PENELOPE-2008: A Code System for Monte Carlo Simulation of Electron and Photon Transport

The computer code system PENELOPE (version 2008) performs Monte Carlo simulation of coupledelectron-photon transport in arbitrary materials for a wide energy range, from a few hundred eV toabout 1 GeV. Photon transport is simulated by means of the standard, detailed simulation scheme.Electron and positron histories are generated on the basis of a mixed procedure, which combinesdetailed simulation of hard events with condensed simulation of soft interactions. A geometry packagecalled PENGEOM permits the generation of random electron-photon showers in material systemsconsisting of homogeneous bodies limited by quadric surfaces, i.e., planes, spheres, cylinders, etc. Thisreport is intended not only to serve as a manual of the PENELOPE code system, but also to provide theuser with the necessary information to understand the details of the Monte Carlo algorithm.

Brownian dynamics simulation of DNA condensation.

DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion. The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential. We show afterward that with a sufficient concentration of divalent salt (typically approximately 20 mM MgCl(2)), supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl(2) above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA.

Does Direct Democracy Matters for Political Parties : An Empirical Test in the Swiss Cantons

According to most political scientists and commentators, direct democracy seems to weaken political parties. Our empirical analysis in the 26 Swiss cantons shows that this thesis in its general form cannot be maintained. Political parties in cantons with extensive use of referendums and initiatives are not in all respects weaker than parties in cantons with little use of direct democratic means of participation. On the contrary, direct democracy goes together with more professional and formalized party organizations. Use of direct democracy is associated with more fragmented and volatile party systems, and with greater support for small parties, but causal interpretations of these relationships are difficult.

A game theoretic simulation model for quality oriented timber supply to sawmills

Summary

Direct Fourier Tomographic Reconstruction Image-To-Image Filter

We present an open-source ITK implementation of a directFourier method for tomographic reconstruction, applicableto parallel-beam x-ray images. Direct Fourierreconstruction makes use of the central-slice theorem tobuild a polar 2D Fourier space from the 1D transformedprojections of the scanned object, that is resampled intoa Cartesian grid. Inverse 2D Fourier transform eventuallyyields the reconstructed image. Additionally, we providea complex wrapper to the BSplineInterpolateImageFunctionto overcome ITKâeuro?s current lack for image interpolatorsdealing with complex data types. A sample application ispresented and extensively illustrated on the Shepp-Loganhead phantom. We show that appropriate input zeropaddingand 2D-DFT oversampling rates together with radial cubicb-spline interpolation improve 2D-DFT interpolationquality and are efficient remedies to reducereconstruction artifacts.

Les interventions de soutien direct auprès des aidants naturels réduisent leur détresse psychologique: revue Cochrane pour le praticien.

Cet article présente les résultats de la revue systématique: Candy B, Jones L, Drake R, Leurent B, King M. Interventions for supporting informal caregivers of patients in the terminal phase of a disease. Cochrane Database Syst Rev. 2011 Jun 15;(6):CD007617. PMID: 21678368. Contexte : Les aidants naturels sont des personnes bénévoles qui dispensent des soins physiques et, ou un soutien émotionnel à l'un(e) de leur proche ou ami(e). Ceci peut générer un stress intense tant physique que psychique. Des interventions visant principalement à augmenter la qualité de vie et à soutenir la vie affective des aidants naturels ont été développées. Cette revue systématique évalue l'effet de ces interventions sur la santé physique et psychique des aidants naturels de patients en phase terminale. [Auteurs]

Numerical simulation of ambient seismic wavefield modification caused by pore-fluid effects in an oil reservoir

