Automatic Brain Extraction in Fetal MRI using Multi-Atlas-based Segmentation

In fetal brain MRI, most of the high-resolution reconstruction algorithms rely on brain segmentation as a preprocessing step. Manual brain segmentation is however highly time-consuming and therefore not a realistic solution. In this work, we assess on a large dataset the performance of Multiple Atlas Fusion (MAF) strategies to automatically address this problem. Firstly, we show that MAF significantly increase the accuracy of brain segmentation as regards single-atlas strategy. Secondly, we show that MAF compares favorably with the most recent approach (Dice above 0.90). Finally, we show that MAF could in turn provide an enhancement in terms of reconstruction quality.

Preconcentration of copper from natural water samples using ligand-less in situ surfactant-based solid phase extraction prior to FAAS determination

In the present work, a simple and rapid ligand-less, in situ, surfactant-based solid phase extraction for the preconcentration of copper in water samples was developed. In this method, a cationic surfactant (n-dodecyltrimethylammonium bromide) was dissolved in an aqueous sample followed by the addition of an appropriate ion-pairing agent (ClO4-). Due to the interaction between the surfactant and ion-pairing agent, solid particles were formed and subsequently used for the adsorption of Cu(OH)2 and CuI. After centrifugation, the sediment was dissolved in 1.0 mL of 1 mol L-1 HNO3 in ethanol and aspirated directly into the flame atomic absorption spectrometer. In order to obtain the optimum conditions, several parameters affecting the performance of the LL-ISS-SPE, including the volumes of DTAB, KClO4, and KI, pH, and potentially interfering ions, were optimized. It was found that KI and phosphate buffer solution (pH = 9) could extract more than 95% of copper ions. The amount of copper ions in the water samples varied from 3.2 to 4.8 ng mL-1, with relative standard deviations of 98.5%-103%. The determination of copper in water samples was linear over a concentration range of 0.5-200.0 ng mL-1. The limit of detection (3Sb/m) was 0.1 ng mL-1 with an enrichment factor of 38.7. The accuracy of the developed method was verified by the determination of copper in two certified reference materials, producing satisfactory results.

Recovery of norbixin from a raw extraction solution of annatto pigments using colloidal gas aphrons (CGAs)

Annatto dyes are widely used in food and are finding increasing interest also for their application in the pharmaceutical and cosmetics industry. Bixin is the main pigment extracted from annatto seeds and accounts for 80% of the carotenoids in the outer coat of the seeds; norbixin being the water-soluble form of the bixin. Typically annatto dyes are extracted from the seeds by mechanical means or solutions of alkali, edible oil or organic solvents, or a combination of the two depending on the desired final product. In this work CGAs are investigated as an alternative separation method for the recovery of norbixin from a raw extraction solution of annatto pigments in KOH. A volume of CGAs generated from a cationic surfactant (CTAB) solution is mixed with a volume of annatto solution and when the mixture is allowed to settle it separates into the top aphron phase and the bottom liquid phase. Potassium norbixinate presented in the annatto solution will interact with the surfactant in the aphron phase, which results in the effective separation of norbixin. Recovery= 94% was achieved at a CTAB to norbixin molar ratio of 3.3. In addition a mechanism of separation is proposed here based on the separation results with the cationic surfactant and an anionic surfactant (bis-2-ethyl hexyl sulfosuccinate, AOT) and measurements of surfactant to norbixin ratio in the aphron phase; electrostatic interactions between the surfactant and norbixin molecules result in the fort-nation of a coloured complex and effective separation of norbixin. (c) 2005 Elsevier B.V. All rights reserved.

A new and improved strategy combining a dispersive-solid phase extraction-based multiclass method with ultra high pressure liquid chromatography for analysis of low molecular weight polyphenols in vegetables

This paper reports on the development and optimization of a modified Quick, Easy, Cheap Effective, Rugged and Safe (QuEChERS) based extraction technique coupled with a clean-up dispersive-solid phase extraction (dSPE) as a new, reliable and powerful strategy to enhance the extraction efficiency of free low molecular-weight polyphenols in selected species of dietary vegetables. The process involves two simple steps. First, the homogenized samples are extracted and partitioned using an organic solvent and salt solution. Then, the supernatant is further extracted and cleaned using a dSPE technique. Final clear extracts of vegetables were concentrated under vacuum to near dryness and taken up into initial mobile phase (0.1% formic acid and 20% methanol). The separation and quantification of free low molecular weight polyphenols from the vegetable extracts was achieved by ultrahigh pressure liquid chromatography (UHPLC) equipped with a phodiode array (PDA) detection system and a Trifunctional High Strength Silica capillary analytical column (HSS T3), specially designed for polar compounds. The performance of the method was assessed by studying the selectivity, linear dynamic range, the limit of detection (LOD) and limit of quantification (LOQ), precision, trueness, and matrix effects. The validation parameters of the method showed satisfactory figures of merit. Good linearity (View the MathML sourceRvalues2>0.954; (+)-catechin in carrot samples) was achieved at the studied concentration range. Reproducibility was better than 3%. Consistent recoveries of polyphenols ranging from 78.4 to 99.9% were observed when all target vegetable samples were spiked at two concentration levels, with relative standard deviations (RSDs, n = 5) lower than 2.9%. The LODs and the LOQs ranged from 0.005 μg mL−1 (trans-resveratrol, carrot) to 0.62 μg mL−1 (syringic acid, garlic) and from 0.016 μg mL−1 (trans-resveratrol, carrot) to 0.87 μg mL−1 ((+)-catechin, carrot) depending on the compound. The method was applied for studying the occurrence of free low molecular weight polyphenols in eight selected dietary vegetables (broccoli, tomato, carrot, garlic, onion, red pepper, green pepper and beetroot), providing a valuable and promising tool for food quality evaluation.

