Now showing items 5621-5640 of 14018

    • Institutions and the performance of coupled infrastructure systems

      Anderies, John M.; Janssen, Marco A.; Schlager, Edella; Univ Arizona, Sch Govt & Publ Policy (IGITUR, UTRECHT PUBLISHING & ARCHIVING SERVICES, 2016-09-23)
      Institutions, the rules of the game that shape repeated human interactions, clearly play a critical role in helping groups avoid the inefficient use of shared resources such as fisheries, freshwater, and the assimilative capacity of the environment. Institutions, however, are intimately intertwined with the human, social, and biophysical context within which they operate. Scholars typically are careful to take this context into account when studying institutions and Ostrom's Institutional Design Principles are a case in point. Scholars have tested whether Ostrom's Design Principles, which specify broad relationships between institutional arrangements and context, actually support successful governance of shared resources. This article further contributes to this line of research by leveraging the notion of institutional design to outline a research trajectory focused on coupled infrastructure systems in which institutions are seen as one class of infrastructure among many that dynamically interact to produce outcomes over time.
    • Instruction and Service Time Decisions: Itinerant Services to Deaf and Hard-of-Hearing Students

      Antia, Shirin D.; Rivera, M. Christina; Univ Arizona (OXFORD UNIV PRESS, 2016-07)
      The purpose of this study was to (a) describe the specific kinds of services provided by itinerant teachers to deaf and hard-of-hearing (DHH) students in general education settings, (b) examine the relationship between student academic performance and instructional support provided by the itinerant teacher, and (c) examine how service provision decisions are made by itinerant teachers. We used quantitative and qualitative data collected during a 5-year longitudinal study. Data were obtained from teacher questionnaires, standardized achievement tests, and interviews. Results indicated that itinerant teachers of DHH students provided direct academic instruction to 60% of students with the majority of students receiving instruction in reading and writing. They provided instruction in nonacademic areas to 80% of students with a majority of students receiving instruction in self-advocacy. Low-achieving students were the most likely to receive academic instruction from the itinerant teacher. Decisions regarding service time were influenced by student needs and performance, age, parental request, and transitions.
    • Instructional Level and Engagement in Students With Behavioral Disorders

      Carr, Chelsea E.; Umbreit, John; Hartzell, Rebecca; University of Arizona (SAGE Publications, 2021-10-08)
      This study examined the effects of adjusting the difficulty level of instructional materials on the time on-task and comprehension of four students with emotional and behavioral disorders. All participants previously exhibited low rates of on-task behavior during reading assignments. Students were presented with reading materials at their instructional, frustration, and independent levels to assess the effect on time on-task and comprehension. All four students demonstrated the highest percent of on-task behavior when presented with reading materials at their instructional level. Comprehension scores were highest for all four students at the independent level and lowest at the frustration level. © Hammill Institute on Disabilities 2021.
    • Insulin Induces Microtubule Stabilization and Regulates the Microtubule Plus-end Tracking Protein Network in Adipocytes

      Parker, Sara S; Krantz, James; Kwak, Eun-A; Barker, Natalie K; Deer, Chris G; Lee, Nam Y; Mouneimne, Ghassan; Langlais, Paul R; Univ Arizona, Coll Med, Dept Cellular & Mol Med; Univ Arizona, Coll Med, Dept Med, Div Endocrinol; et al. (AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 2019-07)
      Insulin-stimulated glucose uptake is known to involve microtubules, although the function of microtubules and the microtubule-regulating proteins involved in insulin action are poorly understood. CLASP2, a plus-end tracking microtubule-associated protein (+TIP) that controls microtubule dynamics, was recently implicated as the first +TIP associated with insulin-regulated glucose uptake. Here, using protein-specific targeted quantitative phosphoproteomics within 3T3-L1 adipocytes, we discovered that insulin regulates phosphorylation of the CLASP2 network members G2L1, MARK2, CLIP2, AGAP3, and CKAP5 as well as EB1, revealing the existence of a previously unknown microtubule-associated protein system that responds to insulin. To further investigate, G2L1 interactome studies within 3T3-L1 adipocytes revealed that G2L1 coimmunoprecipitates CLASP2 and CLIP2 as well as the master integrators of +TIP assembly, the end binding (EB) proteins. Live-cell total internal reflection fluorescence microscopy in adipocytes revealed G2L1 and CLASP2 colocalize on microtubule plus-ends. We found that although insulin increases the number of CLASP2-containing plus-ends, insulin treatment simultaneously decreases CLASP2-containing plus-end velocity. In addition, we discovered that insulin stimulates redistribution of CLASP2 and G2L1 from exclusive plus-end tracking to "trailing" behind the growing tip of the microtubule. Insulin treatment increases alpha-tubulin Lysine 40 acetylation, a mechanism that was observed to be regulated by a counterbalance between GSK3 and mTOR, and led to microtubule stabilization. Our studies introduce insulin-stimulated microtubule stabilization and plus-end trailing of +TIPs as new modes of insulin action and reveal the likelihood that a network of microtubule-associated proteins synergize to coordinate insulin-regulated microtubule dynamics.
    • Insulin injection technique in the western region of Algeria, Tlemcen

