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These collections include publications and data from University of Arizona faculty, staff and researchers. The UA Faculty Publications collection consists primarily of open access versions of published journal articles, but also contains conference proceedings and other unique materials from faculty, staff and researchers. Organizational collections, such as the College of Agricultural and Life Sciences Publications, and Water Resources Research Center, contain additional faculty publications such as departmentally produced technical bulletins, technical reports, and working papers.
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Revealing Earth science code and data-use practices using the Throughput Graph DatabaseThe increased use of complex programmatic workflows and open data within the Earth sciences has led to an increase in the need to find and reuse code, whether as examples, templates, or code snippets that can be used across projects. The “Throughput Graph Database” project offers a platform for discovery that links research objects by using structured annotations. Throughput was initially populated by scraping GitHub for code repositories that reference the names or URLs of data archives listed on the Registry of Research Data Repositories (https://re3data.org). Throughput annotations link the research data archives to public code repositories, which makes data-relevant code repositories easier to find. Linking code repositories in a queryable, machine-readable way is only the first step to improving discoverability. A better understanding of the ways in which data is used and reused in code repositories is needed to better support code reuse. In this paper, we examine the data practices of Earth science data reusers through a classification of GitHub repositories that reference geology and paleontology data archives. A typology of seven reuse classes was developed to describe how data were used within a code repository, and it was applied to a subset of 129 public code repositories on GitHub. Code repositories could have multiple typology assignments. Data use for Software Development dominated (n = 44), followed by Miscellaneous Links to Data Archives (n = 41), Analysis (n = 22), and Educational (n = 20) uses. GitHub repository features show some relationships to the assigned typologies, which indicates that these characteristics may be leveraged to systematically predict a code repository’s category or discover potentially useful code repositories for certain data archives.
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Ar-Ar and U-Pb ages of Chelyabinsk and a re-evaluation of its impact chronologyThe LL5 chondrite Chelyabinsk has had numerous isotopic studies since its fall in 2013. These data have been used to suggest ~8 impact events recorded from multiple isotopic systems (e.g., Ar-Ar, U–Pb, Sm-Nd, Rb-Sr, among others). We report details of Ar-Ar and U-Pb results and re-evaluate the geochronology of Chelyabinsk. Argon has the youngest Ar-Ar age recorded in meteorites, 25 ± 11 Ma, and an older resetting event at ~2550 Ma. The U-Pb analysis has an upper concordia age of 4456 ± 23 Ma and a lower concordia age of 184 ± 200 Ma. The lower concordia intercept represents a later thermal event (e.g., an impact), the most recent time that lead loss occurred, and could represent resetting by the youngest event recorded by Ar-Ar. Combining our data with literature results, we find strong evidence of at least four impact events (~4450, 2550, 1700, 25 Ma), with some evidence for two additional impacts (~3700, 1000 Ma).
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An Examination of Affiliate and Network Television Channels’ Facebook Use for Addressing Audiences’ Critical Information NeedsBased on the principles of localism and Critical Information Needs (CIN), this study analyzed the news content posted on Facebook by three television news channels—one local ABC affiliate each in Phoenix, Arizona and Kearney, Nebraska, and ABC News network channel — to examine the extent to which these posts fulfilled the critical information needs of audiences via social media. Results showed the local channel in Phoenix posted more CIN content than both, national network ABC and the local television channel in Kearney. Audience engagement with CIN posts differed across communities, with some categories increasing engagement in Phoenix and the same categories decreasing engagement in Kearney. This finding highlights not all critical information posts lead to increased audience engagement on social media and it is important for television channels to pay attention to content format and user feedback to further increase audience engagement with critical information.