A stable liquid-liquid extraction system for clavulanic acid using polymer-based aqueous two-phase systems

The partitioning of Clavulanic Acid (CA) in a novel inexpensive and stable aqueous two-phase system (ATPS) composed by poly(ethylene glycol) (PEG) and sodium polyacrylate (NaPA) has been studied. The aqueous two-phase systems are formed by mixing both polymers with a salt (NaCl or Na2SO4) and an aqueous solution of CA. The stability of CA on the presence of both polymers was investigated and it was observed that these polymers do not degrade the biomolecule. The effect of PEG-molecular size, polymer concentrations on the commercial CA partitioning has been studied, at 25 degrees C. The data showed that commercial CA was preferentially partitioned for the PEG-rich phase with a partition coefficient (K-CA) between 1 and 12 in the PEG/NaPA aqueous two phase systems supplemented with NaCl and Na2SO4. The partition to the PEG phase was increased in the systems with high polymer concentrations. Furthermore, Na2SO4 caused higher CA preference for the PEG-phase than NaCl. The systems having a composition with 10 wt.% of PEG4000, 20 wt.% of NaPA8000 and 6 wt.% of Na2SO4 were selected as the optimal ones in terms of recovery of CA from fermented broth of Streptomyces clavuligerus. The partitioning results (K-CA = 9.15 +/- 1.06) are competitive with commercial extraction methods of CA (K-CA = 11.91 +/- 2.08) which emphasizes that the system PEG/NaPA/Na2SO4 can be used as a new process to CA purification/concentration from fermented broth. (C) 2012 Elsevier B.V. All rights reserved.

DNA sequencing by delayed extraction-matrix-assisted laser desorption/ionization time of flight mass spectrometry.

Matrix-assisted laser desorption/ionization (MALDI) time of flight mass spectrometry was used to detect and order DNA fragments generated by Sanger dideoxy cycle sequencing. This was accomplished by improving the sensitivity and resolution of the MALDI method using a delayed ion extraction technique (DE-MALDI). The cycle sequencing chemistry was optimized to produce as much as 100 fmol of each specific dideoxy terminated fragment, generated from extension of a 13-base primer annealed on 40- and 50-base templates. Analysis of the resultant sequencing mixture by DE-MALDI identified the appropriate termination products. The technique provides a new non-gel-based method to sequence DNA which may ultimately have considerable speed advantages over traditional methodologies.

Screen-printed electrode based electrochemical detector coupled with ionic liquid dispersive liquid–liquid microextraction and microvolume back-extraction for determination of mercury in water samples

A novel approach is presented, whereby gold nanostructured screen-printed carbon electrodes (SPCnAuEs) are combined with in-situ ionic liquid formation dispersive liquid–liquid microextraction (in-situ IL-DLLME) and microvolume back-extraction for the determination of mercury in water samples. In-situ IL-DLLME is based on a simple metathesis reaction between a water-miscible IL and a salt to form a water-immiscible IL into sample solution. Mercury complex with ammonium pyrrolidinedithiocarbamate is extracted from sample solution into the water-immiscible IL formed in-situ. Then, an ultrasound-assisted procedure is employed to back-extract the mercury into 10 µL of a 4 M HCl aqueous solution, which is finally analyzed using SPCnAuEs. Sample preparation methodology was optimized using a multivariate optimization strategy. Under optimized conditions, a linear range between 0.5 and 10 µg L−1 was obtained with a correlation coefficient of 0.997 for six calibration points. The limit of detection obtained was 0.2 µg L−1, which is lower than the threshold value established by the Environmental Protection Agency and European Union (i.e., 2 µg L−1 and 1 µg L−1, respectively). The repeatability of the proposed method was evaluated at two different spiking levels (3 and 10 µg L−1) and a coefficient of variation of 13% was obtained in both cases. The performance of the proposed methodology was evaluated in real-world water samples including tap water, bottled water, river water and industrial wastewater. Relative recoveries between 95% and 108% were obtained.

