Chemistry in Second Life

This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students

Draft genome sequence of Curtobacterium flaccumfaciens strain UCD-AKU (phylum Actinobacteria)

© 2013 Flanagan et al. Here we present the draft genome of an actinobacterium, Curtobacterium flaccumfaciens strain UCD-AKU, isolated from a residential carpet. The genome assembly contains 3,692,614 bp in 130 contigs. This is the first member of the Curtobacterium genus to be sequenced

Anti-phospholipid-antibodies in patients with relapsing polychondritis

Relapsing polychondritis (RP) is an extremly rare multisystemic disease thought to be of autoimmune origin. In order to assess if RP is associated with anti-phospholipid antibodies (aPL), clinical data and sera of 21 patients with RP were collected in a multicentre study. Concentration of anti-cardiolipin antibodies (aCL) (IgG-, IgM-and IgA-isotypes), anti-phosphatidylserine-antibodies (aPS) (IgG-and IgM-isotypes) and anti-β-2-glycoprotein I-antibodies (aβ2 GPI) were measured by ELISA. In eight patients aCL were found to be elevated. One patient had elevated aPS. No patient had elevated aβ2 GPI. No patient had clinical signs and symptoms of a aPL syndrome. Interestingly, the two RP patients with the highest aPL had concomitant systemic lupus erythematosus (SLE). Therefore the presence of elevated aPL in RP is probably more closely related to an associated SLE than to RP itself. There is no convincing evidence that aPL are associated with RP

Where is my sink? Reconstruction of landscape development in 1 southwestern Africa since the Late Jurassic

Quantifying the rates and timing of landscape denudation provides a means to constrain sediment flux through time to offshore sedimentary basins. The Late Mesozoic evolution of drainage basins in southern Africa is poorly constrained despite the presence of several onshore and offshore sedimentary basins. A novel approach has been developed to calculate the volume of material eroded since the Late Jurassic at different time steps by constructing structural cross-sections and extrapolating thicknesses of eroded material. Using different assumptions, the calculated volumes of material eroded from southwestern Africa range from 2.52x10⁶ km³ (11.3 km of vertical thickness removed) to 8.87 x10⁵ km³ (4.0 km of vertical thickness removed). For the southward draining systems alone, the calculated removal of 7.81 x10⁵ – 2.60 x10⁵ km³ of material is far greater than the volumes of sediment recorded in offshore sedimentary basins (268 500 km³). Reconstruction of the drainage systems using geomorphic indicators and clast provenance of the Uitenhage Group, as well as extrapolated surface exposure ages, indicate the southern draining systems were active from the Late Jurassic with coeval activity in axial and transverse drainage systems. The calculated volumes are tied to published apatite fission track (AFT) dates to constrain the changes in exhumation rate through time (using multiple scenarios), which indicate a significant amount of Early Cretaceous exhumation (up to 1.26 x10⁶ km³, equivalent to 5.70km of vertical thickness). For the first time, this has permitted long-term landscape evolution to be used to support the interpretation that some of the ‘missing’ sediment was deposited in sedimentary basins on the Falkland Plateau as it moved past southern Africa during the Early Cretaceous. This implies that in this instance, the sinks are separated from their source areas by ~6000 km

The use of protocol in breaking bad news: evidence and ethos

This article discusses health professionals use of protocol in the breaking of bad news, focusing particularly on the well-known SPIKES framework. The evidence of impact on the patient experience is examined and recommendations are made for further outcome-based research. Existing evidence suggests that the model as commonly interpreted may not fully meet the needs of patients or reflect the clinical experience of breaking bad news for some professionals and further guidance may be needed to support them in their practice. The ethos of the step-wise protocol is debated, questioning whether it helps or hinders individualised care and the formation of a genuine relationship between patient and professional. Finally, recommendations for practice are offered

Lung sealant and morbidity after pleural decortication: a prospective randomized, blinded study

<p>Abstract</p> <p>Objectives</p> <p>Prolonged postoperative air leaks (AL) are a major cause of morbidity. Aim of this work was evaluating use of a Lung Sealant System (Pleuraseal™, Covidien, Mansfield, MA, U.S.A.) in pleural decortications for empyema thoracis.</p> <p>Methods</p> <p>From January 2008 to December 2008, 46 consecutive patients received pleural decortications for empyema thoracis. Post-procedural and malignancy-related empyemas were excluded. After hydro-pneumatic test and surgical correction of AL (until satisfaction), patients were assigned (23 per group) to Control or Sealant group. Control group underwent no additional interventions. In Sealant group, lung sealant was applied over AL areas. Following variables were measured daily: patients with AL; time to chest drainage (CD) removal; CD drainage volume at removal, postoperative length of hospital stay, postoperative C-reactive protein (CRP), and leukocyte counts. Personnel recording parameters were blinded to intervention. Two-tailed t-tests (normally distributed data) or Mann - Whitney U-test (not-normally distributed data) were used for evaluating significance of differences between group means or medians. Significance of any proportional differences in attributes were evaluated using Fisher's Exact Test. Statistical analysis was carried out using R-software (version 2.8.1).</p> <p>Results</p> <p>Groups were similar regarding demographic and baseline characteristics. No patients were withdrawn from study; no adverse effects were recorded. There were no significative differences on CRP and leukocyte levels between two groups. Compared with the Control group, in Sealant group significantly fewer patients had AL (30 versus 78%, <it>p = 0.012</it>), and drains were inserted for a shorter time (medians, 3 versus 5 days, <it>p = 0.05</it>). Postoperative hospitalization time was shorter in Sealant group than in control group, but difference was not significant (0.7 days, <it>p = 0.121</it>).</p> <p>Conclusions</p> <p>Pleuraseal™ Lung Sealant System significantly reduces AL following pleural decortications for empyema and, despite of not-increased infectious indexes, is suitable for routinely use, even in procedures with contaminated pleura.</p

