Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform

The availability of crop specimens archived in herbaria and old seed collections represent valuable resources for the analysis of plant genetic diversity and crop domestication. The ability to extract ancient DNA (aDNA) from such samples has recently allowed molecular genetic investigations to be undertaken in ancient materials. While analyses of aDNA initially focused on the use of markers which occur in multiple copies such as the internal transcribed spacer region (ITS) within ribosomal DNA and those requiring amplification of short DNA regions of variable length such as simple sequence repeats (SSRs), emphasis is now moving towards the genotyping of single nucleotide polymorphisms (SNPs), traditionally undertaken in aDNA by Sanger sequencing. Here, using a panel of barley aDNA samples previously surveyed by Sanger sequencing for putative causative SNPs within the flowering-time gene PPD-H1, we assess the utility of the Kompetitive Allele Specific PCR (KASP) genotyping platform for aDNA analysis. We find KASP to out-perform Sanger sequencing in the genotyping of aDNA samples (78% versus 61% success, respectively), as well as being robust to contamination. The small template size (≥46 bp) and one-step, closed-tube amplification/genotyping process make this platform ideally suited to the genotypic analysis of aDNA, a process which is often hampered by template DNA degradation and sample cross-contamination. Such attributes, as well as its flexibility of use and relatively low cost, make KASP particularly relevant to the genetic analysis of aDNA samples. Furthermore, KASP provides a common platform for the genotyping and analysis of corresponding SNPs in ancient, landrace and modern plant materials. The extended haplotype analysis of PPD-H1 undertaken here (allelic variation at which is thought to be important for the spread of domestication and local adaptation) provides further resolution to the previously identified geographic cline of flowering-time allele distribution, illustrating how KASP can be used to aid genetic analyses of aDNA from plant species. We further demonstrate the utility of KASP by genotyping ten additional genetic markers diagnostic for morphological traits in barley, shedding light on the phenotypic traits, alleles and allele combinations present in these unviable ancient specimens, as well as their geographic distributions.

Note: Active optical detection of cloud from a balloon platform

A disposable backscatter instrument is described for optical detection of cloud in the atmosphere from a balloon-carried platform. It uses an ultra-bright light emitting diode (LED) illumination source with a photodiode detector. Scattering of the LED light by cloud droplets generates a small optical signal which is separated from background light fluctuations using a lock-in technique. The signal to noise obtained permits cloud detection using the scattered LED light, even in daytime. The response is interpreted in terms of the equivalent visual range within the cloud. The device is lightweight (150 g) and low power (∼30 mA), for use alongside a conventional meteorological radiosonde.

Using standby generators in support of an electricity network: logistics and experience

Electricity load shifting is becoming a big topic in the world of ‘green’ retail. Marks & Spencer (M&S) aim to become the world’s most sustainable retailer (1) and part of that commitment means contributing to the future electricity network. While intelligent operation of fridges and Heating, Ventilation and Air Conditioning (HVAC) systems are a wide area of research, standby generators should be considered too, as they are the most widely adopted form of distributed generation. In this paper, the experience of using standby generators in Northern Ireland to support the grid is shared and the logistics of future projects are discussed. Interactions with maintenance schedules, electricity costs, grid code, staffing and store opening times are discussed as well as the financial implications associated with running generators for grid support.

TESSA - Toolkit for experimentation with multimodal sensory substitution and augmentation

TESSA is a toolkit for experimenting with sensory augmentation. It includes hardware and software to facilitate rapid prototyping of interfaces that can enhance one sense using information gathered from another sense. The toolkit contains a range of sensors (e.g. ultrasonics, temperature sensors) and actuators (e.g. tactors or stereo sound), designed modularly so that inputs and outputs can be easily swapped in and out and customized using TESSA’s graphical user interface (GUI), with “real time” feedback. The system runs on a Raspberry Pi with a built-in touchscreen, providing a compact and portable form that is amenable for field trials. At CHI Interactivity, the audience will have the opportunity to experience sensory augmentation effects using this system, and design their own sensory augmentation interfaces.

