cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Voltaire's "Candide" and the Methodology of Dramatic Adaptation
Creators: name: Ballachey, Catherine
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2016
Subjects: adaptation
Voltaire
dramaturgy
theatre

description: This thesis details the search for dramaturgical methodologies of adaptation with the additional component of a creative project used to put those methodologies into practice. In particular, my research has been focused on the methodologies available for transforming static or descriptive moments of literature into compelling works of drama. My discussion on this process begins by tracing the scholarly developments in the field of adaptation studies, which have led away from what Linda Hutcheon calls “fidelity criticism” and have opened up a new vein of praxis-based research in recent years. Specifically, I trace the path to a four-step formula for the development of theory first suggested by Edward Said and later tailored to the process of adaptation by Linda Hutcheon. The formula itself advocates the balance of research and creativity, which has been an ideal framework for this thesis document. The second chapter of this thesis focuses on an application of this formula for a dramatic adaptation of Voltaire’s notorious novella Candide, or All for the Best, which presents the particular problematic of a densely philosophical novella. Candide also furnishes an interesting case study for the four-step formula as it presents both a rich historical context and a complicated narrative structure. The third and final chapter details the specific dramaturgical choices made in working with the formula to create a new adaptation entitled Survival of the Optimistic, and the implications these choices create for the adaptation process as a whole. The adaptation itself follows at the end of this thesis document.
The Power of a Small Green Place – A Case Study of Ottawa's Fletcher Wildlife Garden
Creators: name: Sander-Regier, Renate
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2013
Subjects: place
nature
urban green space
human-nature relations
human-nature reconciliation
human-nature reciprocity
case study
ethnography
autoethnography

description: The Power of a Small Green Place is an ethnographic case study among the volunteers and urban wilds of Ottawa’s Fletcher Wildlife Garden (FWG). Through the conceptual lens of the geographical concept of place – with its wide range of physical, relational and deeper meaningful considerations – this urban wildlife habitat project emerged as a place of profound significance. Volunteers working to create and maintain the FWG’s diverse habitats benefit from opportunities to engage in physical outdoor activity, establish social connections, make contact with the natural world, find deep personal satisfaction and meaning, and experience healthier and mutually beneficial relations with nature. This case study fills a knowledge gap in geography regarding the significant relationships that can emerge between people and the land they work with, thereby contributing to geography’s “latest turn earthward” examining practices and relationships of cultivation with the land. The case study also contributes to a growing interdisciplinary dialogue on human-nature relations and their implications in the context of future environmental and societal uncertainties.
UNCOVERing the High-redshift AGN Population among Extreme UV Line Emitters
Creators: name: Treiber, Helena
name: Greene, Jenny
name: Weaver, John R.
name: Miller, Tim B.
name: Furtak, Lukas J.
name: Setton, David J.
name: Wang, Bingjie
name: de Graaff, Anna
name: Bezanson, Rachel
name: Brammer, Gabriel
name: Cutler, Sam E.
name: Dayal, Pratika
name: Feldmann, Robert
name: Fujimoto, Seiji
name: Goulding, Andy D.
name: Kokorev, Vasily
name: Labbe, Ivo
name: Leja, Joel
name: Marchesini, Danilo
name: Nanayakkara, Themiya
name: Nelson, Erica
name: Pan, Richard
name: Price, Sedona H.
name: Siegel, Jared
name: Suess, Katherine
name: Whitaker, Katherine
Publisher: name: arXiv
Year: 2024
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: JWST has revealed diverse new populations of high-redshift ($z\sim4-11$) AGN and extreme star-forming galaxies that challenge current models. In this paper, we use rest-frame UV emission-line diagnostics to identify AGN candidates and other exceptional ionizing sources, complementing previous studies predominantly focused on broad-line AGN. From a parent sample of 205 $\mathrm{z_{spec}}>3$ UNCOVER galaxies with NIRSpec/PRISM follow-up, we identify 12 C IV, He II, and C III] emitters. Three of these galaxies also exhibit clear N III] and/or N IV] lines. Leveraging the combined rest-optical and UV coverage of PRISM, we limit the emission-line model space using the sample's [O III]/H$β$ distribution, significantly decreasing the overlap between AGN and star-formation models in the UV diagnostics. We then find that the five He II emitters are the strongest AGN candidates, with further support from two [Ne V] detections and one X-ray detection from Chandra. Our Balmer line fits also reveal one new broad-line AGN at z=6.87. We cannot robustly quantify the AGN fraction in this sample, but we note that close to 20% of $\mathrm{M_{*}>2\times10^{9}\,M_{\odot}}$ parent sample galaxies are AGN candidates. The lower-mass line emitters, which are consistent with both AGN and star-forming photoionization models, have more compact sizes and higher specific star formation rates than the parent sample. Higher-resolution and deeper data on these UV line emitters should provide much stronger constraints on the obscured AGN fraction at $z > 3$.
description: Accepted to ApJ
Aligning text mining and machine learning algorithms with best practices for study selection in systematic literature reviews
Creators: name: Popoff, E.
name: Besada, M.
name: Jansen, J. P
name: Cope, S.
name: Kanters, Steve
Publisher: name: BioMed Central
Year: 2020

