Spud 1.0: generalising and automating the user interfaces of scientific computer models

The interfaces by which users specify the scenarios to be simulated by scientific computer models are frequently primitive, under-documented and ad-hoc text files which make using the model in question difficult and error-prone and significantly increase the development cost of the model. In this paper, we present a model-independent system, Spud, which formalises the specification of model input formats in terms of formal grammars. This is combined with an automated graphical user interface which guides users to create valid model inputs based on the grammar provided, and a generic options reading module, libspud, which minimises the development cost of adding model options. <br><br> Together, this provides a user friendly, well documented, self validating user interface which is applicable to a wide range of scientific models and which minimises the developer input required to maintain and extend the model interface

The lunar wake at 6.8 R(L): WIND magnetic field observations

We report on WIND magnetic field observations at ∼6.8 RL downstream of the moon on 27th December 1994. The moon was in the solar wind during the encounter. IMP‐8 observations are used to determine baseline IMF conditions, and therefore determine those features in the WIND data which are related to its proximity to the moon. Previous Explorer 35 observations suggest that the lunar wake is not detectable beyond a downstream distance of ∼4 RL. However, despite the distance of WIND from the moon, we observe a slight decrease in field intensity just prior to the spacecraft entering the optical shadow, a slight field strength enhancement whilst in shadow, and perhaps a weak depression once the spacecraft reemerges into sunlight. These signatures closely resemble, but are weaker than, the previous observations. We conclude that a lunar wake did extend to these distances at the time of this encounter. We also note a rotation in field direction some distance outside of the wake signature which may be attributed to the crossing of the lunar mach cone boundary. We discuss the observations in terms of simple models of the solar wind interaction with an insulating body

Ethnicity, socioeconomic status, transfusions and risk of hepatitis B and hepatitis C infection

This study identifies the risk factors for hepatitis B virus (HBV) and hepatitis C virus (HCV) and measures the prevalence of hepatitis B surface antigen (HBsAg) and antibody to hepatitis C (anti-HCV) in the general population of Jakarta. A population-based sample of 985 people aged 15 and above was surveyed. Risk factors were identified through questionnaires and home visits. Serum was analysed for HBsAg, antibody to hepatitis B surface antigen (anti-HBs), anti-HCV, aspartate aminotransferase (AST) and alanine aminotransferase (ALT). The seroprevalence was: 4.0% (39/985) for HBsAg, 17.2% (170/985) for anti-HBs, and 3.9% (38/985) for anti-HCV. The risk factors for hepatitis B and hepatitis C infection had little in common. Low socioeconomic status was a strong risk factor for HBsAg (adjusted odds ratio (OR) 18.09; 95% confidence interval (CI) 2.35–139.50). In addition, the Chinese group has 2.97 higher risk of having HBV infection compared with the Malayan ethnic group (adjusted OR 2.97; 95% CI 1.22–7.83). There was moderate positive trend between family size and risk of HBsAg positivity ( P = 0.130). Age over 50 (adjusted OR 14.72; 95% CI 4.35–49.89) and history of transfusion were significant risk factors for hepatitis C (adjusted OR 3.03; 95% CI 1.25–7.33). Hepatitis B and hepatitis C infections have different risk factors in Jakarta, a high risk in population for both diseases. Hepatitis B transmission is associated with low socioeconomic status, Chinese ethnic group and large family size, while hepatitis C is associated with an older age and a history of transfusions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72591/1/j.1440-1746.1997.tb00365.x.pd

Observations of the lunar plasma wake from the WIND spacecraft on December 27, 1994

On December 27, 1994, the WIND spacecraft crossed the lunar wake at a distance of 6.5 lunar radii ( RL ) behind the moon. The observations made were the first employing modem instruments and a high data rate. The SWE plasma instrument on WIND observed new aspects of the interaction between the solar wind and unmagnetized dielectric bodies. The plasma density decreased exponentially from the periphery of the wake towards its center as predicted by simple theory. Behind the moon two distinct cold ion beams were observed refilling the lunar cavity. The ions were accelerated along the direction of the magnetic field by an electric field of the order 2 × 10−4 volts/m. The region of plasma depletion was observed to extend beyond the light shadow, consistent with a rarefaction wave moving out from the wake into the undisturbed solar wind

Upstream ULF waves and energetic electrons associated with the lunar wake: Detection of precursor activity

We present observations of precursor ULF wave activity and energetic electron flows detected by the WIND spacecraft just prior to entry of the lunar wake on 27 December 1994. This activity occurs upstream of the wake on field lines directly connected to the wake penumbra region. The activity ceases near the penumbra entrance. The observations of upstream ULF wave activity and solar wind counterstreaming electron flows is similar to observations made upstream of collisionless bow shocks. Analogously, the wake precursor region is characterized by thermalization and information propagation ahead of the wake structure

