Improving molecular detection of Candida DNA in whole blood:comparison of seven fungal DNA extraction protocols using real-time PCR

The limitations of classical diagnostic methods for invasive Candida infections have led to the development of molecular techniques such as real-time PCR to improve diagnosis. However, the detection of low titres of Candida DNA in blood from patients with candidaemia requires the use of extraction methods that efficiently lyse yeast cells and recover small amounts of DNA suitable for amplification. In this study, a Candida-specific real-time PCR assay was used to detect Candida albicans DNA in inoculated whole blood specimens extracted using seven different extraction protocols. The yield and quality of total nucleic acids were estimated using UV absorbance, and specific recovery of C. albicans genomic DNA was estimated quantitatively in comparison with a reference (Qiagen kit/lyticase) method currently in use in our laboratory. The extraction protocols were also compared with respect to sensitivity, cost and time required for completion. The TaqMan PCR assay used to amplify the DNA extracts achieved high levels of specificity, sensitivity and reproducibility. Of the seven extraction protocols evaluated, only the MasterPure yeast DNA extraction reagent kit gave significantly higher total nucleic acid yields than the reference method, although nucleic acid purity was highest using either the reference or YeaStar genomic DNA kit methods. More importantly, the YeaStar method enabled C. albicans DNA to be detected with highest sensitivity over the entire range of copy numbers evaluated, and appears to be an optimal method for extracting Candida DNA from whole blood.

Synthesis of caffeic acid and p-hydroxybenzoic acid molecularly imprinted polymers and their application for the selective extraction of polyphenols from olive mill waste waters

Using caffeic acid and p-hydroxybenzoic acid as templates, two molecularly imprinted polymers (MIPs) were prepared that were used for isolation of polyphenols from olive mill waste water samples (OMWWs) without previous pre-treatment. For the preparation of the caffeic acid MIPs 4-vinylpyridine, allylurea, allylaniline and methacrylic acid were tested as functional monomers, ethylene glycol dimethylacrylate (EDMA), pentaerythritol trimethylacrylate (PETRA) and divinylbenzene 80 (DVB80) as cross-linkers and tetrahydrofuran as porogen. For p-hydroxybenzoic acid 4-vinylpyridine, allylurea and allylaniline were tested as functional monomers, EDMA and PETRA as cross-linkers and acetonitrile as porogen. The performance of the synthesized polymers was evaluated against seven structurally related compounds by means of polymer-based HPLC. The two polymers that presented the most interesting properties were further evaluated by batch rebinding and from the derived isotherms their capacity and binding strength were determined. Using solid-phase extraction (SPE), their ability to recognize and bind the template molecule from an aqueous solution as well as the pH dependence of the binding strength were explored. After establishing the best SPE protocol, an aqueous model mixture of compounds and a raw OMWWs sample were loaded on the two best polymers. The result of the consecutive use of the two polymers on the same sample was explored. It was concluded that acidic conditions favour the recognition abilities of both polymers and that they can be used for a quick and efficient isolation of the polyphenol fraction directly from raw OMWW.

Selective solid-phase extraction sorbent for caffeine made by molecular imprinting

A molecularly imprinted polymer (MIP) was prepared with caffeine as the template molecule. Thermal polymerisation (60°C) was optimised, varying ratios of monomer, cross linker and template. The polymer was used as a solid-phase extraction (SPE) sorbent, for selective trapping and pre-concentration of caffeine. Caffeine was loaded on the MIP-SPE cartridge using different loading conditions (solvents, pH value). Washing and elution of the caffeine bound to the MIP was studied utilising different protocols. The extraction protocol was successfully applied to the direct extraction of caffeine from beverages and spiked human plasma.

Preparation of a molecularly imprinted polymer for the solid-phase extraction of scopolamine with hyoscyamine as a dummy template molecule

Molecularly imprinted polymers (MIPs) selective for scopolamine were produced using hyoscyamine (a close structural analogue) as template molecule. The produced polymers were used as media for solid-phase extraction, exhibiting selective binding properties for the analyte from biological samples. Human and calf urine and serum were processed on the MIP under various extraction protocols. The best performance was observed after loading the analyte in aqueous environment facilitating retention on the MIP by non-selective hydrophobic interactions. The MIPs were subsequently washed using an optimised solvent system to enable selective desorption of the analyte. Other related and non-related compounds were accessed to evaluate molecular recognition properties. Recoveries of up to 79% were achieved for the analyte of interest from biological samples.