Fluorescent microplate-based analysis of protein-DNA interactions I:immobilized protein

A simple protein-DNA interaction analysis has been developed using a high-affinity/high-specificity zinc finger protein. In essence, purified protein samples are immobilized directly onto the surface of microplate wells, and fluorescently labeled DNA is added in solution. After incubation and washing, bound DNA is detected in a standard microplate reader. The minimum sensitivity of the assay is approximately 0.2 nM DNA. Since the detection of bound DNA is noninvasive and the protein-DNA interaction is not disrupted during detection, iterative readings may be taken from the same well, after successive alterations in interaction conditions, if required. In this respect, the assay may therefore be considered real time and permits appropriate interaction conditions to be determined quantitatively. The assay format is ideally suited to investigate the interactions of purified unlabeled DNA binding proteins in a high-throughput format.

Fluorescent microplate-based analysis of protein-DNA interactions II:immobilized DNA

A simple protein-DNA interaction analysis has been developed using both a high-affinity/high-specificity zinc finger protein and a low-specificity zinc finger protein with nonspecific DNA binding capability. The latter protein is designed to mimic background binding by proteins generated in randomized or shuffled gene libraries. In essence, DNA is immobilized onto the surface of microplate wells via streptavidin capture, and green fluorescent protein (GFP)-labeled protein is added in solution as part of a crude cell lysate or protein mixture. After incubation and washing, bound protein is detected in a standard microplate reader. The minimum sensitivity of the assay is approximately 0.4 nM protein. The assay format is ideally suited to investigate the interactions of DNA binding proteins from within crude cell extracts and/or mixtures of proteins that may be encountered in protein libraries generated by codon randomization or gene shuffling.

Optical fibre-based detection of DNA hybridization

A dual-peak LPFG (long-period fibre grating), inscribed in an optical fibre, has been employed to sense DNA hybridization in real time, over a 1 h period. One strand of the DNA was immobilized on the fibre, while the other was free in solution. After hybridization, the fibre was stripped and repeated detection of hybridization was achieved, so demonstrating reusability of the device. Neither strand of DNA was fluorescently or otherwise labelled. The present paper will provide an overview of our early-stage experimental data and methodology, examine the potential of fibre gratings for use as biosensors to monitor both nucleic acid and other biomolecular interactions and then give a summary of the theory and fabrication of fibre gratings from a biological standpoint. Finally, the potential of improving signal strength and possible future directions of fibre grating biosensors will be addressed.

Phylogenetics, Ancestral State Reconstruction, And A New Infrafamilial Classification Of The Pantropical Ochnaceae (medusagynaceae, Ochnaceae S.str., Quiinaceae) Based On Five Dna Regions.

Ochnaceae s.str. (Malpighiales) are a pantropical family of about 500 species and 27 genera of almost exclusively woody plants. Infrafamilial classification and relationships have been controversial partially due to the lack of a robust phylogenetic framework. Including all genera except Indosinia and Perissocarpa and DNA sequence data for five DNA regions (ITS, matK, ndhF, rbcL, trnL-F), we provide for the first time a nearly complete molecular phylogenetic analysis of Ochnaceae s.l. resolving most of the phylogenetic backbone of the family. Based on this, we present a new classification of Ochnaceae s.l., with Medusagynoideae and Quiinoideae included as subfamilies and the former subfamilies Ochnoideae and Sauvagesioideae recognized at the rank of tribe. Our data support a monophyletic Ochneae, but Sauvagesieae in the traditional circumscription is paraphyletic because Testulea emerges as sister to the rest of Ochnoideae, and the next clade shows Luxemburgia+Philacra as sister group to the remaining Ochnoideae. To avoid paraphyly, we classify Luxemburgieae and Testuleeae as new tribes. The African genus Lophira, which has switched between subfamilies (here tribes) in past classifications, emerges as sister to all other Ochneae. Thus, endosperm-free seeds and ovules with partly to completely united integuments (resulting in an apparently single integument) are characters that unite all members of that tribe. The relationships within its largest clade, Ochnineae (former Ochneae), are poorly resolved, but former Ochninae (Brackenridgea, Ochna) are polyphyletic. Within Sauvagesieae, the genus Sauvagesia in its broad circumscription is polyphyletic as Sauvagesia serrata is sister to a clade of Adenarake, Sauvagesia spp., and three other genera. Within Quiinoideae, in contrast to former phylogenetic hypotheses, Lacunaria and Touroulia form a clade that is sister to Quiina. Bayesian ancestral state reconstructions showed that zygomorphic flowers with adaptations to buzz-pollination (poricidal anthers), a syncarpous gynoecium (a near-apocarpous gynoecium evolved independently in Quiinoideae and Ochninae), numerous ovules, septicidal capsules, and winged seeds with endosperm are the ancestral condition in Ochnoideae. Although in some lineages poricidal anthers were lost secondarily, the evolution of poricidal superstructures secured the maintenance of buzz-pollination in some of these genera, indicating a strong selective pressure on keeping that specialized pollination system.

