Mechanical Translation

Contains reports on two research projects.National Science Foundation (Grant GN-244

Service-enabling legacy applications for the GENIE project

Abstract. We present work done within the Grid ENabled Integrated Earth system model (GENIE) project to take the original, complex, tightly-coupled Fortran earth modeling application that has been developed by the GENIE team and enable it for execution within a component-based execution environment. Further we have aimed to show that by representing the application as a set of high-level Java Web Service components, execution and management of the application can be made much more flexible. We show how the application has been built into higher-level components and how these have been wrapped within the Java Web Service abstraction. We then look at how these components can be composed into workflows and executed within a Grid environment

MP3 - A meteorology and physical properties package to explore air-sea interaction on Titan

The exchange of mass, heat and momentum at the air:sea interface are profound influences on the terrestrial environment, affecting the intensity of hurricanes, the size of waves and lake-effect precipitation. Titan presents us with an opportunity to study these processes in a novel physical context, with a different sea, atmosphere and gravity. The MP3 instrument, under development for the proposed Discovery mission TiME (Titan Mare Explorer [1,2]) is an integrated suite of small, simple sensors that combines the function of traditional meteorology packages with liquid physical properties and depth-sounding : these latter functions follow the concept of - and indeed use spare elements from - the Huygens Surface Science Package (SSP,[3]). However, unlike Huygens’ brief and dynamic 3 hours of measurement, in TiME’s 6-Titan-day (96 Earth day) nominal mission enabled by radioisotope power, MP3 will have an unprecedented long-term measurement opportunity in one of the most evocative environments in the solar system, Titan’s sea Ligeia Mare

The hepatoadrenal syndrome: A common yet unrecognized clinical condition

Objective: Adrenal failure is common in critically ill patients, particularly those with sepsis. As liver failure and sepsis are both associated with increased circulating levels of endotoxin and proinflammatory mediators and reduced levels of apoprotein-1/ high-density lipoprotein, we postulated that adrenal failure may be common in patients with liver disease. Design: Clinical study. Setting: Liver transplant intensive care unit. Patients: The study cohort included 340 patients with liver disease. Interventions: Based on preliminary observational data, all patients admitted to our 28-bed liver transplant intensive care unit (LTICU) undergo adrenal function testing. An honest broker system was used to extract clinical, hemodynamic, medication, and laboratory data on patients admitted to the LTICU from March 2002 to March 2004. A random (stress) cortisol level <20 μg/dL in a highly stressed patient (respiratory failure, hypotension) was used to diagnose adrenal insufficiency. In all other patients, a random cortisol level <15 μg/dL or a 30-min level <20 μg/dL post-low-dose (1 μg) cosyntropin was considered diagnostic of adrenal insufficiency. Patients were grouped as follows: a) chronic liver failure; b) fulminant hepatic failure; c) patients immediately status post-orthotopic liver transplantation receiving a steroid-free protocol of immunosuppression; and d) patients status post-remote liver transplant (≥6 months). The decision to treat patients with stress doses of hydrocortisone was at the discretion of the treating intensivist and transplant surgeon. Measurements and Main Results: Two-hundred and forty-five (72%) patients met our criteria for adrenal insufficiency (the hepatoadrenal syndrome). Eight (33%) patients with fulminant hepatic failure, 97 (66%) patients with chronic liver disease, 31(61%) patients with a remote history of liver transplantation, and 109 (92%) patients who had undergone liver transplantation under steroid-free immunosuppression were diagnosed with adrenal insufficiency. The high-density lipoprotein level at the time of adrenal testing was the only variable predictive of adrenal insufficiency (p < .0001). In vasopressor-dependent patients with adrenal insufficiency, treatment with hydrocortisone was associated with a significant reduction (p = .02) in the dose of norepinephrine at 24 hrs, whereas the dose of norepinephrine was significantly higher (p = .04) in those patients with adrenal failure not treated with hydrocortisone. In vasopressor-dependent patients without adrenal insufficiency, treatment with hydrocortisone did not affect vasopressor dose at 24 hrs. One hundred and forty-one patients (26.4%) died during their hospitalization. The baseline serum cortisol was 18.8 ± 16.2 μg/dL in the nonsurvivors compared with 13.0 ± 11.8 μg/dL in the survivors (p < .001). Of those patients with adrenal failure who were treated with glucocorticoids, the mortality rate was 26% compared with 46% (p = .002) in those who were not treated. In those patients receiving vasopressor agents at the time of adrenal testing, the baseline cortisol was 10.0 ± 4.8 μg/dL in those with adrenal insufficiency compared with 35.6 ± 21.2 μg/dL in those with normal adrenal function. Vasopressor-dependent patients who did not have adrenal failure had a mortality rate of 75%. Conclusions: Patients with liver failure and patients post-liver transplantation have an exceedingly high incidence of adrenal failure, which may be pathophysiologically related to low levels of high-density lipoprotein. Treatment of patients with adrenal failure may improve outcome. High baseline serum cortisol levels may be a maker of disease severity and portend a poor prognosis. Copyright © 2005 by the Society of Critical Care Medicine and Lippincott Williams & Wilkins

Who bullies whom at a garden feeder? Interspecific agonistic interactions of small passerines during a cold winter

Interspecific agonistic interactions are important selective factors for maintaining ecological niches of different species, but their outcome is difficult to predict a priori. Here, we examined the direction and intensity of interspecific interactions in an assemblage of small passerines at a garden feeder, focussing on three finch species of various body sizes. We found that large and mediumsized birds usually initiated and won agonistic interactions with smaller species. Also, the frequency of fights increased with decreasing differences in body size between the participants. Finally, the probability of engaging in a fight increased with the number of birds at the feeder