Dioxouranium(VI) extraction in microchannels using ionic liquids

The extraction of uranium(VI) from aqueous nitric acid solutions by tributylphosphate {TBP; 30%(v/v)} dissolved in the ionic liquid 1-butyl-3-methylimidazolium bis{(trifluoromethyl)sulfonyl}amide was investigated. The experiments were performed in a Teflon microchannel of 0.5 mm internal diameter, while the dioxouranium(VI) concentrations in the aqueous and the ionic liquid phases were determined by UV-Vis spectroscopy. The effects of initial nitric acid concentration (0.01-3 M), residence time, and phase flow rate ratio were studied. It was found that, with increasing nitric acid concentration, the percentage of dioxouranium(VI) extracted decreased and then increased again, while the extraction efficiency followed a slightly different trend. Overall mass transfer coefficients varied between 0.049 s and 0.312 s . © 2012 Elsevier B.V. All rights reserved.

Adaptive Dialogue Strategy Selection through Imprecise Probabilistic Query Answering

In a human-computer dialogue system, the dialogue strategy can range from very restrictive to highly flexible. Each specific dialogue style has its pros and cons and a dialogue system needs to select the most appropriate style for a given user. During the course of interaction, the dialogue style can change based on a user’s response and the system observation of the user. This allows a dialogue system to understand a user better and provide a more suitable way of communication. Since measures of the quality of the user’s interaction with the system can be incomplete and uncertain, frameworks for reasoning with uncertain and incomplete information can help the system make better decisions when it chooses a dialogue strategy. In this paper, we investigate how to select a dialogue strategy based on aggregating the factors detected during the interaction with the user. For this purpose, we use probabilistic logic programming (PLP) to model probabilistic knowledge about how these factors will affect the degree of freedom of a dialogue. When a dialogue system needs to know which strategy is more suitable, an appropriate query can be executed against the PLP and a probabilistic solution with a degree of satisfaction is returned. The degree of satisfaction reveals how much the system can trust the probability attached to the solution.

Extracting Query Interfaces Based on Form Structures and Semantic Similarity

Web databases are now pervasive. Such a database can be accessed via its query interface (usually HTML query form) only. Extracting Web query interfaces is a critical step in data integration across multiple Web databases, which creates a formal representation of a query form by extracting a set of query conditions in it. This paper presents a novel approach to extracting Web query interfaces. In this approach, a generic set of query condition rules are created to define query conditions that are semantically equivalent to SQL search conditions. Query condition rules represent the semantic roles that labels and form elements play in query conditions, and how they are hierarchically grouped into constructs of query conditions. To group labels and form elements in a query form, we explore both their structural proximity in the hierarchy of structures in the query form, which is captured by a tree of nested tags in the HTML codes of the form, and their semantic similarity, which is captured by various short texts used in labels, form elements and their properties. We have implemented the proposed approach and our experimental results show that the approach is highly effective.

Optimisation and scaling of interfacial GeO2 layers for high-k gate stacks on germanium and extraction of dielectric constant of GeO2

Germanium is an attractive channel material for MOSFETs because of its higher mobility than silicon. In this paper, GeO2 has been investigated as an interfacial layer for high-kappa gate stacks on germanium. Thermally grown GeO2 layers have been prepared at 550 degrees C to minimise GeO volatilisation. GeO2 growth has been performed in both pure O-2 ambient and O-2 diluted with N-2. GeO2 thickness has been scaled down to approximately 3 nm. MOS capacitors have been fabricated using different GeO2 thicknesses with a standard high-kappa dielectric on top. Electrical properties and thermal stability have been tested up to at least 350 degrees C. The K value of GeO2 was experimentally determined to be 4.5. Interface state densities (D-it) of less than 10(12) CM-2 eV(-1) have been extracted for all devices using the conductance method.

WIQ:Work-intensive query scheduling for in-memory database systems

We propose a novel admission control policy for database queries. Our methodology uses system measurements of CPU utilization and query backlogs to determine interference between queries in execution on the same database server. Query interference may arise due to the concurrent access of hardware and software resources and can affect performance in positive and negative ways. Specifically our admission control considers the mix of jobs in service and prioritizes the query classes consuming CPU resources more efficiently. The policy ignores I/O subsystems and is therefore highly appropriate for in-memory databases. We validate our approach in trace-driven simulation and show performance increases of query slowdowns and throughputs compared to first-come first-served and shortest expected processing time first scheduling. Simulation experiments are parameterized from system traces of a SAP HANA in-memory database installation with TPC-H type workloads. © 2012 IEEE.