Human Herpesvirus Infections Of The Central Nervous System: Laboratory Diagnosis Based On Dna Detection By Nested Pcr In Plasma And Cerebrospinal Fluid Samples.

Infections of the central nervous systems (CNS) present a diagnostic problem for which an accurate laboratory diagnosis is essential. Invasive practices, such as cerebral biopsy, have been replaced by obtaining a polymerase chain reaction (PCR) diagnosis using cerebral spinal fluid (CSF) as a reference method. Tests on DNA extracted from plasma are noninvasive, thus avoiding all of the collateral effects and patient risks associated with CSF collection. This study aimed to determine whether plasma can replace CSF in nested PCR analysis for the detection of CNS human herpesvirus (HHV) diseases by analysing the proportion of patients whose CSF nested PCR results were positive for CNS HHV who also had the same organism identified by plasma nested PCR. In this study, CSF DNA was used as the gold standard, and nested PCR was performed on both types of samples. Fifty-two patients with symptoms of nervous system infection were submitted to CSF and blood collection. For the eight HHV, one positive DNA result-in plasma and/or CSF nested PCR-was considered an active HHV infection, whereas the occurrence of two or more HHVs in the same sample was considered a coinfection. HHV infections were positively detected in 27/52 (51.9%) of the CSF and in 32/52 (61.5%) of the plasma, difference not significant, thus nested PCR can be performed on plasma instead of CSF. In conclusion, this findings suggest that plasma as a useful material for the diagnosis of cases where there is any difficulty to perform a CSF puncture.

Species determination of Brazilian mammals implicated in the epidemiology of rabies based on the control region of mitochondrial DNA

Identification of animals that are decomposing or have been run over or burnt and cannot be visually identified is a problem in the surveillance and control of infectious diseases. Many of these animals are wild and represent a valuable source of information for epidemiologic research as they may be carriers of an infectious agent. This article discusses the results obtained using a method for identifying mammals genetically by sequencing their mitochondrial DNA control region. Fourteen species were analyzed and identified. These included the main reservoirs and transmitters of rabies virus, namely, canids, chiroptera and primates. The results prove that this method of genetic identification is both efficient and simple and that it can be used in the surveillance of infectious diseases which includes mammals in their epidemiologic cycle, such as rabies.

DNA-based ionic conducting membranes

Deoxyribonucleic acid based gel solid electrolytes were prepared and their electric properties were characterized. Their ionic conductivity is in the range of 10(-4)-10(-5) S/cm at room temperature and increases linearly in function of temperature, obeying an Arrhenius-like relationship. The present study, combined with the literature data, suggests that the electrical conduction mechanism in these membranes involve ion motion and/or charge hopping, promoted most likely by a significant interaction between the membrane components. The good conductivity results, as found here, together with the good transparency and good adhesion to the electrodes show that the DNA-based gel polymer electrolytes are very promising materials for application in various electrochromic devices. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3610951]

Simultaneous preconcentration of copper, zinc, cadmium, and nickel in water samples by cloud point extraction using 4-(2-pyridylazo)-resorcinol and their determination by inductively coupled plasma optic emission spectrometry

A procedure for simultaneous separation/preconcentration of copper. zinc, cadmium, and nickel in water samples, based on cloud point extraction (CPE) as a prior step to their determination by inductively coupled plasma optic emission spectrometry (ICP-OES), has been developed. The analytes reacted with 4-(2-pyridylazo)-resorcinol (PAR) at pH 5 to form hydrophobic chelates, which were separated and preconcentrated in a surfactant-rich phase of octylphenoxypolyethoxyethanol (Triton X-I 14). The parameters affecting the extraction efficiency of the proposed method, such as sample pH, complexing agent concentration, buffer amount, surfactant concentration, temperature, kinetics of complexation reaction, and incubation time were optimized and their respective values were 5, 0.6 mmol L(-1). 0.3 mL, 0.15% (w/v), 50 degrees C, 40 min, and 10 min for 15 mL of preconcentrated solution. The method presented precision (R.S.D.) between 1.3% and 2.6% (n = 9). The concentration factors with and without dilution of the surfactant-rich phase for the analytes ranged from 9.4 to 10.1 and from 94.0 to 100.1, respectively. The limits of detection (L.O.D.) obtained for copper, zinc, cadmium, and nickel were 1.2, 1.1, 1.0. and 6.3 mu g L(-1), respectively. The accuracy of the procedure was evaluated through recovery experiments on aqueous samples. (C) 2009 Published by Elsevier B.V.