A multiplex real-time PCR assay for rapid detection and differentiation of 25 bacterial and fungal pathogens from whole blood samples

Early detection of bloodstream infections (BSI) is crucial in the clinical setting. Blood culture remains the gold standard for diagnosing BSI. Molecular diagnostic tools can contribute to a more rapid diagnosis in septic patients. Here, a multiplex real-time PCR-based assay for rapid detection of 25 clinically important pathogens directly from whole blood in <6 h is presented. Minimal analytical sensitivity was determined by hit rate analysis from 20 independent experiments. At a concentration of 3 CFU/ml a hit rate of 50% was obtained for E. aerogenes and 100% for S. marcescens, E. coli, P. mirabilis, P. aeruginosa, and A. fumigatus. The hit rate for C. glabrata was 75% at 30 CFU/ml. Comparing PCR identification results with conventional microbiology for 1,548 clinical isolates yielded an overall specificity of 98.8%. The analytical specificity in 102 healthy blood donors was 100%. Although further evaluation is warranted, our assay holds promise for more rapid pathogen identification in clinical sepsis.

Will Whole-Tree Harvest of Jack Pine (Pinus banksiana) deplete soil nutrients in low-productivity sand soils?

In 2009 and 2010 a study was conducted on the Hiawatha National Forest (HNF) to determine if whole-tree harvest (WTH) of jack pine would deplete the soil nutrients in the very coarse-textured Rubicon soil. WTH is restricted on Rubicon sand in order to preserve the soil fertility, but the increasing construction of biomass-fueled power plants is expected to increase the demand for forest biomass. The specific objectives of this study were to estimate biomass and nutrient content of above- and below-ground tree components in mature jack pine (Pinus banksiana) stands growing on a coarse-textured, low-productivity soil, determine pools of total C and N and exchangeable soil cations in Rubicon sand, and to compare the possible impacts of conventional stem-only harvest (CH) and WTH on soil nutrient pools and the implications for productivity of subsequent rotations. Four even-aged jack pine stands on Rubicon soil were studied. Allometric equations were used to estimate above-ground biomass and nutrients, and soil samples from each stand were taken for physical and chemical analysis. Results indicate that WTH will result in cation deficits in all stands, with exceptionally large Ca deficits occurring in two stands. Where a deficit does not occur, the cation surplus is small and, chemical weathering and atmospheric deposition is not anticipated to replace the removed cations. CH will result in a surplus of cations, and will likely not result in productivity declines during the first rotation. However even under CH, the surplus is small, and chemical weathering and atmospheric deposition will not supply enough cations for the second rotation.

The long-term effects of whole-tree harvest at final felling on soil properties in a Norway Spruce (Picea Abies (L) Karst.) Stand

Increased demand for forest-derived biomass has resulted in changes in harvest intensities in Finland. Conventional stem-only harvest (CH) has to some extent been replaced with whole-tree harvest (WTH). The latter involves a greater removal of nutrients from the forest ecosystem, as all the above ground biomass is exported from the site. This has raised concerns that WTH could result in large changes in the nutrient dynamics of a forest stand and could eventually lower its site productivity. Little empirical data exists to support this assumption as only a limited number of studies have been conducted on the topic. A majority of these discuss the short-term effects, thus the long-term consequences remain unknown. The objective of this study was to compare differences in soil properties after CH and WTH in a fertile Norway spruce (Picea abies (L) Karst.) stand in Southern Finland. The site was clear-felled in August 2000 and spruce seedlings were planted in the following summer. Soil sampling in the form of systematic randomized sampling was carried out in May 2011. Changes in base saturation, cation exchange capacity, elemental pools (total and exchangeable) and acidity were studied in both organic and mineral horizons. The results indicate that WTH lowered effective cation exchange capacity and base saturation particularly in the humus layer. The pools of exchangeable Al and Fe were increased in the humus layer, whereas the amount of exchangeable Ca decreased in both layers. WTH also resulted in lower Ca/Al-ratios across the sampled layers. Treatment did not have a significant effect on pH, total pools of elements or on the C/N-ratio of the soil. The results suggest that although the stand possesses significant pools of nutrients at present, WTH, if continued, could have long-term effects on site productivity.

