Synergies: University-Museum Collaborations

The purpose of this report is to provide documentation of the University-Museums Synergies Initiative between a Department of Marine, Earth, and Atmospheric Sciences and a Museum of Natural Sciences. The goals of this initiative were to 1)identify specific projects and opportunities might be developed to strengthen the collaboration between institutions and 2) gain a better understanding of MEAS researchers’ and Museum employees\u27 perspectives on university-museum partnerships

Adverse associations of car time with markers of cardio-metabolic risk.

OBJECTIVE: To examine associations of time spent sitting in cars with markers of cardio-metabolic risk in Australian adults. METHOD: Data were from 2800 participants (age range: 34-65) in the 2011-12 Australian Diabetes, Obesity and Lifestyle Study. Self-reported time spent in cars was categorized into four groups: ≤15min/day; >15 to ≤30min/day; >30 to ≤60min/day; and >60min/day. Markers of cardio-metabolic risk were body mass index (BMI), waist circumference, systolic and diastolic blood pressure, triglycerides, HDL (high-density lipoprotein)-cholesterol, fasting plasma glucose, 2-h plasma glucose, a clustered cardio-metabolic risk score, and having the metabolic syndrome or not. Multilevel linear and logistic regression analyses examined associations of car time with each cardio-metabolic risk outcome, adjusting for socio-demographic and behavioral variables and medication use for blood pressure and cholesterol/triglycerides. RESULTS: Compared to spending 15min/day or less in cars, spending more than 1h/day in cars was significantly associated with higher BMI, waist circumference, fasting plasma glucose, and clustered cardio-metabolic risk, after adjusting for socio-demographic attributes and potentially relevant behaviors including leisure-time physical activity and dietary intake. Gender interactions showed car time to be associated with higher BMI in men only. CONCLUSIONS: Prolonged time spent sitting in cars, in particular over 1h/day, was associated with higher total and central adiposity and a more-adverse cardio-metabolic risk profile. Further studies, ideally using objective measures of sitting time in cars and prospective designs, are needed to confirm the impact of car use on cardio-metabolic disease risk.The AusDiab study was co-coordinated by the Baker IDI Heart and Diabetes Institute. We gratefully acknowledge the support and assistance given by: K. Anstey, B. Atkins, B. Balkau, E. Barr, A. Cameron, S. Chadban, M. de Courten, A. Kavanagh, D. Magliano, S. Murray, K. Polkinghorne, J. Shaw, T. Welborn, P. Zimmet and all the study participants. For funding or logistical support, we are grateful to: National Health and Medical Research Council (NHMRC: #233200, #1007544), Australian Government Department of Health and Ageing, Abbott Australasia Pty Ltd, Alphapharm Pty Ltd, Amgen Australia, AstraZeneca, Bristol-Myers Squibb, City Health Centre-Diabetes Service-Canberra, Department of Health and Community Services – Northern Territory, Department of Health and Human Services – Tasmania, Department of Health – New South Wales, Department of Health – Western Australia, Department of Health – South Australia, Department of Human Services – Victoria, Diabetes Australia, Diabetes Australia Northern Territory, Eli Lilly Australia, Estate of the Late Edward Wilson, GlaxoSmithKline, Jack Brockhoff Foundation, Janssen-Cilag, Kidney Health Australia, Marian & FH Flack Trust, Menzies Research Institute, Merck Sharp & Dohme, Novartis Pharmaceuticals, Novo Nordisk Pharmaceuticals, Pfizer Pty Ltd, Pratt Foundation, Queensland Health, Roche Diagnostics Australia, Royal Prince Alfred Hospital, Sydney, Sanofi Aventis, and sanofi-synthelabo. Wijndaele was supported by a BHF Intermediate Basic Science Research Fellowship #FS/12/58/29709. Koohsari was supported by NHMRC Program Grant #569940. Dunstan was supported by a National Health and Medical Research Council Senior Research Fellowship (#1078360). Owen was supported by NHMRC ProgramGrant #569940, NHMRC Senior Principal Research Fellowship#1003960, and NHMRC Centre of Research Excellence#1057608. Authors from Baker IDI were supported by the Victorian Government's Operational Infrastructure Support Program.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.ypmed.2015.11.02

