Development and evaluation of a multiple-locus variable-number tandem-repeats analysis assay for subtyping Salmonella Typhi strains from sub-Saharan Africa

Purpose: Molecular epidemiological investigations of the highly clonal Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) are important in outbreak detection and in tracking disease transmission. In this study, we developed and evaluated a multiple-locus variable-number tandem-repeats (VNTR) analysis (MLVA) assay for characterization of S. Typhi isolates from sub-Saharan Africa. Methodology: Twelve previously reported VNTR loci were evaluated and an MLVA assay consisting of five polymorphic loci was adopted. The MLVA assay was developed for use on capillary electrophoresis systems by testing a collection of 50 S. Typhi isolates. This S. Typhi strain panel consisted of six outbreak related isolates and 44 epidemiologically unlinked isolates. Amongst these were nine S.Typhi haplotype H58 isolates. Results: The MLVA assay characterized the 50 isolates into 47 MLVA profiles while PFGE analysis of the same isolates revealed 34 pulsotypes. MLVA displayed higher discriminatory power (Simpson’s index of diversity (DI) 0.998 [95% confidence interval (CI) 0.995–1.000)] as compared to pulsed-field gel electrophoresis [Simpson’s DI 0.984 (95% CI 0.974–0.994)]. Conclusion: The MLVA assay presented in this study is a simple, rapid and more accessible tool that serves as a good alternative to other molecular subtyping methods for S. Typhi

Moving charged particles in fluctuating and disordered energy landscapes

In this thesis various experiments are performed that concern the moving of charged particles in fluctuating and disordered energy landscapes. We clarified the working of a Brownian on/off ratchet for suspended particles, studied its potential as a particle separator and determined its potential for improvement. We used the thermoelectric effect to study charge transport in disordered semiconductors, and determined how the temperature dependence relates to different charge transport models. Finally we used admittance spectroscopy to determine the effect of disorder on the differential capacitance and to describe charge carrier relaxation

System occupancy of a two-class batch-service queue with class-dependent variable server capacity

Due to their wide area of applications, queueing models with batch service, where the server can process several customers simultaneously, have been studied frequently. An important characteristic of such batch-service systems is the size of a batch, that is the number of customers that are processed simultaneously. In this paper, we analyse a two-class batch-service queueing model with variable server capacity, where all customers are accommodated in a common first-come-first served single-server queue. The server can only process customers that belong to the same class, so that the size of a batch is determined by the number of consecutive same-class customers. After establishing the system equations that govern the system behaviour, we deduce an expression for the steady-state probability generating function of the system occupancy at random slot boundaries. Also, some numerical examples are given that provide further insight in the impact of the different parameters on the system performance

Controlling the order pool in make-to-order production systems

Voor ‘Make-To-Order’ (MTO, oftewel klantordergestuurde) productiesystemen is de tijd die orders moeten wachten op beschikbare productiecapaciteit cruciaal. Het beheersen van die wachttijd is van groot belang om zowel korte als betrouwbare doorlooptijden te realiseren. Daarom analyseerde en ontwierp Remco Germs regels voor orderacceptatie en ordervrijgave, om daarmee de wachttijden te beheersen. Orderacceptatie en -vrijgave zijn de twee belangrijkste mechanismen om de lengte van wachttijden te beïnvloeden en zodoende de productie te sturen. De logistieke prestatie hangt in grote mate af van specifieke kenmerken van MTO-systemen, zoals routing variabiliteit, beperkte productiecapaciteit, omsteltijden, strikte leveringsvoorwaarden en onzekerheid in het aankomstpatroon van orders. Om een beter begrip te krijgen van de afwegingen die MTO-bedrijven in dit opzicht moeten maken richt het proefschrift zich op de modellering van de belangrijkste kenmerken van MTO-systemen. De inzichten die dat oplevert worden vervolgens gebruikt om orderacceptatie- en ordervrijgaveregels te ontwikkelen die eenvoudig te begrijpen en daarom makkelijk in praktijksituaties te implementeren zijn. Deze relatief eenvoudige beslissingsregels kunnen al leiden tot significante verbeteringen in de logistieke prestaties van MTO-bedrijven. The thesis of Remco Germs analyses and develops order acceptance and order release policies to control queues in make-to-order (MTO) production systems. Controlling the time orders spend waiting in queues is crucial for realizing short and reliable delivery times, two performance measures which are of strategic importance for many MTO com-panies. Order acceptance and order release are the two most important production con-trol mechanisms to influence the length of these queues. Their performance depends on typical characteristics of MTO systems, such as random (batch) order arrival, routing variability, fixed capacities, setup times and (strict) due-dates. To better understand the underlying mechanisms of good order acceptance and order release policies the models in this thesis focus on the main characteristics of MTO systems. The insights obtained from these models are then used to develop order acceptance and order release policies that are easy to understand and thereby easy to implement in practice. The results show that these relatively simple policies may already lead to significant performance improvements for MTO companies.

