EpiCollect+: linking smartphones to web applications for complex data collection projects.

© 2014 Aanensen DM et al.Previously, we have described the development of the generic mobile phone data gathering tool, EpiCollect, and an associated web application, providing two-way communication between multiple data gatherers and a project database. This software only allows data collection on the phone using a single questionnaire form that is tailored to the needs of the user (including a single GPS point and photo per entry), whereas many applications require a more complex structure, allowing users to link a series of forms in a linear or branching hierarchy, along with the addition of any number of media types accessible from smartphones and/or tablet devices (e.g., GPS, photos, videos, sound clips and barcode scanning). A much enhanced version of EpiCollect has been developed (EpiCollect+). The individual data collection forms in EpiCollect+ provide more design complexity than the single form used in EpiCollect, and the software allows the generation of complex data collection projects through the ability to link many forms together in a linear (or branching) hierarchy. Furthermore, EpiCollect+ allows the collection of multiple media types as well as standard text fields, increased data validation and form logic. The entire process of setting up a complex mobile phone data collection project to the specification of a user (project and form definitions) can be undertaken at the EpiCollect+ website using a simple drag and drop procedure, with visualisation of the data gathered using Google Maps and charts at the project website. EpiCollect+ is suitable for situations where multiple users transmit complex data by mobile phone (or other Android devices) to a single project web database and is already being used for a range of field projects, particularly public health projects in sub-Saharan Africa. However, many uses can be envisaged from education, ecology and epidemiology to citizen science

Air Flow Measurements During Medium-Voltage Load Current Interruptions

Air has been considered a good alternative to SF6 as arc quenching medium for load break switchgear at medium voltage ratings. In this work, the air flow characteristics and influence from the electric arc have been studied for typical currents and over-pressures. The cooling air velocity is typically in the range 150 - 200 m/s and thus well below supersonic speed. The arc and the surrounding hot air severely affect the air flow pattern by causing clogging in the contact and nozzle region

The development and use of bioinformatic web applications for infectious disease microbiology

The ever-increasing generation and submission of DNA sequences, and associated biological data, to publicly available databases demands software for the analysis of the biological meanings held within. The web provides a common platform for the provision of tools enabling the concurrent deposition, visualisation and analysis of data collected by many users from many different locations. Open programmatic web standards allow the development of applications addressing diverse biological questions and, more recently, are providing methods enabling functionality more traditionally associated with desktop software to be provided via the internet. In this work I detail the development and use of web applications addressing different, but not exclusive, areas of infectious disease microbiology. Firstly, an application utilised by a group of researchers (including myself) to undertake a comparative genetic analysis of the capsular biosynthetic locus from serotypes of the pathogen Streptococcus pneumoniae is detailed. Secondly, an application widely used by communities of researchers and public health laboratories for the assignment of microbial isolates to strains via the internet: mlst.net is described. Thirdly, I describe a generic electronic taxonomy application for assigning strains to bacterial species, exemplified using sequences from the viridans group streptococci, the taxonomy of which is notoriously difficult to define. Lastly, I describe the use of web mapping tools for molecular epidemiological databases, such as mlst.net, and further detail their application to the European distribution of genotypes of Staphylococcus aureus, to catalogue the global distribution of the emerging amphibian fungal pathogen Batrachochytrium dendrobatidis and to provide geocoding tools to encourage users to submit and explore their own data in the geographical context they were collected. Each application has been designed with generality in mind and through reference to user workflows and biological examples, I demonstrate the extensibility and general applicability of current web development methodologies to enable the provision of applications addressing a diversity of biological questions

Air Flow Measurements During Medium-Voltage Load Current Interruptions

Air has been considered a good alternative to SF6 as arc quenching medium for load break switchgear at medium voltage ratings. In this work, the air flow characteristics and influence from the electric arc have been studied for typical currents and over-pressures. The cooling air velocity is typically in the range 150 - 200 m/s and thus well below supersonic speed. The arc and the surrounding hot air severely affect the air flow pattern by causing clogging in the contact and nozzle region

Vurdering av metoder for økologisk produksjon av storfekjøtt. Fordeler og ulemper ved ulike produksjonssystemer for økologisk storfekjøtt.