      Hacene, Mohammed Nassim Boukli; Saker, Meriem; Youcef, Amina; Koudri, Soumia; Cheriet, Souad; Merzouk, Hafida; Lounici, Ali; Alkhatib, Nimer; Univ Arizona, Coll Pharm, Ctr Hlth Outcomes & PharmacoEcon Res (AFRICAN FIELD EPIDEMIOLOGY NETWORK-AFENET, 2020-08-24)
      Introduction: Algeria has more than 1.7 million diabetic patients on to whom a descriptive assessment particularly on the insulin usage behaviors has not yet been initiated, although is needed. This study aims to provide a descriptive analysis of how Algerian diabetic patients perceive and apply insulin injection techniques. Methods: using the "patient" questionnaire within the Injection Technique Questionnaire (ITQ) 2016 survey, this study assessed the insulin injection practices of 100 patients recruited over a seven-month period in western Algeria at the Tlemcen University Hospital Center. The results of this study are compared to those of the ITQ 2016 survey. Results: pens are the instruments of injection for 98% of Algerians who continue to use mostly long needles of 6- and 8-mm, although 4mm needles are the recommended safer option. Insulin analogues (fast and basal) are plebiscite. Arms and thighs are the preferred injection sites; the abdomen (the preferred site elsewhere) is neglected for reasons to be investigated. The correct re-suspension technique for cloudy insulin is unknown. Extensive pen needle re-use (10+ times) for over half of the patients exposes them to both higher intramuscular (IM) injection risk and lipohypertrophy (LH). Injection training is performed in Algeria by the diabetologist. Conclusion: this study describes for the first time Algerian patients' insulin injection technique. It highlights their skills and identifies many deficiencies which patients and professionals must correct given the issues in this area.
    • Insulin receptor substrate 1 is a substrate of the Pim protein kinases

      Song, Jin H.; Padi, Sathish K. R.; Luevano, Libia A.; Minden, Mark D.; DeAngelo, Daniel J.; Hardiman, Gary; Ball, Lauren E.; Warfel, Noel A.; Kraft, Andrew S.; Univ Arizona, Dept Cellular & Mol Med; et al. (IMPACT JOURNALS LLC, 2016-03-04)
      The Pim family of serine/threonine protein kinases (Pim 1, 2, and 3) contribute to cellular transformation by regulating glucose metabolism, protein synthesis, and mitochondrial oxidative phosphorylation. Drugs targeting the Pim protein kinases are being tested in phase I/II clinical trials for the treatment of hematopoietic malignancies. The goal of these studies was to identify Pim substrate(s) that could help define the pathway regulated by these enzymes and potentially serve as a biomarker of Pim activity. To identify novel substrates, bioinformatics analysis was carried out to identify proteins containing a consensus Pim phosphorylation site. This analysis identified the insulin receptor substrate 1 and 2 (IRS1/2) as potential Pim substrates. Experiments were carried out in tissue culture, animals, and human samples from phase I trials to validate this observation and define the biologic readout of this phosphorylation. Our study demonstrates in both malignant and normal cells using either genetic or pharmacological inhibition of the Pim kinases or overexpression of this family of enzymes that human IRS1S1101 and IRS2S1149 are Pim substrates. In xenograft tumor experiments and in a human phase I clinical trial, a pan-Pim inhibitor administered in vivo to animals or humans decreased IRS1S1101 phosphorylation in tumor tissues. This phosphorylation was shown to have effects on the half-life of the IRS family of proteins, suggesting a role in insulin or IGF signaling. These results demonstrate that IRS1S1101 is a novel substrate for the Pim kinases and provide a novel marker for evaluation of Pim inhibitor therapy.
    • Insulin sensitivity is normalized in the third generation (F3) offspring of developmentally programmed insulin resistant (F2) rats fed an energy-restricted diet