Molecularly imprinted polymers for the extraction of imiquimod from biological samples using a template analogue strategy

Molecularly Imprinted Polymers (MIPs) against imiquimod, a highly potent immune response modifier used in the treatment of skin cancer, were synthesised using a template analogue strategy and were compared with imprints of the drug itself. An investigation of the complexation between the functional monomer and the template analogue revealed an association constant of 1,376 ± 122 M-1, significantly higher than previously reported values for similar systems. The binding characteristics of the synthesised imprinted polymers were evaluated and extremely strong binding for imiquimod was observed while imprinting factors as high as 17 were calculated. When applied as sorbents in solid-phase extraction of imiquimod from aqueous, urine and blood serum samples, clean extracts and recoveries up to 95% were achieved, and it is concluded that while imiquimod imprints exhibited higher capacity for the drug, template analogue imprints are more selective. The results obtained suggest potential applications of imiquimod imprints as sorbents in rapid extraction and monitoring of undesirable systemic release of the drug.

Effect of cataract extraction on SITA perimetry in patients with glaucoma

PURPOSE: To evaluate the effect of cataract extraction on Swedish Interactive Thresholding Algorithm (SITA) perimetry in patients with coexisting cataract and glaucoma. PATIENTS AND METHODS: This is a retrospective noncomparative interventional study. Thirty-seven consecutive patients with open-angle glaucoma who had cataract extraction alone or combined with trabeculectomy were included. All patients had SITA-standard 24-2 visual fields before and after the surgery. The main outcome measures were changes in mean deviation (MD) and pattern standard deviation (PSD). Additionally, changes in best-corrected visual acuity, intraocular pressure, and number of glaucoma medications were also studied. RESULTS: Visual field tests were performed 3.9±4.4 months before surgery and 4.1±2.8 months after surgery. Mean visual acuity improved after the surgery, from 0.41±0.21 to 0.88±0.32 (P

Effect of cataract extraction on frequency doubling technology perimetry in patients with glaucoma

Aim: To evaluate the effect of cataract surgery on frequency doubling technology (FDT) perimetry in patients with coexisting cataract and glaucoma. Methods: In this consecutive prospective cohort study 27 patients with open angle glaucoma scheduled for cataract extraction alone or combined with trabeculectomy were enrolled. All patients underwent FDT threshold C-20 visual fields within 3 months before and 3 months after surgery. Changes in mean deviation (MD) and pattern standard deviation (PSD) were evaluated. Additionally, changes in best corrected logMAR visual acuity (VA), intraocular pressure (IOP), and number of glaucoma medications were also studied. Results: 22 patients completed the study. VA improved after surgery, from 0.47 (SD 0.19) to 0.12 (0.17) (p

The outcome of the functioning filter after subsequent cataract extraction

OBJECTIVE: To evaluate and compare the outcome of functioning filtration surgery followed by cataract surgery with posterior intraocular lens implantation by both phacoemulsification and extracapsular cataract extraction (ECCE) techniques in glaucomatous eyes. PATIENTS AND METHODS: We retrospectively evaluated the clinical course of 77 eyes (68 patients) that after successful trabeculectomy, underwent cataract surgery by either phacoemulsification or ECCE techniques. We determined the frequency of partial and absolute failure following cataract surgery by either phacoemulsification or ECCE in eyes with functioning trabeculectomies. Partial failure of intraocular pressure (IOP), control after cataract extraction was defined as the need for an increased number of antiglaucoma medications or argon laser trabeculoplasty to maintain IOP =21mm Hg. Complete failure of IOP control after cataract surgery was defined as an IOP >21 mm Hg on at least two consecutive measurements one or more weeks apart or the performance of additional filtration surgery. Failure rates were calculated using the Kaplan-Meier actuarial method. Failure rates between phacoemulsification and ECCE subgroups were compared using the log rank test. RESULTS: The probability of partial failure by the third postoperative year after cataract surgery was 39.5% in the phacoemulsification subgroup and 37.3% in the ECCE subgroup. This small difference is not statistically significant (P = 0.48). The probability of complete failure by the fourth postoperative year after cataract surgery was 12.0% in the phacoemulsification subgroup and 12.5% in the ECCE subgroup. This difference is also not statistically significant (P = 0.77). At the 6-month follow-up visit, visual acuity of both groups improved one or more lines in 87.0% of patients, and worsened one or more lines in 3.9% of patients. Sixty-one percent achieved visual acuity of 20/40 or better. The most frequent complication was posterior capsular opacification requiring laser capsulotomy that occurred in 31.2% of patients. CONCLUSION: Cataract extraction by either phacoemulsification or ECCE following trabeculectomy surgery may be associated with a partial loss of the previously functioning filter and the need for more antiglaucoma medications to control IOP.

