CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

<p>Abstract</p> <p>Background</p> <p>The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce <smcaps>CLOTU</smcaps>, an online and open access pipeline for processing 454 amplicon reads. C<smcaps>LOTU</smcaps> has been constructed to be highly user-friendly and flexible, since different types of analyses are needed for different datasets.</p> <p>Results</p> <p>In <smcaps>CLOTU</smcaps>, the user can filter out low quality sequences, trim tags, primers, adaptors, perform clustering of sequence reads, and run <smcaps>BLAST</smcaps> against NCBInr or a customized database in a high performance computing environment. The resulting data may be browsed in a user-friendly manner and easily forwarded to downstream analyses. Although <smcaps>CLOTU</smcaps> is specifically designed for analyzing 454 amplicon reads, other types of DNA sequence data can also be processed. A fungal ITS sequence dataset generated by 454 sequencing of environmental samples is used to demonstrate the utility of <smcaps>CLOTU</smcaps>.</p> <p>Conclusions</p> <p>C<smcaps>LOTU</smcaps> is a flexible and easy to use bioinformatics pipeline that includes different options for filtering, trimming, clustering and taxonomic annotation of high throughput sequence reads. Some of these options are not included in comparable pipelines. C<smcaps>LOTU</smcaps> is implemented in a Linux computer cluster and is freely accessible to academic users through the Bioportal web-based bioinformatics service (<url>http://www.bioportal.uio.no</url>).</p

Modellering og simulering av jernbanesystemer : En lagdelt tilnærming

Oppgaven tar for seg petrinet, og ser på hvordan dette verktøyet egner seg til å modellere større nett. Som eksempel på en type store nett er det brukt jernbanenett. Oppgaven presenterer også noen teknikker for å forenkle modelleringen

Investigation of unsteady and turbulent flow int the jet flow injection swirl rig using LDV, pressure measurements and CFD

Diplomoppgava fortsetter arbeidet som blei starta i prosjektoppgava høsten 2008. Det er utført laboratorieforsøk på en minirigg der spinn settes opp i et vertikalt rør. Nedstrøms kan vann injiseres tangentielt gjennom ei dyse i motsatt retning av spinnet. Strømningsbildet og trykksvingninger er tidligere undersøkt ved hjelp av pitot og trykkmålinger. Arbeidet i denne oppgava omfatter utbedring av miniriggen for måling med LDV, samt supplerende målinger av hastighet med LDV og trykkmålinger. En rekke målinger av hastighet og trykk er gjort for å undersøke strømningsbildet uten og med vanninjeksjon. De eksperimentelle resultata er sammenligna med numeriske beregninger gjort i ANSYS CFX. Det er funnet at vanninjeksjon dreper spinnet i strømninga, og gir lavere tangentiell hastighet. I flere tilfeller minsker trykkpulsasjonene, men det er også funnet at vanninjiseringa kan ha motsatt effekt. Dette avhenger av swirlnummer og trykk i strømninga. Det er ikke funnet sammenfallende frekvenser for trykkpulsasjona og det turbulente hastighetsleddet. De numeriske simuleringene beskriver strømningsbildet på en tilfredsstillende måte uten vanninjeksjon. Spinnet underpredikerers, i tillegg til at profilformen avviker noe. Ved vanninjeksjon dempes spinnet betraktelig mer i de numeriske simuleringene enn hva som virkelig er målt i lab. Særlig den tangentielle hastigheta og det tangentielle momentet avviker mye i verdi

Secondary flow fields in Francis turbines : mapping and analyzing dynamics in rotor-stator interaction and draft tube flow with novel methods