      Benyshek, Daniel; Johnston, Carol; Martin, John; Ross, William; Department of Anthropology, University of Nevada Las Vegas, 4505 Maryland, Parkway, Box 455003, Las Vegas, NV 89154-5003, USA; Department of Nutrition, Arizona State University, Mesa, AZ, USA; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA; College of Medicine, University of Arizona, Tucson, AZ, USA (BioMed Central, 2008)
      BACKGROUND/AIMS:The offspring and grandoffspring of female rats fed low protein diets during pregnancy and lactation, but fed nutritionally adequate diets thereafter, have been shown to exhibit altered insulin sensitivity in adulthood. The current study investigates the insulin sensitivity of the offspring and grandoffspring of female rats fed low protein diets during pregnancy, and then maintained on energy-restricted diets post weaning over three generations.METHODS:Female Sprague Dawley rats (F0) were mated with control males and protein malnourished during pregnancy/lactation. F1 offspring were then weaned to adequate but energy-restricted diets into adulthood. F1 dams were fed energy-restricted diets throughout pregnancy/lactation. F2 offspring were also fed energy-restricted diets post weaning. F2 pregnant dams were maintained as described above. Their F3 offspring were split into two groups
    • Integral Field Spectroscopy of the Low-mass Companion HD 984 B with the Gemini Planet Imager

      Johnson-Groh, Mara; Marois, Christian; De Rosa, Robert J.; Nielsen, Eric L.; Rameau, Julien; Blunt, Sarah; Vargas, Jeffrey; Ammons, S. Mark; Bailey, Vanessa P.; Barman, Travis S.; et al. (IOP PUBLISHING LTD, 2017-03-31)
      We present new observations of the low-mass companion to HD 984 taken with the Gemini Planet Imager (GPI) as a part of the GPI Exoplanet Survey campaign. Images of HD 984 B were obtained in the J (1.12-1.3 mu m) and H (1.50-1.80 mu m) bands. Combined with archival epochs from 2012 and 2014, we fit the first orbit to the companion to find an 18 au (70-year) orbit with a 68% confidence interval between 14 and 28 au, an eccentricity of 0.18 with a 68% confidence interval between 0.05 and 0.47, and an inclination of 119 degrees with a 68% confidence interval between 114 degrees and 125 degrees. To address the considerable spectral covariance in both spectra, we present a method of splitting the spectra into low and high frequencies to analyze the spectral structure at different spatial frequencies with the proper spectral noise correlation. Using the split spectra, we compare them to known spectral types using field brown dwarf and low-mass star spectra and find a best-fit match of a field gravity M6.5 +/- 1.5 spectral type with a corresponding temperature of 2730(-180)(+120)K. Photometry of the companion yields a luminosity of log(L-bol/L-circle dot) = -2.88 +/- 0.07 dex with DUSTY models. Mass estimates, again from DUSTY models, find an age-dependent mass of 34 +/- 1 to 95 +/- 4 M-Jup. These results are consistent with previous measurements of the object.
    • An Integrated Analysis with Predictions on the Architecture of the τ Ceti Planetary System, Including a Habitable Zone Planet

      Dietrich, Jeremy; Apai, Dániel; Univ Arizona, Dept Astron; Univ Arizona, Lunar & Planetary Lab (IOP PUBLISHING LTD, 2020-12-07)
      tau Ceti is the closest single Sun-like star to the solar system and hosts a multiplanet system with four confirmed planets. The possible presence of additional planets, especially potentially habitable worlds, remains of great interest. We analyze the structure of the tau Ceti planetary system via the DYNAMITE algorithm, combining information from exoplanet population statistics and orbital dynamics with measurements of this specific system. We also expand DYNAMITE to incorporate radial velocity information. Our analysis suggests the presence of four additional planets, three of which match closely with the periods of three tentative planet candidates reported previously. We also predict at least one more planet candidate with an orbital period between similar to 270 and 470 days, in the habitable zone for tau Ceti. Based on the measured m sin i values of the confirmed planets, we also assess the possible masses and nature of the detected and undetected planets. The least massive planets and candidates are likely to be rocky, while the other planets and candidates could either be rocky or contain a significant gaseous envelope. The radial velocity observable signature from the predicted habitable zone planet candidate would likely be at or just above the noise level in current data, but should be detectable in future extremely high-precision radial velocity and direct-imaging studies.
    • An Integrated Approach to Improve Maternal Mental Health and Well-Being During the COVID-19 Crisis