Food supply depends on seagrass meadows in the coral triangle

The tropical seascape provides food and livelihoods to hundreds of millions of people, but the support of key habitats to this supply remains ill appreciated. For fisheries and conservation management actions to help promote resilient ecosystems, sustainable livelihoods, and food supply, knowledge is required about the habitats that help support fisheries productivity and the consequences of this for food security. This paper provides an interdisciplinary case study from the coral triangle of how seagrass meadows provide support for fisheries and local food security. We apply a triangulated approach that utilizes ecological, fisheries and market data combined with over 250 household interviews. Our research demonstrates that seagrass associated fauna in a coral triangle marine protected area support local food supply contributing at least 50% of the fish based food. This formed between 54% and 99% of daily protein intake in the area. Fishery catch was found to significantly vary with respect to village (p < 0.01) with habitat configuration a probable driver. Juvenile fish comprised 26% of the fishery catch and gear type significantly influenced this proportion (<0.05). Limited sustainability of fishery practices (high juvenile catch and a 51% decline in CPUE for the biggest fishery) and poor habitat management mean the security of this food supply has the potential to be undermined in the long-term. Findings of this study have implications for the management and assessment of fisheries throughout the tropical seascape. Our study provides an exemplar for why natural resource management should move beyond biodiversity and consider how conservation and local food security are interlinked processes that are not mutually exclusive. Seagrass meadows are under sustained threat worldwide, this study provides evidence of the need to conserve these not just to protect biodiversity but to protect food security

Chemical Amendments of Dryland Saline–Sodic Soils Did Not Enhance Productivity and Soil Health in Fields without Effective Drainage

A common restoration treatment for saline–sodic soils involves improving soil drainage, applying soil amendments (e.g., CaSO4, CaCl2, or elemental S), and leaching with water that has a relatively low electrical conductivity. However, due to high subsoil bulk densities and low drainable porosities, these treatments many not be effective in glaciated dryland systems. A 3-yr field study conducted in three model systems determined the impact of chemical amendments (none, CaCl2, CaSO4, and elemental S) on plant growth, microbial composition, temporal changes in electrical conductivity (ECe ), and the relative sodium content (%Na). Chemical amendments (i) either reduced or did not increase maize (Zea mays), soybean (Glycine max), and sorghum (Sorghum bicolor) yields; (ii) did not increase water infiltration or microbial biomass as determined using the phospholipid-derived fatty acid (PLFA) technique; and (iii) did not reduce ECe or %Na. These results were attributed to high bulk densities and low drainable porosities that reducing the drainage effectiveness in the model backslope and footslope soils, the presence of subsurface marine sediments that provided a source for sodium and other salts that could be transported through capillary action to the surface soil, high sulfate and gypsum contents in the surface soil, and relatively low microbial biomass values. The results suggests that an alternative multistep saline sodic soil restoration approach that involves increasing exchangeable Ca+2 through enhanced microbial and root respiration and increasing transpiration and soil drainage by seeding full season deep rooted perennial vegetation should be tested

Neighborhood environmental attributes and adults\u27 maintenance of regular walking

Environmental initiatives to support walking are keys to non-communicable disease prevention, but the relevant evidence comes mainly from cross-sectional studies. We examined neighborhood environmental attributes associated cross-sectionally with walking and those associated prospectively with walking maintenance

T cell antigen discovery via trogocytosis

T cell receptor (TCR) ligand discovery is essential for understanding and manipulating immune responses to tumors. We developed a cell-based selection platform for TCR ligand discovery that exploits a membrane transfer phenomenon called trogocytosis. We discovered that T cell membrane proteins are transferred specifically to target cells that present cognate peptide–major histocompatibility complex (MHC) molecules. Co-incubation of T cells expressing an orphan TCR with target cells collectively presenting a library of peptide–MHCs led to specific labeling of cognate target cells, enabling isolation of these target cells and sequencing of the cognate TCR ligand. We validated this method for two clinically employed TCRs and further used the platform to identify the cognate neoepitope for a subject-derived neoantigen-specific TCR. Thus, target cell trogocytosis is a robust tool for TCR ligand discovery that will be useful for studying basic tumor immunology and identifying new targets for immunotherapy