The biomechanics of amnion rupture: an X-ray diffraction study

Pre-term birth is the leading cause of perinatal and neonatal mortality, 40% of which are attributed to the pre-term premature rupture of amnion. Rupture of amnion is thought to be associated with a corresponding decrease in the extracellular collagen content and/or increase in collagenase activity. However, there is very little information concerning the detailed organisation of fibrillar collagen in amnion and how this might influence rupture. Here we identify a loss of lattice like arrangement in collagen organisation from areas near to the rupture site, and present a 9% increase in fibril spacing and a 50% decrease in fibrillar organisation using quantitative measurements gained by transmission electron microscopy and the novel application of synchrotron X-ray diffraction. These data provide an accurate insight into the biomechanical process of amnion rupture and highlight X-ray diffraction as a new and powerful tool in our understanding of this process

Epstein-Barr virus (EBV) deletions as biomarkers of response to treatment of chronic active EBV

Chronic active Epstein–Barr virus (CAEBV) disease is a rare condition characterised by persistent EBV infection in previously healthy individuals. Defective EBV genomes were found in East Asian patients with CAEBV. In the present study, we sequenced 14 blood EBV samples from three UK patients with CAEBV, comparing the results with saliva CAEBV samples and other conditions. We observed EBV deletions in blood, some of which may disrupt viral replication, but not saliva in CAEBV. Deletions were lost overtime after successful treatment. These findings are compatible with CAEBV being associated with the evolution and persistence of EBV+ haematological clones that are lost on successful treatment

A solution to Nature's haemoglobin knockout: a plasma-accessible carbonic anhydrase catalyses CO₂ excretion in Antarctic icefish gills

In all vertebrates studied to date, CO₂ excretion depends on the enzyme carbonic anhydrase (CA) that catalyses the rapid conversion of HCO₃− to CO₂ at the gas-exchange organs. The largest pool of CA is present within red blood cells (RBC) and, in some vertebrates, plasma-accessible CA (paCA) isoforms participate in CO₂ excretion. However, teleost fishes typically do not have paCA at the gills and CO₂ excretion is reliant entirely on RBC CA; a strategy that is not possible in icefishes. As the result of a natural knockout, Antarctic icefishes (Channichthyidae) are the only known vertebrates that do not express haemoglobin (Hb) as adults, and largely lack RBC in the circulation (haematocrit<1%). Previous work has indicated the presence of high levels of membrane-bound CA activity in the gills of icefishes, but without determining its cellular orientation. Thus, we hypothesised that icefishes express a membrane-bound CA isoform at the gill that is accessible to the blood plasma. The CA distribution was compared in the gills of two closely-related notothenioid species, one with Hb and RBCs (Notothenia rossii) and one without (Champsocephalus gunnari). Molecular, biochemical and immunohistochemical markers indicate high levels of a Ca4 isoform in the gills of the icefish (but not the red-blooded N. rossii), in a plasma-accessible location that is consistent with a role in CO₂ excretion. Thus, in the absence of RBC CA, the icefish gill could exclusively provide the catalytic activity necessary for CO₂ excretion; a pathway that is unlike that of any other vertebrate

Clinically Translatable Cell Tracking and Quantification by MRI in Cartilage Repair Using Superparamagnetic Iron Oxides

Background: Articular cartilage has very limited intrinsic regenerative capacity, making cell-based therapy a tempting approach for cartilage repair. Cell tracking can be a major step towards unraveling and improving the repair process of these therapies. We studied superparamagnetic iron oxides (SPIO) for labeling human bone marrow-derived mesenchymal stem cells (hBMSCs) regarding effectivity, cell viability, long term metabolic cell activity, chondrogenic differentiation and hBMSC secretion profile. We additionally examined the capacity of synovial cells to endocytose SPIO from dead, labeled cells, together with the use of magnetic resonance imaging (MRI) for intra-articular visualization and quantification of SPIO labeled cells. Methodology/Prinicipal Findings: Efficacy and various safety aspects of SPIO cell labeling were determined using appropriate assays. Synovial SPIO re-uptake was investigated in vitro by co-labeling cells with SPIO and green fluorescent protein (GFP). MRI experiments were performed on a clinical 3.0T MRI scanner. Two cell-based cartilage repair techniques were mimicked for evaluating MRI traceability of labeled cells: intra-articular cell injection and cell implantation in cartilage defects. Cells were applied ex vivo or in vitro in an intra-articular environment and immediately scanned. SPIO labeling was effective and did not impair any of the studied safety aspects, including hBMSC secretion profile. SPIO from dead, labeled cells could be taken up by synovial cells. Both injected and implanted SPIO-labeled cells could accurately be visualized by MRI in a clinically relevant sized joint model using clinically applied cell doses. Finally, we quantified the amount of labeled cells seeded in cartilage defects using MR-based relaxometry. Conclusions: SPIO labeling appears to be safe without influencing cell behavior. SPIO labeled cells can be visualized in an intra-articular environment and quantified when seeded in cartilage defects.Biomechanical EngineeringMechanical, Maritime and Materials Engineerin