A simple and versatile 2-dimensional platform to study plant germination and growth under controlled humidity

We describe a simple, inexpensive, but remarkably versatile and controlled growth environment for the observation of plant germination and seedling root growth on a flat, horizontal surface over periods of weeks. The setup provides to each plant a controlled humidity (between 56% and 91% RH), and contact with both nutrients and atmosphere. The flat and horizontal geometry of the surface supporting the roots eliminates the gravitropic bias on their development and facilitates the imaging of the entire root system. Experiments can be setup under sterile conditions and then transferred to a non-sterile environment. The system can be assembled in 1-2 minutes, costs approximately 8.78$ per plant, is almost entirely reusable (0.43$ per experiment in disposables), and is easily scalable to a variety of plants. We demonstrate the performance of the system by germinating, growing, and imaging Wheat (Triticum aestivum), Corn (Zea mays), and Wisconsin Fast Plants (Brassica rapa). Germination rates were close to those expected for optimal conditions.

Robust multimodal face and fingerprint fusion in the presence of spoofing attacks

Anti-spoofing is attracting growing interest in biometrics, considering the variety of fake materials and new means to attack biometric recognition systems. New unseen materials continuously challenge state-of-the-art spoofing detectors, suggesting for additional systematic approaches to target anti-spoofing. By incorporating liveness scores into the biometric fusion process, recognition accuracy can be enhanced, but traditional sum-rule based fusion algorithms are known to be highly sensitive to single spoofed instances. This paper investigates 1-median filtering as a spoofing-resistant generalised alternative to the sum-rule targeting the problem of partial multibiometric spoofing where m out of n biometric sources to be combined are attacked. Augmenting previous work, this paper investigates the dynamic detection and rejection of livenessrecognition pair outliers for spoofed samples in true multi-modal configuration with its inherent challenge of normalisation. As a further contribution, bootstrap aggregating (bagging) classifiers for fingerprint spoof-detection algorithm is presented. Experiments on the latest face video databases (Idiap Replay- Attack Database and CASIA Face Anti-Spoofing Database), and fingerprint spoofing database (Fingerprint Liveness Detection Competition 2013) illustrate the efficiency of proposed techniques.

Bone Remodeling Adjacent to Morse Cone-Connection Implants with Platform Switch: A Fluorescence Study in the Dog Mandible

Purpose: The aim of this study was to evaluate, through fluorescence analysis, the effect that different interimplant distances, after prosthetic restoration, will have on bone remodeling in submerged and nonsubmerged implants restored with a ""platform switch."" Materials and Methods: Fifty-six Ankylos implants were placed 1.5 mm subcrestally in seven dogs. The implants were placed so that two fixed prostheses, with three interimplant contacts separated by 1-mm, 2-mm, and 3-mm distances, could be fabricated for each side of the mandible. The sides and the positions of the groups were selected randomly. To better evaluate bone remodeling, calcein green was injected 3 days before placement of the prostheses at 12 weeks postimplantation. At 3 days before sacrifice (8 weeks postloading), alizarin red was injected. The amounts of remodeled bone within the different interimplant areas were compared statistically before and after loading in submerged and nonsubmerged implants. Results: Statistically significant differences existed in the percentage of remodeled bone seen in the different regions. Mean percentages of remodeled bone in the submerged and nonsubmerged groups, respectively, were as follows: for the 1-mm distance, 23.0% +/- 0.05% and 23.1% +/- 0.03% preloading and 27.0% +/- 0.03% and 25.2% +/- 0.04% postloading, for the 2-mm distance, 18.2% +/- 0.05% and 18.1% +/- 0.04% preloading and 21.3% +/- 0.07% and 19.9% +/- 0.03% postloading, for the 3-mm distance, 18.3% +/- 0.03% and 18.3% +/- 0.03% preloading and 18.8% +/- 0.04% and 19.8% +/- 0.04% postloading, for distal-extension regions, 16.6% +/- 0.02% and 17.4% +/- 0.04% preloading and 17.0% +/- 0.04% and 18.4% +/- 0.04% postloading. Conclusions: Based upon this animal study, loading increases bone formation for submerged or nonsubmerged implants, and the interimplant distance of 1 mm appears to result in more pronounced bone remodeling than the 2-mm or 3-mm distances in implants with a ""platform switch."" INT J ORAL MAXILLOFAC IMPLANTS 2009;24:257-266

Upper-mantle seismic anisotropy from SKS splitting in the South American stable platform: A test of asthenospheric flow models beneath the lithosphere