Effect of cataract extraction on the Glaucoma Progression Index (GPI) in glaucoma patients

PURPOSE: To determine the effect of cataract extraction on the glaucoma progression index (GPI) in glaucoma patients with coexisting cataract.

PATIENTS AND METHODS: This is a retrospective noncomparative study. Consecutive eligible patients with glaucoma who underwent phacoemulsification alone or in combination with augmented trabeculectomy were included. All patients had Swedish Interactive Threshold Algorithm-standard 24-2 visual fields within 10 months of surgery. Exclusion criteria included other ocular morbidity, intraoperative complications, and perimetric reliability indices greater than 33%. Comparison was made between the immediate visual fields before and after surgery. The main outcome measure was the change in GPI. Changes in the pattern standard deviation (PSD) and mean deviation (MD) were also assessed. Comparison of means was performed with the paired t test.

RESULTS: Thirty-three eyes of 33 patients (all Whites) were analyzed. The mean age at surgery was 77.0+/-8.7 years. Visual field tests were performed 3.3+/-3.0 months SD before surgery and 5.4+/-2.6 months after surgery. There was a statistically significant increase in the GPI after cataract surgery (from 71.5+/-18.5% to 74.6+/-17.1%; P=0.02). The improvement in MD was also statistically significant (from -11.8+/-5.3 to -10.2+/-5.3 dB; P <0.01), but the change in PSD did not reach statistical significance.

CONCLUSIONS: Uncomplicated cataract extraction resulted in a statistically significant improvement in the 24-2 Swedish Interactive Threshold Algorithm-standard GPI and MD, but not in PSD. Both the MD and the GPI may be influenced by lens opacities, which could make detection of glaucoma visual field progression more difficult for clinicians in glaucoma patients with concurrent cataract.

The effectiveness of early lens extraction with intraocular lens implantation for the treatment of primary angle-closure glaucoma (EAGLE): Study protocol for a randomized controlled trial

BACKGROUND: Glaucoma is the leading cause of irreversible blindness. Although primary open-angle glaucoma is more common, primary angle-closure glaucoma (PACG) is more likely to result in irreversible blindness. By 2020, 5·3 million people worldwide will be blind because of PACG. The current standard care for PACG is a stepped approach of a combination of laser iridotomy surgery (to open the drainage angle) and medical treatment (to reduce intraocular pressure). If these treatments fail, glaucoma surgery (eg, trabeculectomy) is indicated. It has been proposed that, because the lens of the eye plays a major role in the mechanisms leading to PACG, early clear lens extraction will improve glaucoma control by opening the drainage angle. This procedure might reduce the need for drugs and glaucoma surgery, maintain good visual acuity, and improve quality of life compared with standard care.EAGLE aims to evaluate whether early lens extraction improves patient-reported, clinical outcomes, and cost-effectiveness, compared with standard care.

METHODS/DESIGN: EAGLE is a multicentre pragmatic randomized trial. All people presenting to the recruitment centres in the UK and east Asia with newly diagnosed PACG and who are at least 50 years old are eligible.The primary outcomes are EQ-5D, intraocular pressure, and incremental cost per quality adjusted life year (QALY) gained. Other outcomes are: vision and glaucoma-specific patient-reported outcomes, visual acuity, visual field, angle closure, number of medications, additional surgery (e.g., trabeculectomy), costs to the health services and patients, and adverse events.A single main analysis will be done at the end of the trial, after three years of follow-up. The analysis will be based on all participants as randomized (intention to treat). 400 participants (200 in each group) will be recruited, to have 90% power at 5% significance level to detect a difference in EQ-5D score between the two groups of 0·05, and a mean difference in intraocular pressure of 1·75 mm Hg. The study will have 80% power to detect a difference of 15% in the glaucoma surgery rate.

TRIAL REGISTRATION: ISRCTN44464607.