description: Background: Despite existing research on text mining and machine learning for title and abstract screening, the role of machine learning within systematic literature reviews (SLRs) for health technology assessment (HTA) remains unclear given lack of extensive testing and of guidance from HTA agencies. We sought to address two knowledge gaps: to extend ML algorithms to provide a reason for exclusion—to align with current practices—and to determine optimal parameter settings for feature-set generation and ML algorithms. Methods: We used abstract and full-text selection data from five large SLRs (n = 3089 to 12,769 abstracts) across a variety of disease areas. Each SLR was split into training and test sets. We developed a multi-step algorithm to categorize each citation into the following categories: included; excluded for each PICOS criterion; or unclassified. We used a bag-of-words approach for feature-set generation and compared machine learning algorithms using support vector machines (SVMs), naïve Bayes (NB), and bagged classification and regression trees (CART) for classification. We also compared alternative training set strategies: using full data versus downsampling (i.e., reducing excludes to balance includes/excludes because machine learning algorithms perform better with balanced data), and using inclusion/exclusion decisions from abstract versus full-text screening. Performance comparisons were in terms of specificity, sensitivity, accuracy, and matching the reason for exclusion. Results: The best-fitting model (optimized sensitivity and specificity) was based on the SVM algorithm using training data based on full-text decisions, downsampling, and excluding words occurring fewer than five times. The sensitivity and specificity of this model ranged from 94 to 100%, and 54 to 89%, respectively, across the five SLRs. On average, 75% of excluded citations were excluded with a reason and 83% of these citations matched the reviewers’ original reason for exclusion. Sensitivity significantly improved when both downsampling and abstract decisions were used. Conclusions: ML algorithms can improve the efficiency of the SLR process and the proposed algorithms could reduce the workload of a second reviewer by identifying exclusions with a relevant PICOS reason, thus aligning with HTA guidance. Downsampling can be used to improve study selection, and improvements using full-text exclusions have implications for a learn-as-you-go approach.
Generalized Numerical semigroups up to isomorphism
Creators: name: Cisto, Carmelo
name: Failla, Gioia
name: Navarra, Francesco
Publisher: name: arXiv
Year: 2024
Subjects: subject: Combinatorics (math.CO)
subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics
subject: 20M14, 05A15, 11D07, 20-04

description: A generalized numerical semigroup is a submonoid $S$ of $\mathbb{N}^d$ with finite complement in it. We characterize isomorphisms between these monoids in terms of permutation of coordinates. Considering the equivalence relation that identifies the monoids obtained by the action of a permutation and establishing a criterion to select a representative from each equivalence class, we define some procedures for generating the set of all generalized numerical semigroups of given genus up to isomorphism. Finally, we present computational data and explore properties related to the number of generalized numerical semigroups of a given genus up to isomorphism.
description: 18 pages
Size, Age, Distribution and Mass Accumulation Rates of Seafloor Hydrothermal Sulfide Deposits
Creators: name: Jamieson, John William
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2013
Subjects: Seafloor Massive Sulfides
Hydrothermal
Marine Resources

description: Hydrothermal discharge on the seafloor results in significant accumulation of base- and precious-metal-rich sulfide material. Technological advances as well as elevated metal prices have led to a growing interest in the direct mining of these deposits from the modern ocean floor. The research presented in this thesis details an investigation of the size, grades, distribution, and accumulation rates of these deposits on the seafloor. A three-part resource assessment, originally designed for land-based ore deposits, was used to generate a predictive framework for the global seafloor sulfide resource. Using detailed descriptions of sizes, grades and locations for 92 known deposits, a resource estimate was generated that predicts a total of ~1,000 deposits and a total global abundance of 600 Mt of sulfide within the neovolcanic zones of the modern ocean floor. A detailed study of the hydrothermal sulfide deposits along the Endeavour Segment of the Juan de Fuca Ridge was carried out to investigate the processes of sulfide accumulation at the ridge-segment scale. Results of 226Ra/Ba dating of barite within the deposits indicate that hydrothermal activity has been ongoing for ~6,000 years and venting has been continuous at the Main Endeavour and High Rise vent fields for ~2,300 and 850 years, respectively. Abundant older sulfide samples from inactive sites outside of the main vent fields indicate a complex history of venting along the ridge segment. Analysis of high-resolution bathymetry of the Endeavour Segment, generated from eight autonomous underwater vehicle surveys, revealed the location of 581 individual hydrothermal sulfide edifices along 15 km of ridge length. Using GIS-based software, the volume of each edifice was calculated, and the total amount of sulfide at Endeavour is estimated to be 1.2 Mt. This estimate is the first comprehensive resource evaluation on the seafloor at this scale. Sulfide has been accumulating within the Endeavour axial valley at a rate of ~400 tonnes per year, which is similar to estimates for the TAG deposit on the Mid-Atlantic Ridge. Using endmember hydrothermal fluid chemistry data and estimates of fluid discharge rates, the mass accumulation rate calculated for Endeavour corresponds to a sulfide depositional efficiency of 6%.
Polarized radiation from the spreading layer of the weakly magnetized neutron stars
Creators: name: Bobrikova, Anna
name: Poutanen, Juri
name: Loktev, Vladislav
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Observations show that the X-ray emission of the accreting weakly magnetized neutron stars is polarized. Here, we develop a theoretical model, where we assume the emission of the accreting neutron star coming from the spreading layer, the extension of the boundary between the disk and the neutron star surface onto the surface. We then calculate the Stokes parameters of the emission accounting for relativistic aberration and gravitational light bending in the Schwarzschild metric. We show that regardless of the geometry, for the spreading layer, we cannot expect the polarization degree to be higher than 1.5%. Our results have implications with regard to the understanding of the X-ray polarization from weakly magnetized neutron stars observed with the Imaging X-ray Polarimetry Explorer and the future enhanced X-ray Timing and Polarimetry mission.
description: 9 pages, 7 figures
Modelling Human Risk of West Nile Virus Using Surveillance and Environmental Data
Creators: name: Mallya, Shruti
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2017
Subjects: West Nile Virus
Spatial Analysis
Generalized Linear Mixed Modelling
Public Health