Upper-mantle seismic anisotropy has been extensively used to infer both present and past deformation processes at lithospheric and asthenospheric depths. Analysis of shear-wave splitting (mainly from core-refracted SKS phases) provides information regarding upper-mantle anisotropy. We present average measurements of fast-polarization directions at 21 new sites in poorly sampled regions of intra-plate South America, such as northern and northeastern Brazil. Despite sparse data coverage for the South American stable platform, consistent orientations are observed over hundreds of kilometers. Over most of the continent, the fast-polarization direction tends to be close to the absolute plate motion direction given by the hotspot reference model HS3-NUVEL-1A. A previous global comparison of the SKS fast-polarization directions with flow models of the upper mantle showed relatively poor correlation on the continents, which was interpreted as evidence for a large contribution of ""frozen"" anisotropy in the lithosphere. For the South American plate, our data indicate that one of the reasons for the poor correlation may have been the relatively coarse model of lithospheric thicknesses. We suggest that improved models of upper-mantle flow that are based on more detailed lithospheric thicknesses in South America may help to explain most of the observed anisotropy patterns.

A full family of multimodal maps on the circle

We exhibit a family of trigonometric polynomials inducing a family of 2m-multimodal maps on the circle which contains all relevant dynamical behavior.

GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

Nanoparticle Platform to Modulate Reaction Mechanism of Phenothiazine Photosensitizers

Herein, we report on the synthesis of photosensitizing nanoparticles in which the generation of different oxidizing species, i.e., singlet oxygen ((1)O(2)) or radicals, was modulated. Sol gel and surface chemistry were used to obtain nanoparticles with specific ratios of dimer to monomer species of phenothiazine photosensitizers (PSs). Due to competition between the reactions involving electron transfer within dimer species and energy transfer from monomer triplets to oxygen, the efficiency of (1)O(2) generation could be controlled. Nanoparticles with an excess of dimer have an (1)O(2) generation efficiency (S(Delta)) of 0.01 while those without dimer have a S, value of 0.4. Furthermore, we demonstrate that the PS properties of the nanoparticles are not subjected to interference from the external medium as is commonly the case for free PSs, i.e., PS ground and triplet states are not reduced by NADH and ascorbate, respectively, and singlet excited states are less suppressed by bromide. The modulated (1)O(2) generation and the PS protection from external interferences make this nanoparticle platform a promising tool to aid in performing mechanistic studies in biological systems. Also, it offers potential application in technological areas in which photo-induced processes take place.

RailsTNE : En multimodal informationsplattform i ett interorganisatoriskt nätverk

Att utreda möjligheterna att etablera dataförsörjning riktade mot multimodala transporttjänster är idag av största intresse. Det är också intressant att försöka utnyttja de standarder som tagits fram när en dataförsörjningskedja ska etableras. Detta examensarbete genomfördes på Triona AB i Borlänge. Triona har utvecklat databasen Transport Network Engine (TNE), som idag används för att läsa in data från Nationella VägDataBasen (NVDB) och från skogsnäringen. Målet med arbetet var att ta fram en informationsmodell, som beskriver hur ett transportnät med nätanknutna data, som stödjer multimodala transporter och resor, kan lagras i TNE. En förlängning av målet blev att, utifrån ett givet användarfall, etablera dataförsörjning till TNE och lägga in de nödvändiga datamängderna. TNE bygger på ESRI:s produkter och funktionalitet för hantering av geografisk information och informationsmodell och datahantering i TNE baseras på internationella och svenska standarder. Idag finns all information om järnvägsnätet hos Banverket och det finns ingen koppling mellan Banverkets databas Baninformationssystemet (BIS) och Vägverkets databas NVDB. För att den kopplingen ska kunna ske, krävs att de båda verken kan samarbeta som två stora organisationer i ett väl fungerande nätverk. Ett så kallat interorganisatoriskt nätverk. Det akademiska syftet var att föreslå en arkitekturstrategi som stödjer ett sådant nätverk. Vi upptäckte att arkitekturstrategierna IRM och VBS är uppbyggda för att inrikta sig på enskilda organisationer, och det visade sig svårt att följa en specifik strategi inom ett nätverk med flera organisationer. I vårt användarfall måste nätverket mellan Banverket, Vägverket och Stora Enso samarbeta över organisationsgränserna. Därför behövs en strategi för ett interorganisatoriskt samarbete så att informationen kan struktureras på ett gemensamt sätt. Vi föreslår ett antal idealtypskriterier som vi utgått efter i struktureringen av systemarkitekturen. Den innehåller en informationsmodell för både väg- och järnvägsdata som följer standarden SS 63 70 04. Arbetet avgränsades till att endast innehålla de datamängder som användarfallet kräver. Vi har analyserat KombiTIF-rapporten som är ett avslutat projekt styrt av Banverket på uppdrag av Näringsdepartementet. Rapporten ger ett förslag på en lösning i form av en arena som ska göra data tillgänglig för användning. Vi väljer att se TNE-plattformen som en realisering av denna arena. Enligt vårt förslg så ska TNE-plattformen hämta in det mest grundläggande datat om järnvägsnät och nätanknuten data från BIS och standardiserad information om vägnät och nätanknuten data från NVDB via ett gränssnitt. I framtiden är det möjligt att på samma sätt ta in andra trafiknät såsom Sjöfartsverket, Luftfartsverket och Rikstrafiken. Vi arbetade efter en egen metod som vi tog fram med valda delar från andra metoder; kartläggning, perspektivanalys, verksamhetsanalys, utveckling och utvärdering. Arbetet genomfördes iterativt i de fem olika faserna.

