Enzyme-induced Aggregation of Plasmonic Nanoparticles for the Development of Label-free and Ultrasensitive Detection of Bacterial DNA

Sensitive detection of pathogens is critical to ensure the safety of food supplies and to prevent bacterial disease infection and outbreak at the first onset. While conventional techniques such as cell culture, ELISA, PCR, etc. have been used as the predominant detection workhorses, they are however limited by either time-consuming procedure, complicated sample pre-treatment, expensive analysis and operation, or inability to be implemented at point-of-care testing. Here, we present our recently developed assay exploiting enzyme-induced aggregation of plasmonic gold nanoparticles (AuNPs) for label-free and ultrasensitive detection of bacterial DNA. In the experiments, AuNPs are first functionalized with specific, single-stranded RNA probes so that they exhibit high stability in solution even under high electrolytic condition thus exhibiting red color. When bacterial DNA is present in a sample, a DNA-RNA heteroduplex will be formed and subsequently prone to the RNase H cleavage on the RNA probe, allowing the DNA to liberate and hybridize with another RNA strand. This continuously happens until all of the RNA strands are cleaved, leaving the nanoparticles ‘unprotected’. The addition of NaCl will cause the ‘unprotected’ nanoparticles to aggregate, initiating a colour change from red to blue. The reaction is performed in a multi-well plate format, and the distinct colour signal can be discriminated by naked eye or simple optical spectroscopy. As a result, bacterial DNA as low as pM could be unambiguously detected, suggesting that the enzyme-induced aggregation of AuNPs assay is very easy to perform and sensitive, it will significantly benefit to development of fast and ultrasensitive methods that can be used for disease detection and diagnosis.

Conservative fluid management or deresuscitation for patients with sepsis or acute respiratory distress syndrome following the resuscitation phase of critical illness: a systematic review and meta-analysis

Background

It is unknown whether a conservative approach to fluid administration or deresuscitation (active removal of fluid using diuretics or renal replacement therapy) is beneficial following haemodynamic stabilisation of critically ill patients.

Purpose

To evaluate the efficacy and safety of conservative or deresuscitative fluid strategies in adults and children with acute respiratory distress syndrome (ARDS), sepsis or systemic inflammatory response syndrome (SIRS) in the post-resuscitation phase of critical illness.

Methods

We searched Medline, EMBASE and the Cochrane central register of controlled trials from 1980 to June 2016, and manually reviewed relevant conference proceedings from 2009 to the present. Two reviewers independently assessed search results for inclusion and undertook data extraction and quality appraisal. We included randomised trials comparing fluid regimens with differing fluid balances between groups, and observational studies investigating the relationship between fluid balance and clinical outcomes.

Results

Forty-nine studies met the inclusion criteria. Marked clinical heterogeneity was evident. In a meta-analysis of 11 randomised trials (2051 patients) using a random-effects model, we found no significant difference in mortality with conservative or deresuscitative strategies compared with a liberal strategy or usual care [pooled risk ratio (RR) 0.92, 95 % confidence interval (CI) 0.82–1.02, I2 = 0 %]. A conservative or deresuscitative strategy resulted in increased ventilator-free days (mean difference 1.82 days, 95 % CI 0.53–3.10, I2 = 9 %) and reduced length of ICU stay (mean difference −1.88 days, 95 % CI −0.12 to −3.64, I2 = 75 %) compared with a liberal strategy or standard care.

Conclusions

In adults and children with ARDS, sepsis or SIRS, a conservative or deresuscitative fluid strategy results in an increased number of ventilator-free days and a decreased length of ICU stay compared with a liberal strategy or standard care. The effect on mortality remains uncertain. Large randomised trials are needed to determine optimal fluid strategies in critical illness.