description: Limited research has been performed in Ontario to ascertain risk factors for West Nile Virus (WNV) and to develop a unified risk prediction strategy. The aim of the current body of work was to use spatio-temporal modelling in conjunction with surveillance and environmental data to determine which pre-WNV season factors could forecast a high risk season and to explore how well mosquito surveillance data could predict human cases in space and time during the WNV season. Generalized linear mixed modelling found that mean minimum monthly temperature variables and annual WNV-positive mosquito pools were most significantly predictive of number of human WNV cases (p<0.001). Spatio-temporal cluster analysis found that positive mosquito pool clusters could predict human case clusters up to one month in advance. These results demonstrate the usefulness of mosquito surveillance data as well as publicly available climate data for assessing risk and informing public health practice.
Fractonic Coset Construction for Spontaneously Broken Translations
Creators: name: Chavda, Ameya
name: Naegels, Daniel
name: Staunton, John
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We study the homogeneous breaking of spatial translation symmetry concomitantly with the spontaneous breaking of other internal and spacetime symmetries, including dilations. We use the symmetry-breaking pattern as the only input to derive, via the coset construction, general effective field theories for the symmetry-originated modes associated with Goldstone's theorem, namely the Nambu-Goldstone candidates. Through explicit computations, we show that integrating out the explicit massive Nambu-Goldstone candidates or imposing symmetric constraints, namely the inverse Higgs constraints, to express massive modes in terms of the massless ones leads to physically distinct effective field theories. This sensitivity to the chosen method can be traced back to the homogeneous breaking of translations, the homogeneous aspect of the breaking induces a mixing between internal and spacetime symmetries at the level of the Lie algebra. This, in turn, leads to subtle discussions about the inverse Higgs constraints, in particular that they lead to a loss of generality in our specific examples. The derived general effective field theories also give rise to a broad class of theories exhibiting emergent enhanced shift symmetries, which constrain the mobility of the modes. The latter are referred to as fractonic modes.
description: 56 pages, 1 figure, 2 supplemental Mathematica notebooks
VAFB-2013-21: Section 106 Consultation Package For The Santa Ynez Band of Chumash Indians Temporary Construction Easement Grant For The Union Pacific Railroad’s Narlon Bridge Replacement Vandenberg Air Force Base Santa Barbara County, California
Creators: name: Ryan, Christopher
Year: 2013

description: This document is the Section 106 consultation package submitted by Vandenberg Air Force Base (VAFB) to the Santa Ynez Band of Chumash Indians for the Union Pacific Narlon Bridge Replacement Project. VAFB applied the criteria of adverse effect and determined granting a temporary construction easement to the UPRR to support their replacement of the Narlon Bridge would not alter, directly or indirectly, any of the characteristics of the historic properties within the APE that qualify those properties for inclusion in the National Register. As such, VAFB’s Section 106 finding for the proposed undertaking is no adverse effect to historic properties.
VAFB-2000-19: Survey and Testing of Proposed Bore Site Location, Vandenberg Air Force Base, South of San Antonio Creek
Creators: name: DeMar, David
Year: 2000

description: This brief letter report details the results of a cultural resource inspection performed on 31 July 2000 for a proposed bore site and access within the Union Pacific railroad right of way.
An Infrastructure Based Worm Spreading Countermeasure for Vehicular Ad Hoc Networks
Creators: name: Zhang, Qi
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2017
Subjects: VANETs
Worm Spreading
Infrastructure Deployment
Minimum Contamination Problem

description: VANETs are the essential component of the intelligent transport system, which attract research and industrial interests increasingly. As the multifunctional mobile nodes integrating transporting, sensing, information processing, and wireless communication capabilities, vehicular nodes are facing remarkable security issues and more vulnerable to malware attack than conventional communication nodes. In this thesis, the behavior and the security issues of the worm spreading on VANETs are studied. The approaches of the worm spreading on VANETs are discussed and an infrastructure based worm containment strategy is proposed. The infrastructure based worm containment problem is modeled as minimum contamination problem by introducing the expected contamination degree. Then the existing greedy method is applied to solve the proposed problem in VANETs scenario. After that, the Grid-shrinking Greedy Method and the Simplified Greedy Method are proposed which incorporate the characteristics of road networks and VANETs respectively. Simulation results show the two proposed methods outperform the existing greedy method and the comparison method from both complexity and solution quality aspects.
Fine-Grained, Unsupervised, Context-based Change Detection and Adaptation for Evolving Categorical Data
Creators: name: D'Ettorre, Sarah
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2016
Subjects: concept drift
context-based
categorical data

