Sensitive bioassay for determination of fluconazole concentrations in plasma using a Candida albicans mutant hypersusceptible to azoles.

The antifungal agent fluconazole (FLC) is widely used in clinical practice. Monitoring FLC levels is useful in complicated clinical settings and in experimental infection models. A bioassay using Candida pseudotropicalis, a simple and cost-effective method, is validated only for FLC levels ranging from 5 to 40 mg/liter. An extension of the analytical range is needed to cover most yeast MICs. A new bioassay in RPMI agar containing methylene blue was developed using C. albicans DSY1024, a mutant rendered hypersusceptible to FLC constructed by the deletion of the multidrug efflux transporter genes CDR1, CDR2, CaMDR1, and FLU1. Reproducible standard curves were obtained with FLC concentrations in plasma ranging from 1 to 100 mg/liter (quadratic regression coefficient > 0.997). The absolute sensitivity was 0.026 microg of FLC. The method was internally validated according to current guidelines for analytical method validation. Both accuracy and precision lied in the required +/-15% range. FLC levels measured by bioassay and by high-performance liquid chromatography (HPLC) performed with 62 plasma samples from humans and rats showed a strong correlation (coefficients, 0.979 and 0.995, respectively; percent deviations of bioassay from HPLC values, 0.44% +/- 15.31% and 2.66% +/- 7.54%, respectively). In summary, this newly developed bioassay is sensitive, simple, rapid, and inexpensive. It allows nonspecialized laboratories to determine FLC levels in plasma to within the clinically relevant concentration range and represents a useful tool for experimental treatment models.

Sensitive determination of D-lactic acid and L-lactic acid in urine by high-performance liquid chromatography-tandem mass spectrometry.

D-lactic acid in urine originates mainly from bacterial production in the intestinal tract. Increased D-lactate excretion as observed in patients affected by short bowel syndrome or necrotizing enterocolitis reflects D-lactic overproduction. Therefore, there is a need for a reliable and sensitive method able to detect D-lactic acid even at subclinical elevation levels. A new and highly sensitive method for the simultaneous determination of L- and D-lactic acid by a two-step procedure has been developed. This method is based on the concentration of lactic acid enantiomers from urine by supported liquid extraction followed by high-performance liquid chromatography-tandem mass spectrometry. The separation was achieved by the use of an Astec Chirobiotic? R chiral column under isocratic conditions. The calibration curves were linear over the ranges of 2-400 and 0.5-100 µmol/L respectively for L- and D-lactic acid. The limit of detection of D-lactic acid was 0.125 µmol/L and its limit of quantification was 0.5 µmol/L. The overall accuracy and precision were well within 10% of the nominal values. The developed method is suitable for production of reference values in children and could be applied for accurate routine analysis.

Lack of original antigenic sin in recall CD8(+) T cell responses.

In the real world, mice and men are not immunologically naive, having been exposed to numerous antigenic challenges. Prior infections sometimes negatively impact the response to a subsequent infection. This can occur in serial infections with pathogens sharing cross-reactive Ags. At the T cell level it has been proposed that preformed memory T cells, which cross-react with low avidity to epitopes presented in subsequent infections, dampen the response of high-avidity T cells. We investigated this with a series of related MHC class-I restricted Ags expressed by bacterial and viral pathogens. In all cases, we find that high-avidity CD8(+) T cell precursors, either naive or memory, massively expand in secondary cross-reactive infections to dominate the response over low-avidity memory T cells. This holds true even when >10% of the CD8(+) T cell compartment consists of memory T cells that cross-react weakly with the rechallenge ligand. Occasionally, memory cells generated by low-avidity stimulation in a primary infection recognize a cross-reactive epitope with high avidity and contribute positively to the response to a second infection. Taken together, our data show that the phenomenon of original antigenic sin does not occur in all heterologous infections.

Precision and scaling in morphogen gradient read-out.

Morphogen gradients infer cell fate as a function of cellular position. Experiments in Drosophila embryos have shown that the Bicoid (Bcd) gradient is precise and exhibits some degree of scaling. We present experimental results on the precision of Bcd target genes for embryos with a single, double or quadruple dose of bicoid demonstrating that precision is highest at mid-embryo and position dependent, rather than gene dependent. This confirms that the major contribution to precision is achieved already at the Bcd gradient formation. Modeling this dynamic process, we investigate precision for inter-embryo fluctuations in different parameters affecting gradient formation. Within our modeling framework, the observed precision can only be achieved by a transient Bcd profile. Studying different extensions of our modeling framework reveals that scaling is generally position dependent and decreases toward the posterior pole. Our measurements confirm this trend, indicating almost perfect scaling except for anterior most expression domains, which overcompensate fluctuations in embryo length.

Conduit artery compliance and distensibility are not necessarily reduced in hypertension.

