Subversion Over OpenNetInf and CCNx

We describe experiences and insights from adapting the Subversion version control system to use the network service of two information-centric networking (ICN) prototypes: OpenNetInf and CCNx. The evaluation is done using a local collaboration scenario, common in our own project work where a group of people meet and share documents through a Subversion repository. The measurements show a performance benefit already with two clients in some of the studied scenarios, despite being done on un-optimised research prototypes. The conclusion is that ICN clearly is beneficial also for non mass-distribution applications. It was straightforward to adapt Subversion to fetch updated files from the repository using the ICN network service. The adaptation however neglected access control which will need a different approach in ICN than an authenticated SSL tunnel. Another insight from the experiments is that care needs to be taken when implementing the heavy ICN hash and signature calculations. In the prototypes, these are done serially, but we see an opportunity for parallelisation, making use of current multi-core processors

Experiments with Subversion Over OpenNetInf and CCNx

We describe experiences and insights from adapting the Subversion version control system to use the network service of two information-centric networking (ICN) prototypes: OpenNetInf and CCNx. The evaluation is done using a local collaboration scenario, common in our own project work where a group of people meet and share documents through a Subversion repository. The measurements show a performance benefit already with two clients in some of the studied scenarios, despite being done on un-optimised research prototypes. The conclusion is that ICN clearly is beneficial also for non mass-distribution applications

Global transcriptome response in Lactobacillus sakei during growth on ribose

<p>Abstract</p> <p>Background</p> <p><it>Lactobacillus sakei </it>is valuable in the fermentation of meat products and exhibits properties that allow for better preservation of meat and fish. On these substrates, glucose and ribose are the main carbon sources available for growth. We used a whole-genome microarray based on the genome sequence of <it>L. sakei </it>strain 23K to investigate the global transcriptome response of three <it>L. sakei </it>strains when grown on ribose compared with glucose.</p> <p>Results</p> <p>The function of the common regulated genes was mostly related to carbohydrate metabolism and transport. Decreased transcription of genes encoding enzymes involved in glucose metabolism and the L-lactate dehydrogenase was observed, but most of the genes showing differential expression were up-regulated. Especially transcription of genes directly involved in ribose catabolism, the phosphoketolase pathway, and in alternative fates of pyruvate increased. Interestingly, the methylglyoxal synthase gene, which encodes an enzyme unique for <it>L. sakei </it>among lactobacilli, was up-regulated. Ribose catabolism seems closely linked with catabolism of nucleosides. The deoxyribonucleoside synthesis operon transcriptional regulator gene was strongly up-regulated, as well as two gene clusters involved in nucleoside catabolism. One of the clusters included a ribokinase gene. Moreover, <it>hprK </it>encoding the HPr kinase/phosphatase, which plays a major role in the regulation of carbon metabolism and sugar transport, was up-regulated, as were genes encoding the general PTS enzyme I and the mannose-specific enzyme II complex (EII^man). Putative catabolite-responsive element (<it>cre</it>) sites were found in proximity to the promoter of several genes and operons affected by the change of carbon source. This could indicate regulation by a catabolite control protein A (CcpA)-mediated carbon catabolite repression (CCR) mechanism, possibly with the EII^manbeing indirectly involved.</p> <p>Conclusions</p> <p>Our data shows that the ribose uptake and catabolic machinery in <it>L. sakei </it>is highly regulated at the transcription level. A global regulation mechanism seems to permit a fine tuning of the expression of enzymes that control efficient exploitation of available carbon sources.</p

Exploring Pre-Colonial Resource Control of Individual Sami Households

In order to understand the use and control of resources by indigenous households and bands, information on territorial division is crucial. However, although indigenous resource use has been quantified in several studies, such information has usually been lacking. A unique map provides this kind of information for the Swedish Sami. Drawn by Jonas Persson Gedda in 1671, before the Swedish state started to interfere with Sami territorial division, it shows the borders of 37 household territories. We have combined the geographical information from Gedda’s map with historical sources and modern land survey data to quantify the resources controlled by each household and relate them to taxation. Three crucial resources are identified: alpine heath together with subalpine birch forest, pine-dominated forests, and fishing waters. Only the fishing resource showed any correlation to taxation, which underlines its importance as the main subsistence mode, at least for the forest Sami. Mountain Sami, who lived primarily on reindeer husbandry, controlled abundant alpine heath and subalpine birch forests that were used as summer pastures, but virtually no pine-dominated forests with winter pastures. The necessary winterpastures were located in the territories of the forest Sami, who controlled extensive pine-dominated forests and who were able to combine reindeer herding and wild reindeer hunting.Pour comprendre l’utilisation et la gestion des ressources des groupes de peuples indigènes, il est essentiel de disposer d’informations sur la division territoriale. Cependant, si l’utilisation des ressources des peuples indigènes a fait l’objet de plusieurs analyses quantitatives, les informations sur la division territoriale font le plus souvent défaut. Pour les Samis de Suède, une carte unique fournit ce genre d’information. Établie par Jonas Persson Gedda en 1671, avant que l’État suédois n’ait commencé à intervenir dans la division territoriale des Samis, la carte montre les limites de 37 territoires familiaux. Nous avons allié les informations géographiques de la carte de Gedda à des sources historiques et à des données topographiques modernes pour quantifier les ressources contrôlées par chaque famille et les lier au système de taxation. Trois ressources naturelles fondamentales ont ainsi été identifiées : les landes alpines avec les forêts subalpines de bouleau, les pinèdes et les pêcheries. Il appert que seules les pêcheries étaient corrélées au système de taxation, ce qui souligne leur importance en tant que mode de subsistance, pour les Samis de la forêt à tout le moins. Les Samis des montagnes, qui vivaient surtout de l’élevage des rennes, contrôlaient les landes alpines et les forêts subalpines de bouleau abondantes qui étaient utilisées comme pâturages estivaux, mais pratiquement pas de pinèdes offrant des pâturages hivernaux. Les pâturages nécessaires se trouvaient chez les Samis de la forêt, qui contrôlaient de vastes pinèdes et savaient combiner tant l’élevage des rennes que la chasse aux rennes sauvages