description: Concept drift detection, the identfication of changes in data distributions in streams, is critical to understanding the mechanics of data generating processes and ensuring that data models remain representative through time [2]. Many change detection methods utilize statistical techniques that take numerical data as input. However, many applications produce data streams containing categorical attributes. In this context, numerical statistical methods are unavailable, and different approaches are required. Common solutions use error monitoring, assuming that fluctuations in the error measures of a learning system correspond to concept drift [4]. There has been very little research, though, on context-based concept drift detection in categorical streams. This approach observes changes in the actual data distribution and is less popular due to the challenges associated with categorical data analysis. However, context-based change detection is arguably more informative as it is data-driven, and more widely applicable in that it can function in an unsupervised setting [4]. This study offers a contribution to this gap in the research by proposing a novel context-based change detection and adaptation algorithm for categorical data, namely Fine-Grained Change Detection in Categorical Data Streams (FG-CDCStream). This unsupervised method exploits elements of ensemble learning, a technique whereby decisions are made according to the majority vote of a set of models representing different random subspaces of the data [5]. These ideas are applied to a set of concept drift detector objects and merged with concepts from a recent, state-of-the-art, context-based change detection algorithm, the so-called Change Detection in Categorical Data Streams (CDCStream) [4]. FG-CDCStream is proposed as an extension of the batch-based CDCStream, providing instance-by-instance analysis and improving its change detection capabilities especially in data streams containing abrupt changes or a combination of abrupt and gradual changes. FG-CDCStream also enhances the adaptation strategy of CDCStream producing more representative post-change models.
Identification and classification of marine bacteria associated with poly(ethylene terephthalate) degradation
Creators: name: Ng, Hooi Jun
Publisher: name: Swinburne
Year: 2024

description: Poly(ethylene terephthalate) (PET) is a manmade synthetic polymer that has been widely used in a variety of industries. The high production and usage of PET, together with the inappropriate handling of PET wastes are becoming a global environmental issue, especially in the marine environment. Detailed taxonomic investigations of marine bacteria that have the potential to degrade PET were the focus of this thesis. Taxonomic studies based on comparative phylogenetic and genomic analyses, traditional physiological and biochemical studies, together with newly developed modern taxonomic tools, namely multi-locus sequence analysis and MALDI-TOF MS revealed three novel bacterial species, Alteromonas australica H17T, Marinobacter similis A3d10T and Marinobacter salarius R9SW1T, in which M. similis A3d10T has shown to have the ability to degrade the PET trimer in this study.
The Roles of Stop Codons and 3’ Flanking Base in Bacterial Translation Termination Efficiency
Creators: name: Wei, Yulong
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2016
Subjects: translation termination
gene expression
termination read-through

description: Understanding translation efficiency is crucial to pharmaceutical companies that have invested substantial time and effort in engineering bacteria to produce recombinant proteins. While translation initiation and elongation have been studied intensively, much remains obscure in the subprocess of translation termination. We aim to understand how stop codons and the first 3’ flanking (+4) base affect translation termination efficiency. In chapter two, we hypothesized that stop codon usage of UAG and UGA is dependent on the abundance of their respective decoders, RF1 and RF2. We predicted and observed that bacterial species with high relative proportions of RF1 uses UAG more, and vice versa for UGA. In addition, the usage of UGA, not UAG, is always avoided in highly expressed genes. Thus, we argued against the claim made by a recent study that UAG is a minor stop codon in bacteria. The claim is incorrect because UAG does not meet the two criteria of a minor codon: i) it is most avoided in highly expressed genes, and ii) it corresponds to the least abundant decoder. Interestingly, we found that the proportion of RF2 decreases rapidly towards zero in species with high AT contents; this explains why UGA is reassigned to a sense codon in bacterial lineages with high AT content. In chapter three, we examined the role of the first downstream (+4) base Uracil in bacterial translation termination. The +4U is associated with a decrease in stop codon read-through in bacteria and yeast. We hypothesized that i) +4U enhances the termination efficiency of stop signals, and ii) +4U may serve to prevent stop codon misreading by near cognate tRNAs (nc_tRNAs). We predicted that i) +4U is preferred in highly expressed genes (HEGs) than lowly expressed genes (LEGs), and ii) +4U usage increases with the frequency of stop codon nc_tRNAs. We found +4U consistently over-represented in HEGs in contrast to LEGs; however, +4U usage in HEGs decreases in GC-rich species where most stop codons are UGA and UAG. In addition, +4U usage increases significantly with UAA usage in the known highly expressed ribosomal protein genes. These results suggest that +4U is a strong stop signal enhancer for UAA, not UAG or UGA. Furthermore, in HEGs, +4U usage also increases significantly with the abundance of UAA nc_tRNAs, suggesting that +4U increases UAA termination efficiency presumably by reducing misreading of UAA by nc_tRNAs.
VAFB-2013-17: Supplemental National Register of Historic Places Evaluation Report for Union Pacific Railroad, Santa Barbara Subdivision, Milepost 291.33, Narlon Bridge Replacement Project at Vandenberg Air Force Base, California
Creators: name: Price, Lori D.
Year: 2013

