MolabIS - An integrated information system for storing and managing molecular genetics data

BACKGROUND: Long-term sample storage, tracing of data flow and data export for subsequent analyses are of great importance in genetics studies. Therefore, molecular labs do need a proper information system to handle an increasing amount of data from different projects. RESULTS: We have developed a molecular labs information management system (MolabIS). It was implemented as a web-based system allowing the users to capture original data at each step of their workflow. MolabIS provides essential functionality for managing information on individuals, tracking samples and storage locations, capturing raw files, importing final data from external files, searching results, accessing and modifying data. Further important features are options to generate ready-to-print reports and convert sequence and microsatellite data into various data formats, which can be used as input files in subsequent analyses. Moreover, MolabIS also provides a tool for data migration. CONCLUSIONS: MolabIS is designed for small-to-medium sized labs conducting Sanger sequencing and microsatellite genotyping to store and efficiently handle a relative large amount of data. MolabIS not only helps to avoid time consuming tasks but also ensures the availability of data for further analyses. The software is packaged as a virtual appliance which can run on different platforms (e.g. Linux, Windows). MolabIS can be distributed to a wide range of molecular genetics labs since it was developed according to a general data model. Released under GPL, MolabIS is freely available at http://www.molabis.org

Verkenning sensorgestuurde dosering van loofdodingsmiddelen in pootaardappelen

In 2008 is een verkenning gedaan naar haalbaarheid van sensorgestuurde dosering van loofdodingsmiddelen in pootgoedteelt van aardappelen. Er werd een prototype gebouwd en getest waarmee Finale pleksgewijs gedoseerd werd d.m.v. Greenseeker-sensoren op een klap-spuit-combinatie en een rekenregel die plaatspecifieke meetwaarden doorvertaalde in een minimum effectieve dosering. Ook werden dosis-response proeven uitgevoerd. De eerste resultaten met het prototype en systeem waren positief. Met de sensoren konden variatie in gewasstand in kaart gebracht worden, en deze bleek groter dan verwacht. Bovendien kon de dosering effectief gestuurd worden met de sensormeetwaarden. Het onderzoek laat zien dat reductie in loofdodingsmiddel met sensorsturing mogelijk is. In het onderzoek bleken ras en dosering van Finale geen effect te hebben op verkleuring van navels van knollen. Nader onderzoek aan de beslisregels, validatie in de praktijk inclusief effecten op kwaliteit van de aardappelen is nodig voor implementatie in de praktij

Renormalization Group Study of the soliton mass on the (lambda Phi^4)_{1+1} lattice model

We compute, on the $(\lambda \Phi^4)_{1+1}$ model on the lattice, the soliton mass by means of two very different numerical methods. First, we make use of a ``creation operator'' formalism, measuring the decay of a certain correlation function. On the other hand we measure the shift of the vacuum energy between the symmetric and the antiperiodic systems. The obtained results are fully compatible. We compute the continuum limit of the mass from the perturbative Renormalization Group equations. Special attention is paid to ensure that we are working on the scaling region, where physical quantities remain unchanged along any Renormalization Group Trajectory. We compare the continuum value of the soliton mass with its perturbative value up to one loop calculation. Both quantities show a quite satisfactory agreement. The first is slightly bigger than the perturbative one; this may be due to the contributions of higher order corrections.Comment: 19 pages, preprint DFTUZ/93/0

Ultrafast quasiparticle relaxation dynamics in normal metals and heavy fermion materials

We present a detailed theoretical study of the ultrafast quasiparticle relaxation dynamics observed in normal metals and heavy fermion materials with femtosecond time-resolved optical pump-probe spectroscopy. For normal metals, a nonthermal electron distribution gives rise to a temperature (T) independent electron-phonon relaxation time at low temperatures, in contrast to the T^{-3}-divergent behavior predicted by the two-temperature model. For heavy fermion compounds, we find that the blocking of electron-phonon scattering for heavy electrons within the density-of-states peak near the Fermi energy is crucial to explain the rapid increase of the electron-phonon relaxation time below the Kondo temperature. We propose the hypothesis that the slower Fermi velocity compared to the sound velocity provides a natural blocking mechanism due to energy and momentum conservation laws.Comment: 10 pages, 11 figure

Size-Dependent Surface Plasmon Dynamics in Metal Nanoparticles

We study the effect of Coulomb correlations on the ultrafast optical dynamics of small metal particles. We demonstrate that a surface-induced dynamical screening of the electron-electron interactions leads to quasiparticle scattering with collective surface excitations. In noble-metal nanoparticles, it results in an interband resonant scattering of d-holes with surface plasmons. We show that this size-dependent many-body effect manifests itself in the differential absorption dynamics for frequencies close to the surface plasmon resonance. In particular, our self-consistent calculations reveal a strong frequency dependence of the relaxation, in agreement with recent femtosecond pump-probe experiments.Comment: 8 pages + 4 figures, final version accepted to PR

Low tidal volume ventilation ameliorates left ventricular dysfunction in mechanically ventilated rats following LPS-induced lung injury