Numerical and experimental study of ethanol combustion in an industrial gas turbine

The application of ethanol as a biomass-derived fuel in OPRA’s 2 MWe class OP16 radial gas turbine has been studied both numerically and experimentally. The main purpose of this work is to validate the numerical model for future work on biofuel combustion. For the experimental investigation a modified OP16 gas turbine combustor has been used. This reverse-flow tubular combustor is a diffusion type combustor that has been adjusted to be suitable for numerical validation. Two series of ethanol burning experiments have been conducted at atmospheric pressure with a thermal input ranging from 16 to 72 kW. Exhaust gas temperature and emissions (CO, CO2, O2, NOx) were measured at various fuel flow rates while keeping the air flow rate and air temperature constant. In addition, the temperature profile of the combustor liner has been determined by applying thermochromic paint. CFD simulations have been performed in Ansys Fluent for four different operating conditions considered in the experiments. The simulations are based on a 3D RANS code. Fuel droplets representing the fuel spray are tracked throughout the domain while they interact with the gas phase. A temperature profile based on measurements has been prescribed on the liner to account for heat transfer through the flame tube wall. Detailed combustion chemistry is included by using the steady laminar flamelet model. The predicted levels of CO2 and O2 in the exhaust gas are in good agreement with the experimental results. The calculated and measured exhaust gas temperatures show a close match for the low power condition, but more significant deviations are observed in the higher load cases. Also, the comparison pointed out that the CFD model needs to be improved regarding the prediction of the pollutants CO and NOx. Chemiluminescence of CH radicals in the flame front indicated that the flame extends up to the liner, suggesting the presence of fuel near the surface. However, this result was not confirmed by liner temperature measurements using thermochromic paint.</jats:p

Primary metabolism in Lactobacillus sakei food isolates by proteomic analysis

<p>Abstract</p> <p>Background</p> <p><it>Lactobacillus sakei </it>is an important food-associated lactic acid bacterium commonly used as starter culture for industrial meat fermentation, and with great potential as a biopreservative in meat and fish products. Understanding the metabolic mechanisms underlying the growth performance of a strain to be used for food fermentations is important for obtaining high-quality and safe products. Proteomic analysis was used to study the primary metabolism in ten food isolates after growth on glucose and ribose, the main sugars available for <it>L. sakei </it>in meat and fish.</p> <p>Results</p> <p>Proteins, the expression of which varied depending on the carbon source were identified, such as a ribokinase and a D-ribose pyranase directly involved in ribose catabolism, and enzymes involved in the phosphoketolase and glycolytic pathways. Expression of enzymes involved in pyruvate and glycerol/glycerolipid metabolism were also affected by the change of carbon source. Interestingly, a commercial starter culture and a protective culture strain down-regulated the glycolytic pathway more efficiently than the rest of the strains when grown on ribose. The overall two-dimensional gel electrophoresis (2-DE) protein expression pattern was similar for the different strains, though distinct differences were seen between the two subspecies (<it>sakei </it>and <it>carnosus</it>), and a variation of about 20% in the number of spots in the 2-DE gels was observed between strains. A strain isolated from fermented fish showed a higher expression of stress related proteins growing on both carbon sources.</p> <p>Conclusions</p> <p>It is obvious from the data obtained in this study that the proteomic approach efficiently identifies differentially expressed proteins caused by the change of carbon source. Despite the basic similarity in the strains metabolic routes when they ferment glucose and ribose, there were also interesting differences. From the application point of view, an understanding of regulatory mechanisms, actions of catabolic enzymes and proteins, and preference of carbon source is of great importance.</p

Quantitative Assessment of 99mTc-Depreotide Uptake in Oesophageal Cancer and Precursor Conditions and Its Reflection in Immunohistochemically Detected Somatostatin Receptors