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LINNA: Likelihood Inference Neural Network AcceleratorBayesian posterior inference of modern multi-probe cosmological analyses incurs massive computational costs. For instance, depending on the combinations of probes, a single posterior inference for the Dark Energy Survey (DES) data had a wall-clock time that ranged from 1 to 21 days using a state-of-the-art computing cluster with 100 cores. These computational costs have severe environmental impacts and the long wall-clock time slows scientific productivity. To address these difficulties, we introduce LINNA: the Likelihood Inference Neural Network Accelerator. Relative to the baseline DES analyses, LINNA reduces the computational cost associated with posterior inference by a factor of 8–50. If applied to the first-year cosmological analysis of Rubin Observatory's Legacy Survey of Space and Time (LSST Y1), we conservatively estimate that LINNA will save more than U.S. $300,000 on energy costs, while simultaneously reducing CO2 emission by 2,400 tons. To accomplish these reductions, LINNA automatically builds training data sets, creates neural network emulators, and produces a Markov chain that samples the posterior. We explicitly verify that LINNA accurately reproduces the first-year DES (DES Y1) cosmological constraints derived from a variety of different data vectors with our default code settings, without needing to retune the algorithm every time. Further, we find that LINNA is sufficient for enabling accurate and efficient sampling for LSST Y10 multi-probe analyses. We make LINNA publicly available at https://github.com/chto/linna, to enable others to perform fast and accurate posterior inference in contemporary cosmological analyses.
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Quercus rubra invasion of temperate deciduous forest stands alters the structure and functions of the soil microbiomeInvasive plants can modify the diversity and taxonomical structure of soil microbiomes. However, it is difficult to generalize the underlying factors as their influence often seems to depend on the complex plant-soil-microbial interactions. In this paper, we investigated how Quercus rubra impacts on the soil microbiome across two soil horizons in relation to native woodland. Five paired adjacent invaded vs native vegetation plots in a managed forest in southern Poland were investigated. Soil microbial communities were assessed along with soil enzyme activities and soil physicochemical parameters, separately for both organic and mineral horizons, as well as forest stand characteristics to explore plant-soil-microbe interactions. Although Q. rubra did not significantly affect pH, organic C, total N, available nutrients nor enzymatic activity, differences in soil abiotic properties (except C to N ratio) were primarily driven by soil depth for both vegetation types. Further, we found significant differences in soil microbiome under invasion in relation to native vegetation. Microbial richness and diversity were lower in both horizons of Q. rubra vs control plots. Moreover, Q. rubra increased relative abundance of unique amplicon sequence variants in both horizons and thereby significantly changed the structure of the core soil microbial communities, in comparison to the control plots. In addition, predicted microbial functional groups indicated a predominant soil depth effect in both vegetation plots with higher abundance of aerobic chemoheterotrophic bacteria and endophytic fungi in the organic horizon and greater abundance of methanotrophic and methylotrophic bacteria, and ectomycorrhizal fungi in the mineral horizon. Overall, our results indicate strong associations between Q. rubra invasion and changes in soil microbiome and associated functions, a finding that needs to be further investigated to predict modifications in ecosystem functioning caused by this invasive species.
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The Craft and Coordination of Data Curation: Complicating Workflow Views of Data ScienceData curation is the process of making a dataset fit-for-use and archivable. It is critical to data-intensive science because it makes complex data pipelines possible, studies reproducible, and data reusable. Yet the complexities of the hands-on, technical, and intellectual work of data curation is frequently overlooked or downplayed. Obscuring the work of data curation not only renders the labor and contributions of data curators invisible but also hides the impact that curators' work has on the later usability, reliability, and reproducibility of data. To better understand the work and impact of data curation, we conducted a close examination of data curation at a large social science data repository, the Inter-university Consortium for Political and Social Research (ICPSR). We asked: What does curatorial work entail at ICPSR, and what work is more or less visible to different stakeholders and in different contexts? And, how is that curatorial work coordinated across the organization? We triangulated accounts of data curation from interviews and records of curation in Jira tickets to develop a rich and detailed account of curatorial work. While we identified numerous curatorial actions performed by ICPSR curators, we also found that curators rely on a number of craft practices to perform their jobs. The reality of their work practices defies the rote sequence of events implied by many life cycle or workflow models. Further, we show that craft practices are needed to enact data curation best practices and standards. The craft that goes into data curation is often invisible to end users, but it is well recognized by ICPSR curators and their supervisors. Explicitly acknowledging and supporting data curators as craftspeople is important in creating sustainable and successful curatorial infrastructures.