Stomatin-like Protein 2 Links Mitochondria to T-Cell Receptor Signalosomes at the Immunological Synapse and Enhances T-Cell Activation

T cell activation through the antigen receptor (TCR) requires sustained signalling from microclusters in the peripheral region of the immunological synapse (IS). The bioenergetics of such prolonged signaling have been linked to the redistribution of mitochondria to the IS. Here, we report that stomatin-like protein-2 (SLP-2) plays an important role in this process by bridging polarized mitochondria to these signaling TCR microclusters or signalosomes in the IS in a polymerized actin-dependent manner. In this way, SLP-2 helps to sustain TCR-dependent signalling and enhances T cell activation

Human Cytomegalovirus: detection of congenital and perinatal infection in Argentina

BACKGROUND: Human cytomegalovirus (CMV) is one of the most commonly found agents of congenital infections. Primary maternal infection is associated with risk of symptomatic congenital diseases, and high morbidity is frequently associated with very low birth weight. Neonates with asymptomatic infection develop various sequelae during infancy. This is the first Argentine study performed in neonates with congenital and postnatal HCMV infection. The purpose of this study was to evaluate the performance of the polymerase chain reaction (PCR) technique with different pairs of primers, to detect cytomegalovirus isolated in tissue cultures and directly in urine and dried blood spot (DBS) specimens. Results were compared with IgM detection. METHODS: The study was performed between 1999 and 2001 on routine samples in the Laboratory. A total of 61 urine and 56 serum samples were selected from 61 newborns/infants, 33 patients whose samples were analyzed during the first two to three weeks of life were considered congenital infections; the remaining 28 patients whose samples were taken later than the third week were grouped as perinatal infections, although only in 4 the perinatal transmission of infection was determined unequivocally Cytomegalovirus diagnosis was made by isolating the virus from urine samples in human foreskin fibroblast cells. Three different primer pairs directed to IE, LA and gB genes were used for the HCMV PCR assay in viral isolates. Subsequently, PCR and nested PCR (nPCR) assays with gB primers were performed directly in urine and in 11 samples of dried blood spot (DBS) on Guthrie Card, these results were then compared with serology. RESULTS: The main clinical manifestations of the 33 patients with congenital infection were purpura, jaundice, hepatomegaly and anaemia. Three patients presented low birth weight as single symptom, 10, intracranial calcifications, and 2, kidney failure. In the 28 patients grouped as with perinatal infection, anaemia, hepatosplenomegaly and enzymatic alteration were predominant, and 4 patients were HIV positive. The primers used to amplify the gB region had a PCR positivity rate of 100%, whereas those that amplified IE and LA regions had a PCR positivity rate of 54% and 61% respectively, in CMV isolates. Amplification by PCR of urine samples (with no previous DNA extraction), using primers for the gB region, detected 34/61 positive samples. Out of the 33 samples from patients with congenital infection, 24 (73%) were positive. When nPCR was used in these samples, all were positive, whereas in the remaining 28 patients, two negative cases were found. Cytomegalovirus DNA detection in 11 samples was also carried out in DBS: 7 DBS samples were positive and 4 were negative. CONCLUSIONS: Primers directed to the gB fragment region were the best choice for the detection of CMV DNA in positive isolates. In congenital infections, direct PCR in urine was positive in a high percentage (73%) of samples; however, in patients grouped as with perinatal infection only 36% of the cases were positive. With n-PCR, total sample positivity reached 97%. PCR technique performed in DBS allowed identifying congenital infection in four patients and to be confirmed in 3. These results show the value of nPCR for the detection of all cases of CMV infection. The assay offers the advantage that it may be performed within the normal working day and provides reliable results in a much shorter time frame than that required for either traditional tissue culture or the shell-viral assay

Theoretical determination of the Raman spectra of MgSiO3 perovskite and post-perovskite at high pressure

We use the density functional perturbation theory to determine for the first time the pressure evolution of the Raman intensities for a mineral, the two high-pressure structures of MgSiO3 perovskite and post-perovskite. At high pressures, the Raman powder spectra reveals three main peaks for the perovskite structure and one main peak for the post-perovskite structure. Due to the large differences in the spectra of the two phases Raman spectroscopy can be used as a good experimental indication of the phase transition.Comment: 16 pages, submitted to Geophysical Research Letter

Transition from School to University Mathematics: Manifestations of Unresolved Commognitive Conflict in First Year Students’ Examination Scripts

We explore the transition from school to university through a commognitive (Sfard 2008) analysis of twenty-two students’ examination scripts from the end of year examination of a first year, year-long module on Sets, Numbers, Proofs and Probability in a UK mathematics department. Our analysis of the scripts relies on a preliminary analysis of the tasks and the lecturers’ (also exam setters’) assessment practices, and focuses on manifestations of unresolved commognitive conflict in students’ engagement with the tasks. Here we note four such manifestations concerning the students’ identification of and consistent work with: the appropriate numerical context of the examination tasks; the visual mediators and the rules of school algebra and Set Theory discourses; the visual mediators of the Probability and Set Theory discourses; and, with the visual mediators and rules of the Probability Theory discourse. Our analysis suggests that, despite lecturers’ attempts to assist students towards a smooth transition to the different discourses of university mathematics, students’ errors at the final examination reveal unresolved commognitive conflicts. A pedagogical implication of our analysis is that a more explicit and systematic presentation of the distinctive differences between these discourses, along with facilitation of the flexible moves between them, is needed