Enhancing Quality of Life for People who are Blind or Low Vision Using Computing Technology

Thesis (Ph.D.)--University of Washington, 2016-08

Three-dimensional free surface modelling in an unstructured mesh environment for metal processing applications

In the casting of metals, tundish flow, welding, converters, and other metal processing applications, the behaviour of the fluid surface is important. In aluminium alloys, for example, oxides formed on the surface may be drawn into the body of the melt where they act as faults in the solidified product affecting cast quality. For this reason, accurate description of wave behaviour, air entrapment, and other effects need to be modelled, in the presence of heat transfer and possibly phase change. The authors have developed a single-phase algorithm for modelling this problem. The Scalar Equation Algorithm (SEA) (see Refs. 1 and 2), enables the transport of the property discontinuity representing the free surface through a fixed grid. An extension of this method to unstructured mesh codes is presented here, together with validation. The new method employs a TVD flux limiter in conjunction with a ray-tracing algorithm, to ensure a sharp bound interface. Applications of the method are in the filling and emptying of mould cavities, with heat transfer and phase change.

Low- vs. high-glycemic load diets: effects on postprandial plasma free fatty acids

Thesis (Master's)--University of Washington, 2016-06

Teaching Rules or Teaching Creativity: a Paradigm Shift

Structure is everything in a screenplay we are told. If indeed there are any rules to screenwriting then this would be carved in tablets of stone. Within pedagogical frameworks we are diligent in our instruction of the three acts, advocating it as a paradigm. We pass on tools for the analysis of character that are gleaned from psychology. But I have seen students struggle with this toolbox. They feel constrained by concrete techniques. So often seeing principles as rules, structure as restriction. The stifling of free-form ideas is further compounded by the plethora of books that claim the path to glory lies only in structural devices. Some even purport to have a formula, a simple prescriptive model that will bestow almost certain success. Yet this is an industry that abhors formula, that hungers for the fresh and the new. Without bravado, imagination and experimentation with character and form, the best structured screenplay in the world is merely a typing exercise. As educators we have a duty to retain a balance between letting a student’s mind dance and keeping them to the tempo. This study will compare a variety of diverse structures, from Hegel to Alcoholics Anonymous, Kubler Ross to Jung. It will analyse recent journal articles, on both new techniques in teaching creativity and new approaches to the instruction of screenwriting, to suggest a model of how best to inform the application of structure to HE students and keep creativity uppermost. A structure of emotional truth. An equal appreciation of both the tools of our craft and an imaginative exploration of character and world that can unlock our originality and our artistry.

Higher Education - Border or Boundary? Can Theatre in Education Help Promote a University Education?

With the expansion and increased availability of Higher Education the progression to study for an undergraduate degree has been viewed as a simple stepping stone with examination success a straight - forward border pass. Changes in the funding of degree courses has established a series of more challenging boundaries to entry which demand a rigorous assessment of the benefits of Higher Education. The Widening Participation Unit at The University of Worcester has sought to ease this border crossing for pupils whose parents have not been to university. Their experience from previous projects was that school pupils more easily relate to undergraduate students whose experience of Higher Education is recent and relevant. With this in mind they commissioned the Drama and Performance Department to create a Theatre in Education programme that introduced an awareness of post sixteen options and future choices to challenge Higher Education stereotypes. As a result of this collaboration Why Bother? was created, directed by myself and devised and researched with four students who were studying drama. Their own experiences were used to inform the character development and dealt with worrying as a mature student about integration into full – time education, loss of income after working, the pressures of emotional commitments to partners and being away from home. The programme toured to two thousand year 9 – 11 pupils in Worcestershire and Herefordshire schools in January and May 2011. Devising and touring Why Bother provided students with an opportunity to work as a professional paid TIE team that it is not possible for them to do as part of their undergraduate degree course. My initial research looks at the effectiveness and limitations of this project based on pupil questionnaires and the experiences of the team which are explored within the broader context of TIE and its potential for affecting attitudinal change. This has given rise to a number of questions that need consideration in the development of a new TIE programme aimed at raising the awareness of sixth form students who are about to make the decision whether to apply to university or not. Collaboration with university students in exploring the value of an education that they have subscribed to raises issues of bias and whether their powers of persuasion actually prevent pupils from making their own individual decision. The ethics of promoting a “free” university education seem much less complex than the decision required now which involves balancing the real value against the high financial cost suggested in the working title of Is it Worth it? This paper will present my first attempts to develop research methods and methodologies that will enable me to evaluate the success of this and future TIE.