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Vocabulary Acquisition and Usage for Late Talkers: The Feasibility of a Caregiver-Implemented Telehealth ModelPurpose: This feasibility study examined a caregiver-implemented telehealth model of the Vocabulary Acquisition and Usage for Late Talkers (VAULT) proto-col. We asked whether caregivers could reach fidelity on VAULT, if the protocol was socially and ecologically valid, and if late-talking toddlers could learn new words with this model. Method: Five late-talking monolingual and bilingual toddlers and four caregivers participated. The caregiver-related research questions involved measurements taken at multiple time points and replication across subjects but did not follow a specific research design. The toddler-related research questions included ele-ments of a single-case design. Caregivers completed self-paced online training modules and then provided 8 weeks of VAULT to their children with remote coaching. Fidelity data were collected during coached sessions and through rating scales. Social and ecological validity data were collected via surveys and interviews. Children’s word learning was measured before, during, and after treatment via production of targets and controls and via standardized vocabulary inventories. Results: Caregivers demonstrated high fidelity to VAULT throughout treatment. They reported being comfortable with many aspects of VAULT. Feedback was mixed regarding the time required. Many reported their child was talking more as a result of the program. Visual analysis revealed that toddlers learned more target than control words, which was corroborated by Tau-U and d effect size analyses. Conclusion: A caregiver-implemented telehealth model of VAULT was feasible, was socially and ecologically valid, and benefited toddlers, making this a worth-while model for future studies to examine.
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T-cell cellular stress and reticulocyte signatures, but not loss of naïve T lymphocytes, characterize severe COVID-19 in older adultsIn children and younger adults up to 39 years of age, SARS-CoV-2 usually elicits mild symptoms that resemble the common cold. Disease severity increases with age starting at 30 and reaches astounding mortality rates that are ~330 fold higher in persons above 85 years of age compared to those 18–39 years old. To understand age-specific immune pathobiology of COVID-19, we have analyzed soluble mediators, cellular phenotypes, and transcriptome from over 80 COVID-19 patients of varying ages and disease severity, carefully controlling for age as a variable. We found that reticulocyte numbers and peripheral blood transcriptional signatures robustly correlated with disease severity. By contrast, decreased numbers and proportion of naïve T-cells, reported previously as a COVID-19 severity risk factor, were found to be general features of aging and not of COVID-19 severity, as they readily occurred in older participants experiencing only mild or no disease at all. Single-cell transcriptional signatures across age and severity groups showed that severe but not moderate/mild COVID-19 causes cell stress response in different T-cell populations, and some of that stress was unique to old severe participants, suggesting that in severe disease of older adults, these defenders of the organism may be disabled from performing immune protection. These findings shed new light on interactions between age and disease severity in COVID-19.
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Non-reciprocal acoustoelectric microwave amplifiers with net gain and low noise in continuous operationPiezoelectric acoustic devices that are integrated with semiconductors can leverage the acoustoelectric effect, allowing functionalities such as gain and isolation to be achieved in the acoustic domain. This could lead to performance improvements and miniaturization of radio-frequency electronic systems. However, acoustoelectric amplifiers that offer a large acoustic gain with low power consumption and noise figure at microwave frequencies in continuous operation have not yet been developed. Here we report non-reciprocal acoustoelectric amplifiers that are based on a three-layer heterostructure consisting of an indium gallium arsenide (In0.53Ga0.47As) semiconducting film, a lithium niobate (LiNbO3) piezoelectric film, and a silicon substrate. The heterostructure can continuously generate 28.0 dB of acoustic gain (4.0 dB net radio-frequency gain) for 1 GHz phonons with an acoustic noise figure of 2.8 dB, while dissipating 40.5 mW of d.c. power. We also create a device with an acoustic gain of 37.0 dB (11.3 dB net gain) at 1 GHz with 19.6 mW of d.c. power dissipation and a non-reciprocal transmission of over 55 dB.
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Student Feedback Regarding Online Course Production Value: A Case Study from ClassicsThis paper employs a data-driven approach to understanding the relationship between online course production quality, instructional effectiveness, and student satisfaction. To accomplish this, it assesses data from six years of student evaluations for online courses and compares it to the production style and quality present in those courses. The quantitative multiple choice course evaluation questions speak to issues of overall quality and satisfaction, student learning, and content and lesson clarity. Qualitative student comments are also assessed to understand the degree to which production quality is highlighted as a driving factor in both student enjoyment and instructional effectiveness. Finally, trends in evaluation data are analyzed in conjunction with the quality and style of each course to provide a better understanding of how students perceive the value of production quality. This project serves as an important step in furthering evidence-based online pedagogy and provides valuable insights for how to best allocate time and resources with regard to online course production.