Separation and Execution of graphical engine on a cross platform IDE to enhance performance

“Biosim” is a simulation software which works to simulate the harvesting system.This system is able to design a model for any logistic problem with the combination of several objects so that the artificial system can show the performance of an individual model. The system will also describe the efficiency, possibility to be chosen for real life application of that particular model. So, when any one wish to setup a logistic model like- harvesting system, in real life he/she may be noticed about the suitable prostitution for his plants and factories as well as he/she may get information about the least number of objects, total time to complete the task, total investment required for his model, total amount of noise produced for his establishment in advance. It will produce an advance over view for his model. But “Biosim” is quite slow .As it is an object based system, it takes long time to make its decision. Here the main task is to modify the system so that it can work faster than the previous. So, the main objective of this thesis is to reduce the load of “Biosim” by making some modification of the original system as well as to increase its efficiency. So that the whole system will be faster than the previous one and performs more efficiently when it will be applied in real life. Theconcept is to separate the execution part of ”Biosim” form its graphical engine and run this separated portion in a third generation language platform. C++ is chosenhere as this external platform. After completing the proposed system, results with different models have been observed. The results show that, for any type of plants of fields, for any number of trucks, the proposed system is faster than the original system. The proposed system takes at least 15% less time “Biosim”. The efficiency increase with the complexity of than the original the model. More complex the model, more efficient the proposed system is than original “Biosim”.Depending on the complexity of a model, the proposed system can be 56.53 % faster than the original “Biosim”.

Multimodal Literacy as a form of Communication : What is the state of the students at Dalarna University multimodal literacy?

Literacy is an invaluable asset to have, and has allowed for communication, documentation and the spreading of ideas since the beginning of the written language. With technological advancements, and new possibilities to communicate, it is important to question the degree to which people’s abilities to utilise these new methods have developed in relation to these emerging technologies. The purpose of this bachelor’s thesis is to analyse the state of students’ at Dalarna University mulitimodal literacy, as well as their experience of multimodality in their education. This has led to the two main research questions: What is the state of the students at Dalarna University multimodal literacy? And: How have the students at Dalarna University experienced multimodality in education? The paper is based on a mixed-method study that incorporates both a quantitative and qualitative aspect to it. The main thrust of the research paper is, however, based on a quantitative study that was conducted online and emailed to students via their program coordinators. The scope of the research is in audio-visual modes, i.e. audio, video and images, while textual literacy is presumed and serves as an inspiration to the study. The purpose of the study is to analyse the state of the students’ multimodal literacy and their experience of multimodality in education. The study revealed that the students at Dalarna University have most skill in image editing, while not being very literate in audio or video editing. The students seem to have had mediocre experience creating meaning through multimodality both in private use and in their respective educational institutions. The study also reveals that students prefer learning by means of video (rather than text or audio), yet are not able to create meaning (communicate) through it.