description: This document is the Supplemental National Register of Historic Places Evaluation Report for Union Pacific Railroad, Santa Barbara Subdivision, Milepost 291.33, Narlon Bridge Replacement Project at Vandenberg Air Force Base, California. This project proposed replacing the existing Narlon Bridge, built in 1896, and its adjacent access bring. Consultation between VAFB, the SHPO, and the ACHP led to a revision of the APE to include privately-owned UPRR land. This revision incorporated three additional unevaluated cultural resources into the APE: Narlon Bridge and its small access bridge, and Site CA-SBA-3733. This report concluded that the three cultural resources be found not eligible for listing in the National Register of Historic Places (NRHP).
Early Childhood Educators' Constructions of Play Beliefs and Practice
Creators: name: Parsons, Amy L.
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2013

description: This qualitative study was designed to explore the constructions of Early Childhood Educators’ (ECE) beliefs about play and how they translate these beliefs into practice. Guided by a teachers’ beliefs framework (Sanger & Osguthorpe, 2011; Haney & McArthur, 2001; Richards & Lockheart, 1994; Pajares, 1992) and a constructivist philosophical lens, the study sought to identify (a) ECE educators’ beliefs about play, (b) how the educators practice play, and (c) how they incorporate both theoretical and practical components of play beliefs into the early childhood education classroom. A postmodern orientation and rigorous qualitative research methods were employed. Data were collected in three phases: an in-depth open-ended interview was conducted, followed by classroom observation over the course of 6 weeks, and finally a second interview was conducted using the process of Interpersonal Process Recall (IPR) with four purposefully selected participants. The interview data were transcribed and categories were co-constructed with the participants. Findings revealed that the educators came into their training programs with certain core beliefs about play that were developed in pre-service experience (upbringing, culture, childhood memories). These core beliefs played an important role in the information that these educators were able to filter into their previous beliefs about play. Further, the educators’ beliefs about play appeared to be reinforced and even magnified through their training programs, as they were able to take specific techniques and approaches and apply them in their practice. Two of the educators had previous experience working in daycare, hence facilitating the application of new knowledge to their pre-existing beliefs. The study findings add to a small growing body of research that furthers our understanding of the construction of early childhood educator beliefs. This research also helps us understand how educators’ pre-service and in-service experience contributes to the development of play beliefs and helps in the transfer of beliefs into practice. In addition, the findings give a voice to the early childhood educators, making a valuable contribution to the literature.
PDB validation report_EM-1 from Structural and functional characterisation of nanobodies that neutralize Omicron variants of SARS-CoV-2
Creators: name: Cornish, Katy
name: Huo, Jiandong
name: Jones, Luke
name: Sharma, Parul
name: Thrush, Joseph W.
name: Abdelkarim, Sahar
name: Kipar, Anja
name: Ramadurai, Siva
name: Weckener, Miriam
name: Mikolajek, Halina
name: Liu, Sai
name: Buckle, Imogen
name: Bentley, Eleanor
name: Kirby, Adam
name: Han, Ximeng
name: Laidlaw, Stephen M.
name: Eyssen, Lauren
name: Hill, Michelle
name: Norman, Chelsea
name: Le Bas, Audrey
name: Clarke, John Douglas
name: James, William
name: Stewart, James
name: Carroll, Miles
name: Naismith, James H.
name: Owens, Ray
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 310112
subject: Structural biology (incl. macromolecular modelling)