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The Cost of High Production Quality: A Preliminary Discussion of the Value of Production in Asynchronous Online ModalitiesWhat would happen if online course content was produced at television-or even cinematic-level quality? Would students become more engaged? Would they learn more and more deeply? If so, would the gains be worth the expenditure of time and funds that higher video production quality requires? To put it another way: Do investments in video production quality result in measurable increases in students' achievement of learning outcomes and objectives? Questions such as these are at the heart of this preliminary discussion of production value for online content creation, which investigates a grand challenge facing higher education and society generally, as we navigate the spectrum of modalities in a post-pandemic world. This questions that this paper proposes stands at the intersection of educational scholarship, course content creation, student retention and persistence, and the achievement of learning outcomes and objectives. It, therefore, seeks to push forward a model for change and improvement in university education and teaching and learning on our campuses.
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A Descriptive Study of Speech Breathing in Children With Cerebral Palsy During Two Types of Connected Speech TasksPurpose: This study examined speech breathing during two connected speech tasks in children with cerebral palsy (CP) and typically developing (TD) peers. Understanding how the respiratory system supports speech production during various speech tasks can help researchers construct appropriate models of speech production and clinicians remediate speech disorders effectively. Method: Four children with CP and four age-and sex-matched TD peers completed two speech tasks, reading and extemporaneous speech. Respiratory kinematic and acoustic data were collected. Dependent variables included utterance length, speech rate, sound pressure level, and lung volume variables. Results: Based on descriptive results, children with CP and speech motor involvement demonstrated reduced utterance length and speech rate, equivalent intensity levels, and changes in lung volume variables indicative of respiratory physiological impairment as compared to their TD peers. However, children with CP and no speech motor involvement exhibited speech production and speech breathing variables in the more typical range. In relation to task effects, the majority of children (CP and TD) produced shorter utterances, slower speech rates, equivalent intensity levels, higher lung volume initiation, termination, excursion, higher percent vital capacity per syllable, and longer inspiratory duration during extemporaneous speech as compared to reading. Conclusions: Two major themes emerged from the data: (a) Children with CP, particularly those with concomitant speech motor involvement, demonstrate different speech production and speech breathing patterns than their TD peers. (b) Speech task impacts speech production and speech breathing variables in both children with CP and their TD peers, but the extemporaneous speech task did not seem to exaggerate group differences.
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Clinically Relevant Drug Interactions with Monoamine Oxidase InhibitorsMonoamine oxidase inhibitors (MAOI) are a class of drugs that were originally developed for the treatment of depression but have since been expanded to be used in management of affective and neurological disorders, as well as stroke and aging-related neurocognitive changes. Ranging from irreversible to reversible and selective to non-selective, these drugs target the monoamine oxidase (MAO) enzyme and prevent the oxidative deamination of various monoamines and catecholamines such as serotonin and dopamine, respectively. Tyramine is a potent releaser of norepinephrine (NE) and is found in high concentrations in foods such as aged cheeses and meats. Under normal conditions, NE is unable to accumulate to toxic levels due to the presence of MAO-A, an enzyme that degrades neurotransmitters, including NE. When MAO-A is inhibited, the capacity to handle tyramine intake from the diet is significantly reduced causing the brain to be vulnerable to overstimulation of postsynaptic adrenergic receptors with as little as 8-10 mg of tyramine ingested and can result in life-threatening blood pressure elevations. In addition to adverse reactions with certain foods, both older and newer MAOIs can negatively interact with both sympathomimetic and serotonergic drugs. In general, patients on a MAOI want to avoid two types of medications: those that can elevate blood pressure via sympathomimetic actions (e.g., phenylephrine and oxymetazoline) and those that can increase serotonin levels via 5-HT reuptake inhibition (e.g., dextromethorphan, chlorpheniramine, and brompheniramine). Illicit drugs that stimulate the central nervous system such as ecstasy (MDMA, 3,4-methylenedioxymethamphetamine) act as serotonin releasers. Patient involvement is also crucial to ensure any interaction within the healthcare setting includes making other providers aware of a MAOI prescription as well as avoiding certain OTC medications that can interact adversely with MAOIs. © 2022, Open Medical Publishing. All rights reserved.
