The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Comparison of Setting Time Measured Using Ultrasonic Wave Propagation with Saw-Cutting Times on Pavements, TR-675, 2015

At present, there is little fundamental guidance available to assist contractors in choosing when to schedule saw cuts on joints. To conduct pavement finishing and sawing activities effectively, however, contractors need to know when a concrete mixture is going to reach initial set, or when the sawing window will open. Previous research investigated the use of the ultrasonic pulse velocity (UPV) method to predict the saw-cutting window for early entry sawing. The results indicated that the method has the potential to provide effective guidance to contractors as to when to conduct early entry sawing. The aim of this project was to conduct similar work to observe the correlation between initial setting and conventional sawing time. Sixteen construction sites were visited in Minnesota and Missouri over a two-year period. At each site, initial set was determined using a p-wave propagation technique with a commercial device. Calorimetric data were collected using a commercial semi-adiabatic device at a majority of the sites. Concrete samples were collected in front of the paver and tested using both methods with equipment that was set up next to the pavement during paving. The data collected revealed that the UPV method looks promising for early entry and conventional sawing in the field, both early entry and conventional sawing times can be predicted for the range of mixtures tested.

The diagnosis of chronic inflammatory demyelinating polyneuropathy: a Delphi-method approach.

The diagnosis of chronic inflammatory demyelinating polyneuropathy (CIDP) is based on a set of clinical and neurophysiological parameters. However, in clinical practice, CIDP remains difficult to diagnose in atypical cases. In the present study, 32 experts from 22 centers (the French CIDP study group) were asked individually to score four typical, and seven atypical, CIDP observations (TOs and AOs, respectively) reported by other physicians, according to the Delphi method. The diagnoses of CIDP were confirmed by the group in 96.9 % of the TO and 60.1 % of the AO (p < 0.0001). There was a positive correlation between the consensus of CIDP diagnosis and the demyelinating features (r = 0.82, p < 0.004). The European CIDP classification was used in 28.3 % of the TOs and 18.2 % of the AOs (p < 0.002). The French CIDP study group diagnostic strategy was used in 90 % of the TOs and 61 % of the AOs (p < 0.0001). In 3 % of the TOs and 21.6 % of the AOs, the experts had difficulty determining a final diagnosis due to a lack of information. This study shows that a set of criteria and a diagnostic strategy are not sufficient to reach a consensus for the diagnosis of atypical CIDP in clinical practice.

A simple halide-to-anion exchange method for heteroaromatic salts and ionic liquids

A broad and simple method permitted halide ions in quaternary heteroaromatic and ammonium salts to be exchanged for a variety of anions using an anion exchange resin (A− form) in non-aqueous media. The anion loading of the AER (OH− form) was examined using two different anion sources, acids or ammonium salts, and changing the polarity of the solvents. The AER (A− form) method in organic solvents was then applied to several quaternary heteroaromatic salts and ILs, and the anion exchange proceeded in excellent to quantitative yields, concomitantly removing halide impurities. Relying on the hydrophobicity of the targeted ion pair for the counteranion swap, organic solvents with variable polarity were used, such as CH3OH, CH3CN and the dipolar nonhydroxylic solvent mixture CH3CN:CH2Cl2 (3:7) and the anion exchange was equally successful with both lipophilic cations and anions.

Analysis of Markers for Recent Alcohol Consumption by Capillary Zone Electrophoresis and an Immunochemical Method

Le but de ce travail doctoral était le développement de méthodes analytiques pour la détermination dethyl glucuronide et dethyl sulfate. Ces deux substances sont des métabolites directs de lethanol qui peuvent être détectées pendant des heures jusqu'à des jours dans des fluides corporels, après que léthanol ait été complètement éliminé du corps humain. Ce sont donc des marqueurs de consommation récente d'alcool.La majorité des expériences ont été effectuées en utilisant l'électrophorèse capillaire. Il était envisagé de fournir des méthodes utilisables dans des laboratoires de routine. Des méthodes électrophorétiques ont été développées et optimisées pour la détermination dethyl sulfate dans le sérum et l'urine ainsi que pour lethyl glucuronide dans le sérum. Lethyl glucuronide urinaire a pu être déterminé par un immunoassay commerciale qui a en plus été adapté avec succès pour des échantillons de sérum. Avec toutes ces méthodes d'analyse il était possible d'observer les deux marqueurs de consommation d'alcool récente, même une consommation aussi basse qu'un verre de boissons alcooliques.Finalement, une étude englobant plus de 100 échantillons aété effectuée avec l'ambition de déterminer les valeurs de référence pour lethyl glucuronide dans le sérum et l'urine. De plus, la nécessité de normaliser les échantillons d'urine par rapport à la dilution a été investiguée. Grâce à cette étude des valeurs de cut-off et une base statistique pour l'interprétation probabiliste ont pu être proposées.

Atrial arrhythmias in adult patients with right- versus left-sided congenital heart disease anomalies.

