Exploring the Challenges of a Flexible, Feature Rich IoT Testbed

IoT is a field of technology of ever growing importance in our daily lives. From smart cities, health devices, climate observations, appliances, and so much more, IoT surrounds us now more than ever. The types of devices being added to IoT networks is ever growing, and as this variety of hardware and software increases, so does the difficulty of working with them. Ensuring inter-compatibility between devices, testing new communication protocols, and writing software for emerging technologies becomes a complex challenge. To help solve this challenge are IoT Testbeds. IoT Testbeds help developers, researchers, and many more groups of people explore and test their IoT solutions in contexts of real IoT Devices. These testbeds exist today, but as far as we know, no Jack of all trades testbed exists that supports all features one might want from a testbed. This thesis will introduce a first draft of a new testbed. Introducing a system design, architecture, and implementation that theoretically and practically implements all these features. Also highlighting issues with this design and ways to tackle them. In the end contributing a foundation onto which a powerful system could be built. The challenge the thesis aims to tackle is, in short: What are the needed features that make up a good testbed? And how can we incorporate these features into a simple, flexible, unified system

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

<p>Abstract</p> <p>Background</p> <p>Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques.</p> <p>Results</p> <p>Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (<100,000 CFU/ml) healthy female urine specimens. Sequences were compared to 16S rRNA databases and showed significant diversity, with the predominant genera detected being <it>Lactobacillus</it>, <it>Prevotella </it>and <it>Gardnerella</it>. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20 - 500.</p> <p>Conclusions</p> <p>Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.</p

A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain

<p>Abstract</p> <p>Background</p> <p>Cyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS). Although some cyanobacterial NRPS gene cluster types are well described, the entire NRPS genomic content within a single cyanobacterial strain has never been investigated. Here we have combined a genome-wide analysis using massive parallel pyrosequencing ("454") and mass spectrometry screening of oligopeptides produced in the strain <it>Planktothrix rubescens </it>NIVA CYA 98 in order to identify all putative gene clusters for oligopeptides.</p> <p>Results</p> <p>Thirteen types of oligopeptides were uncovered by mass spectrometry (MS) analyses. Microcystin, cyanopeptolin and aeruginosin synthetases, highly similar to already characterized NRPS, were present in the genome. Two novel NRPS gene clusters were associated with production of anabaenopeptins and microginins, respectively. Sequence-depth of the genome and real-time PCR data revealed three copies of the microginin gene cluster. Since NRPS gene cluster candidates for microviridin and oscillatorin synthesis could not be found, putative (gene encoded) precursor peptide sequences to microviridin and oscillatorin were found in the genes <it>mdn</it>A and <it>osc</it>A, respectively. The genes flanking the microviridin and oscillatorin precursor genes encode putative modifying enzymes of the precursor oligopeptides. We therefore propose ribosomal pathways involving modifications and cyclisation for microviridin and oscillatorin. The microviridin, anabaenopeptin and cyanopeptolin gene clusters are situated in close proximity to each other, constituting an oligopeptide island.</p> <p>Conclusion</p> <p>Altogether seven nonribosomal peptide synthetase (NRPS) gene clusters and two gene clusters putatively encoding ribosomal oligopeptide biosynthetic pathways were revealed. Our results demonstrate that whole genome shotgun sequencing combined with MS-directed determination of oligopeptides successfully can identify NRPS gene clusters and the corresponding oligopeptides. The analyses suggest independent evolution of all NRPS gene clusters as functional units. Our data indicate that the <it>Planktothrix </it>genome displays evolution of dual pathways (NRPS and ribosomal) for production of oligopeptides in order to maximize the diversity of oligopeptides with similar but functional discrete bioactivities.</p

Concluding destructive investigation of a nine-year-old marine-exposed cracked concrete panel

This study undertaken on a nine-year-old cracked concrete panel further investigates the impact of cracks on the corrosion performance of conventional steel reinforcement in marine-exposed concrete to explain observed monitoring data. The present data covers seven 1.80 m long (12.6 m) reinforcing bars embedded in good quality concrete (w/b = 0.40 and cover >75 mm). Each bar was crossed by two horizontal cracks (surface crack widths 0.20–0.30 mm). The investigation showed no corrosion on the surface of the reinforcing bars, in either cracked or uncracked areas. Two of the seven reinforcing bars were instrumented in the vicinity of the cracks. Extensive corrosion was found in the interior of all instrumented parts of these bars. This may explain the monitoring data despite the lack of corrosion on the exterior surface of the two instrumented rebars. However, with no other weaknesses, the remaining conventional rebars showed no impact from the cracks.publishedVersio