Physicochemical characterisation of protein ingredients prepared from milk by ultrafiltration or microfiltration for application in formulated nutritional products

Formulated food systems are becoming more sophisticated as demand grows for the design of structural and nutritional profiles targeted at increasingly specific demographics. Milk protein is an important bio- and techno-functional component of such formulations, which include infant formula, sports supplements, clinical beverages and elderly nutrition products. This thesis outlines research into ingredients that are key to the development of these products, namely milk protein concentrate (MPC), milk protein isolate (MPI), micellar casein concentrate (MCC), β-casein concentrate (BCC) and serum protein concentrate (SPC). MPC powders ranging from 37 to 90% protein (solids basis) were studied for properties of relevance to handling and storage of powders, powder solubilisation and thermal processing of reconstituted MPCs. MPC powders with ≥80% protein were found to have very poor flowability and high compressibility; in addition, these high-protein MPCs exhibited poor wetting and dispersion characteristics during rehydration in water. Heat stability studies on unconcentrated (3.5%, 140°C) and concentrated (8.5%, 120°C) MPC suspensions, showed that suspensions prepared from high-protein MPCs coagulated much more rapidly than lower protein MPCs. β-casein ingredients were developed using membrane processing. Enrichment of β-casein from skim milk was performed at laboratory-scale using ‘cold’ microfiltration (MF) at <4°C with either 1000 kDa molecular weight cut-off or 0.1 µm pore-size membranes. At pilot-scale, a second ‘warm’ MF step at 26°C was incorporated for selective purification of micellised β-casein from whey proteins; using this approach, BCCs with β-casein purity of up to 80% (protein basis) were prepared, with the whey protein purity of the SPC co-product reaching ~90%. The BCC ingredient could prevent supersaturated solutions of calcium phosphate (CaP) from precipitating, although the amorphous CaP formed created large micelles that were less thermo-reversible than those in CaP-free systems. Another co-product of BCC manufacture, MCC powder, was shown to have superior rehydration characteristics compared to traditional MCCs. The findings presented in this thesis constitute a significant advance in the research of milk protein ingredients, in terms of optimising their preparation by membrane filtration, preventing their destabilisation during processing and facilitating their effective incorporation into nutritional formulations designed for consumers of a specific age, lifestyle or health status

Effect of galactose metabolising and non-metabolising strains of Streptococcus thermophilus as a starter culture adjunct on the properties of Cheddar cheese made with low or high pH at whey drainage

Cheddar cheese was made using control culture (Lactococcus lactis subsp. lactis), or with control culture plus a galactose-metabolising (Gal+) or galactose-non-metabolising (Gal-) Streptococcus thermophilus adjunct; for each culture type, the pH at whey drainage was either low (pH 6.15) or high (pH 6.45). Sc. thermophilus affected the levels of residual lactose and galactose, and the volatile compound profile and sensory properties of the mature cheese (270 d) to an extent dependent on the drain pH and phenotype (Gal+ or Gal-). For all culture systems, reducing drain pH resulted in lower levels of moisture and lactic acid, a higher concentration of free amino acids, and higher firmness. The results indicate that Sc. thermophilus may be used to diversify the sensory properties of Cheddar cheese, for example from a fruity buttery odour and creamy flavour to a more acid taste, rancid odour, and a sweaty cheese flavour at high drain pH.

Zero-rating in emerging mobile markets: Free Basics and Wikipedia Zero in Ghana

Despite widespread controversy surrounding zero-rating—that is, the practice of subsidizing mobile data—the field suffers from a lack of inquiry into user understanding of and experience with zero-rated services. This paper explores how Ghanaian mobile users interact with zero-rated mobile applications Free Basics and Wikipedia Zero. Based on semi-structured interviews with users and non-users of the applications, I discuss how mobile phone users perceive Free Basics and Wikipedia Zero, what motivates them to use or not use the applications, and how the availability of the applications influences their data-buying strategies. Findings suggest that respondents, including those who did not actively use the applications, understood and experienced Free Basics and Wikipedia Zero in ways divergent from the providers’ aim of expanding access to online content and services.