Trace fossils and the agronmomic revolution at the Neoproterozoic – Cambrian transition in Southwest Gondwana

The Ediacaran-Early Cambrian transition in the southwestern margin of Gondwana is represented in the Andean Margin of South America by the thick sequence of the Puncoviscana Basin. In southern Africa, the Nama and Vanrhynsdorp groups display partially equivalent successions. Trace fossil assemblages are well known from both regions, with relatively simple, low diversity forms in the lower stratigraphic levels. An increase in complexity is recorded in the upper sector of the Andean and African sequences, with a variety of Treptichnus-type traces that denotes a more gradual diversity increase towards the Cambrian than generally accepted. Trace fossil associations indicate that the fossiliferous levels of the Puncoviscana Basin may predate the uppermost lower Cambrian (pre-trilobite) successions of the Nama and Vanrhynsdorp groups, and lasted into the ‘trilobitic’ Cambrian. Intergradations between Treptichnus and different ichnogenera cast doubts on using related ichnospecies in Ediacaran-Early Cambrian biozonation.Fil: Aceñolaza, Guillermo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Correlación Geológica. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Departamento de Geología. Cátedra Geología Estructural. Instituto Superior de Correlación Geológica; ArgentinaFil: Germs, Gerard. University of Johannesburg; SudáfricaFil: Aceñolaza, Florencio Gilberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Correlación Geológica. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo. Departamento de Geología. Cátedra Geología Estructural. Instituto Superior de Correlación Geológica; Argentin

Approaching disorder-free transport in high-mobility conjugated polymers.

Conjugated polymers enable the production of flexible semiconductor devices that can be processed from solution at low temperatures. Over the past 25 years, device performance has improved greatly as a wide variety of molecular structures have been studied. However, one major limitation has not been overcome; transport properties in polymer films are still limited by pervasive conformational and energetic disorder. This not only limits the rational design of materials with higher performance, but also prevents the study of physical phenomena associated with an extended π-electron delocalization along the polymer backbone. Here we report a comparative transport study of several high-mobility conjugated polymers by field-effect-modulated Seebeck, transistor and sub-bandgap optical absorption measurements. We show that in several of these polymers, most notably in a recently reported, indacenodithiophene-based donor-acceptor copolymer with a near-amorphous microstructure, the charge transport properties approach intrinsic disorder-free limits at which all molecular sites are thermally accessible. Molecular dynamics simulations identify the origin of this long sought-after regime as a planar, torsion-free backbone conformation that is surprisingly resilient to side-chain disorder. Our results provide molecular-design guidelines for 'disorder-free' conjugated polymers.We gratefully acknowledge financial support from the Engineering and Physical Sciences Research Council (EPSRC) through a programme grant (EP/G060738/1) and the Technology Strategy Board (TSB) (PORSCHED project). D. Venkateshvaran acknowledges financial support from the Cambridge Commonwealth Trust through a Cambridge International Scholarship. K. Broch acknowledges post-doctoral fellowship support from the German Research Foundation (DFG). Mateusz Zelazny acknowledges funding from the NanoDTC in Cambridge. The work in Mons was supported by the European Commission / Région Wallonne (FEDER – Smartfilm RF project), the Interuniversity Attraction Pole program of the Belgian Federal Science Policy Office (PAI 7/05), Programme d’Excellence de la Région Wallonne (OPTI2MAT project) and FNRS-FRFC. D.B. and J.C. are FNRS Research Fellows.This is the accepted manuscript. The final version's available from Nature at http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13854.html

A geochemical investigation into the occurrence and fate of nitrogen and phosphorus in the lower Oliphants River, Western Cape

Bibliography: leaves 69-76.Knowledge of nutrient dynamics within aquatic ecosystems are of fundamental importance for water quality management, especially in cultivated areas where irrigation farming pose a salinization and eutrophication risk to water bodies. A range of water quality problems is associated with eutrophication, which is generally controlled by the nutrients nitrogen and phosphorus. The lower Olifants River is situated in an arid region with intensive irrigation agriculture. This study set out to investigate the loading and fate of nitrogen and phosphorus in the lower Olifants River