På oppdrag fra Relelverksutvalget for økologisk produksjon (RVU) har Bioforsk utført en vurdering av fordeler og ulemper knyttet til luftekravet for okser i økologisk produksjon, samt en utredning av mulige løsninger for lufting av okser. I tillegg er det utført en vudering av alternative metoder for produksjon av økologisk storfekjøtt, for eksempel produksjon av kastrat-, kvige- og kalvekjøtt. Økologisk produksjon av storfekjøtt er vurdert med bakgrunn i kravet om lufting av okser. Regelverket for økologisk produksjon(EU-reg. 2091/92) sier at "(...) okser skal ha tilgang til beiter eller luftegårder. Okser over ett år gamle kan holdes i et husdyrrom med fri adgang til en luftegård hele året, i stedet for å gå på beite i sommerperioden." Nytt regelverk som vil bli gjeldende i løpet av 2011 (EU-reg 834/2007 og 889/2008) vil mest sannsynlig ha samme ordlyd. Tilgang på luftegård/større plass er positivt for helse og velferd hos storfe, og det finnes flere alternative og gode måter å oppstalle okser på som både tilfredsstiller dyrenes krav til lufting og mulighet for naturlig atferd, uten at det går på bekostning av produksjon og sikkerhet. Beitebasert kjøttproduksjon på kastrater, kviger og kalver kan være gode alternativer til kjøttproduksjon på okser. Slike produksjoner gir mulighet for å produsere kjøtt av god kvalitet på en bærekraftig måte samtidig som en hindrer gjengroing av kulturlandskapet. Hovedtanken bak økologisk kjøttproduksjon på storfe må være at produksjonen tar hensyn til det økologiske regelverket og IFOAM sine økologiske prinsipper. Produksjonen skal være miljøvennlig, tilpasset naturens kretsløp og økologiske balanse, samt ha fokus på god dyrevelferd. Hvilken produksjonsform den enkelte kjøttprodusenten velger avhenger av hva slags ressurser den enkelte produsent/gårdsbruk har tilgang på. Det er viktig at rådgivningstjenesten har oversikt over de alternative produksjonsformene og kommer med de riktige rådene for den enkelte besetningen

The multilocus sequence typing network: mlst.net

The unambiguous characterization of strains of a pathogen is crucial for addressing questions relating to its epidemiology, population and evolutionary biology. Multilocus sequence typing (MLST), which defines strains from the sequences at seven house-keeping loci, has become the method of choice for molecular typing of many bacterial and fungal pathogens (and non-pathogens), and MLST schemes and strain databases are available for a growing number of prokaryotic and eukaryotic organisms. Sequence data are ideal for strain characterization as they are unambiguous, meaning strains can readily be compared between laboratories via the Internet. Laboratories undertaking MLST can quickly progress from sequencing the seven gene fragments to characterizing their strains and relating them to those submitted by others and to the population as a whole. We provide the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated sequences, and a recently developed method (eBURST) for identifying clonal complexes within a species and displaying the overall structure of the population. This network of MLST websites is available a

Air Flow Measurements during Medium-Voltage Load Current Interruptions

Air has been considered a good alternative to SF6 as arc quenching medium for load break switchgear at medium voltage ratings. In this work, the air flow characteristics and influence from the electric arc have been studied for typical currents and over-pressures. The cooling air velocity is typically in the range 150 - 200 m/s and thus well below supersonic speed. The arc and the surrounding hot air severely affect the air flow pattern by causing clogging in the contact and nozzle region

Contact and Nozzle Wear from 100 Interruptions for a Puffer-Type Air Load Break Switch

One type test requirement for medium voltage load break switches is to interrupt 100 consecutive "mainly active loads". A puffer-type switch with axial-blown arc has been tested according to the 630 A/24 kV ratings. The nozzle and contact wear were measured regularly to investigate design requirements and the impact from nozzle wear on gas flow. The contact wear is only moderate, while the nozzle wear causes a decrease in pressure build-up, which in turn may influence the interruption performance

Deep clustering of bacterial tree images

The field of genomic epidemiology is rapidly growing as many jurisdictions begin to deploy whole-genome sequencing (WGS) in their national or regional pathogen surveillance programmes. WGS data offer a rich view of the shared ancestry of a set of taxa, typically visualized with phylogenetic trees illustrating the clusters or subtypes present in a group of taxa, their relatedness and the extent of diversification within and between them. When methicillin-resistant Staphylococcus aureus (MRSA) arose and disseminated widely, phylogenetic trees of MRSA-containing types of S. aureus had a distinctive 'comet' shape, with a 'comet head' of recently adapted drug-resistant isolates in the context of a 'comet tail' that was predominantly drug-sensitive. Placing an S. aureus isolate in the context of such a 'comet' helped public health laboratories interpret local data within the broader setting of S. aureus evolution. In this work, we ask what other tree shapes, analogous to the MRSA comet, are present in bacterial WGS datasets. We extract trees from large bacterial genomic datasets, visualize them as images and cluster the images. We find nine major groups of tree images, including the 'comets', star-like phylogenies, 'barbell' phylogenies and other shapes, and comment on the evolutionary and epidemiological stories these shapes might illustrate. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'