description: PDB validation report for deposited EM structure 8OYU
StratLearn-z: Improved photo-$z$ estimation from spectroscopic data subject to selection effects
Creators: name: Moretti, Chiara
name: Autenrieth, Maximilian
name: Serra, Riccardo
name: Trotta, Roberto
name: van Dyk, David A.
name: Mesinger, Andrei
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: A precise measurement of photometric redshifts (photo-z) is key for the success of modern photometric galaxy surveys. Machine learning (ML) methods show great promise in this context, but suffer from covariate shift (CS) in training sets due to selection bias where interesting sources are underrepresented, and the corresponding ML models show poor generalisation properties. We present an application of the StratLearn method to the estimation of photo-z, validating against simulations where we enforce the presence of CS to different degrees. StratLearn is a statistically principled approach that relies on splitting the source and target datasets into strata based on estimated propensity scores (i.e. the probability for an object to be in the source set given its observed covariates). After stratification, two conditional density estimators are fit separately to each stratum, then combined via a weighted average. We benchmark our results against the GPz algorithm, quantifying the performance of the two codes with a set of metrics. Our results show that the StratLearn-z metrics are only marginally affected by the presence of CS, while GPz shows a significant degradation of performance in the photo-z prediction for fainter objects. For the strongest CS scenario, StratLearn-z yields a reduced fraction of catastrophic errors, a factor of 2 improvement for the RMSE and one order of magnitude improvement on the bias. We also assess the quality of the conditional redshift estimates with the probability integral transform (PIT). The PIT distribution obtained from StratLearn-z features fat fewer outliers and is symmetric, i.e. the predictions appear to be centered around the true redshift value, despite showing a conservative estimation of the spread of the conditional redshift distributions. Our julia implementation of the method is available at https://github.com/chiaramoretti/StratLearn-z.
description: Accepted for publication on the Open Journal of Astrophysics
Quantum Annealing with chaotic driver Hamiltonians
Creators: name: Schlömer, Henning
name: Sachdev, Subir
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Quantum annealing is a computational approach designed to leverage quantum fluctuations for solving large-scale classical optimization problems. Although incorporating standard transverse field (TF) terms in the annealing process can help navigate sharp minima, the potential for achieving a scalable quantum advantage for general optimization problems remains uncertain. Here, we examine the effectiveness of including chaotic quantum driver Hamiltonians in the annealing dynamics. Specifically, we investigate driver Hamiltonians based on a bosonic spin version of the Sachdev-Ye-Kitaev (SYK) model, which features a high degree of non-locality and non-commutativity. Focusing on MaxCut instances on regular graphs, we find that a considerable proportion of SYK model instances demonstrate significant speedups, especially for challenging graph configurations. Additionally, our analysis of time-to-solution scalings for the low autocorrelation binary sequence (LABS) problem suggests that SYK-type fluctuations can outperform traditional transverse field annealing schedules in large-scale optimization tasks.
description: 9+2 pages
Quasinormal modes of a charged loop quantum black hole
Creators: name: Zhu, Li-Gang
name: Fu, Guoyang
name: Li, Shulan
name: Zhang, Dan
name: Wu, Jian-Pin
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: This study presents a systematic investigation of quasinormal modes (QNMs) for probe fields-massless/massive scalar and Dirac fields-around a charged loop quantum gravity black hole (LQG-BH) characterized by the quantum parameter $b_0$ and the charge parameter $Q$. Through spectral analysis of quasinormal frequencies (QNFs), we uncover a distinct overtone outburst driven by quantum gravity effects, prominently manifested in the scalar field spectrum with the multipole quantum number $l=0$. Both the outburst and its accompanying oscillatory patterns grow more pronounced with increasing overtone numbers. In contrast, massless scalar fields with $l>1$ and Dirac fields exhibit delayed outburst development, with non-monotonic behavior dominating the first two overtones. Notably, increasing the charge $Q$ universally suppresses quantum-gravity-induced features, including outbursts, non-monotonicity, and oscillations. Furthermore, we present evidence suggesting the presence of quasi-resonances in the massive scalar QNM spectrum, thereby illustrating the potential for the emergence of arbitrarily long-lived modes in this charged LQG spacetime. These findings establish a robust and universal interplay between quantum gravity effects and charge dynamics, providing new insights into the spectral properties of quantum-corrected BHs.
VAFB-1989-21: Archaeological Test at Titan Pasture A (Gate location)
Creators: name: Osland, Karen
Year: 1989

description: This document is a one page report for the excavation of 6 shovel test pits at the Titan Pasture A (Gate location). The report provides a breakdown of the 6 STPS including the artifacts that were observed.
Superfield twist-$2$ operators in $\mathcal{N} = 1$ SCFTs and their renormalization-group improved generating functional in $\mathcal{N} = 1$ SYM theory
Creators: name: Santoni, Giacomo
name: Scardino, Francesco
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We provide a new construction of superfield collinear twist-$2$ operators as infinite-dimensional, irreducible representations of the collinear superconformal algebra in $\mathcal{N}=1$ superconformal field theories. As an application, we realize the above representations in terms of free superfields, in a manifestly gauge-invariant and supersymmetric-covariant fashion, in the zero coupling limit of $\mathcal{N}=1$ supersymmetric Yang-Mills (SYM) theory. This realization makes manifest their mixing and renormalization properties at one loop. We also extend to the superfield formalism the perturbative and nonperturbative techniques in [1-7] to a large class of supersymmetric theories that are superconformal in the zero-coupling limit. Specifically, we compute the generating functional of superfield twist-$2$ operators in $\mathcal{N}=1$ SU($N$) SYM theory in the zero coupling limit. We also work out in a closed form the corresponding asymptotic renormalization-group improved generating functional in Euclidean superspace and its planar and leading nonplanar large-$N$ expansion. We verify -- as originally predicted in [5] and verified in the component formalism [3, 4, 6, 7] -- that the leading nonplanar asymptotic RG-improved generating functional matches the structure of logarithm of a functional superdeterminant of the corresponding nonperturbative object, which it should be asymptotic to at short distances because of the asymptotic freedom. Hence, our large-$N$ computation sets strong ultraviolet asymptotic constraints on the nonperturbative solution of large-$N$ $\mathcal{N} = 1$ SYM theory that may be a pivotal guide for the search of such a solution.
description: 96 pages
Zebrafish (Danio rerio) Aquaporin 1a as a Multi-functional Transporter of Water, CO2, and Ammonia
Creators: name: Talbot, Krystle
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2014
Subjects: zebrafish
ammonia
AQP1a
aquaporin
carbon dioxide
gas channel