Influence of hyperhomocysteinemia on the cellular redox state - Impact on homocysteine-induced endothelial dysfunction

Hyperhomocysteinemia is an independent risk factor for the development of atherosclerosis. An increasing body of evidence has implicated oxidative stress as being contributory to homocysteines deleterious effects on the vasculature. Elevated levels of homocysteine may lead to increased generation of superoxide by a biochemical mechanism involving nitric oxide synthase, and, to a lesser extent, by an increase in the chemical oxidation of homocysteine and other aminothiols in the circulation. The resultant increase in superoxide levels is further amplified by homocysteinedependent alterations in the function of cellular antioxidant enzymes such as cellular glutathione peroxidase or extracellular superoxide dismutase. One direct clinical consequence of elevated vascular superoxide levels is the inactivation of the vasorelaxant messenger nitric oxide, leading to endothelial dysfunction. Scavenging of superoxide anion by either superoxide dismutase or 4,5-dihydroxybenzene 1,3-disulfonate (Tiron) reverses endothelial dysfunction in hyperhomocysteinemic animal models and in isolated aortic rings incubated with homocysteine. Similarly, homocysteineinduced endothelial dysfunction is also reversed by increasing the concentration of the endogenous antioxidant glutathione or overexpressing cellular glutathione peroxidase in animal models of mild hyperhomocysteinemia. Taken together, these findings strongly suggest that the adverse vascular effects of homocysteine are at least partly mediated by oxidative inactivation of nitric oxide

Sequential Deliberation for Social Choice

In large scale collective decision making, social choice is a normative study of how one ought to design a protocol for reaching consensus. However, in instances where the underlying decision space is too large or complex for ordinal voting, standard voting methods of social choice may be impractical. How then can we design a mechanism - preferably decentralized, simple, scalable, and not requiring any special knowledge of the decision space - to reach consensus? We propose sequential deliberation as a natural solution to this problem. In this iterative method, successive pairs of agents bargain over the decision space using the previous decision as a disagreement alternative. We describe the general method and analyze the quality of its outcome when the space of preferences define a median graph. We show that sequential deliberation finds a 1.208- approximation to the optimal social cost on such graphs, coming very close to this value with only a small constant number of agents sampled from the population. We also show lower bounds on simpler classes of mechanisms to justify our design choices. We further show that sequential deliberation is ex-post Pareto efficient and has truthful reporting as an equilibrium of the induced extensive form game. We finally show that for general metric spaces, the second moment of of the distribution of social cost of the outcomes produced by sequential deliberation is also bounded

The actions of methotrexate on endothelial cells are dependent on the shear stress-induced regulation of one carbon metabolism

Objectives: The disease-modifying anti-rheumatic drug methotrexate (MTX) is recognized to reduce cardiovascular risk in patients with systemic inflammatory diseases. However, the molecular basis for these cardioprotective effects remains incompletely understood. This study evaluated the actions of low-dose MTX on the vascular endothelium. Methods: Human endothelial cells (EC) were studied under in vitro conditions relevant to inflammatory arthritis. These included culture in a pro-inflammatory microenvironment and exposure to fluid shear stress (FSS) using a parallel plate model. Respectively treated cells were analyzed by RNA sequencing and quantitative real-time PCR for gene expression, by immunoblotting for protein expression, by phosphokinase activity arrays, by flow cytometry for cell cycle analyses and by mass spectrometry to assess folate metabolite levels. Results: In static conditions, MTX was efficiently taken up by EC and caused cell cycle arrest concurrent with modulation of cell signaling pathways. These responses were reversed by folinic acid (FA), suggesting that OCM is a predominant target of MTX. Under FSS, MTX did not affect cell proliferation or pro-inflammatory gene expression. Exposure to FSS downregulated endothelial one carbon metabolism (OCM) as evidenced by decreased expression of key OCM genes and metabolites. Conclusion: We found that FSS significantly downregulated OCM and thereby rendered EC less susceptible to the effects of MTX treatment. The impact of shear stress on OCM suggested that MTX does not directly modulate endothelial function. The cardioprotective actions of MTX likely reflect direct actions on inflammatory cells and indirect benefit on the vascular endothelium