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

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

Environmental and diagenetic controls on the morphology and calcification of the Ediacaran metazoan Cloudina

Abstract Cloudina is a globally distributed Ediacaran metazoan, with a tubular, funnel-in-funnel form built of thin laminae (ca. 1–10 μm). To what degree local environmental controlled morphology, and whether early diagenesis controlled the degree of calcification of Cloudina, is debated. Here we test these hypotheses by considering assemblages from four, coeval localities from the Upper Omkyk Member, Nama Group, Namibia, from inner ramp to mid-ramp reef across the Zaris Subbasin. We show that sinuosity of the Cloudina tube is variable between sites, as is the relative thickness of the tube wall, suggesting these features were environmentally controlled. Walls are thickest in high-energy reef settings, and thinnest in the low-energy, inner ramp. While local diagenesis controls preservation, all diagenetic expressions are consistent with the presence of weakly calcified, organic-rich laminae, and lamina thicknesses are broadly constant. Finally, internal ‘cements’ within Cloudina are found in all sites, and pre-date skeletal breakage, transport, as well as syn-sedimentary botryoidal cement precipitation. Best preservation shows these to be formed by fine, pseudomorphed aragonitic acicular crystals. Sr concentrations and Mg/Ca show no statistically significant differences between internal Cloudina cements and botryoidal cements, but we infer all internal cements to have precipitated when Cloudina was still in-situ and added considerable mechanical strength, but may have formed post-mortem or in abandoned parts of the skeleton

Dynamic redox conditions control late Ediacaran metazoan ecosystems in the Nama Group, Namibia

The first appearance of skeletal metazoans in the late Ediacaran (~550 million years ago; Ma) has been linked to the widespread development of oxygenated oceanic conditions, but a precise spatial and temporal reconstruction of their evolution has not been resolved. Here we consider the evolution of ocean chemistry from ~550 to ~541. Ma across shelf-to-basin transects in the Zaris and Witputs Sub-Basins of the Nama Group, Namibia. New carbon isotope data capture the final stages of the Shuram/Wonoka deep negative C-isotope excursion, and these are complemented with a reconstruction of water column redox dynamics utilising Fe-S-C systematics and the distribution of skeletal and soft-bodied metazoans. Combined, these inter-basinal datasets provide insight into the potential role of ocean redox chemistry during this pivotal interval of major biological innovation.The strongly negative δ13C values in the lower parts of the sections reflect both a secular, global change in the C-isotopic composition of Ediacaran seawater, as well as the influence of 'local' basinal effects as shown by the most negative δ13C values occurring in the transition from distal to proximal ramp settings. Critical, though, is that the transition to positive δ13C values postdates the appearance of calcified metazoans, indicating that the onset of biomineralization did not occur under post-excursion conditions.Significantly, we find that anoxic and ferruginous deeper water column conditions were prevalent during and after the transition to positive δ13C that marks the end of the Shuram/Wonoka excursion. Thus, if the C isotope trend reflects the transition to global-scale oxygenation in the aftermath of the oxidation of a large-scale, isotopically light organic carbon pool, it was not sufficient to fully oxygenate the deep ocean.Both sub-basins reveal highly dynamic redox structures, where shallow, inner ramp settings experienced transient oxygenation. Anoxic conditions were caused either by episodic upwelling of deeper anoxic waters or higher rates of productivity. These settings supported short-lived and monospecific skeletal metazoan communities. By contrast, microbial (thrombolite) reefs, found in deeper inner- and mid-ramp settings, supported more biodiverse communities with complex ecologies and large skeletal metazoans. These long-lived reef communities, as well as Ediacaran soft-bodied biotas, are found particularly within transgressive systems, where oxygenation was persistent. We suggest that a mid-ramp position enabled physical ventilation mechanisms for shallow water column oxygenation to operate during flooding and transgressive sea-level rise. Our data support a prominent role for oxygen, and for stable oxygenated conditions in particular, in controlling both the distribution and ecology of Ediacaran skeletal metazoan communities

