Strong pathogen competition in neonatal gut colonisation

Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.Peer reviewe

Electrical and thermal applications of carbon nanotube films

Abstract Carbon nanotubes (CNTs) have fascinating mechanical, electrical and thermal properties, all of which significantly depend on structural properties such as nanotube length, number of walls, lattice defect densities, impurities and surface functional groups. A number of different applications of carbon nanotubes have been demonstrated during the past two decades including electrical interconnects, transistors, heating and cooling devices, sensors and various actuators. However, further studies on the structure-dependent properties and innovative handling techniques of these materials are needed in order to explore the limitations of use and to be able fully to exploit the advantageous properties of such one-dimensional sp2 hybridized carbon nanomaterials. In this thesis, random networks of single-wall and multi-walled carbon nanotubes (SWCNTs and MWCNTs, respectively) and aligned films of multi-walled carbon nanotubes are studied in the context of three main application fields: gas sensing, electrical interconnects/electrodes and thermal cooling elements. Analyses of associated material properties and some feasible integration techniques are discussed. Single-wall and multi-walled carbon nanotube films cast from aqueous dispersions are shown to be selective nitric oxide sensing components in Taguchi-type sensor devices, in which films based on SWCNTs outperformed those made of MWCNTs. The thickness dependent electrical conduction mechanism of inkjet-printed SWCNT films is also discussed. Robust aligned MWCNT films are demonstrated as soft electrical contact brushes in DC motors and in other moving electrical contacts. The thermal properties of freestanding aligned MWCNT forests are analyzed and shown to be potential alternatives to copper or aluminium in the thermal management of electrical components.Tiivistelmä Hiilinanoputkien kiehtovat mekaaniset, sähköiset ja lämmönjohto-ominaisuudet ovat kiinnostaneet tutkijoita suuresti viimeisten kahden vuosikymmenen ajan. Monia erilaisia applikaatioita on demonstroitu tänä aikana: mukaan lukien sähköiset kontaktit, transistori-rakenteet, lämmitys- ja jäähdytyslaitteet, anturirakenteet sekä erilaiset aktuaattori-rakenteet. Tämän väitöskirjan päätavoitteena on tutkia hiilinanoputkien toiminnollisuutta ja käytännöllisyyttä erilaisissa sovelluskohteissa. Tässä työssä käytettävät hiilinanoputkirakenteet ovat joko satunnaisjärjestyksessä olevia nanoputkista koostuvia verkostorakenteita tai yhdensuuntaisia, makroskooppisia hiilinanoputkikalvoja. Nanoputkia tutkitaan kolmessa erityyppisessä sovelluskohteessa: kaasuanturisovelluksessa, sähköisissä kontaktirakenteissa sekä jäähdytyselementteinä. Työssä analysoidaan hiilinanoputkirakenteiden ominaisuuksia eri sovelluskohteissa sekä esitetään joitain käyttökelpoisia tekniikoita hiilinanoputkien integroimiseen olemassa oleviin tekniikoihin. Hiilinanoputkien osoitetaan olevan käyttökelpoisia aktiivisia materiaaleja typpioksidille resistiivisessä kaasuanturirakenteessa. Tulosten perusteella yksiseinämäiset hiilinanoputket ovat moniseinämäisiä herkempiä ja parempia kyseisessä sovelluksessa. Lisäksi tutkitaan ja analysoidaan mustesuihku-tulostettujen yksiseinämäisten hiilinanoputkifilmien sähköisten ominaisuuksien riippuvuutta filmin paksuudesta. Vantterien yhdensuuntaisten moniseinämäisten hiilinanoputkirakenteiden osoitetaan toimivan erinomaisesti pehmeinä sähköisinä kontaktielementteinä liikkuvissa sähköisissä kontakteissa. Vapaasti seisovien yhdensuuntaisten, moniseinämäisten hiilinanoputkirakenteiden lämmönjohto-ominaisuuksien tutkiminen ja analysointi osoittaa, että kyseisiä rakenteita voidaan käyttää tehokkaina jäähdytyselementteinä ja mahdollisesti korvaavana vaihtoehtona alumiinille ja kuparille sähköisten komponenttien lämmönhallinta sovelluksissa