Atrial arrhythmias (AAs) are a common complication in adult patients with congenital heart disease. We sought to compare the lifetime prevalence of AAs in patients with right- versus left-sided congenital cardiac lesions and their effect on the prognosis. A congenital heart disease diagnosis was assigned using the International Disease Classification, Ninth Revision, diagnostic codes in the administrative databases of Quebec, from 1983 to 2005. Patients with AAs were those diagnosed with an International Disease Classification, Ninth Revision, code for atrial fibrillation or intra-atrial reentry tachycardia. To ensure that the diagnosis of AA was new, a washout period of 5 years after entry into the database was used, a period during which the patient could not have received an International Disease Classification, Ninth Revision, code for AA. The cumulative lifetime risk of AA was estimated using the Practical Incidence Estimators method. The hazard ratios (HRs) for mortality, morbidity, and cardiac interventions were compared between those with right- and left-sided lesions after adjustment for age, gender, disease severity, and cardiac risk factors. In a population of 71,467 patients, 7,756 adults developed AAs (isolated right-sided, 2,229; isolated left-sided, 1,725). The lifetime risk of developing AAs was significantly greater in patients with right- sided than in patients with left-sided lesions (61.0% vs 55.4%, p <0.001). The HR for mortality and the development of stroke or heart failure was similar in both groups (HR 0.96, 95% confidence interval [CI] 0.86 to 1.09; HR 0.94, 95% CI 0.80 to 1.09; and HR 1.10, 95% CI 0.98 to 1.23, respectively). However, the rates of cardiac catheterization (HR 0.63, 95% CI 0.55 to 0.72), cardiac surgery (HR 0.40, 95% CI 0.36 to 0.45), and arrhythmia surgery (HR 0.77, 95% CI 0.6 to 0.98) were significantly less for patients with right-sided lesions. In conclusion, patients with right-sided lesions had a greater lifetime burden of AAs. However, their morbidity and mortality were no less than those with left-sided lesions, although the rate of intervention was substantially different.

A new method to simulate the hydrological state of soil under natural conditions

Micro, macro and mesofauna in the soil often respond to fluctuating environmental conditions, resulting in changes of abundance and community structure. Effects of changing soil parameters are normally determined with samples taken in the field and brought to the laboratory, i.e. where natural environmental conditions may not apply. We devised a method (STAFD - soil tubes for artificial flood and drought), which simulates the hydrological state of soil in situ using implanted cores. Control tubes were compared with treatment tubes in which floods of 15, 30, 60 and 90 days, and droughts of 60, 90 and 120 days were simulated in the field. Flooding and drought were found to reduce number of individuals in all soil faunal groups, but the response to drought was slower and not in proportion to the expected decrease of the water content. The results of the simulated floods in particular show the value of the STAFD method for the investigation of such extreme events in natural habitats.

Mineralogical alteration of artificial meteorites during atmospheric entry. The STONE-5 experiment

The generic concept of the artificial meteorite experiment STONE is to fix rock samples bearing microorganisms on the heat shield of a recoverable space capsule and to study their modifications during atmospheric re-entry. The STONE-5 experiment was performed mainly to answer astrobiological questions. The rock samples mounted on the heat shield were used (i) as a carrier for microorganisms and (ii) as internal control to verify whether physical conditions during atmospheric re-entry were comparable to those experienced by "real" meteorites. Samples of dolerite (an igneous rock), sandstone (a sedimentary rock), and gneiss impactite from Haughton Crater carrying endolithic cyanobacteria were fixed to the heat shield of the unmanned recoverable capsule FOTON-M2. Holes drilled on the back side of each rock sample were loaded with bacterial and fungal spores and with dried vegetative cryptoendoliths. The front of the gneissic sample was also soaked with cryptoendoliths. <p>The mineralogical differences between pre- and post-flight samples are detailed. Despite intense ablation resulting in deeply eroded samples, all rocks in part survived atmospheric re-entry. Temperatures attained during re-entry were high enough to melt dolerite, silica, and the gneiss impactite sample. The formation of fusion crusts in STONE-5 was a real novelty and strengthens the link with real meteorites. The exposed part of the dolerite is covered by a fusion crust consisting of silicate glass formed from the rock sample with an admixture of holder material (silica). Compositionally, the fusion crust varies from silica-rich areas (undissolved silica fibres of the holder material) to areas whose composition is "basaltic". Likewise, the fusion crust on the exposed gneiss surface was formed from gneiss with an admixture of holder material. The corresponding composition of the fusion crust varies from silica-rich areas to areas with "gneiss" composition (main component potassium-rich feldspar). The sandstone sample was retrieved intact and did not develop a fusion crust. Thermal decomposition of the calcite matrix followed by disintegration and liberation of the silicate grains prevented the formation of a melt.</p> <p>Furthermore, the non-exposed surface of all samples experienced strong thermal alterations. Hot gases released during ablation pervaded the empty space between sample and sample holder leading to intense local heating. The intense heating below the protective sample holder led to surface melting of the dolerite rock and to the formation of calcium-silicate rims on quartz grains in the sandstone sample. (c) 2008 Elsevier Ltd. All rights reserved.</p>

Suprachoroidal electrotransfer: a nonviral gene delivery method to transfect the choroid and the retina without detaching the retina.