Chronic Muscle Weakness and Mitochondrial Dysfunction in the Absence of Sustained Atrophy in a Preclinical Sepsis Model

Chronic critical illness is a global clinical issue affecting millions of sepsis survivors annually. Survivors report chronic skeletal muscle weakness and development of new functional limitations that persist for years. To delineate mechanisms of sepsis-induced chronic weakness, we first surpassed a critical barrier by establishing a murine model of sepsis with ICU-like interventions that allows for the study of survivors. We show that sepsis survivors have profound weakness for at least 1 month, even after recovery of muscle mass. Abnormal mitochondrial ultrastructure, impaired respiration and electron transport chain activities, and persistent protein oxidative damage were evident in the muscle of survivors. Our data suggest that sustained mitochondrial dysfunction, rather than atrophy alone, underlies chronic sepsis-induced muscle weakness. This study emphasizes that conventional efforts that aim to recover muscle quantity will likely remain ineffective for regaining strength and improving quality of life after sepsis until deficiencies in muscle quality are addressed

Clustering of glycoprotein VI (GPVI) dimers upon adhesion to collagen as a mechanism to regulate GPVI signaling in platelets

Background: Platelet glycoprotein VI (GPVI) binding to subendothelial collagen exposed upon blood vessel injury initiates thrombus formation. Dimeric GPVI has high affinity for collagen, and occurs constitutively on resting platelets. Objective: To identify higher-order oligomerization (clustering) of pre-existing GPVI dimers upon interaction with collagen as a mechanism to initiate GPVI-mediated signaling. Methods: GPVI was located by use of fluorophore-conjugated GPVI dimer-specific Fab (antigen-binding fragment). The tested substrates include Horm collagen I fibers, soluble collagen III, GPVI-specific collagen peptides, and fibrinogen. GPVI dimer clusters on the platelet surface interacting with these substrates were visualized with complementary imaging techniques: total internal reflection fluorescence microscopy to monitor real-time interactions, and direct stochastic optical reconstruction microscopy (dSTORM), providing relative quantification of GPVI cluster size and density. Confocal microscopy was used to locate GPVI dimer clusters, glycoprotein Ib, integrin α2β1, and phosphotyrosine. Results: Upon platelet adhesion to all collagenous substrates, GPVI dimers coalesced to form clusters; notably clusters formed along the fibers of Horm collagen. dSTORM revealed that GPVI density within clusters depended on the substrate, collagen III being the most effective. Clusters on fibrinogen-adhered platelets were much smaller and more numerous; whether these are pre-existing oligomers of GPVI dimers or fibrinogen-induced is not clear. Some GPVI dimer clusters colocalized with areas of phosphotyrosine, indicative of signaling activity. Integrin α2β1 was localized to collagen fibers close to GPVI dimer clusters. GPVI clustering depends on a dynamic actin cytoskeleton. Conclusions: Platelet adhesion to collagen induces GPVI dimer clustering. GPVI clustering increases both avidity for collagen and the proximity of GPVI-associated signaling molecules, which may be crucial for the initiation and persistence of signalingThese studies were supported by a Project Grant (PG/10/ 011/28199, to S. M. Jung, M. Moroi, R. W. Farndale, and S. P. Watson) and a Special Project Grant (SP/13/7/ 30575, to S. M. Jung) from the British Heart Foundation and a Wellcome Trust Biomedical Resource Grant (09440/Z/10/Z, to R. W. Farndale). S. P. Watson and N. S. Poulter are supported by the British Heart Foundation (CH/03/003). A. Y. Pollitt was funded by Wellcome Trust Grant 088410 (to S. P. Watson)

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A