Themisto : a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes

Publisher Copyright: © 2023 The Author(s). Published by Oxford University Press.Motivation: Huge datasets containing whole-genome sequences of bacterial strains are now commonplace and represent a rich and important resource for modern genomic epidemiology and metagenomics. In order to efficiently make use of these datasets, efficient indexing data structures-that are both scalable and provide rapid query throughput-are paramount.Results: Here, we present Themisto, a scalable colored k-mer index designed for large collections of microbial reference genomes, that works for both short and long read data. Themisto indexes 179 thousand Salmonella enterica genomes in 9 h. The resulting index takes 142 gigabytes. In comparison, the best competing tools Metagraph and Bifrost were only able to index 11 000 genomes in the same time. In pseudoalignment, these other tools were either an order of magnitude slower than Themisto, or used an order of magnitude more memory. Themisto also offers superior pseudoalignment quality, achieving a higher recall than previous methods on Nanopore read sets.Availability and implementation: Themisto is available and documented as a C++ package at available under the GPLv2 license.Peer reviewe

High-resolution sweep metagenomics using fast probabilistic inference

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.Peer reviewe

High-resolution sweep metagenomics using fast probabilistic inference

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.Peer reviewe

Influence of different curing conditions on the pore structure and the early age properties of mortars with fly ash and blast-furnace slag

En este trabajo se ha estudiado la evolución de la microestructura, propiedades de durabilidad y resistencias mecánicas de morteros preparados con cementos comerciales, que contienen ceniza volante (entre un 21% y un 35%) y escoria de alto horno (entre un 66% y un 80%), expuestos a tres ambientes, un ambiente óptimo de laboratorio, y dos ambientes representativos del clima Atlántico y Mediterráneo respectivamente. Como referencia de comportamiento, también se ensayaron morteros de cemento Portland. La microestructura se caracterizó mediante porosimetría de intrusión de mercurio. En lo referente a la durabilidad, se estudiaron los coeficientes de absorción capilar y de migración de cloruros en estado no estacionario. También se determinó la resistencia a compresión de los morteros. Los ensayos se realizaron a 7, 28 y 90 días. La principal conclusión alcanzada es que los cementos con cenizas y escorias expuestos a condiciones ambientales representativas de los climas Atlántico y Mediterráneo, pueden desarrollar unas propiedades en servicio adecuadas al cabo de tres meses.In this work, the evolution of the microstructure, durability properties and mechanical strength of mortars made with commercial cements, which contain fly ash (between 21% and 35%) and ground granulated blast-furnace slag (between 66% and 80%), were studied. These mortars were exposed to three different environments during their hardening, an optimum laboratory condition, and two environments representing a mild Atlantic climate and a Mediterranean climate, respectively. As a reference, ordinary Portland cement mortars were also tested. The microstructure was characterized using mercury intrusion porosimetry. Regarding durability, the capillary suction coefficient and non-steady-state chloride migration coefficient were determined. Compressive strength was studied too. The tests were performed at 7, 28 and 90 days. The main conclusion of this work is that cements with slag and fly ash hardened under environmental conditions of Atlantic and Mediterranean climates, can develop good service properties after three months of hardening.Este trabajo ha sido financiado por el Ministerio de Ciencia e Innovación y Economía y Competitividad del Gobierno de España a través de los proyectos BIA2010-20548 y BIA2011-25721. J.M. Ortega ha sido beneficiario de una beca predoctoral perteneciente al programa de “Formación de Personal Investigador (FPI)” (referencia BES-2008-002650)

Novel printed nanostructured gas sensors

AbstractThere is a need for low-cost mass-production circuits on various substrates, possibly performing some simple functions as switches, antennas, displays, and sensors. Also in the field of gas sensors widely used in several applications there is a need for such novel fabrication technologies and materials. In this paper, we present three gas sensor structures fabricated using novel printing techniques. Inkjet and gravure printing techniques were used for fabrication of resistive WO3 nanoparticle gas sensors for detection of NO, and inkjet printing was utilized for fabrication of solid electrolyte (mixture of H3PW12O40 and PVC) in a nanostructured Metal-Electrolyte-Insulator- Semiconductor (MEIS) transistor for detection of H2. The sensor structures were found to be sensitive for detection of NO below 10ppm, and H2 below 100ppm concentrations in synthetic air, respectively