description: Previous in vitro studies have demonstrated that AQP1, traditionally viewed as a water channel, also facilitates the passage of CO2 and ammonia across cell membranes. This thesis summarizes the first in vivo studies confirming a physiologically-relevant role for AQP1 in acid-base balance and nitrogenous waste excretion. Zebrafish embryos were microinjected with a translation-blocking morpholino oligonucleotide targeted to the zebrafish AQP1 paralog, AQP1a. Closed-system respirometry, total CO2 analysis, tritiated water fluxes and measurement of ammonia excretion were performed on larvae at 4 days post-fertilization (dpf). Knockdown of AQP1a significantly reduced rates of water, CO2 and ammonia excretion. Use of phenylhydrazine, a haemolytic agent, provided evidence that the yolk sac epithelium AQP1a (and not erythrocyte AQP1a) is the major site of CO2 and ammonia movements. Further, the hypothesis that AQP1a and the Rh glycoprotein Rhcg1, another multi-functional gas channel, act in concert to regulate CO2 and ammonia excretion was explored. Exposure to conditions impairing ammonia excretion (such as high external ammonia (HEA) or alkaline water) modulated AQP1a protein expression in 4 dpf zebrafish larvae experiencing knockdown of Rhcg1. Chronic HEA exposure triggered a significant compensatory increase in AQP1a protein abundance in Rhcg1 morphants. Exposure of Rhcg1 morphants to pH 10 water, however, caused a significant decrease in AQP1a protein expression. Interestingly, when AQP1a mRNA and protein levels were examined in Rhcg1 morphants and vice versa, no changes were observed. Overall, zebrafish AQP1a was found to be a multi-functional transporter of water, CO2 and ammonia, though the exact relationship it holds with other such gas channels bears further exploration.
Factors associated with drug checking service utilization among people who use drugs in a Canadian setting
Creators: name: Long, Viseth
name: Arredondo, Jaime
name: Ti, Lianping
name: Grant, Cameron
name: DeBeck, Kora
name: Milloy, M-J
name: Lysyshyn, Mark
name: Wood, Evan
name: Kerr, Thomas
name: Hayashi, Kanna
Publisher: name: BioMed Central
Year: 2020

description: Background: The United States and Canada are amidst an opioid overdose crisis, with the Canadian province of British Columbia (BC) among the hardest hit. In response, drug checking services (DCS) have been introduced in this setting as a novel pilot harm reduction intervention though little is known about usage rates. Therefore, we sought to identify factors associated with drug checking uptake among people who use drugs (PWUD) in Vancouver, BC. Methods: Data were derived from three ongoing prospective cohort studies of PWUD in Vancouver between June and November 2018. Multivariable logistic regression was used to determine factors associated with self-reported DCS utilization in the past 6 months among participants at high risk of fentanyl exposure (i.e., those self-reporting illicit opioid use or testing positive for fentanyl via urine drug screen). Results: Among 828 eligible participants, including 451 (55%) males, 176 (21%) reported recent use of DCS. In multivariable analyses, factors significantly associated with DCS utilization included: homelessness (Adjusted Odds Ratio [AOR] 1.47; 95% Confidence Interval [CI] 1.01–2.13) and involvement in drug dealing (AOR 1.59; 95% CI 1.05–2.39). Conclusions: In our sample of PWUD, uptake of DCS was low, although those who were homeless, a sub-population known to be at a heightened risk of overdose, were more likely to use the services. Those involved in drug dealing were also more likely to use the services, which may imply potential for improving drug market safety. Further evaluation of drug checking is warranted.
Cornish et al Supplementary_Information from Structural and functional characterisation of nanobodies that neutralize Omicron variants of SARS-CoV-2
Creators: name: Cornish, Katy
name: Huo, Jiandong
name: Jones, Luke
name: Sharma, Parul
name: Thrush, Joseph W.
name: Abdelkarim, Sahar
name: Kipar, Anja
name: Ramadurai, Siva
name: Weckener, Miriam
name: Mikolajek, Halina
name: Liu, Sai
name: Buckle, Imogen
name: Bentley, Eleanor
name: Kirby, Adam
name: Han, Ximeng
name: Laidlaw, Stephen M.
name: Eyssen, Lauren
name: Hill, Michelle
name: Norman, Chelsea
name: Le Bas, Audrey
name: Clarke, John Douglas
name: James, William
name: Stewart, James
name: Carroll, Miles
name: Naismith, James H.
name: Owens, Ray
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 310112
subject: Structural biology (incl. macromolecular modelling)

description: Compilation of 10 supplementary figures and 2 supplementary tables
The Role of Heme Oxygenase-1 and the CD163 Pathway in Type 1 Diabetes Pathogenesis
Creators: name: Husseini, Mahmoud
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2013
Subjects: Type 1 Diabetes
M2 Macrophages
BBdp rat
Cobalt protoporphyrin
Heme oxygenase-1