Langsiktige likevektsforhold mellom aksjemarked og makroøkonomi i Norge og USA

Masteroppgave i bedriftsøkonomi - Universitetet i Nordland, 2012Vi har i denne masteroppgaven hatt som formål å avdekke om det eksisterer langsiktige likevektsforhold mellom aksjemarkedet og de makroøkonomiske variablene kredittvekst, sysselsetting og rentespread. Dette er en undersøkelse vi har utført på både det norske og amerikanske markedet. En grunnleggende antakelse som ligger bak vår utredning er at utviklingen i økonomien kan forklares av de uobserverbare variablene forventning og usikkerhet. Vi antar videre at aksjemarkedet vil opptre som en god indikator for å fange opp publikums forventninger og usikkerhet rettet til den fremtidige økonomiske utviklingen. Gjennom vårt teoretiske rammeverk argumenterer vi for hva som er viktige premisser og komponenter for prisfastsettelse i et aksjemarkedet og hvordan våre utvalgte makroøkonomiske variabler kan ha innflytelse i denne sammenhengen. Dataanalysen har avdekket at aksjemarkedet har et forhold til alle våre tre utvalgte makroøkonomiske variabler. Vi har gjennom å estimere totalt 14 feilkorreksjonsmodeller funnet at aksjemarkedet virker å inngå i en positiv langsiktig likevekt med kredittveksten og sysselsettingens vekstrate på både det norske og amerikanske markedet.Videre finner vi indikasjoner om et inverst langsiktig likevektsforhold mellom aksjemarkedet og rentens terminstruktur i begge markedene. Eksistensen av langsiktige likevektsforhold mellom aksjemarkedet og våre variabler impliserer at den usikkerheten og de forventningene vi antar gjenspeiles i aksjemarkedet også vil komme til uttrykk gjennom de makroøkonomiske variablene vi har presentert. Indikasjonene vi da vil få er at en økning i kredittveksten eller en økning i sysselsettingens vekstrate kan gi oss signaler om at forventningene til økonomisk utvikling hos befolkningen stiger samtidig som usikkerheten avtar. Motsatt vil en økning i rentens terminstruktur indikere en økende usikkerhet blant befolkningen samtidig som forventningene til den fremtidige økonomiske situasjonen reduseres. Vi finner av justeringsmekanismene i modellene at aksjemarkedet virker å drive utviklingen av alle de tre makroøkonomiske variablene på det norske markedet. På det amerikanske markedet virker aksjemarkedet å drive utviklingen i kredittveksten og sysselsettingens vekstrate, mens vi der finner at rentens terminstruktur virker å drive utviklingen i aksjemarkedet. Dette kan tyde på at aksjemarkedet er den beste indikatoren for å hurtig fange opp endringen i publikums forventninger og usikkerhet rettet mot fremtidig økonomisk utvikling i det norske markedet, mens rentespreaden tyder på å være den beste indikatoren på det amerikanske markedet

Intraoperative milrinone versus dobutamine in cardiac surgery patients:a retrospective cohort study on mortality

Abstract Background Several choices of inotropic therapy are available and used in relation to cardiac surgery. Comparisons are necessary to select optimal therapy. In Denmark, dobutamine and milrinone are the two inotropic agents most commonly used to treat post-bypass low cardiac output syndrome. This study compares all-cause mortality with these drugs. Methods In a retrospective observational study we investigated 10,700 consecutive patients undergoing cardiac surgery from 1 April 2006 to 31 December 2013 at Aarhus and Aalborg University Hospitals in the Central and Northern Denmark Region. Prospectively entered data in the Western Danish Heart Registry on intraoperative use of inotropes were used to identify 952 patients treated with milrinone, 418 patients treated with dobutamine, and 82 patients receiving a combination of the two inotropes. All-cause mortality among patients receiving dobutamine was compared to all-cause mortality among milrinone receivers. Multiple logistic regression analyses including preoperative and intraoperative variables along with g-formula analyses were used to model 30-day and 1-year mortality risks. Reported were standardized mortality risk differences between the treatment groups. Results Among patients receiving intraoperative dobutamine, 18 (4.3%) died within 30 days and 49 (11.7%) within 1 year. Corresponding 30-day and 1-year mortality for milrinone receivers were 81 (8.5%) and 170 (17.9%). Risk of death within 30 days and 1 year was increased for intraoperative milrinone compared to dobutamine with a standardized risk difference of 4.06% (confidence interval (CI) 1.23; 6.89, p = 0.005) and 4.77% (CI 0.39; 9.15, p = 0.033), respectively. Sensitivity analyses including adjustment for milrinone preference, hemodynamic instability prior to cardiopulmonary bypass, and separate analyses on hospital level all confirmed a sign toward increased mortality among milrinone receivers. Conclusions Intraoperative use of milrinone in cardiac surgery may be associated with an increase in all-cause mortality compared to use of dobutamine

