Phosphorus saturation of Finnish soils : evaluating an easy oxalate extraction method

Selostus: Alumiini- ja rautaoksidien fosforikyllästysasteen arvioiminen suomalaisista peltomaista

DNA extraction using the QIAsymphony: Evaluation of PCR inhibitor removal

The goal of this study was to compare the quantity and purity of DNA extracted from biological tracesusing the QIAsymphony robot with that of the manual QIAamp DNA mini kit currently in use in ourlaboratory. We found that the DNA yield of robot was 1.6-3.5 times lower than that of the manualprotocol. This resulted in a loss of 8% and 29% of the alleles correctly scored when analyzing 1/400 and 1/800 diluted saliva samples, respectively. Specific tests showed that the QIAsymphony was at least 2-16times more efficient at removing PCR inhibitors. The higher purity of the DNA may therefore partlycompensate for the lower DNA yield obtained. No case of cross-contamination was observed amongsamples. After purification with the robot, DNA extracts can be automatically transferred in 96-wellsplates, which is an ideal format for subsequent RT-qPCR quantification and DNA amplification. Lesshands-on time and reduced risk of operational errors represent additional advantages of the robotic platform.

Transvaginal specimen extraction in colorectal surgery: current state of the art.

Aim  Background The expected benefit of transvaginal specimen extraction is reduced incision-related morbidity. Objectives A systematic review of transvaginal specimen extraction in colorectal surgery was carried out to assess this expectation. Method  Search strategy The following keywords, in various combinations, were searched: NOSE (natural orifices specimen extraction), colorectal, colon surgery, transvaginal, right hemicolectomy, left hemicolectomy, low anterior resection, sigmoidectomy, ileocaecal resection, proctocolectomy, colon cancer, sigmoid diverticulitis and inflammatory bowel diseases. Selection criteria Selection criteria included large bowel resection with transvaginal specimen extraction, laparoscopic approach, human studies and English language. Exclusion criteria were experimental studies and laparotomic approach or local excision. All articles published up to February 2011 were included. Results  Twenty-three articles (including a total of 130 patients) fulfilled the search criteria. The primary diagnosis was colorectal cancer in 51% (67) of patients, endometriosis in 46% (60) of patients and other conditions in the remaining patients. A concurrent gynaecological procedure was performed in 17% (22) of patients. One case of conversion to laparotomy was reported. In two patients, transvaginal extraction failed. In left- and right-sided resections, the rate of severe complications was 3.7% and 2%, respectively. Two significant complications, one of pelvic seroma and one of rectovaginal fistula, were likely to have been related to transvaginal extraction. The degree of follow up was specified in only one study. Harvested nodes and negative margins were adequate and reported in 70% of oncological cases. Conclusion  Vaginal extraction of a colorectal surgery specimen shows potential benefit, particularly when associated with a gynaecological procedure. Data from prospective randomized trials are needed to support the routine use of this technique.

Ex-PRESS R-50 miniature glaucoma implant insertion under the conjunctiva combined with cataract extraction

Rapport de synthèse : Le glaucome à angle ouvert est une neuropathie optique chronique progressive pour laquelle de nombreux traitements tant médicaux que chirurgicaux ont été proposés. La prise en charge chirurgicale s'articule principalement autour de deux chirurgies filtrantes, la trabéculectomie et la sclérectomie profonde avec implant de collagène. Cependant, les complications postopératoires de ces deux interventions étant relativement fréquentes, la recherche s'est orientée vers des traitements alternatifs dont la mise en place de micro-drains. Ces implants de drainage diminuent la pression intraoculaire en créant un court-circuit du flux d'humeur aqueuse de la chambre antérieure vers l'espace sous-conjonctival avec formation d'une bulle de filtration. L'implant Ex-PRESS R-50 est un implant miniature (2.5 mm de long pour 400 µm de diamètre) en acier inoxydable et biocompatible. La présente étude s'est proposée d'étudier l'efficacité et la sécurité de l'implant miniature Ex-Press R-50 lors d'une opération combinée cataracte-glaucome. Trente-cinq yeux de 35 patients (âge moyen: 75 ans) ont été inclus dans l'étude. Tous les patients ont bénéficié d'une opération de la cataracte par phacoemulsification et mise en place d'un implant de chambre postérieure suivie de l'implantation du micro-drain. Les pressions intraoculaires préopératoires et postopératoires, la meilleure acuité visuelle corrigée, le nombre de médicaments anti-glaucomateux ainsi que le type et le nombre de complications ont été évalués mensuellement puis tous les 6 mois pendant 4 ans. Le succès total a été défini par une pression postopératoire finale inférieure à 18mmHg sans traitement médical associé, le succès partiel par une pression postopératoire finale inférieure à 18mmHg avec ou sans traitement médical associé.. Le suivi moyen a été de 36.9 mois avec une baisse de la pression intraoculaire significative d'environ 25%. Une augmentation de l'acuité visuelle a été observée après l'opération de la cataracte et le nombre de médicaments anti-glaucomateux a été réduit de 57%. Dix patients ont bénéficié d'un traitement supplémentaire de la bulle de filtration par injection d'anti-métabolite (mitomycine C). Nous avons observé 8 complications majeures (4 érosions conjonctivales et 4 obstructions de l'orifice interne du micro-drain), toutes suivies de l'ablation de l'implant et de la réalisation d'une chirurgie classique du glaucome. En se basant sur les courbes de Kaplan-Meier à 48 mois, le taux de succès total était de 32.7% et le succès partiel de 53.7%. Nous pouvons conclure suite à ce travail que l'implant miniature Ex-PRESS R-50 est associé à un nombre trop élevé de complications, même si les cas non compliqués ont bénéficié d'une baisse significative de la pression intraoculaire. La modification de l'architecture du micro-drain ainsi que de la technique chirurgicale devrait augmenter le taux de succès.