Free surface and mesh control for the FV simulation of semi-levitation melting

Abstract not available

Topics in equilibrium and nonequilibrium thermodynamics: computing crystalline free energies and engineering Maxwell’s demon.

This dissertation covers two separate topics in statistical physics. The first part of the dissertation focuses on computational methods of obtaining the free energies (or partition functions) of crystalline solids. We describe a method to compute the Helmholtz free energy of a crystalline solid by direct evaluation of the partition function. In the many-dimensional conformation space of all possible arrangements of N particles inside a periodic box, the energy landscape consists of localized islands corresponding to different solid phases. Calculating the partition function for a specific phase involves integrating over the corresponding island. Introducing a natural order parameter that quantifies the net displacement of particles from lattices sites, we write the partition function in terms of a one-dimensional integral along the order parameter, and evaluate this integral using umbrella sampling. We validate the method by computing free energies of both face-centered cubic (FCC) and hexagonal close-packed (HCP) hard sphere crystals with a precision of $10^{-5}k_BT$ per particle. In developing the numerical method, we find several scaling properties of crystalline solids in the thermodynamic limit. Using these scaling properties, we derive an explicit asymptotic formula for the free energy per particle in the thermodynamic limit. In addition, we describe several changes of coordinates that can be used to separate internal degrees of freedom from external, translational degrees of freedom. The second part of the dissertation focuses on engineering idealized physical devices that work as Maxwell's demon. We describe two autonomous mechanical devices that extract energy from a single heat bath and convert it into work, while writing information onto memory registers. Additionally, both devices can operate as Landauer's eraser, namely they can erase information from a memory register, while energy is dissipated into the heat bath. The phase diagrams and the efficiencies of the two models are solved and analyzed. These two models provide concrete physical illustrations of the thermodynamic consequences of information processing.

Testing the universality of free fall with rubidium and ytterbium in a very large baseline atom interferometer

We propose a very long baseline atom interferometer test of Einstein's equivalence principle (EEP) with ytterbium and rubidium extending over 10m of free fall. In view of existing parametrizations of EEP violations, this choice of test masses significantly broadens the scope of atom interferometric EEP tests with respect to other performed or proposed tests by comparing two elements with high atomic numbfers. In the first step, our experimental scheme will allow us to reach an accuracy in the Eotvos ratio of 7 . 10(-13). This achievement will constrain violation scenarios beyond our present knowledge and will represent an important milestone for exploring a variety of schemes for further improvements of the tests as outlined in the paper. We will discuss the technical realisation in the new infrastructure of the Hanover Institute of Technology (HITec) and give a short overview of the requirements needed to reach this accuracy. The experiment will demonstrate a variety of techniques, which will be employed in future tests of EEP, high-accuracy gravimetry and gravity gradiometry. It includes operation of a force-sensitive atom interferometer with an alkaline earth-like element in free fall, beam splitting over macroscopic distances and novel source concepts.

A representation-free description of the Kasevich-Chu interferometer: a resolution of the redshift controversy

Motivated by a recent claim by Muller et al (2010 Nature 463 926-9) that an atom interferometer can serve as an atom clock to measure the gravitational redshift with an unprecedented accuracy, we provide a representation-free description of the Kasevich-Chu interferometer based on operator algebra. We use this framework to show that the operator product determining the number of atoms at the exit ports of the interferometer is a c-number phase factor whose phase is the sum of only two phases: one is due to the acceleration of the phases of the laser pulses and the other one is due to the acceleration of the atom. This formulation brings out most clearly that this interferometer is an accelerometer or a gravimeter. Moreover, we point out that in different representations of quantum mechanics such as the position or the momentum representation the phase shift appears as though it originates from different physical phenomena. Due to this representation dependence conclusions concerning an enhanced accuracy derived in a specific representation are unfounded.