Open Science: Tools, approaches, and implications

The Pacific Symposium on Biocomputing is an annual meeting whose topics are determined by proposals submitted by members of the community. This document is the proposal for a session on Open Science, submitted for consideration for the PSB meeting in 2009

Cultivating capitalism: Sea Island Cotton, planter identity, and Atlantic connections in Antebellum Beaufort County, South Carolina

Studies of southern planters and cotton litter the scholarship about antebellum America. These works often debate the capitalist, pre-capitalist, or anti-capitalist nature of the southern economy and slave-based plantation agriculture. This study examines how antebellum sea island cotton planters in South Carolina identified themselves and practiced as capitalists in the Atlantic World. Their identity was shaped by ongoing discussions in The Southern Agriculturalist which was published in Charleston between 1828 and 1846, and the periodical was dedicated to agricultural improvement. The ideal planter capitalist identity was defined by a dedication to agricultural innovation, an understanding of domestic and foreign markets, the successful management of enslaved labor, and advocacy for increased formal agricultural education at South Carolina College. One primary example of the planter capitalist class was William Elliott III from Beaufort, South Carolina. Through careful analysis of Elliott’s personal and published writings, this project shows the ways Elliott dealt with various challenges in putting his identity into practice. Domestically, he was met increasing challenges from a rising professional class, state and federal governments, and his enslaved labor force. However, when he left the United States and traveled to Paris in the summer of 1855, Elliott gained a strong reputation as an agriculturalist and demonstrated a clear and calculated understanding of the potential threats of a French-controlled Algerian sea island cotton market. The international stage provided a unique opportunity for Elliott to demonstrate his role as a planter capitalist

Learning design research in action

The new field of Learning Design is gaining traction in higher education, aiming to address a number of challenges in technology enhanced learning and teaching. This symposium seeks to build on the national Learning Design Research strengths and help highlight Australian Learning Design theory and practice expertise. It also aims to further consolidate the Australian and international Learning Design community. The content of this submission directly addresses the following topics: An introduction of the Learning Design Framework, Generic Templates, Teacher Design Thinking in Higher Education, Connecting Connectivism and Learning Design, and Translating Learning Outcomes into Learning Designs. The symposium will be divided into five topic-based presentations. The topic discussions will be led by members of the Australian Learning Design network. Discussion will be open and audience interaction will be encouraged

Wound care in the geriatric client

With our aging population, chronic diseases that compromise skin integrity such as diabetes, peripheral vascular disease (venous hypertension, arterial insufficiency) are becoming increasingly common. Skin breakdown with ulcer and chronic wound formation is a frequent consequence of these diseases. Types of ulcers include pressure ulcers, vascular ulcers (arterial and venous hypertension), and neuropathic ulcers. Treatment of these ulcers involves recognizing the four stages of healing: coagulation, inflammation, proliferation, and maturation. Chronic wounds are frequently stalled in the inflammatory stage. Moving past the inflammation stage requires considering the bacterial burden, necrotic tissue, and moisture balance of the wound being treated. Bacterial overgrowth or infection needs to be treated with topical or systemic agents. In most cases, necrotic tissue needs to be debrided and moisture balance needs to be addressed by wetting dry tissue and drying wet tissue. Special dressings have been developed to accomplish these tasks. They include films, hydrocolloids, hydrogel dressings, foams, hydrofibers, composite and alginate dressings

Endoscopic Management of Cavernous Carotid Surgical Complications: Evaluation of a Simulated Perfusion Model