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A comprehensive review of intraarticular knee injection therapy, geniculate injections, and peripheral nerve stimulation for knee pain in clinical practiceThe knee is the most common joint in adults associated with morbidity. Many pathologies are associated with knee damage, such as gout or rheumathoid arthritis, but the primary condition is osteoarthritis (OA). Not only can osteoarthritis cause significant pain, but it also can result in signficant disability as well. Treatment for this condition varies, starting off with oral analgesics and physical therapy to surgical total knee replacmenet. In the gamut of this various treatments, a conservative approach has included intra articular steroid injections. With time, researchers and clinicians determined that other components injected to the knee may additionally provide relief of this condition. In this investigation, we describe different types of knee injections such as platelet-rich plasma (PRP), hyaluronic acid, stem cells, and prolotherapy. Additionally, we describe the role of geniculate knee injections, radiofrequency, and periopheral nerve stimulation. These treatments should be considered for patients with knee pain refractory to conservative therapies. © 2022, Open Medical Publishing. All rights reserved.
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The Value of Classical Islamic Thoufor Muslims TodayThis article challenges the assertion, found in the writings Dr. Taha Jabir Al-Alwani and other Muslim reformers, that Islamic thought declined precipitously in the early centuries of Islam and is of little value to contemporary Muslims. It introduces readers to the sophis-ticated thought of four diverse Muslim thinkers from the 5th/11th century who each wrote about topics that remain important to Muslims today, such as the nature of the soul, ethics, the purpose of knowledge, and spirituality. These thinkers are the philosopher-his-torian Miskawayh, the Sunni Mu‘tazili al-Ḥākim al-Jishumī, the Zahiri Ibn Ḥazm, and the Hadith scholar al-Khaṭīb al-Baghdādī. In addition to drawing specific lessons from these classical thinkers’ writings, the article encourages contemporary Muslims to emulate their practice of reading widely, including works of Muslim phi-losophy and theology, and to appreciate the significant connection they made between the acquisition of knowledge and its application to daily life. © 2020 International Institute of Islamic Though.
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Future Directions for Digital Literacy Fluency using Cognitive Flexibility Research: A Review of Selected Digital Literacy Paradigms and Theoretical FrameworksAs learners engage, test, and apply new subject knowledge, they often expend their cognitive capacity on the technological tools designed to capture their learning progress and outcomes. The energy and attention spent on these tools reduces their capacity to engage deeply with new learning concepts. Digital literacy skills require both cognitive and technical skills to develop a learner’s ability to locate, use, and communicate information. Increasingly complex information environments create various barriers for student learning, and as our learning and working industries continue to evolve and integrate technologies, students must overcome these barriers by bridging learning needs and technology expectations. This research explores the value of developing digital literacy to improve learners’ cognitive flexibility by decreasing technological cognitive load and increasing learning fluency. The findings highlight the need for establishing scaffolded digital literacy skills and digital tool selection, and expand college readiness requirements to include digital literacy as a prerequisite skill for learners. © 2022, Commonwealth of Learning. All rights reserved.
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An Evaluation of Electrostatic Lofting and Subsequent Particle Motion on BennuElectrostatic lofting is the detachment of particles from a surface that occurs if the electrostatic force on the particles is greater than the forces binding the particles to the surface. Electrostatic lofting has been hypothesized to occur on the Moon and observed in the laboratory environment. Because gravity is much weaker on asteroids than on the Moon, the hypothesis of electrostatic lofting has naturally been extended to these smaller airless bodies. We evaluate the feasibility of electrostatic lofting on Bennu using two formulations of the patched charge model. We find that submillimeter particles can be lofted from Bennu’s dayside and, depending on their initial conditions, will reimpact or escape. The size and speed of the predicted electrostatically lofted particles are compared to those of the particle ejection events recently observed on Bennu. We find that dayside electrostatic lofting is not consistent with the size and speed of particles in the largest ejection events observed by the OSIRIS-REx mission. However, the escape of submillimeter particles has implications for the particle size distribution on Bennu’s surface. Additionally, we model particle charging on Bennu’s nightside due to secondary electron emission and find the resulting electrostatic force to be too weak to produce electrostatic lofting on the nightside. © 2022. The Author(s). Published by the American Astronomical Society.