Determination of the Enantiomers of Mianserin and its Metabolites in Plasma by Capillary Electrophoresis After Liquid-Liquid Extraction and On-Column Sample Preconcentration

Capillary electrophoresis has drawn considerable attention in the past few years, particularly in the field of chiral separations because of its high separation efficiency. However, its routine use in therapeutic drug monitoring is hampered by its low sensitivity due to a short optical path. We have developed a capillary zone electrophoresis (CZE) method using 2mM of hydroxypropyl-β-cyclodextrin as a chiral selector, which allows base-to-base separation of the enantiomers of mianserin (MIA), desmethylmianserin (DMIA), and 8-hydroxymianserin (OHMIA). Through the use of an on-column sample concentration step after liquid-liquid extraction from plasma and through the presence of an internal standard, the quantitation limits were found to be 5 ng/mL for each enantiomer of MIA and DMIA and 15 ng/mL for each enantiomer of OHMIA. To our knowledge, this is the first published CE method that allows its use for therapeutic monitoring of antidepressants due to its sensitivity down to the low nanogram range. The variability of the assays, as assessed by the coefficients of variation (CV) measured at two concentrations for each substance, ranged from 2 to 14% for the intraday (eight replicates) and from 5 to 14% for the interday (eight replicates) experiments. The deviations from the theoretical concentrations, which represent the accuracy of the method, were all within 12.5%. A linear response was obtained for all compounds within the range of concentrations used for the calibration curves (10-150 ng/mL for each enantiomer of MIA and DMIA and 20-300 ng/mL for each enantiomer of OHMIA). Good correlations were calculated between [(R) + (S)]-MIA and DMIA concentrations measured in plasma samples of 20 patients by a nonchiral gas chromatography method and CZE, and between the (R)- and (S)-concentrations of MIA and DMIA measured in plasma samples of 37 patients by a previously described chiral high-performance liquid chromatography method and CZE. Finally, no interference was noted from more than 20 other psychotropic drugs. Thus, this method, which is both sensitive and selective, can be routinely used for therapeutic monitoring of the enantiomers of MIA and its metabolites. It could be very useful due to the demonstrated interindividual variability of the stereoselective metabolism of MIA.

Polyethylene glycol and polyvinylpirrolidone effect on bacterial rRNA extraction and hybridization from cells exposed to tannins

In order to detect fluctuations in ruminal microbial populations due to forage tannins using 16S ribosomal RNA (rRNA) probes, recovery of intact rRNA is required. The objective of this work was to evaluate the effect of polyethylene glycol (PEG) and polyvinylpirrolidone (PVP) on extraction of bacterial rRNA, in the presence of tannins from tropical legume forages and other sources, that hybridize with oligonucleotide probes. Ruminococcus albus 8 cells were exposed to 8 g/L tannic acid or 1 g/L condensed tannins extracted from Acacia angustissima, banana (Musa sp.) skin, Desmodium ovalifolium, red grape (Vitis vinifera) skin and Inga edulis, or no tannins. Cells were rinsed with Tris buffer pH 7 containing either 8% PEG or 6% PVP prior to cell lysis. Total RNA samples rinsed with either PEG or PVP migrated through denaturing agarose gels. The 16S rRNA bands successfully hybridized with a R. albus species-specific oligonucleotide probe, regardless of tannin source. The effect of rinsing buffers on the density of 16S rRNA bands, as well as on the hybridization signals was compared. There were significant effects (P<0.01) when the controls were compared to either buffer treatments due to tannin type, buffer used and the interaction of tannin type and buffer. The significant interaction indicates the influence of tannin type on the parameters evaluated.