Analysis of finite-buffer state-dependent bulk queues

<p>In this paper, we consider a general state-dependent finite-buffer bulk queue in which the rates and batch sizes of arrivals and services are allowed to depend on the number of customers in queue and service batch sizes. Such queueing systems have rich applications in manufacturing, service operations, computer and telecommunication systems. Interesting examples include batch oven processes in the aircraft and semiconductor industry; serving of passengers by elevators, shuttle buses, and ferries; and congestion control mechanisms to regulate transmission rates in packet-switched communication networks. We develop a unifying method to study the performance of this general class of finite-buffer state-dependent bulk queueing systems. For this purpose, we use semi-regenerative analysis to develop a numerically stable method for calculating the limiting probability distribution of the queue length process. Based on the limiting probabilities, we present various performance measures for evaluating admission control and batch service policies, such as the loss probability for an arriving group of customers and for individual customers within a group. We demonstrate our method by means of numerical examples.</p>

Análisis paleontológicos a través límite Ediacárico-Cámbrico, Grupo Alto Corumbá, Brasil

This work presents the results of a palaeontological analysis focused on twenty-six species sampled in five sections of the Tamengo and Guaicurus formations, Corumbá and Ladário regions: Corcal and Laginha quarries, Porto Sobramil, Porto Figueiras and Ecoparque Cacimba. Besides, palaeoecological and palaeoenvironmental inferences are presented based on the occurrence of this fossil assemblage. Cloudina carinata Cortijo et al., 2010, previously documented in Spain and Siberia, presents an unprecedented occurrence in the American continent, in siltstones of the Tamengo Formation at Porto Figueiras section, Municipality of Corumbá, Mato Grosso do Sul State, Brazil. The biota of the Tamengo Formation is updated and composed of three biomineralizing metazoans, including poriferan spicules, putative sponge gemmule, and a sessile epibiontic prokaryotic colony. The present work also deals with the taxonomy and stratigraphic distribution of four ichnospecies and three vendotaenid species that integrate the updated benthic fauna for the upper portion of Corumbá Group. The species diversity of the Tamengo Formation was complemented by the occurrence of sixteen microfossil species that possibly represent a marine planktic assemblage. A dramatic change was identified in the palaeoenvironmental conditions of the Tamengo to Guaicurus formations, followed by a mass extinction event, possibly linked to the global Ediacaran- Cambrian mass extinction. In addition, organic-walled microfossils were prepared and analyzed from sections of three countries: nine species from the Nomtsas Formation, Namibia; four species from the Tagatiya Guazu Formation, Paraguay; and six species from the Dengying Formation, China. An international biostratigraphic essay consisting of six biozones is proposed for the uppermost Ediacaran and one biozone for the earliest Cambrian.Se presenta en este trabajo el análisis paleontológico de 26 especies fósiles muestradas en cinco cortes de las Formaciones de Tamengo y Guaicurus en las regines de Corumbá y Ladário: canteras de Corcal y Laginha, Porto Sobramil, Porto Figueiras y Ecoparque Cacimba. Además, se añaden varias interpretaciones paleoecológicas y ambientales, basadas en el registro fósil. Cloudina carinata Cortijo et al., 2010, previamente citada en España y Siberia, aparece por primera vez en el continente Americano, concretamente en limolitas de la Formación Tamengo en el corte de Porto Figueiras, Corumbá, Estado de Mato Grosso do Sul, Brasil. La biota de la Formación Tamengo incluye tres metazoos mineralizados, que incluyen espículas de poríferos, posibles gémulas de esponjas y una colonia sésil de procaiotas epibentónicos. Este trabajo se centra en la taxonomía y distribución estratigráfica de cuatro icnoespecies y tres especies de vendoténidos que forman la fauna bentónica de la parte superior del Grupo de Corumbá. La biodiversidad de la Formación Tamengo ha sido completada con el registro de 16 especies microfósiles que representan posiblemente una asociación plantónica marina. Se ha identificado un cambio drástico en las condiciones ambientales de las Formaciones Tamengo y Guaicurus, que culminan en un evento de extincinón masiva posiblemente relacionado con la extincición en masa que marca el tránsito global Ediácarico- Cámbrico. Por otro lado, se han extraído microfósiles de pared orgánica de varios afloramientos: nueve especies de la Formación de Nomtsas (Namibia), cuatro de la Formación Tagatiya Guazu (Paraguay) y seis de la Formación Dengying (China). Se propone un marco bioestratigráfico para el Ediacárico terminal que incluye seis biozonas y una biozona para el Cámbrico basal

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