Objective—Endoscopic surgical treatment of pituitary tumors, lateral invading tumors, or aneurysms requires surgeons to operate adjacent to the cavernous sinus. During these endoscopic endonasal procedures, the carotid artery is vulnerable to surgical injury at its genu. The objective of this simulation model was to evaluate trainees regarding management of a potentially lifethreatening vascular injury. Methods—Cadaveric heads were prepared in accordance with the Oregon Health & Science University body donation program. An endoscopic endonasal approach was used, and a perfusion pump with a catheter was placed in the ipsilateral common carotid artery at its origin in the neck. Learners used a muscle graft to establish vascular control and were evaluated over 3 training sessions. Simulation assessment, blood loss during sessions, and performance metric data were collected for learners. Results—Vascular control was obtained at a mean arterial pressure of 65 mm Hg using a muscle graft correctly positioned at the arteriotomy site. Learners improved over the course of training, with senior residents (n = 4) performing better across all simulation categories (situation awareness, decision making, communications and teamwork, and leadership); the largest mean difference was in communication and teamwork. Additionally, learner performance concerning blood loss improved between sessions (t = 3.667, P \u3c 0.01). Conclusions—In this pilot endoscopic endonasal simulation study, we successfully demonstrate a vascular complication perfusion model. Learners were able to gain direct applicable expertise in endoscopic endonasal techniques, instrumentation use, and teamwork required to optimize the technique. Learners gained skills of vascular complication management that transcend this model

Triggering Collapse of the Presolar Dense Cloud Core and Injecting Short-Lived Radioisotopes with a Shock Wave. I. Varied Shock Speeds

The discovery of decay products of a short-lived radioisotope (SLRI) in the Allende meteorite led to the hypothesis that a supernova shock wave transported freshly synthesized SLRI to the presolar dense cloud core, triggered its self-gravitational collapse, and injected the SLRI into the core. Previous multidimensional numerical calculations of the shock-cloud collision process showed that this hypothesis is plausible when the shock wave and dense cloud core are assumed to remain isothermal at ~10 K, but not when compressional heating to ~1000 K is assumed. Our two-dimensional models (Boss et al. 2008) with the FLASH2.5 adaptive mesh refinement (AMR) hydrodynamics code have shown that a 20 km/sec shock front can simultaneously trigger collapse of a 1 solar mass core and inject shock wave material, provided that cooling by molecular species such as H2O, CO, and H2 is included. Here we present the results for similar calculations with shock speeds ranging from 1 km/sec to 100 km/sec. We find that shock speeds in the range from 5 km/sec to 70 km/sec are able to trigger the collapse of a 2.2 solar mass cloud while simultaneously injecting shock wave material: lower speed shocks do not achieve injection, while higher speed shocks do not trigger sustained collapse. The calculations continue to support the shock-wave trigger hypothesis for the formation of the solar system, though the injection efficiencies in the present models are lower than desired.Comment: 39 pages, 14 figures. in press, Ap

The clustering of Galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : including covariance matrix errors

JP acknowledges support from the UK Science & Technology Facilities Council (STFC) through the consolidated grant ST/K0090X/1 and from the European Research Council through the ‘Starting Independent Research’ grant 202686, MDEPUGS. AGS acknowledges support from the Trans-regional Collaborative Research Centre TR33 ‘The Dark Universe’ of the German Research Foundation (DFG).We present improved methodology for including covariance matrices in the error budget of Baryon Oscillation Spectroscopic Survey (BOSS) galaxy clustering measurements, revisiting Data Release 9 (DR9) analyses, and describing a method that is used in DR10/11 analyses presented in companion papers. The precise analysis method adopted is becoming increasingly important, due to the precision that BOSS can now reach: even using as many as 600 mock catalogues to estimate covariance of two-point clustering measurements can still lead to an increase in the errors of ∼20 per cent, depending on how the cosmological parameters of interest are measured. In this paper, we extend previous work on this contribution to the error budget, deriving formulae for errors measured by integrating over the likelihood, and to the distribution of recovered best-fitting parameters fitting the simulations also used to estimate the covariance matrix. Both are situations that previous analyses of BOSS have considered. We apply the formulae derived to baryon acoustic oscillation (BAO) and redshift-space distortion (RSD) measurements from BOSS in our companion papers. To further aid these analyses, we consider the optimum number of bins to use for two-point measurements using the monopole power spectrum or correlation function for BAO, and the monopole and quadrupole moments of the correlation function for anisotropic-BAO and RSD measurements.Publisher PDFPeer reviewe