We have modeled numerically the seismic response of a poroelastic inclusion with properties applicable to an oil reservoir that interacts with an ambient wavefield. The model includes wave-induced fluid flow caused by pressure differences between mesoscopic-scale (i.e., in the order of centimeters to meters) heterogeneities. We used a viscoelastic approximation on the macroscopic scale to implement the attenuation and dispersion resulting from this mesoscopic-scale theory in numerical simulations of wave propagation on the kilometer scale. This upscaling method includes finite-element modeling of wave-induced fluid flow to determine effective seismic properties of the poroelastic media, such as attenuation of P- and S-waves. The fitted, equivalent, viscoelastic behavior is implemented in finite-difference wave propagation simulations. With this two-stage process, we model numerically the quasi-poroelastic wave-propagation on the kilometer scale and study the impact of fluid properties and fluid saturation on the modeled seismic amplitudes. In particular, we addressed the question of whether poroelastic effects within an oil reservoir may be a plausible explanation for low-frequency ambient wavefield modifications observed at oil fields in recent years. Our results indicate that ambient wavefield modification is expected to occur for oil reservoirs exhibiting high attenuation. Whether or not such modifications can be detected in surface recordings, however, will depend on acquisition design and noise mitigation processing as well as site-specific conditions, such as the geologic complexity of the subsurface, the nature of the ambient wavefield, and the amount of surface noise.

Bone marrow dosimetry in rats using direct tissue counting after injection of radio-iodinated intact monoclonal antibodies or F(ab')2 fragments.

Normal rats were injected intravenously with 131I- and 125I-labeled intact murine and chimeric mouse-human monoclonal antibodies directed against carcinoembryonic antigen or with the corresponding F(ab')2 fragments. At different times after injection, individual animals were killed and radioactivity of blood and major organs, including bones and bone marrow, was determined. Ratios comparing radioactivity concentration in different tissues with that of bone marrow were calculated and found to remain stable during several effective half-lives of the antibodies. Mean bone marrow radioactivity was 35% (range, 29%-40%) of that of blood and 126% (range, 108%-147%) of that of liver after injection of intact Mabs or F(ab')2 fragments. In nude rats bearing human colon carcinoma xenografts producing carcinoembryonic antigen, relative bone marrow radioactivity was slightly lower than that in normal rats.

The Sequential Organ Failure Assessment score and copeptin for predicting survival in ventilator-associated pneumonia.

INTRODUCTION: Ventilator-associated pneumonia remains the most common nosocomial infection in the critically ill and contributes to significant morbidity. Eventual decisions regarding withdrawal or maximal therapy are demanding and rely on physicians' experience. Additional objective tools for risk assessment may improve medical judgement. Copeptin, reflecting vasopressin release, as well as the Sequential Organ Failure Assessment (SOFA) score, reflecting the individual degree of organ dysfunction, might qualify for survival prediction in ventilator-associated pneumonia. We investigated the predictive value of the SOFA score and copeptin in ventilator-associated pneumonia. METHODS: One hundred one patients with ventilator-associated pneumonia were prospectively assessed. Death within 28 days after ventilator-associated pneumonia onset was the primary end point. RESULTS: The SOFA score and the copeptin levels at ventilator-associated pneumonia onset were significantly elevated in nonsurvivors (P = .002 and P = .017, respectively). Both markers had different time courses in survivors and nonsurvivors (P < .001 and P = .006). Mean SOFA (average SOFA of 10 days after VAP onset) was superior in predicting 28-day survival as compared with SOFA and copeptin at ventilator-associated pneumonia onset (area under the curve, 0.90 vs 0.73 and 0.67, respectively). CONCLUSIONS: The predictive value of serial-measured SOFA significantly exceeds those of single SOFA and copeptin measurements. Serial SOFA scores accurately predict outcome in ventilator-associated pneumonia.

Influence of the menstrual cycle on the sweating response measured by direct calorimetry in women exposed to warm environmental conditions.

The whole body sweating response was measured at rest in eight women during the follicular (F) and the luteal (L) phases of the menstrual cycle. Subjects were exposed for 30-min to neutral (N) environmental conditions [ambient temperature (Ta) 28 degrees C] and then for 90-min to warm (W) environmental conditions (Ta, 35 degrees C) in a direct calorimeter. At the end of the N exposure, tympanic temperature (Tty) was 0.18 (SEM 0.06) degrees C higher in the L than in the F phase (P less than 0.05), whereas mean skin temperature (Tsk) was unchanged. During W exposure, the time to the onset of sweating as well as the concomitant increase in body heat content were similar in both phases. At the onset of sweating, the tympanic threshold temperature (Tty,thresh) was higher in the L phase [37.18 (SEM 0.08) degrees C] than in the F phase [36.95 (SEM 0.07) degrees C; P less than 0.01]. The magnitude of the shift in Tty,thresh [0.23 (SEM 0.07) degrees C] was similar to the L-F difference in Tty observed at the end of the N exposure. The mean skin threshold temperature was not statistically different between the two phases. The slope of the relationship between sweating rate and Tty was similar in F and L. It was concluded that the internal set point temperature of resting women exposed to warm environmental conditions shifted to a higher value during the L phase compared to the F phase of the menstrual cycle; and that the magnitude of the shift corresponded to the difference in internal temperature observed in neutral environmental conditions between the two phases.