      Shidhaye, Rahul; Madhivanan, Purnima; Shidhaye, Pallavi; Krupp, Karl; Univ Arizona, Mel & Enid Zuckerman Coll Publ Hlth, Dept Hlth Promot Sci; Univ Arizona, Coll Med, Div Infect Dis; Univ Arizona, Coll Med, Dept Family & Community Med (FRONTIERS MEDIA SA, 2020-11-24)
      The ongoing COVID-19 pandemic has led to disruption of normal life across the globe, severely affecting the already vulnerable populations such as the pregnant women. Maternal mental health and well-being is a public health priority and the evidence about the impact of COVID-19 on mental health status of pregnant women is gradually emerging. The findings of the recently published studies suggest that increased risk perception about contracting COVID-19, reduced social support, increase in domestic violence, disruption of antenatal care, and economic consequences of COVID-19 mitigation strategies can lead to adverse mental health outcomes in antenatal period. There is a significant increase in antenatal depression and anxiety since the onset of COVID-19 and social determinants of health (e.g., younger age, lower education, lower income) are associated with these poor outcomes. In this paper, we propose an integrated approach to improve the mental health and well-being of pregnant women. Physical activity and/or mind-body interventions like yoga can be practiced as self-care interventions by pregnant women. Despite social distancing being the current norm, efforts should be made to strengthen social support. Evidence-based interventions for perinatal depression should be integrated within the health system and stepped, collaborative care using non-specialist health workers as key human resource be utilized to improve access to mental health services. Use of digital platforms and smartphone enabled delivery of services has huge potential to further improve the access to care. Most importantly, the COVID-19 related policy guidelines should categorically include maternal mental health and well-being as a priority area.
    • Integrated Framework of Vehicle Dynamics, Instabilities, Energy Models, and Sparse Flow Smoothing Controllers

      Lee, J.W.; Gunter, G.; Ramadan, R.; Almatrudi, S.; Arnold, P.; Aquino, J.; Barbour, W.; Bhadani, R.; Carpio, J.; Chou, F.-C.; et al. (Association for Computing Machinery, Inc, 2021)
      This work presents an integrated framework of: vehicle dynamics models, with a particular attention to instabilities and traffic waves; vehicle energy models, with particular attention to accurate energy values for strongly unsteady driving profiles; and sparse Lagrangian controls via automated vehicles, with a focus on controls that can be executed via existing technology such as adaptive cruise control systems. This framework serves as a key building block in developing control strategies for human-in-the-loop traffic flow smoothing on real highways. In this contribution, we outline the fundamental merits of integrating vehicle dynamics and energy modeling into a single framework, and we demonstrate the energy impact of sparse flow smoothing controllers via simulation results. © 2021 Owner/Author.
    • Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection

      Stewart, David B; Wright, Justin R; Fowler, Maria; McLimans, Christopher J; Tokarev, Vasily; Amaniera, Isabella; Baker, Owen; Wong, Hoi-Tong; Brabec, Jeff; Drucker, Rebecca; et al. (AMER SOC MICROBIOLOGY, 2019-08-28)
      There has been no prior application of matched metagenomics and metatranscriptomics in Clostridioides difficile infection (CDI) evaluating the role of fungi in CDI or identifying community functions that contribute to the development of this disease. We collected diarrheal stools from 49 inpatients (18 of whom tested positive for CDI) under stringent inclusion criteria. We utilized a tiered sequencing approach to identify enriched bacterial and fungal taxa, using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing, with matched metagenomics and metatranscriptomics performed on a subset of the population. Distinct bacterial and fungal compositions distinguished CDI-positive and -negative patients, with the greatest differentiation between the cohorts observed based on bacterial metatranscriptomics. Bipartite network analyses demonstrated that Aspergillus and Penicillium taxa shared a strong positive relationship in CDI patients and together formed negative cooccurring relationships with several bacterial taxa, including the Oscillospira, Comamonadaceae, Microbacteriaceae, and Cytophagaceae Metatranscriptomics revealed enriched pathways in CDI patients associated with biofilm production primarily driven by Escherichia coli and Pseudomonas, quorum-sensing proteins, and two-component systems related to functions such as osmotic regulation, linoleic acid metabolism, and flagellar assembly. Differential expression of functional pathways unveiled a mechanism by which the causal dysbiosis of CDI may self-perpetuate, potentially contributing to treatment failures. We propose that CDI has a distinct fungus-associated bacteriome, and this first description of metatranscriptomics in human subjects with CDI demonstrates that inflammation, osmotic changes, and biofilm production are key elements of CDI pathophysiology.IMPORTANCE Our data suggest a potential role for fungi in the most common nosocomial bacterial infection in the United States, introducing the concept of a transkingdom interaction between bacteria and fungi in this disease. We also provide the first direct measure of microbial community function in Clostridioides difficile infection using patient-derived tissue samples, revealing antibiotic-independent mechanisms by which C. difficile infection may resist a return to a healthy gut microbiome.
    • Integrated mitochondrial function and cancer-related fatigue in men with prostate cancer undergoing radiation therapy