Whole body postmortem angiography with a high viscosity contrast agent solution using poly ethylene glycol as contrast agent dissolver

Postmortem minimal invasive angiography has already been implemented to support virtual autopsy examinations. An experimental approach in a porcine model to overcome an initially described artificial tissue edema artifact by using a poly ethylene glycol (PEG) containing contrast agent solution showed promising results. The present publication describes the first application of PEG in a whole corpse angiographic CT examination. A minimal invasive postmortem CT angiography was performed in a human corpse utilizing the high viscosity contrast agent solution containing 65% of PEG. Injection was carried out via the femoral artery into the aortic root in simulated cardiac output conditions. Subsequent CT scanning delivered the 3D volume data of the whole corpse. Visualization of the human arterial anatomy was excellent and the contrast agent distribution was generally limited to the arterial system as intended. As exceptions an enhancement of the brain, the left ventricular myocardium and the renal cortex became obvious. This most likely represented the stage of centralization of the blood circulation at the time of death with dilatation of the precapillary arterioles within these tissues. Especially for the brain this resulted in a distinctively improved visualization of the intracerebral structures by CT. However, the general tissue edema artifact of postmortem minimal invasive angiography examinations could be distinctively reduced.

Monitoring thrombin generation by electrochemistry: development of an amperometric biosensor screening test for plasma and whole blood

BACKGROUND: Complete investigation of thrombophilic or hemorrhagic clinical presentations is a time-, apparatus-, and cost-intensive process. Sensitive screening tests for characterizing the overall function of the hemostatic system, or defined parts of it, would be very useful. For this purpose, we are developing an electrochemical biosensor system that allows measurement of thrombin generation in whole blood as well as in plasma. METHODS: The measuring system consists of a single-use electrochemical sensor in the shape of a strip and a measuring unit connected to a personal computer, recording the electrical signal. Blood is added to a specific reagent mixture immobilized in dry form on the strip, including a coagulation activator (e.g., tissue factor or silica) and an electrogenic substrate specific to thrombin. RESULTS: Increasing thrombin concentrations gave standard curves with progressively increasing maximal current and decreasing time to reach the peak. Because the measurement was unaffected by color or turbidity, any type of blood sample could be analyzed: platelet-poor plasma, platelet-rich plasma, and whole blood. The test strips with the predried reagents were stable when stored for several months before testing. Analysis of the combined results obtained with different activators allowed discrimination between defects of the extrinsic, intrinsic, and common coagulation pathways. Activated protein C (APC) predried on the strips allowed identification of APC-resistance in plasma and whole blood samples. CONCLUSIONS: The biosensor system provides a new method for assessing thrombin generation in plasma or whole blood samples as small as 10 microL. The assay is easy to use, thus allowing it to be performed in a point-of-care setting.

Whole-body vibration dosage alters leg blood flow

The effect of whole-body vibration dosage on leg blood flow was investigated. Nine healthy young adult males completed a set of 14 random vibration and non-vibration exercise bouts whilst squatting on a Galileo 900 plate. Six vibration frequencies ranging from 5 to 30 Hz (5 Hz increments) were used in combination with a 2.5 mm and 4.5 mm amplitude to produce twelve 1-min vibration bouts. Subjects also completed two 1-min bouts where no vibration was applied. Systolic and diastolic diameters of the common femoral artery and blood cell velocity were measured by an echo Doppler ultrasound in a standing or rest condition prior to the bouts and during and after each bout. Repeated measures MANOVAs were used in the statistical analysis. Compared with the standing condition, the exercise bouts produced a four-fold increase in mean blood cell velocity (P<0.001) and a two-fold increase in peak blood cell velocity (P<0.001). Compared to the non-vibration bouts, frequencies of 10-30 Hz increased mean blood cell velocity by approximately 33% (P<0.01) whereas 20-30 Hz increased peak blood cell velocity by approximately 27% (P<0.01). Amplitude was additive to frequency but only achieved significance at 30 Hz (P<0.05). Compared with the standing condition, squatting alone produced significant increases in mean and peak blood cell velocity (P<0.001). The results show leg blood flow increased during the squat or non-vibration bouts and systematically increased with frequency in the vibration bouts.

Personal experience with whole-body, low-dosage, digital X-ray scanning (LODOX-Statscan) in trauma

BACKGROUND: Lodox-Statscan is a whole-body, skeletal and soft-tissue, low-dose X-ray scanner Anterior-posterior and lateral thoraco-abdominal studies are obtained in 3-5 minutes with only about one-third of the radiation required for conventional radiography. Since its approval by the Food and Drug Administration (FDA) in the USA, several trauma centers have incorporated this technology into their Advanced Trauma Life Support protocols. This review provides a brief overview of the system, and describes the authors' own experience with the system. METHODS: We performed a PubMed search to retrieve all references with 'Lodox' and 'Stat-scan' used as search terms. We furthermore used the google search engine to identify existing alternatives. To the best of our knowledge, this is the only FDA-approved device of its kind currently used in trauma. RESULTS AND CONCLUSION: The intention of our review has been to sensitize the readership that such alternative devices exist. The key message is that low dosage full body radiography may be an alternative to conventional resuscitation room radiography which is usually a prelude to CT scanning (ATLS algorithm). The combination of both is radiation intensive and therefore we consider any reduction of radiation a success. But only the future will show whether LS will survive in the face of low-dose radiation CT scanners and magnetic resonance imaging devices that may eventually completely replace conventional radiography.