The goal of this study was to investigate whether the elastic behavior of conduit arteries of humans or rats is altered as a result of concomitant hypertension. Forearm arterial cross-sectional compliance-pressure curves were determined noninvasively by means of a high precision ultrasonic echo-tracking device coupled to a photoplethysmograph (Finapres system) allowing simultaneous arterial diameter and finger blood pressure monitoring. Seventeen newly diagnosed hypertensive patients with a humeral blood pressure of 163/103 +/- 4.4/2.2 mm Hg (mean +/- SEM) and 17 age- and sex-matched normotensive controls with a humeral blood pressure of 121/77 +/- 3.2/1.9 mm Hg were included in the study. Compliance-pressure curves were also established at the carotid artery of 16-week-old anesthetized spontaneously hypertensive rats (n = 14) as well as Wistar-Kyoto normotensive animals (n = 15) using the same echo-tracking device. In these animals, intra-arterial pressure was monitored in the contralateral carotid artery. Mean blood pressures averaged 197 +/- 4 and 140 +/- 3 mm Hg in the hypertensive and normotensive rats, respectively. Despite the considerable differences in blood pressure, the diameter-pressure and cross-sectional compliance-pressure and distensibility-pressure curves were not different when hypertensive patients or animals were compared with their respective controls. These results suggest that the elastic behavior of a medium size muscular artery (radial) in humans and of an elastic artery (carotid) in rats is not necessarily altered by an increase in blood pressure.

High precision anatomy for MEG.

Precise MEG estimates of neuronal current flow are undermined by uncertain knowledge of the head location with respect to the MEG sensors. This is either due to head movements within the scanning session or systematic errors in co-registration to anatomy. Here we show how such errors can be minimized using subject-specific head-casts produced using 3D printing technology. The casts fit the scalp of the subject internally and the inside of the MEG dewar externally, reducing within session and between session head movements. Systematic errors in matching to MRI coordinate system are also reduced through the use of MRI-visible fiducial markers placed on the same cast. Bootstrap estimates of absolute co-registration error were of the order of 1mm. Estimates of relative co-registration error were <1.5mm between sessions. We corroborated these scalp based estimates by looking at the MEG data recorded over a 6month period. We found that the between session sensor variability of the subject's evoked response was of the order of the within session noise, showing no appreciable noise due to between-session movement. Simulations suggest that the between-session sensor level amplitude SNR improved by a factor of 5 over conventional strategies. We show that at this level of coregistration accuracy there is strong evidence for anatomical models based on the individual rather than canonical anatomy; but that this advantage disappears for errors of greater than 5mm. This work paves the way for source reconstruction methods which can exploit very high SNR signals and accurate anatomical models; and also significantly increases the sensitivity of longitudinal studies with MEG.

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.

BACKGROUND: The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have developed a system which extracts information from the scientific literature for the most frequently annotated PTMs in UniProtKB. RESULTS: The procedure uses a pattern-matching and rule-based approach to extract sentences with information on the type and site of modification. A ranked list of protein candidates for the modification is also provided. For PTM extraction, precision varies from 57% to 94%, and recall from 75% to 95%, according to the type of modification. The procedure was used to track new publications on PTMs and to recover potential supporting evidence for phosphorylation sites annotated based on the results of large scale proteomics experiments. CONCLUSIONS: The information retrieval and extraction method we have developed in this study forms the basis of a simple tool for the manual curation of protein post-translational modifications in UniProtKB/Swiss-Prot. Our work demonstrates that even simple text-mining tools can be effectively adapted for database curation tasks, providing that a thorough understanding of the working process and requirements are first obtained. This system can be accessed at http://eagl.unige.ch/PTM/.

Equilibrium curves and growth models to deal with forests in transition to uneven-aged structure : application in two sample stands

Abstract

Evaluation of Low-Cost Treatments on Rural Two-Lane Curves, TR-579, 2012

The objective of this project was to evaluate low-cost measures to reduce speeds on high-crash horizontal curves. The researchers evaluated two low-cost treatments in Iowa to determine their effectiveness in reducing speeds on rural two-lane roadways. This report summarizes how the research team selected sites and collected data, and the results. The team selected six sites. Retroreflective post treatments were added to existing chevrons at four sites and on-pavement curve markings were added at two sites. The researchers collected speed data before and after installation of the two treatments. The study compared several speed metrics to assess the effectiveness of the treatments. Overall, both were moderately effective in reducing speeds. The most significant impact of the treatments was in reducing the percentage of vehicles traveling over the posted or advisory speed by 5, 10, 15, or 20 or more mph. This result suggests that the treatments are most effective in reducing high-end speeds.

Speed-cohesion trade-offs in collective decision making in ants and the concept of precision in animal behaviour

In decision making, speed-accuracy trade-offs are well known and often inevitable because accuracy depends on being well informed and gathering information takes time. However, trade-offs between speed and cohesion, that is the degree to which a group remains together as a single entity, as a result of their decision making, have been comparatively neglected. We combine theory and experimentation to show that in decision-making systems, speed-cohesion trade-offs are a natural complement to speed-accuracy trade-offs and are therefore of general importance. We then analyse the decision performance of 32 rock ant, Temnothorax albipennis, colonies in experiments in which accuracy of collective decision making was held constant, but time urgency varied. These experiments reveal for the first time an adaptive speed-cohesion trade-off in collective decision making and how this is achieved. In accord with different time constraints, colonies can decide quickly, at the cost of social unity, or they can decide slowly with much greater cohesion. We discuss the similarity between cohesion and the term precision as used in statistics and engineering. This emphasizes the generality of speed versus cohesion/precision trade-offs in decision making and decision implementation in other fields within animal behaviour such as sexually selected motor displays and even certain aspects of birdsong. We also suggest that speed versus precision trade-offs may occur when individuals within a group need to synchronize their activity, and in collective navigation, cooperative hunting and in certain escape behaviours.