Background: High tidal volume ventilation has shown to cause ventilator-induced lung injury (VILI), possibly contributing to concomitant extrapulmonary organ dysfunction. The present study examined whether left ventricular (LV) function is dependent on tidal volume size and whether this effect is augmented during lipopolysaccharide(LPS)-induced lung injury. Methods: Twenty male Wistar rats were sedated, paralyzed and then randomized in four groups receiving mechanical ventilation with tidal volumes of 6 ml/kg or 19 ml/kg with or without intrapulmonary administration of LPS. A conductance catheter was placed in the left ventricle to generate pressure-volume loops, which were also obtained within a few seconds of vena cava occlusion to obtain relatively load-independent LV systolic and diastolic function parameters. The end-systolic elastance / effective arterial elastance (Ees/Ea) ratio was used as the primary parameter of LV systolic function with the end-diastolic elastance (Eed) as primary LV diastolic function. Results: Ees/Ea decreased over time in rats receiving LPS (p = 0.045) and high tidal volume ventilation (p = 0.007), with a lower Ees/Ea in the rats with high tidal volume ventilation plus LPS compared to the other groups (p < 0.001). Eed increased over time in all groups except for the rats receiving low tidal volume ventilation without LPS (p = 0.223). A significant interaction (p < 0.001) was found between tidal ventilation and LPS for Ees/Ea and Eed, and all rats receiving high tidal volume ventilation plus LPS died before the end of the experiment. Conclusions: Low tidal volume ventilation ameliorated LV systolic and diastolic dysfunction while preventing death following LPS-induced lung injury in mechanically ventilated rats. Our data advocates the use of low tidal volumes, not only to avoid VILI, but to avert ventilator-induced myocardial dysfunction as well

Relaxation Dynamics of Photoinduced Changes in the Superfluid Weight of High-Tc Superconductors

In the transient state of d-wave superconductors, we investigate the temporal variation of photoinduced changes in the superfluid weight. We derive the formula that relates the nonlinear response function to the nonequilibrium distribution function. The latter qunatity is obtained by solving the kinetic equation with the electron-electron and the electron-phonon interaction included. By numerical calculations, a nonexponential decay is found at low temperatures in contrast to the usual exponential decay at high temperatures. The nonexponential decay originates from the nonmonotonous temporal variation of the nonequilibrium distribution function at low energies. The main physical process that causes this behavior is not the recombination of quasiparticles as previous phenomenological studies suggested, but the absorption of phonons.Comment: 18 pages, 12 figures; to be published in J. Phys. Soc. Jpn. Vol. 80, No.

Identity of the universal repulsive-core singularity with Yang-Lee edge criticality

Lattice and continuum fluid models with repulsive-core interactions typically display a dominant, critical-type singularity on the real, negative activity axis. Lai and Fisher recently suggested, mainly on numerical grounds, that this repulsive-core singularity is universal and in the same class as the Yang-Lee edge singularities, which arise above criticality at complex activities with positive real part. A general analytic demonstration of this identification is presented here using a field-theory approach with separate representation of the repulsive and attractive parts of the pair interactions.Comment: 6 pages, 3 figure

Citrate confers less filter-induced complement activation and neutrophil degranulation than heparin when used for anticoagulation during continuous venovenous haemofiltration in critically ill patients

Background: During continuous venovenous haemofiltration (CVVH), regional anticoagulation with citrate may be superior to heparin in terms of biocompatibility, since heparin as opposed to citrate may activate complement (reflected by circulating C5a) and induce neutrophil degranulation in the filter and myeloperoxidase (MPO) release from endothelium. Methods. No anticoagulation (n = 13), unfractionated heparin (n = 8) and trisodium citrate (n = 17) regimens during CVVH were compared. Blood samples were collected pre- and postfilter; C5a, elastase and MPO were determined by ELISA. Additionally, C5a was also measured in the ultrafiltrate. Results: In the heparin group, there was C5a production across the filter which most decreased over time as compared to other groups (P = 0.007). There was also net production of elastase and MPO across the filter during heparin anticoagulation (P = 0.049 or lower), while production was minimal and absent in the no anticoagulation and citrate group, respectively. During heparin anticoagulation, plasma concentrations of MPO at the inlet increased in the first 10 minutes of CVVH (P = 0.024). Conclusion: Citrate confers less filter-induced, potentially harmful complement activation and neutrophil degranulation and less endothelial activation than heparin when used for anticoagulation during continuous venovenous haemofiltration in critically ill patients

The plasma level and biomarker value of neutrophil gelatinase-associated lipocalin in critically ill patients with acute kidney injury are not affected by continuous venovenous hemofiltration and anticoagulation applied

Introduction: Neutrophil gelatinase-associated lipocalin (NGAL) is a biomarker of acute kidney injury (AKI), and levels reflect severity of disease in critically ill patients. However, continuous venovenous hemofiltration (CVVH) may affect plasma levels by clearance or release of NGAL by activated neutrophils in the filter, dependent on the anticoagulation regimen applied. We therefore studied handling of NGAL by CVVH in patients with AKI.Methods: Immediately before initiation of CVVH, prefilter blood was drawn. After 10, 60, 180, and 720 minutes of CVVH, samples were collected from pre- and postfilter (in- and outlet) blood and ultrafiltrate. CVVH with the following anticoagulation regimens was studied: no anticoagulation in case of a high bleeding tendency (n = 13), unfractionated heparin (n = 8), or trisodium citrate (n = 21). NGAL levels were determined with enzyme-linked immunosorbent assay (ELISA).Results: Concentrations of NGAL at inlet and outlet were similar, and concentrations did not change over time in any of the anticoagulation groups; thus no net removal or production of NGAL occurred. Concentrations of NGAL at inlet correlated with disease severity at initiation of CVVH and at the end of a CVVH run. Concentrations of NGAL in the ultrafiltrate were lower with citrate-based CVVH (P = 0.03) and decreased over time, irrespective of anticoagulation administered (P < 0.001). The sieving coefficient and clearance of NGAL were low and decreased over time (P < 0.001).Conclusions: The plasma level and biomarker value of NGAL in critically ill patients with AKI are not affected by CVVH, because clearance by the filter was low. Furthermore, no evidence exists for intrafilter release of NGAL by neutrophils, irrespective of the anticoagulation method applied