      Hsiao, Chao-Pin; Chen, Mei-Kuang; Daly, Barbara; Hoppel, Charles; Univ Arizona, Dept Psychol (DOVE MEDICAL PRESS LTD, 2018-01-01)
      Introduction: Fatigue experienced by cancer patients is one of the most common symptoms with the greatest adverse effect on quality of life, but arguably the least understood. The purpose of this study was to explore changes in integrated mitochondrial function and fatigue in non-metastatic prostate cancer patients receiving localized radiation therapy (XRT). Materials and methods: We proposed a mitochondria' bioenergetics mechanism of radiation-induced fatigue linking impaired oxidative phosphorylation (OXPIIOS) through complex III and decreased adenosine triphosphate (ATP) production as consequences of XRT. Integrated mitochondria' function was measured as mitochondria' OXPHOS from patients' peripheral blood mononuclear cells. Fatigue was measured using the revised Piper Fatigue Scale. Data were collected before (day 0) and at day 21 of XRT. Results: At day 21 of XRT, fatigue symptom intensified in 15 prostate cancer patients (P<0.05). Mitochondrial OXPHOS complex III-linked and uncoupled complex III rates were significantly decreased in mononuclear cells at day 21 during XRT compared to that before XRT (P<0.05). Additionally, increased fatigue appeared to be associated with decreased OXPHOS complex Ill-linked respiration in patients undergoing XRT. Conclusion: Fatigue was associated with OXPHOS complex III-linked oxidation and a defect in oxidation starting at complex III in mononuclear cell mitochondria was revealed at day 21 of XRT in 15 prostate cancer patients. Complex III is a potential target for pharmacological and, in particular, nutraceutical interventions, eg, Q10, for design of interventions for CRF.
    • Integrated Optics Modules Based Proposal for Quantum Information Processing, Teleportation, QKD, and Quantum Error Correction Employing Photon Angular Momentum

      Djordjevic, Ivan B.; Univ Arizona, Dept Elect & Comp Engn; Univ Arizona, Coll Opt Sci (IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2016-02)
      To address key challenges for both quantum communication and quantum computing applications in a simultaneous manner, we propose to employ the photon angular momentum approach by invoking the well-known fact that photons carry both the spin angular momentum (SAM) and the orbital angular momentum (OAM). SAM is associated with polarization, while OAM is associated with azimuthal phase dependence of the complex electric field. Given that OAM eigenstates are mutually orthogonal, in principle, an arbitrary number of bits per single photon can be transmitted. The ability to generate/analyze states with different photon angular momentum, by using either holographic or interferometric methods, allows the realization of quantum states in multidimensional Hilbert space. Because OAM states provide an infinite basis state, while SAM states are 2-D only, the OAM can also be used to increase the security for quantum key distribution (QKD) applications and improve computational power for quantum computing applications. The goal of this paper is to describe photon angular momentum based deterministic universal quantum qudit gates, namely, {generalized-X, generalized-Z, generalized-CNOT} qudit gates, and different quantum modules of importance for various applications, including (fault-tolerant) quantum computing, teleportation, QKD, and quantum error correction. For instance, the basic quantum modules for quantum teleportation applications include the generalized-Bell-state generation module and the QFT-module. The basic quantum module for quantum error correction and fault-tolerant computing is the nonbinary syndrome calculator module. The basic module for entanglement assisted QKD is either the generalized-Bell-state generation module or the Weyl-operator-module. The possibility of implementing all these modules in integrated optics is discussed as well. Finally, we provide security analysis of entanglement assisted multidimensional QKD protocols, employing the proposed qudit modules, by taking into account the imperfect generation of OAM modes.
    • Integrated Patient-Derived Models Delineate Individualized Therapeutic Vulnerabilities of Pancreatic Cancer