Endothelial cell protection and complement inhibition in xenotransplantation: a novel in vitro model using whole blood

BACKGROUND: Studying the interactions between xenoreactive antibodies, complement and coagulation factors with the endothelium in hyperacute and acute vascular rejection usually necessitates the use of in vivo models. Conventional in vitro or ex vivo systems require either serum, plasma or anti-coagulated whole blood, making analysis of coagulation-mediated effects difficult. Here a novel in vitro microcarrier-based system for the study of endothelial cell (EC) activation and damage, using non-anticoagulated whole blood is described. Once established, the model was used to study the effect of the characterized complement- and coagulation inhibitor dextran sulfate (DXS, MW 5000) for its EC protective properties in a xenotransplantation setting. METHODS: Porcine aortic endothelial cells (PAEC), grown to confluence on microcarrier beads, were incubated with non-anticoagulated whole human blood until coagulation occurred or for a maximum of 90 min. PAEC-beads were either pre- or co-incubated with DXS. Phosphate buffered saline (PBS) experiments served as controls. Fluid phase and surface activation markers for complement and coagulation were analyzed as well as binding of DXS to PAEC-beads. RESULTS: Co- as well as pre-incubation of DXS, followed by washing of the beads, significantly prolonged time to coagulation from 39 +/- 12 min (PBS control) to 74 +/- 23 and 77 +/- 20 min, respectively (P < 0.005 vs. PBS). DXS treatment attenuated surface deposition of C1q, C4b/c, C3b/c and C5b-9 without affecting IgG or IgM deposition. Endothelial integrity, expressed by positivity for von Willebrand Factor, was maintained longer with DXS treatment. Compared with PBS controls, both pre- and co-incubation with DXS significantly prolonged activated partial thromboplastin time (>300 s, P < 0.05) and reduced production of thrombin-antithrombin complexes and fibrinopeptide A. Whilst DXS co-incubation completely blocked classical pathway complement activity (CH50 test) DXS pre-incubation or PBS control experiments showed no inhibition. DXS bound to PAEC-beads as visualized using fluorescein-labeled DXS. CONCLUSIONS: This novel in vitro microcarrier model can be used to study EC damage and the complex interactions with whole blood as well as screen ''endothelial protective'' substances in a xenotransplantation setting. DXS provides EC protection in this in vitro setting, attenuating damage of ECs as seen in hyperacute xenograft rejection.

PyGirl Generating Whole-System VMs from high-level models using PyPy

Virtual machines emulating hardware devices are generally implemented in low-level languages and using a low-level style for performance reasons. This trend results in largely difficult to understand, difficult to extend and unmaintainable systems. As new general techniques for virtual machines arise, it gets harder to incorporate or test these techniques because of early design and optimization decisions. In this paper we show how such decisions can be postponed to later phases by separating virtual machine implementation issues from the high-level machine-specific model. We construct compact models of whole-system VMs in a high-level language, which exclude all low-level implementation details. We use the pluggable translation toolchain PyPy to translate those models to executables. During the translation process, the toolchain reintroduces the VM implementation and optimization details for specific target platforms. As a case study we implement an executable model of a hardware gaming device. We show that our approach to VM building increases understandability, maintainability and extendability while preserving performance.

PyGirl: Generating Whole-System VMs from High-Level Prototypes Using PyPy

Virtual machines (VMs) emulating hardware devices are generally implemented in low-level languages for performance reasons. This results in unmaintainable systems that are difficult to understand. In this paper we report on our experience using the PyPy toolchain to improve the portability and reduce the complexity of whole-system VM implementations. As a case study we implement a VM prototype for a Nintendo Game Boy, called PyGirl, in which the high-level model is separated from low-level VM implementation issues. We shed light on the process of refactoring from a low-level VM implementation in Java to a high-level model in RPython. We show that our whole-system VM written with PyPy is significantly less complex than standard implementations, without substantial loss in performance.