Background. Somatostatin receptors (SSTRs) are over-expressed in several tumors making it possible for imaging with labelled SSTR. A previous study showed feasibility to image oesophageal cancer with SSTR analogue 99mTc-depreotide. Purpose. (1) To investigate expression of the SSTRs in different types of esophageal carcinoma and (2) to correlate such an expression with 99mTc-depreotide uptake in these lesions. Material and Methods. Total 28 patients (17 with esophageal cancer and 11 with Barrett's esophagus) were examined with 99mTc-depreotide scintigraphy. The SSTR2A, SSTR2B, SSTR3, and SSTR5 were analyzed immunohistochemically in the lesion samples. Results. Among the patients with adenocarcinoma 10/11 expressed different amounts of SSTRs, while SSTRs were absent in 5/6 patients with Squamous cell carcinoma (Sqcc). There was no correlation neither between the 99mTc-depreotide uptake and the amount of SSTRs nor between the amount of SSTRs and differentiation grade of the tumor. Conclusions. (1) SSTRs are expressed in esophageal carcinoma and more abundantly so in adenocancer specimens; (2) in vivo 99mTc-depreotide uptake does not obviously correlate with the immunohistochemically detection of SSTRs of different subtypes in esophageal carcinoma

Genome-wide analysis of signal peptide functionality in Lactobacillus plantarum WCFS1

<p>Abstract</p> <p>Background</p> <p><it>Lactobacillus plantarum </it>is a normal, potentially probiotic, inhabitant of the human gastrointestinal (GI) tract. The bacterium has great potential as food-grade cell factory and for <it>in situ </it>delivery of biomolecules. Since protein secretion is important both for probiotic activity and in biotechnological applications, we have carried out a genome-wide experimental study of signal peptide (SP) functionality.</p> <p>Results</p> <p>We have constructed a library of 76 Sec-type signal peptides from <it>L. plantarum </it>WCFS1 that were predicted to be cleaved by signal peptidase I. SP functionality was studied using staphylococcal nuclease (NucA) as a reporter protein. 82% of the SPs gave significant extracellular NucA activity. Levels of secreted NucA varied by a dramatic 1800-fold and this variation was shown not to be the result of different mRNA levels. For the best-performing SPs all produced NucA was detected in the culture supernatant, but the secretion efficiency decreased for the less well performing SPs. Sequence analyses of the SPs and their cognate proteins revealed four properties that correlated positively with SP performance for NucA: high hydrophobicity, the presence of a transmembrane helix predicted by TMHMM, the absence of an anchoring motif in the cognate protein, and the length of the H+C domain. Analysis of a subset of SPs with a lactobacillal amylase (AmyA) showed large variation in production levels and secretion efficiencies. Importantly, there was no correlation between SP performance with NucA and the performance with AmyA.</p> <p>Conclusion</p> <p>This is the first comprehensive experimental study showing that predicted SPs in the <it>L. plantarum </it>genome actually are capable of driving protein secretion. The results reveal considerable variation between the SPs that is at least in part dependent on the protein that is secreted. Several SPs stand out as promising candidates for efficient secretion of heterologous proteins in <it>L. plantarum</it>. The results for NucA provide some hints as to the sequence-based prediction of SP functionality, but the general conclusion is that such prediction is difficult. The vector library generated in this study is based on exchangeable cassettes and provides a powerful tool for rapid experimental screening of SPs.</p

Long-term yield and biodiversity in stands managed with the selection system and the rotation forestry system: A qualitative review

There is an increasing interest in implementing Continuous Cover Forestry (CCF) as a tool to mitigate negative effects of the traditional rotation forestry system on biodiversity. However, the effects of CCF on forest growth and yield and on biodiversity is still poorly known. In this qualitative review, we compare biodiversity and longterm yield between the selection system, which is a type of CCF practiced in full-storied forests, and the traditional rotation forestry system. We specifically focus on forests dominated by Picea abies, which is a tree species of high economic relevance. Our literature search resulted in 17 publications on stand growth and yield and 21 publications on biodiversity. A majority of simulation studies found a higher long-term yield in the rotation forestry system, but it is challenging to conclude which system is the most productive. The magnitude of the difference in yield between systems, and how it varies across different environmental conditions, remains to be determined. For biodiversity, comparisons of species assemblage and individual species were only made to certain phases of the rotation cycle (recent clearcuts and middle-aged stands). Nevertheless, two aspects can be highlighted: i) the species assemblage in clearcuts differ substantially from stands managed with the selection system. Some of these effects may however be short lasting as examplified by studies on beetle assamblages showing that middle-aged rotation forestry stands become more similar to stands managed with the selection system, ii) the selection system maintains a similar species assemblage as the uncut control during the first years after cutting. In conclusion, management with the selection system may come with a loss in long-term stand yield, but much of the species assemblage is maintained after logging. We recommend future studies to specifically focus on long-term effects on biodiversity - in particular on species of conservation concern. There is also a need to establish a long-term research infrastructure to further develop the field