description: Type 1 diabetes (T1D) is an autoimmune disease whereby the insulin-producing β-cells of the pancreas are destroyed by the immune system, possibly related to an inappropriate immune reaction to dietary antigens and/or microbes in the gut. We previously observed a deficit in gut-resident CD163+ M2 anti-inflammatory macrophages in BioBreeding diabetes-prone (BBdp) rats. Heme oxygenase-1 (HO-1) is the rate-limiting enzyme of the CD163 pathway and through the breakdown of toxic heme releases potent antioxidants. We hypothesized that the treatment of animals with cobalt protoporphyrin (CoPP), an inducer of HO-1 expression, would inhibit development of T1D through modulation of the CD163/HO-1 pathway and increase M2 macrophages. HO-1 expression was significantly increased in the pancreas and gut. T1D incidence was inhibited in CoPP-treated rats and these animals showed an unexpected increase in cells expressing CD68 (an M1 pro-inflammatory macrophage marker) in the pancreas and gut. CoPP induced the expression of cathelicidin anti-microbial peptide (CAMP) in the jejunum, which co-localized with CD163+ (M2) macrophages. KLF4, an M2 macrophage-specific transcription factor, was significantly upregulated in the pancreas and jejunum of CoPP-treated animals and co-localized with CD68 and HO-1 in the pancreas. We conclude that HO-1 induction prevented T1D through modulation of the gut immune system and potential recruitment of a unique population of anti-inflammatory M2 macrophages in the gut and pancreas
Meissner effect in non-Hermitian superconductors
Creators: name: Tamura, Shun
name: Müller, Helene
name: Aliani, Linus
name: Kornich, Viktoriia
Publisher: name: arXiv
Year: 2024
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study theoretically Meissner effect in non-Hermitian systems of BCS type, i.e., with an electron-electron interaction leading to the mean field description in a Cooper channel, via superfluid stiffness. We show that depending on the values of the mean fields, chemical potential, and temperature, we obtain paramagnetic or diamagnetic Meissner effect. Notably, positive real part of the product of mean fields guarantees diamagnetic Meissner effect in an $s$-wave 3D non-Hermitian superconductor. Once the mean fields are close to being anti-Hermitian, 2D $s$-, $p_x$-, and $d$-wave superconductors exhibit interesting behaviour, including negative superfluid stiffness giving paramagnetic Meissner effect for certain parameters. Negative superfluid stiffness indicates instability of this collective state.
Active Polymer Behavior in Two Dimensions: A Comparative Analysis of Tangential and Push-Pull Models
Creators: name: Janzen, Giulia
name: Miranda, Juan Pablo
name: Martín-Roca, José
name: Malgaretti, Paolo
name: Locatelli, Emanuele
name: Valeriani, Chantal
name: Fernandez, D. A. Matoz
Publisher: name: arXiv
Year: 2024
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: In this work, we compare the structural and dynamic behavior of active filaments in two dimensions using tangential and push-pull models, including a variant with passive end monomers. These models serve as valuable frameworks for understanding self-organization in biological polymers and synthetic materials. At low activity, all models exhibit similar behaviors. Differences emerge in the intermediate range as activity increases, though at higher activity levels, their behaviors converge. Importantly, adjusting for differences in mean active force reveals nearly identical behavior across models. Our results highlight the importance of force definitions in active polymer simulations and provide insights into phase transitions across varying filament configurations.
VAFB-1999-08: Archaeological Investigations for the North Base Fiber-Optic Cable System, Vandenberg Air Force Base, Santa Barbara County, California
Creators: name: Ryan, Christopher
name: Lebow, Clayton G.
name: Harro, Douglas
name: Gerber, Joyce L.
Year: 1999

description: This document is a report that presents the results of archaeological investigations for the North Base Fiber-Optic Cable System Project. The U.S. Air Force proposes to construct the North Base Fiber-Optic Cable System on Vandenberg Air Force Base (AFB) in Santa Barbara County, California. The proposed project will involve placement of approximately 23 miles of cable conduit in trenches a maximum of 42 inches deep and 18 inches wide. Archival research identified multiple archaeological sites near or within the proposed project alignment; however, subsequent consultation between Vandenberg AFB environmental management staff, Applied Earth Works, Inc. personnel, and project engineers resulted in the complete avoidance of all but three sites: CA SBA-990, -992, and -1177.
PDB validation report_EM2 from Structural and functional characterisation of nanobodies that neutralize Omicron variants of SARS-CoV-2
Creators: name: Cornish, Katy
name: Huo, Jiandong
name: Jones, Luke
name: Sharma, Parul
name: Thrush, Joseph W.
name: Abdelkarim, Sahar
name: Kipar, Anja
name: Ramadurai, Siva
name: Weckener, Miriam
name: Mikolajek, Halina
name: Liu, Sai
name: Buckle, Imogen
name: Bentley, Eleanor
name: Kirby, Adam
name: Han, Ximeng
name: Laidlaw, Stephen M.
name: Eyssen, Lauren
name: Hill, Michelle
name: Norman, Chelsea
name: Le Bas, Audrey
name: Clarke, John Douglas
name: James, William
name: Stewart, James
name: Carroll, Miles
name: Naismith, James H.
name: Owens, Ray
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 310112
subject: Structural biology (incl. macromolecular modelling)

description: PDB validation report for deposited EM structure 8OYT