Comparison of thinning methods in a Scots pine stand on drained peatland : a simulation study

Tiivistelmä: Harvennusmenetelmien vertailu ojitetun turvemaan männikössä. Simulointitutkimus

Quantification of brain glycogen concentration and turnover through localized 13C NMR of both the C1 and C6 resonances.

We have recently shown that at isotopic steady state (13)C NMR can provide a direct measurement of glycogen concentration changes, but that the turnover of glycogen was not accessible with this protocol. The aim of the present study was to design, implement and apply a novel dual-tracer infusion protocol to simultaneously measure glycogen concentration and turnover. After reaching isotopic steady state for glycogen C1 using [1-(13)C] glucose administration, [1,6-(13)C(2)] glucose was infused such that isotopic steady state was maintained at the C1 position, but the C6 position reflected (13)C label incorporation. To overcome the large chemical shift displacement error between the C1 and C6 resonances of glycogen, we implemented 2D gradient based localization using the Fourier series window approach, in conjunction with time-domain analysis of the resulting FIDs using jMRUI. The glycogen concentration of 5.1 +/- 1.6 mM measured from the C1 position was in excellent agreement with concomitant biochemical determinations. Glycogen turnover measured from the rate of label incorporation into the C6 position of glycogen in the alpha-chloralose anesthetized rat was 0.7 micromol/g/h.

Nitrogen application timing and soil inorganic nitrogen dynamics under no-till oat/maize sequential cropping

The timing of N application to maize is a key factor to be considered in no-till oat/maize sequential cropping. This study aimed to evaluate the influence of pre-planting, planting and sidedress N application on oat residue decomposition, on soil N immobilisation and remineralisation and on N uptake by maize plants in no-till oat/maize sequential cropping. Undisturbed soil cores of 10 and 20 cm diameter were collected from the 0-15 cm layer of a no-till Red Latossol, when the oat cover crop was in the milk-grain stage. Two greenhouse experiments were conducted simultaneously. Experiment A, established in the 10 cm diameter cores and without plant cultivation, was used to asses N dynamics in soil and oat residues. Experiment B, established in the 20 cm diameter cores and with maize cultivation, was used to assess plant growth and N uptake. An amount of 6.0 Mg ha-1 dry matter of oat residues was spread on the surface of the cores. A rate of 90 kg N ha-1 applied as ammonium sulphate in both experiments was split in pre-planting, planting and sidedress applications as follows: (a) 00-00-00 (control), (b) 90-00-00 (pre-planting application, 20 days before planting), (c) 00-90-00 (planting application), (d) 00-30-60 (split in a planting and a sidedress application 31 days after emergence), (e) 00-00-00* (control, without oat residue) and (f) 90-00-00* (pre-planting application, without oat residue). The N concentration and N content in oat residues were not affected during decomposition by N fertilisation. Most of the fertiliser NH4+-N was converted into NO3--N within 20 days after application. A significant decrease in NO3--N contents in the 0-4 cm layer was observed in all treatments between 40 and 60 days after the oat residue placement on the soil surface, suggesting the occurrence of N immobilisation in this period. Considering that most of the inorganic N was converted into NO3- and that no immobilisation of the pre planting fertiliser N occurred at the time of its application, it was possible to conclude that pre-planting applied N was prone to losses by leaching. On the other hand, with split N applications, maize plants showed N deficiency symptoms before sidedress application. Two indications for fertiliser-N management in no-till oat/maize sequential cropping could be suggested: (a) in case of split application, the sidedress should be earlier than 30 days after emergence, and (b) if integral application is preferred to save field operations, this should be done at planting.