Hydropower, and especially Francis turbines, for electricity production has a history of more than 100 years and has proved to be one of the most efficient ways of utilizing renewable energy for electricity production. Yet, there are several problems to be solved regarding producing and running cost effective, high efficient and durable turbines. Secondary flow fields are all unwanted flow patterns present in the turbine. The major fluctuating flow fields in Francis turbines are caused by rotor‐stator interaction when the runner vane passes the guide vane wake and the swirling flow in the draft tube at off‐design operation. Such flow fields have a negative effect in terms of causing losses, vibrations, noise or damage to the turbine structure. The flow through a Francis turbine, especially at off‐design operation is not optimal, and is characterized by a dynamic and fluctuating flow pattern. It is difficult, but important to understand the behavior of the dynamics to better predict the negative effects of the fluctuating flows, and also in order to minimize or remove the unwanted effects by e.g. geometry modifying or flow control. This work aims to introduce new methods helping to obtain a deeper understanding on the dynamics present in wake flow and in rotor‐stator interaction. It is investigated whether vortex generators, VGs, can have a positive effect on the wake with respect to rotor‐stator interaction. Experimental TRPIV (Transient Particle Image Velocimetry) wake data recorded at 10 000 Samples/sec from a cylinder in a stream at 1‐6 m/s and hydrofoils in a stream at 9 m/s are studied. Both plain hydrofoils, and hydrofoils where Vortex Generators – VGs are mounted are used in the study. The Reynolds number is in the range of 1.2∙104 – 7.3∙105. The velocity fields from both the cylinder and the hydrofoils are used as inlet boundary condition in a 2D CFD‐case simulating rotor‐stator interaction. The characteristic frequencies of the system are the vortex shedding frequency and the rotor passing frequency. The cylinder case shows that leading edge stagnation point moves with the vortex shedding frequency. The shedding frequency is also found in leading edge pressure and lift fluctuations, but the rotor passing frequency is found more dominant. Only the rotor passing frequency and its multiples is observed when looking into the same fluctuations for the hydrofoil case. Vortex shedding is only observed at Angle of Attack ‐ AoA=8 degrees for the hydrofoil. In terms of rotor leading edge pressure reduction, only AoA=0 and AoA=2 showed equal or slightly improvements with VGs. A time averaged wake is also used as input in the CFD for AoA=4 and it shows large amplitude reduction when looking at the leading edge pressure and lift oscillations. Proportional Orthogonal Decomposition – POD is introduced to reveal flow structures and their corresponding energy in the wake flow. POD shows that up to 65 % of the total energy is located in the two first POD modes for the cylinder wake. Up to 18 % of the total energy is located in the two first modes for the hydrofoil at AoA=8 degrees where vortex shedding is present. The vortex generators prove to break the characteristic shedding pattern and move the early mode energy to later modes and reduce the energy content in the two first modes from 18 % to 8 % at AoA=8. At other AoAs only slight change in the energy distribution was observed due to the vortex generators. The second part of the thesis is focusing on measurements and investigation of draft tube flow dynamics. Pairwise radial dynamic measurements of the swirling draft tube flow is done at the 25 MW Svorka power plant in Surnadal operating at 48 % load, at 6 radial and 7 angular positions. The data is analyzed with traditional methods as well as with POD. The pressure fluctuations were found to peak at R5, at 83 % of the radius. The Rheingans frequency is found to be the only distinctive peak, and is very dominant in the pressure signal. The POD addressed 52 % of the total pressure variance to the azimuthal mode 1. As the POD will pin point structures of high energy it is desired to be able to use this information in active flow control applications. This is difficult as the measurements in the draft tube are performed manually and are time consuming. The resulting eigenfunctions from the POD measured at one operating point can later be coupled with a single wall pressure transmitter through Linear Stochastic Estimation – LSE in order to give POD results for other operating points. This work presents the first step of required measurements in one operational point in order to verify the use of POD in draft tube flow. Further development of POD for use in active flow control through LSE will be a continuation of this work

Undersøkelse av ustasjonære og turbulente forhold i minirigg ved hjelp av LDV, trykkmålinger og CFD

Diplomoppgava fortsetter arbeidet som blei starta i prosjektoppgava høsten 2008. Det er utført laboratorieforsøk på en minirigg der spinn settes opp i et vertikalt rør. Nedstrøms kan vann injiseres tangentielt gjennom ei dyse i motsatt retning av spinnet. Strømningsbildet og trykksvingninger er tidligere undersøkt ved hjelp av pitot og trykkmålinger. Arbeidet i denne oppgava omfatter utbedring av miniriggen for måling med LDV, samt supplerende målinger av hastighet med LDV og trykkmålinger. En rekke målinger av hastighet og trykk er gjort for å undersøke strømningsbildet uten og med vanninjeksjon. De eksperimentelle resultata er sammenligna med numeriske beregninger gjort i ANSYS CFX. Det er funnet at vanninjeksjon dreper spinnet i strømninga, og gir lavere tangentiell hastighet. I flere tilfeller minsker trykkpulsasjonene, men det er også funnet at vanninjiseringa kan ha motsatt effekt. Dette avhenger av swirlnummer og trykk i strømninga. Det er ikke funnet sammenfallende frekvenser for trykkpulsasjona og det turbulente hastighetsleddet. De numeriske simuleringene beskriver strømningsbildet på en tilfredsstillende måte uten vanninjeksjon. Spinnet underpredikerers, i tillegg til at profilformen avviker noe. Ved vanninjeksjon dempes spinnet betraktelig mer i de numeriske simuleringene enn hva som virkelig er målt i lab. Særlig den tangentielle hastigheta og det tangentielle momentet avviker mye i verdi