The effects of public spending composition on firm productivity

This paper exploits the unique institutional features of South Africa to estimate the impact of provincial public spending on health, edu- cation and transport on firm productivity. Our identification strategy is based on within industry-province differences between firms of the effects of public spending. We show that public spending composi- tion affects firm productivity depending on the capital intensity of firms relative to the province-industry mean. Our data and empir- ical specification allow us to rule out that these results are affected by econometric problems that are commonly encountered when es- timating the effects of fiscal policy and by unobserved industry- or province-specific productivity shocks. In contrast to related existing microeconomic evidence, we take into account the government budget constraint so that our results have clear policy implications

Health and mortality consequences of abdominal obesity : evidence from the AusDiab study

Objective: To provide an estimate of the morbidity and mortality resulting from abdominal overweight and obesity in the Australian population.Design and setting: Prospective, national, population-based study (the Australian Diabetes, Obesity and Lifestyle [AusDiab] study).Participants: 6072 men and women aged ≥ 25 years at study entry between May 1999 and December 2000, and aged ≤ 75 years, not pregnant and for whom there were waist circumference data at the follow-up survey between June 2004 and December 2005.Main outcome measures: Incident health outcomes (type 2 diabetes, hypertension, dyslipidaemia, the metabolic syndrome and cardiovascular diseases) at 5 years and mortality at 8 years. Comparison of outcome measures between those classified as abdominally overweight or obese and those with a normal waist circumference at baseline, and across quintiles of waist circumference, and (for mortality only) waist-to-hip ratio.Results: Abdominal obesity was associated with odds ratios of between 2 and 5 for incident type 2 diabetes, dyslipidaemia, hypertension and the metabolic syndrome. The risk of myocardial infarction among obese participants was similarly increased in men (hazard ratio [HR], 2.75; 95% CI, 1.08–7.03), but not women (HR, 1.43; 95% CI, 0.37–5.50). Abdominal obesity-related population attributable fractions for these outcomes ranged from 13% to 47%, and were highest for type 2 diabetes. No significant associations were observed between all-cause mortality and increasing quintiles of abdominal obesity.Conclusions: Our findings confirm that abdominal obesity confers a considerably heightened risk for type 2 diabetes, the metabolic syndrome (as well as its components) and cardiovascular disease, and they provide important information that enables a more precise estimate of the burden of disease attributable to obesity in Australia

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : cosmological implications of the full shape of the clustering wedges in the data release 10 and 11 galaxy samples

We explore the cosmological implications of the angle-averaged correlation function, ξ(s), and the clustering wedges, ξ⊥(s) and ξ∥(s), of the LOWZ and CMASS galaxy samples from Data Releases 10 and 11 of the Sloan Digital Sky Survey III (SDSS-III) Baryon Oscillation Spectroscopic Survey. Our results show no significant evidence for a deviation from the standard Λ cold dark matter model. The combination of the information from our clustering measurements with recent data from the cosmic microwave background is sufficient to constrain the curvature of the Universe to Ωk = 0.0010 ± 0.0029, the total neutrino mass to ∑mν < 0.23 eV (95 per cent confidence level), the effective number of relativistic species to Neff = 3.31 ± 0.27 and the dark energy equation of state to wDE = −1.051 ± 0.076. These limits are further improved by adding information from Type Ia supernovae and baryon acoustic oscillations from other samples. In particular, this data set combination is completely consistent with a time-independent dark energy equation of state, in which case we find wDE = −1.024 ± 0.052. We explore the constraints on the growth rate of cosmic structures assuming f(z) = Ωm(z)γ and obtain γ = 0.69 ± 0.15, consistent with the predictions of general relativity of γ = 0.55.Publisher PDFPeer reviewe