Self-organization mechanisms for the formation on nearshore crescentic and transverse sand bars

The formation and development of transverse and crescentic sand bars in the coastal marine environment has been investigated by means of a nonlinear numerical model based on the shallow-water equations and on a simpli ed sediment transport parameterization. By assuming normally approaching waves and a saturated surf zone, rhythmic patterns develop from a planar slope where random perturbations of small amplitude have been superimposed. Two types of bedforms appear: one is a crescentic bar pattern centred around the breakpoint and the other, herein modelled for the rst time, is a transverse bar pattern. The feedback mechanism related to the formation and development of the patterns can be explained by coupling the water and sediment conservation equations. Basically, the waves stir up the sediment and keep it in suspension with a certain cross-shore distribution of depth-averaged concentration. Then, a current flowing with (against) the gradient of sediment concentration produces erosion (deposition). It is shown that inside the surf zone, these currents may occur due to the wave refraction and to the redistribution of wave breaking produced by the growing bedforms. Numerical simulations have been performed in order to understand the sensitivity of the pattern formation to the parameterization and to relate the hydro-morphodynamic input conditions to which of the patterns develops. It is suggested that crescentic bar growth would be favoured by high-energy conditions and ne sediment while transverse bars would grow for milder waves and coarser sediment. In intermediate conditions mixed patterns may occur.

Bump time-frequency toolbox: a toolbox for time-frequency oscillatory bursts extraction in electrophysiological signals

Background: oscillatory activity, which can be separated in background and oscillatory burst pattern activities, is supposed to be representative of local synchronies of neural assemblies. Oscillatory burst events should consequently play a specific functional role, distinct from background EEG activity – especially for cognitive tasks (e.g. working memory tasks), binding mechanisms and perceptual dynamics (e.g. visual binding), or in clinical contexts (e.g. effects of brain disorders). However extracting oscillatory events in single trials, with a reliable and consistent method, is not a simple task. Results: in this work we propose a user-friendly stand-alone toolbox, which models in a reasonable time a bump time-frequency model from the wavelet representations of a set of signals. The software is provided with a Matlab toolbox which can compute wavelet representations before calling automatically the stand-alone application. Conclusion: The tool is publicly available as a freeware at the address: http:// www.bsp.brain.riken.jp/bumptoolbox/toolbox_home.html

Investigation of ICA algorithms for feature extraction of EEG signals in discrimination of Alzheimer disease

In this paper we present a quantitative comparisons of different independent component analysis (ICA) algorithms in order to investigate their potential use in preprocessing (such as noise reduction and feature extraction) the electroencephalogram (EEG) data for early detection of Alzhemier disease (AD) or discrimination between AD (or mild cognitive impairment, MCI) and age-match control subjects.

High-throughput and sensitive quantitation of plasma catecholamines by ultraperformance liquid chromatography-tandem mass spectrometry using a solid phase microwell extraction plate.

Plasma catecholamines provide a reliable biomarker of sympathetic activity. The low circulating concentrations of catecholamines and analytical interferences require tedious sample preparation and long chromatographic runs to ensure their accurate quantification by HPLC with electrochemical detection. Published or commercially available methods relying on solid phase extraction technology lack sensitivity or require derivatization of catecholamine by hazardous reagents prior to tandem mass spectrometry (MS) analysis. Here, we manufactured a novel 96-well microplate device specifically designed to extract plasma catecholamines prior to their quantification by a new and highly sensitive ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. Processing time, which included sample purification on activated aluminum oxide and elution, is less than 1 h per 96-well microplate. The UPLC-MS/MS analysis run time is 2.0 min per sample. This UPLC-MS/MS method does not require a derivatization step, reduces the turnaround time by 10-fold compared to conventional methods used for routine application, and allows catecholamine quantification in reduced plasma sample volumes (50-250 μL, e.g., from children and mice).

Evaluation of Dowel Bar Retrofits for Local Road Pavements, TR-520, 2008

As truck traffic on Iowa secondary roads has increased, engineers have moved to concrete pavements of greater depths. Early designs included thickened edge pavements and depths of seven inches or greater. The designs typically did not have load transfer devices installed in the transverse joints and relied on aggregate interlock for this purpose. In some cases, aggregate interlock was not adequate to deal with the soils and traffic conditions and faulting of the joints has begun to appear. Engineers are now faced with the need to install or retrofit load transfer in the joints to preserve the pavements. Questions associated with this decision range from the type of dowel material to dowel diameter, spacing, number of bars, placement method, and construction techniques to be used to assure reduction or elimination of faulting. Buena Vista County constructed a dowel bar retrofit project on one mile of road. The plan called for addition of the dowels (2, 3, or 4) in the outer wheel path only and surface grinding in lieu of asphalt overlay. The project included the application of elliptical- and round-shaped dowels in a rehabilitation project. Dowel material types included conventional epoxy-coated steel and fiber-reinforced polymer (FRP). This work involved the determination of relative costs in materials to be used in this type of work and performance of FRP and elliptical-shaped steel dowels in the retrofit work. The results indicate good performance from each of the bar configurations and use the results of ride and deflection testing over the research period to project the benefits that can be gained from each configuration vs. the anticipated construction costs. The reader is cautioned that this project could not relate the number of dowels required to the level of anticipated truck traffic for other roads that might be considered.