Photoreceptors and retinal pigment epithelial cells (RPE) targeting remains challenging in ocular gene therapy. Viral gene transfer, the only method having reached clinical evaluation, still raises safety concerns when administered via subretinal injections. We have developed a novel transfection method in the adult rat, called suprachoroidal electrotransfer (ET), combining the administration of nonviral plasmid DNA into the suprachoroidal space with the application of an electrical field. Optimization of injection, electrical parameters and external electrodes geometry using a reporter plasmid, resulted in a large area of transfected tissues. Not only choroidal cells but also RPE, and potentially photoreceptors, were efficiently transduced for at least a month when using a cytomegalovirus (CMV) promoter. No ocular complications were recorded by angiographic, electroretinographic, and histological analyses, demonstrating that under selected conditions the procedure is devoid of side effects on the retina or the vasculature integrity. Moreover, a significant inhibition of laser induced-choroidal neovascularization (CNV) was achieved 15 days after transfection of a soluble vascular endothelial growth factor receptor-1 (sFlt-1)-encoding plasmid. This is the first nonviral gene transfer technique that is efficient for RPE targeting without inducing retinal detachment. This novel minimally invasive nonviral gene therapy method may open new prospects for human retinal therapies.

Role of DC-SIGN in Lassa virus entry into human dendritic cells.

The arenavirus Lassa virus (LASV) causes a severe hemorrhagic fever with high mortality in humans. Antigen-presenting cells, in particular dendritic cells (DCs), are early and preferred targets of LASV, and their productive infection contributes to the virus-induced immunosuppression observed in fatal disease. Here, we characterized the role of the C-type lectin DC-specific ICAM-3-grabbing nonintegrin (DC-SIGN) in LASV entry into primary human DCs using a chimera of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) expressing the LASV glycoprotein (rLCMV-LASVGP). We found that differentiation of human primary monocytes into DCs enhanced virus attachment and entry, concomitant with the upregulation of DC-SIGN. LASV and rLCMV-LASVGP bound to DC-SIGN via mannose sugars located on the N-terminal GP1 subunit of LASVGP. We provide evidence that DC-SIGN serves as an attachment factor for rLCMV-LASVGP in monocyte-derived immature dendritic cells (MDDC) and can accelerate the capture of free virus. However, in contrast to the phlebovirus Uukuniemi virus (UUKV), which uses DC-SIGN as an authentic entry receptor, productive infection with rLCMV-LASVGP was less dependent on DC-SIGN. In contrast to the DC-SIGN-mediated cell entry of UUKV, entry of rLCMV-LASVGP in MDDC was remarkably slow and depended on actin, indicating the use of different endocytotic pathways. In sum, our data reveal that DC-SIGN can facilitate cell entry of LASV in human MDDC but that its role seems distinct from the function as an authentic entry receptor reported for phleboviruses.

Iowa Fen Rapid Assessment Method for Wetlands v. 1 Quantitative Rating, 2016

Rapid assessment methods are valuable tools for collecting information about the quality and status of natural systems. However, they are not a substitute for detailed surveys of those systems. Users of this method should consider that the method may under-score or over-score the site that’s assessed, especially when the site is not a typical fen (i.e. a sedge meadow could score lower than fens, but in-fact be a relatively high quality sedge meadow). This assessment can be used throughout most of the spring, summer and fall period, however the ideal “index period” would be from late May through early October when native plant communities, as well as invasive species, are most apparent.

A fast automated screening method for the detection of blood transfusion in sports.

Currently, there is no simple direct screening method for the misuse of blood transfusions in sports. In this study, we investigated whether the measurement of iron in EDTA-plasma can serve as biomarker for such purpose. Our results revealed an increase of the plasma iron level up to 25-fold 6 h after blood re-infusion. The variable remained elevated 10-fold one day after the procedure. A specificity of 100% and a sensitivity of 93% were obtained with a proposed threshold at 45 µg/dL of plasma iron. Therefore, our test could be used as a simple, cost effective biomarker for the screening for blood transfusion misuse in sports. Copyright © 2014 John Wiley & Sons, Ltd.

Evaluation of the multicriteria approval method for timber-harvesting group decision support

Abstract

A need for determination of arsenic species at low levels in cereal-based food and infant cereals. Validation of a method by LC-ICPMS.

The present study arose from the need to determine inorganic arsenic (iAs) at low levels in cereal-based food. Validated methods with a low limit of detection (LOD) are required to analyse these kinds of food. An analytical method for the determination of iAs, methylarsonic acid (MA) and dimethylarsinic acid (DMA) in cereal-based food and infant cereals is reported. The method was optimised and validated to achieve low LODs. Ion chromatography-inductively coupled plasma mass spectrometry (LC-ICPMS) was used for arsenic speciation. The main quality parameters were established. To expand the applicability of the method, different cereal products were analysed: bread, biscuits, breakfast cereals, wheat flour, corn snacks, pasta and infant cereals. The total and inorganic arsenic content of 29 cereal-based food samples ranged between 3.7-35.6 and 3.1-26.0 microg As kg-1, respectively. The present method could be considered a valuable tool for assessing inorganic arsenic contents in cereal-based foods.