Site quality curves for birch stands in north-western Spain

Abstract

Interlaboratory Study to Determine the Precision of the MIT Scan T2 for PCC Pavement Thickness, MLR 14-01, 2015

The MIT Scan T2 device has been implemented in Iowa as a new method for determining PCC pavement thickness compliance. The T2 device utilizes a magnetic pulse induction technology to measure the distance from a sensor to a metal target. The objective of this project was to conduct an interlaboratory study (ASTM C802) to determine the precision of the test.Fifteen MIT Scan T2 gauges and fifteen operators performed testing on three reference platforms and nine pavement locations of varying thicknesses. The testing was conducted on October 29, 2014 at two sites near Ames, Iowa. Usable data was obtained from every operator at all locations.

Smooth height/age curves from stem analysis with linear programming

[Abstract]

High precision U/Pb zircon dating of the Chalten Plutonic Complex (Cerro Fitz Roy, Patagonia) and its relationship to arc migration in the southernmost Andes

We report new high-precision U/Pb ages and geochemical data from the Chalten Plutonic Complex to better understand the link between magmatism and tectonics in Southern Patagonia. This small intrusion located in the back-arc region east of the Patagonian Batholith provides important insights on the role of arc migration and subduction erosion. The Chalten Plutonic Complex consists of a suite of calc-alkaline gabbroic to granitic rocks, which were emplaced over 530 kyr between 16.90 +/- 0.05 Ma and 16.37 +/- 0.02 Ma. A synthesis of age and geochemical data from other intrusions in Patagonia reveals (a) striking similarities between the Chalten Plutonic Complex and the Neogene intrusions of the batholith and differences to other back-arc intrusions such as Torres del Paine (b) a distinct E-W trend of calc-alkaline magmatic activity between 20 and 17 Ma. We propose that this trend reflects the eastward migration of the magmatic arc, and the consistent age pattern between the subduction segments north and south of the Chile triple junction suggests a causal relation with a period of fast subduction of the Farallon-Nazca plate during the Early Miocene. Previously proposed flat slab models are not consistent with the present location and morphology of the Southern Patagonian Batholith. We advocate, alternatively, that migration of the magmatic arc is caused by subduction erosion due to the increasing subduction velocities during the Early Miocene.

High-precision dating and origin of synsedimentary volcanism in the Late Carboniferous Salvan-Dorenaz basin (Aiguilles-Rouges Massif, Western Alps)

Late Variscan volcanic activity is documented in the Late Carboniferous Salvan-Dorenaz sedimentary basin and in the neighboring basement units of the Aiguilles-Rouges and Mont-Blanc crystalline massifs (Western Alps). Precise U/Pb isotopic dating, zircon morphology and geochemical analyses indicate that volcanism occurred during short-lived pulses and that coexisting crustal and mantle sources were involved in the production of melts. Volcanic and subvolcanic products were emplaced along major N-S to NNE-SSW transtensional fracture zones, similar to the ones that governed intense basement exhumation and that favored the formation and filling of the Late Carboniferous Salvan-Dorenaz continental basin. In the Aiguilles-Rouges massif, dacitic flows outcropping at the base of the Salvan-Dorenaz basin erupted at 308 +/- 3 Ma; they represent the surface equivalent of the nearby Vallorcine peraluminous granite and associated rhyolitic dykes (311 +/- 17 Ma). In the Mont Blanc massif, calc-alkaline rhyolitic dykes were emplaced simultaneously (307 +/- 2 Ma) at shallow crustal levels, but they derive from deeper magma sources denoting enhanced mantellic activity. Recently identified tuffs and volcaniclastic layers embedded at different levels of the Salvan-Dorenaz stratigraphic record testify a 295 +3/-4 Ma old episode of highly explosive volcanism from distant volcanic centers, possibly located in the Aar-Gotthard massifs (Central Alps). Their zircon typology is highly heterogeneous. documenting wall-rock contamination of the melts and/or admixture of crustal sediments, whereas consistent subpopulations point to high-temperature magmas of deep-seated origin and alkaline affinity. The dated volcanic layers from the Salvan-Dorenaz basin set the beginning of the detrital sedimentation at 308 +/- 3 Ma and constrain the deposition of 1.5-1.7 km thick of elastic sediments within a time span of 10-15 Ma. These results infer minimum, long-term subsidence rates during basin evolution in the order of >0.1 mm/a, while in the surrounding basement units estimated exhumation rates are in the range of 1 mm/a. All dated rocks contain inherited zircon populations about 350, 450 or 600 Ma old.