Behavioral side effects of prophylactic therapies against soman-induced seizures and lethality in rats

Four medical therapies previously shown to exert varying degrees of protection against a convulsant dose of soman were assessed for potential behavioral side effects in a novelty test. In Experiment 1, HI-6 (1-[([4-(aminocarbonyl)pyridino] methoxy)methyl]-2-[(hydroxyimino)methyl]pyridinium) (125 mg/kg), scopolamine (1 mg/kg), physostigmine (0.1 mg/kg), levetiracetam (50 mg/kg), and procyclidine (20 mg/kg) were tested separately. In Experiment 2, the combination of HI-6, scopolamine, and physostigmine (termed the physostigmine regimen) or HI-6, levetiracetam, and procyclidine (termed the procyclidine regimen) were tested. In Experiment 3, the metabotropic glutamate modulators DCG-IV ((2S,2′R,3′R)-2-(2′,3′-dicarboxycyclopropyl)glycine) (4 mg/kg) and MPEP (2-Methyl-6-(phenylethynyl)pyridine hydrochloride) (30 mg/kg) were tested separately or each drug in combination with HI-6 and procyclidine (termed the DCG-IV regimen and the MPEP regimen, respectively). The results showed that the physostigmine and procyclidine regimens both produced severe cognitive impairment (lack of preference for novelty) and reduced locomotor and rearing activities. The DCG-IV and MPEP regimens caused milder deficits on the same behavioral measures. Some relations were seen between prophylactic capacity and degree of behavioral side effects. Only HI-6 or levetiracetam had no adverse effects on behavior. DCG-IV or MPEP produced some impairment, whereas the detrimental effects of scopolamine or procyclidine were pronounced. The relatively high dose of procyclidine (anticholinergic and antiglutamatergic) needed for prophylactic efficacy may have played a major role for the side effects of the regimens in which the drug was used. It was concluded that behavioral side effects are inevitable for potent prophylactic therapies against soman intoxication

Carbon capture – from waste to energy: a stylized case from a pioneering initiative at Klemetsrud, Oslo. Report to the CLIMIT – demo project 618215: Potential for financing and pricing Carbon Capture in Waste-to Energy Installations in cities

Oslo has recently been given the European Environmental Capital award for 2019, following its adoption of an ambitious green strategy of reducing CO2 emissions by 50% by 2022, and by 95% by 2030. A core premise for Oslo reaching its goals is, however, that the city’s waste to energy plant installs carbon capture for sequestration (CCS). With 400,000 tons of CO2 emissions per year (Fortum 2019), Oslo’s Klemetsrud waste to energy plant is the largest single point carbon emitter in the city, and with these emissions it will be impossible for Oslo to reach its CO2 targets. However, carbon capture at Klemetsrud also carries significance in a wider global climate perspective. Global climate models are increasingly reverting to CCS in order to arrive at scenarios that are compatible with the Paris Agreement . This has created new pressure for CCS implementation, and Klemetsrud – if successful – could be an important trigger for CCS in Europe. This report is a styilized business case study of the Klemetsrud CCS project in light of four different regulatory scenarios.Carbon capture – from waste to energy: a stylized case from a pioneering initiative at Klemetsrud, Oslo. Report to the CLIMIT – demo project 618215: Potential for financing and pricing Carbon Capture in Waste-to Energy Installations in citiessubmittedVersio

Carbon capture – from waste to energy: a stylized case from a pioneering initiative at Klemetsrud, Oslo. Report to the CLIMIT – demo project 618215: Potential for financing and pricing Carbon Capture in Waste-to Energy Installations in cities

Oslo has recently been given the European Environmental Capital award for 2019, following its adoption of an ambitious green strategy of reducing CO2 emissions by 50% by 2022, and by 95% by 2030. A core premise for Oslo reaching its goals is, however, that the city’s waste to energy plant installs carbon capture for sequestration (CCS). With 400,000 tons of CO2 emissions per year (Fortum 2019), Oslo’s Klemetsrud waste to energy plant is the largest single point carbon emitter in the city, and with these emissions it will be impossible for Oslo to reach its CO2 targets. However, carbon capture at Klemetsrud also carries significance in a wider global climate perspective. Global climate models are increasingly reverting to CCS in order to arrive at scenarios that are compatible with the Paris Agreement . This has created new pressure for CCS implementation, and Klemetsrud – if successful – could be an important trigger for CCS in Europe. This report is a styilized business case study of the Klemetsrud CCS project in light of four different regulatory scenarios