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Quality Assessment of Stereophotoclinometry as a Shape Modeling Method Using a Synthetic AsteroidThe stereophotoclinometry (SPC) software suite has been used to generate global digital terrain models (DTMs) of many asteroids and moons, and was the primary tool used by the Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx) mission to model the shape of asteroid Bennu. We describe the dedicated preflight testing of SPC for the OSIRIS-REx mission using a synthetic “truth” asteroid model. SPC has metrics that determine the internal consistency of a DTM, but it was not known how these metrics are related to the absolute accuracy of a DTM, which was important for the operational needs of the mission. The absolute accuracy of an SPC-generated DTM cannot be determined without knowing the truth topography. Consequently, we developed a realistic, but synthetic, computer-generated representation of asteroid Bennu, photographed this synthetic truth model in an imaging campaign similar to that planned for the OSIRIS-REx mission, and then generated a global SPC DTM from these images. We compared the SPC DTM, which was represented by a radius every 70 cm across the asteroid surface, to the synthetic truth model to assess the absolute accuracy. We found that the internal consistency can be used to determine the 3D root-mean-square accuracy of the model to within a factor of two of the absolute accuracy. © 2022. The Author(s). Published by the American Astronomical Society.
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Near-infrared Spectroscopy of the Nucleus of Low-activity Comet P/2016 BA14 during Its 2016 Close ApproachThe near-Earth comet P/2016 BA14 (PanSTARRS) is a slow-rotating, nearly dormant object, a likely dynamical twin of 252P/LINEAR, and was recently shown to have a mid-infrared spectrum very dissimilar to other comets. Comet BA14 was also recently selected as one of the backup targets for the ESA’s Comet Interceptor, so a clearer understanding of BA14’s modern properties would not just improve our understanding of how comets go dormant but could also aid in planning for a potential spacecraft visit. We present observations of BA14 during its 2016 Earth close approach taken with the NASA Infrared Telescope Facility on two dates, both of which are consistent with direct observations of its nucleus. The reflectance spectrum of BA14 is similar to 67P/Churyumov–Gerasimenko, albeit highly phase-reddened. Thermal emission contaminates the reflectance spectrum at longer wavelengths, which we correct with a new Markov Chain Monte Carlo thermal modeling code. The models suggest that BA14’s visible geometric albedo is pV = 0.01–0.03, consistent with radar observations; its beaming parameter is typical for NEOs observed in its geometry; and its reflectance spectrum is red and linear throughout the H and K bands. It appears very much like a “normal” comet nucleus despite its mid-infrared oddities. A slow loss of fine grains as the object’s activity diminished might help to reconcile some of the lines of evidence, and we discuss other possibilities. A spacecraft flyby past BA14 could get closer to the nucleus than with a more active target, and we highlight some science questions that could be addressed with a visit to a (nearly) dormant comet. © 2022. The Author(s). Published by the American Astronomical Society.
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NEOWISE Observations of the Potentially Hazardous Asteroid (99942) ApophisLarge potentially hazardous asteroids (PHAs) are capable of causing a global catastrophe in the event of a planetary collision. Thus, rapid assessment of such an object’s physical characteristics is crucial for determining its potential risk scale. We treated the near-Earth asteroid (99942) Apophis as a newly discovered object during its 2020–2021 close approach as part of a mock planetary defense exercise. The object was detected by the Near-Earth Object Wide-field Infrared Survey Explorer (NEOWISE), and data collected by the two active bands (3.4 and 4.6 μm) were analyzed using thermal and thermophysical modeling. Our results indicate that Apophis is an elongated object with an effective spherical diameter Deff = 340 ± 70 m, a geometric visual albedo pV = 0.31 ± 0.09, and a thermal inertia Γ ∼ 150–2850 J m−2 s-½ K−1 with a best-fit value of 550 J m−2 s-½K−1. NEOWISE “discovery” observations reveal that (99942) Apophis is a PHA that would likely cause damage at a regional level and not a global one. © 2022. The Author(s). Published by the American Astronomical Society.