Concluding destructive investigation of a nine-year-old marine-exposed cracked concrete panel

This study undertaken on a nine-year-old cracked concrete panel further investigates the impact of cracks on the corrosion performance of conventional steel reinforcement in marine-exposed concrete to explain observed monitoring data. The present data covers seven 1.80 m long (12.6 m) reinforcing bars embedded in good quality concrete (w/b = 0.40 and cover &gt;75 mm). Each bar was crossed by two horizontal cracks (surface crack widths 0.20–0.30 mm). The investigation showed no corrosion on the surface of the reinforcing bars, in either cracked or uncracked areas. Two of the seven reinforcing bars were instrumented in the vicinity of the cracks. Extensive corrosion was found in the interior of all instrumented parts of these bars. This may explain the monitoring data despite the lack of corrosion on the exterior surface of the two instrumented rebars. However, with no other weaknesses, the remaining conventional rebars showed no impact from the cracks

Workrs: Fault Tolerant Horizontal Computation Offloading

The broad development and usage of edge devices has highlighted the importance of creating resilient and computationally advanced environments. When working with edge devices these desiderata are usually achieved through replication and offloading. This paper reports on the design and implementation of Workrs, a fault tolerant service that enables the offloading of jobs from devices with limited computational power. We propose a solution that allows users to upload jobs through a web service, which will be executed on edge nodes within the system. The solution is designed to be fault tolerant and scalable, with no single point of failure as well as the ability to accommodate growth, if the service is expanded. The use of Docker checkpointing on the worker machines ensures that jobs can be resumed in the event of a fault. We provide a mathematical approach to optimize the number of checkpoints that are created along a computation, given that we can forecast the time needed to execute a job. We present experiments that indicate in which scenarios checkpointing benefits job execution. The results achieved are based on a working prototype which shows clear benefits of using checkpointing and restore when the completion jobs' time rises compared with the forecast fault rate. The code of Workrs is released as open source, and it is available at \url{https://github.com/orgs/P7-workrs/repositories}. This paper is an extended version of \cite{edge2023paper}.Comment: extended version of a paper accepted at IEEE Edge 202

Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2)

Background: Systems biology approaches to study metabolic switching in Streptomyces coelicolor A3(2) depend on cultivation conditions ensuring high reproducibility and distinct phases of culture growth and secondary metabolite production. In addition, biomass concentrations must be sufficiently high to allow for extensive time-series sampling before occurrence of a given nutrient depletion for transition triggering. The present study describes for the first time the development of a dedicated optimized submerged batch fermentation strategy as the basis for highly time-resolved systems biology studies of metabolic switching in S. coelicolor A3(2). Results: By a step-wise approach, cultivation conditions and two fully defined cultivation media were developed and evaluated using strain M145 of S. coelicolor A3(2), providing a high degree of cultivation reproducibility and enabling reliable studies of the effect of phosphate depletion and L-glutamate depletion on the metabolic transition to antibiotic production phase. Interestingly, both of the two carbon sources provided, D-glucose and L-glutamate, were found to be necessary in order to maintain high growth rates and prevent secondary metabolite production before nutrient depletion. Comparative analysis of batch cultivations with (i) both L-glutamate and D-glucose in excess, (ii) L-glutamate depletion and D-glucose in excess, (iii) L-glutamate as the sole source of carbon and (iv) D-glucose as the sole source of carbon, reveal a complex interplay of the two carbon sources in the bacterium's central carbon metabolism. Conclusions: The present study presents for the first time a dedicated cultivation strategy fulfilling the requirements for systems biology studies of metabolic switching in S. coelicolor A3(2). Key results from labelling and cultivation experiments on either or both of the two carbon sources provided indicate that in the presence of D-glucose, L-glutamate was the preferred carbon source, while D-glucose alone appeared incapable of maintaining culture growth, likely due to a metabolic bottleneck at the oxidation of pyruvate to acetyl-CoA