      Witkiewicz, Agnieszka K.; Balaji, Uthra; Eslinger, Cody; McMillan, Elizabeth; Conway, William; Posner, Bruce; Mills, Gordon B.; O’Reilly, Eileen M.; Knudsen, Erik S.; Department of Pathology, University of Arizona; et al. (Cell Press, 2016-08)
      Pancreatic ductal adenocarcinoma (PDAC) harbors the worst prognosis of any common solid tumor, and multiple failed clinical trials indicate therapeutic recalcitrance. Here, we use exome sequencing of patient tumors and find multiple conserved genetic alterations. However, the majority of tumors exhibit no clearly defined therapeutic target. High-throughput drug screens using patient-derived cell lines found rare examples of sensitivity to monotherapy, with most models requiring combination therapy. Using PDX models, we confirmed the effectiveness and selectivity of the identified treatment responses. Out of more than 500 single and combination drug regimens tested, no single treatment was effective for the majority of PDAC tumors, and each case had unique sensitivity profiles that could not be predicted using genetic analyses. These data indicate a shortcoming of reliance on genetic analysis to predict efficacy of currently available agents against PDAC and suggest that sensitivity profiling of patient-derived models could inform personalized therapy design for PDAC.
    • Integrated Patient-Derived Models Delineate Individualized Therapeutic Vulnerabilities of Pancreatic Cancer.

      Witkiewicz, Agnieszka K; Balaji, Uthra; Eslinger, Cody; McMillan, Elizabeth; Conway, William; Posner, Bruce; Mills, Gordon B; O'Reilly, Eileen M; Knudsen, Erik S; Univ Arizona, Dept Pathol; et al. (CELL PRESS, 2016-08-16)
      Pancreatic ductal adenocarcinoma (PDAC) harbors the worst prognosis of any common solid tumor, and multiple failed clinical trials indicate therapeutic recalcitrance. Here, we use exome sequencing of patient tumors and find multiple conserved genetic alterations. However, the majority of tumors exhibit no clearly defined therapeutic target. High-throughput drug screens using patient-derived cell lines found rare examples of sensitivity to monotherapy, with most models requiring combination therapy. Using PDX models, we confirmed the effectiveness and selectivity of the identified treatment responses. Out of more than 500 single and combination drug regimens tested, no single treatment was effective for the majority of PDAC tumors, and each case had unique sensitivity profiles that could not be predicted using genetic analyses. These data indicate a shortcoming of reliance on genetic analysis to predict efficacy of currently available agents against PDAC and suggest that sensitivity profiling of patient-derived models could inform personalized therapy design for PDAC.
    • Integrated photonics and application-specific design on a massive open online course platform

      Saini, Sajan; Preble, Stefan; Popović, Miloš; Cardenas, Jaime; Kost, Alan; Verlage, Erik; Howland, Gregory; Kimerling, Lionel C.; Univ Arizona, Coll Opt Sci (SPIE-INT SOC OPTICAL ENGINEERING, 2019-07-02)
      Silicon-based photonics is mobilizing into a manufacturing industry with specialized integrated circuit design requirements for applications in low power cloud computing, high speed wireless, smart sensing, and augmented imaging. The AIM Photonics Manufacturing USA Institute, which operates the world's most advanced 300mm semiconductor research fab, has co-developed a Process Design Kit (PDK) in fabless circuit design for these expanding digital and analog applications; however, there currently isn't available an in-depth curriculum to train engineers (academia, industry) in the AIM PDK process and Electronic Photonic Design Automation (EPDA) software. AIM Photonics Academy, an education initiative of AIM Photonics based at MIT, has collaborated with faculty to create three online MOOC edX courses that (1) introduce integrated photonics devices, and applications performance needs and metrics; and (2) train into the AIM PDK and specialized EPDA tools in a six week design project to lay out an application-specific photonic transceiver. The courses are structured around asynchronous video lectures and exploratory design problems that involve Python and Matlab-based first-principles calculations (systems modeling) or advanced EPDA tools (circuit design and layout). The online MOOC courses can optionally form a tandem blended learning component with two AIM Photonics Academy on-site training programs: the annual AIM Summer Academy one-week intensive program (held every July at MIT), or a photonic integrated circuit testing workshop (the first workshop is planned for fall 2019). These courses are a cornerstone effort at AIM to found and support a specialized cohort community of future integrated photonics designers.
    • Integrated TORC1 and PKA signaling control the temporal activation of glucose-induced gene expression in yeast

