-index prediction
Creators: name: Momeni, Fakhri
name: Mayr, Philipp
name: Dietze, Stefan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Digital Libraries (cs.DL)
subject: FOS: Computer and information sciences

description: Evaluation of researchers' output is vital for hiring committees and funding bodies, and it is usually measured via their scientific productivity, citations, or a combined metric such as h-index. Assessing young researchers is more critical because it takes a while to get citations and increment of h-index. Hence, predicting the h-index can help to discover the researchers' scientific impact. In addition, identifying the influential factors to predict the scientific impact is helpful for researchers seeking solutions to improve it. This study investigates the effect of author, paper and venue-specific features on the future h-index. For this purpose, we used machine learning methods to predict the h-index and feature analysis techniques to advance the understanding of feature impact. Utilizing the bibliometric data in Scopus, we defined and extracted two main groups of features. The first relates to prior scientific impact, and we name it 'prior impact-based features' and includes the number of publications, received citations, and h-index. The second group is 'non-impact-based features' and contains the features related to author, co-authorship, paper, and venue characteristics. We explored their importance in predicting h-index for researchers in three different career phases. Also, we examine the temporal dimension of predicting performance for different feature categories to find out which features are more reliable for long- and short-term prediction. We referred to the gender of the authors to examine the role of this author's characteristics in the prediction task. Our findings showed that gender has a very slight effect in predicting the h-index. We found that non-impact-based features are more robust predictors for younger scholars than seniors in the short term. Also, prior impact-based features lose their power to predict more than other features in the long-term.
description: 14 pages, 1 figure
Hubble and Keck Telescope Observations of Active Asteroid 288P/300163 (2006 VW139)
Creators: name: Agarwal, Jessica
name: Jewitt, David
name: Weaver, Harold
name: Mutchler, Max
name: Larson, Stephen
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present Hubble Space Telescope and Keck 10 meter telescope observations of active asteroid 288P/300163 (2006 VW139) taken to examine ejected dust. The nucleus is a C-type object with absolute magnitude $H_V$ = 17.0$\pm$0.1 and estimated diameter $\sim$2.6 km (for assumed visual geometric albedo $p_V$ = 0.04). Variations in the brightness of the nucleus at the 10% to 15% level are significant in both 2011 December and 2012 October but we possess too few data to distinguish variations caused by activity from those caused by rotation. The dust scattering cross-section in 2011 December is $\sim$40 km$^2$, corresponding to a dust mass $\sim$9$\times$10$^6$ kg (88 $μ$m mean particle radius assumed). The full width at half maximum of the debris sheet varies from $\sim$100 km near the nucleus to $\sim$1000 km 30arcsec (40,000 km) east of it. Dust dynamical models indicate ejection speeds between 0.06 and 0.3 m s$^{-1}$, particle sizes between 10 and 300 $μ$m and an inverse square-root relation between particle size and velocity. Overall, the data are most simply explained by prolonged, low velocity ejection of dust, starting in or before 2011 July and continuing until at least 2011 October. These properties are consistent with the sublimation of near-surface ice aided by centrifugal forces. The high spatial resolution of our HST images (52 km per pixel) reveals details that remained hidden in previous ground-based observations, such as the extraordinarily small vertical extent of the dust sheet, ejection speeds well below the nucleus escape speed, and the possibility of a binary nucleus.
description: Accepted for publication by AJ
Local observability of state variables and parameters in nonlinear modeling quantified by delay reconstruction
Creators: name: Parlitz, Ulrich
name: Schumann-Bischoff, Jan
name: Luther, Stefan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences

description: Features of the Jacobian matrix of the delay coordinates map are exploited for quantifying the robustness and reliability of state and parameter estimations for a given dynamical model using an observed time series. Relevant concepts of this approach are introduced and illustrated for discrete and continuous time systems employing a filtered Hénon map and a Rössler system.
description: 12 pages, 15 figures
Counting sheaves on curves
Creators: name: Bu, Chenjing
Publisher: name: arXiv
Year: 2022
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14H60 (primary), 14C17, 14D20, 14N35, 17B69 (secondary)

description: We compute Joyce's (arXiv:2111.04694) enumerative invariants $[\mathcal{M}^{\mathrm{ss}}_{(r,d)}]_{\mathrm{inv}}$ for semistable rank $r$ degree $d$ coherent sheaves on a complex projective curve. These invariants are a generalization of the fundamental class of the moduli of semistable sheaves. We express the invariants as a regularized sum, which is a way to assign finite values to divergent series, and we obtain explicit expressions for the invariants. From these invariants, one can extract cohomology pairings on the moduli of semistable sheaves. When $r$ and $d$ are coprime, formulae for such pairings were found by Witten and proved by Jeffrey and Kirwan. Our results provide a new point of view on this classical problem, and can be seen as a generalization of this to the case when $r$ and $d$ are not coprime.
description: 83 pages, accepted version
Exploring the comorbidity of personality disorder and musculoskeletal diseases among adults: a scoping review protocol
Creators: name: Quirk, Shae
name: Williams, Lana
name: Koivumaa-Honkanen, Heli
Publisher: name: Open Science Framework
Year: 2022

description: This protocol describes the methodology to undertake the scoping review. It is guided by Arksey and O’Malley’s framework and the extensions recommended by the Joanna Briggs Institute.
Neural Correlates of Emotion Regulation in Schizophrenia
Creators: name: Duffy, Kelly
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The primary aim of the present study is to use the paradigm developed by Kisley
et al. (2011) to determine if, across groups, framing has an effect on the magnitude of
LPP response to neutral and emotionally-salient stimuli. We hypothesize that positive
framing will decrease the magnitude of the LPP response to negative stimuli across
groups, and that there will be no significant difference of framing on neutral stimuli. We
will then use time frequency analysis to determine if, across groups, there are differences
in frontal theta oscillatory activity, either in evoked power or intertrial phase coherence,
in framing conditions for negative and neutral stimuli. We hypothesize that there will be
increased frontal theta evoked power and ITC to positively-, versus negatively-, framed
negative stimuli, and no difference between frames in neutral stimuli.
The secondary aim of the present study is to determine if differences exist
between patient and control groups in either modulation of LPP or frontal theta activity in
response to framing cues on neutral and negative stimuli. We hypothesize that patients
will not have a significant decrease of LPP amplitude to the positively-framed negative
stimuli, as will likely be seen in controls and across groups. Accordingly, we hypothesize
that patients will not have significantly increased theta activity, in either evoked power or
ITC, to the positively-framed negative stimuli, compared to the negatively-framed
negative stimuli, as expected in controls and across groups. Finally, we hypothesize that
there will be no significant differences between patients and controls in the processing of
neutral stimuli.