      Kunkel, Joseph; Luo, Xiangxia; Capaldi, Andrew P; Univ Arizona, Dept Mol & Cellular Biol (NATURE PUBLISHING GROUP, 2019-08-08)
      The growth rate of a yeast cell is controlled by the target of rapamycin kinase complex I (TORC1) and cAMP-dependent protein kinase (PKA) pathways. To determine how TORC1 and PKA cooperate to regulate cell growth, we performed temporal analysis of gene expression in yeast switched from a non-fermentable substrate, to glucose, in the presence and absence of TORC1 and PKA inhibitors. Quantitative analysis of these data reveals that PKA drives the expression of key cell growth genes during transitions into, and out of, the rapid growth state in glucose, while TORC1 is important for the steady-state expression of the same genes. This circuit design may enable yeast to set an exact growth rate based on the abundance of internal metabolites such as amino acids, via TORC1, but also adapt rapidly to changes in external nutrients, such as glucose, via PKA.
    • Integrated water management recommendations in practice: coexistence of old and new ways in Arizona

      Berger, Lena; Henry, Adam Douglas; Pivo, Gary; Univ Arizona, Sch Govt & Publ Policy; Univ Arizona, Coll Architecture Planning & Landscape Architecture (IWA Publishing, 2020-05-15)
      Integrated water management (IWM) is widely regarded as a key strategy in achieving a variety of urban sustainability goals. Despite the promise of this strategy, however, uptake of IWM practices has generally been slow. A central reason for this lies in the divergence of action recommendations in the literature and actual water management praxis. In this paper, we explore how action taken by governments relate (or not) to IWM dimensions found in the literature. We do this by combining a corpus of actions taken by local governments in Arizona with a systematic review of the IWM literature. More precisely, we identify a confined set of IWM action dimensions particularly relevant to current praxis and apply these to water management practices reported by local governments in Arizona. We find that governments in the state systematically use IWM strategies to complement or enhance traditional water management approaches. Uptake differs across management spheres in terms of magnitude and form and is informed by contextual characteristics. Overall, our study indicates that transition may be guided by bottom-up experimentation, context-sensitive selection, and incremental change. This is in contrast to how IWM is often understood in the literature - as sharp shift and break with old traditions.
    • Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits

      Harper, J; De Vega, J; Swain, S; Heavens, D; Gasior, D; Thomas, A; Evans, C; Lovatt, A; Lister, S; Thorogood, D; et al. (OXFORD UNIV PRESS, 2019-05-08)
      Background and Aims Lolium perenne (perennial ryegrass) is the most widely cultivated forage and amenity grass species in temperate areas worldwide and there is a need to understand the genetic architectures of key agricultural traits and crop characteristics that deliver wider environmental services. Our aim was to identify genomic regions associated with agriculturally important traits by integrating a bacterial artificial chromosome (BAC)-based physical map with a genome-wide association study (GWAS). Methods BAC-based physical maps for L. perenne were constructed from similar to 212 000 high-information-content fingerprints using Fingerprint Contig and Linear Topology Contig software. BAC clones were associated with both BAC-end sequences and a partial minimum tiling path sequence. A panel of 716 L. perenne diploid genotypes from 90 European accessions was assessed in the field over 2 years, and genotyped using a Lolium Infinium SNP array. The GWAS was carried out using a linear mixed model implemented in TASSEL, and extended genomic regions associated with significant markers were identified through integration with the physical map. Key Results Between similar to 3600 and 7500 physical map contigs were derived, depending on the software and probability thresholds used, and integrated with similar to 35 k sequenced BAC clones to develop a resource predicted to span the majority of the L. perenne genome. From the GWAS, eight different loci were significantly associated with heading date, plant width, plant biomass and water-soluble carbohydrate accumulation, seven of which could be associated with physical map contigs. This allowed the identification of a number of candidate genes. Conclusions Combining the physical mapping resource with the GWAS has allowed us to extend the search for candidate genes across larger regions of the L. perenne genome and identified a number of interesting gene model annotations. These physical maps will aid in validating future sequence-based assemblies of the L. perenne genome.