An Empirical Investigation of Pull Requests in Partially Distributed BizDevOps Teams

In globally distributed projects, virtual teams are often partially dispersed. One common setup occurs when several members from one company work with a large outsourcing vendor based in another country. Further, the introduction of the popular BizDevOps concept has increased the necessity to cooperate across departments and reduce the age-old disconnection between the business strategy and technical development. Establishing a good collaboration in partially distributed BizDevOps teams requires extensive collaboration and communication techniques. Nowadays, a common approach is to rely on collaboration through pull requests and frequent communication on Slack. To investigate barriers for pull requests in distributed teams, we examined an organization located in Scandinavia where cross-functional BizDevOps teams collaborated with off-site team members in India. Data were collected by conducting 14 interviews, observing 23 entire days with the team, and observing 37 meetings. We found that the pull-request approach worked very well locally but not across sites. We found barriers such as domain complexity, different agile processes (timeboxed vs. flow-based development), and employee turnover. Using an intellectual capital lens on our findings, we discuss barriers and positive and negative effects on the success of the pull-request approach

Learning representations of multivariate time series with missing data

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordLearning compressed representations of multivariate time series (MTS) facilitates data analysis in the presence of noise and redundant information, and for a large number of variates and time steps. However, classical dimensionality reduction approaches are designed for vectorial data and cannot deal explicitly with missing values. In this work, we propose a novel autoencoder architecture based on recurrent neural networks to generate compressed representations of MTS. The proposed model can process inputs characterized by variable lengths and it is specifically designed to handle missing data. Our autoencoder learns fixed-length vectorial representations, whose pairwise similarities are aligned to a kernel function that operates in input space and that handles missing values. This allows to learn good representations, even in the presence of a significant amount of missing data. To show the effectiveness of the proposed approach, we evaluate the quality of the learned representations in several classification tasks, including those involving medical data, and we compare to other methods for dimensionality reduction. Successively, we design two frameworks based on the proposed architecture: one for imputing missing data and another for one-class classification. Finally, we analyze under what circumstances an autoencoder with recurrent layers can learn better compressed representations of MTS than feed-forward architectures.Norwegian Research Counci

The real-time interaction model for transient mode investigations of a dual-piston free-piston engine generator

A free-piston engine generator is being developed worldwide as a novel means of electrical power generator for light vehicle application, which can provide a complementary solution towards reducing carbon dioxide emissions of road vehicles in general. However, the absence of a crank-slider mechanism in free-piston engines resulted in poor transient operations. Transient real-time modelling and simulation can provide the interaction between in-cylinder combustion with dynamics of piston motion, which has not been fully explored previously. This paper presents a real-time interaction model between dynamics of the piston motion and thermodynamics of the in-cylinder combustion of a two-stroke spark ignition dual-piston free-piston engine generator for transient operation investigations. The simulation model was developed based on the working prototype and comprised of zero- and one-dimensional sub-models interacted in real-time governed by a single timestep. The study focuses on three critical transient modes: motoring, starting and generating for the transient performance investigation. A series of experimental results during motoring was used for validating the simulation model, which showed good agreement between simulation and experiment results with 2–5% errors. The targeted brake thermal efficiency is around 20–30% at 50–60 Hz engine speed which has been shown achievable. Transient speeds of 10 and 25 Hz produced higher combustion pressure around the top dead centre but suffered pumping loss at the end of the expansion stroke. The lower peak pressures at 50 and 60 Hz have contributed to the lower brake mean effective pressure values. Maximum brake thermal efficiency of 25.8% lies in the mid-range of compression ratios between 10:1 to 15:1 while at the cyclic speeds of 50 Hz to 60 Hz. Maximum brake mean effective pressure contour occurs between 5 and 12.5 compression ratios and corresponding speeds of 10 to 30 Hz. It was observed that the excess energy from combustion results in piston overshoot condition while insufficient energy prevents the piston from achieving the targeted stroke and compression ratio. Knock events were observed for high compression ratio cases regardless of engine speed. Predictive stroke control and knock detection capability are the main contribution of the real-time interaction model presented in this paper for realistic transient operation investigation and performance prediction of the dual-piston free-piston engine generator

Investigating the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis

Background: The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including antimicrobial resistance genes encoded by mobile genetic elements (MGEs). Here, we investigate this mobilome in successful hospital associated genetic lineages, E. faecium sequence type (ST)17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) by DNA microarray analyses. Results: The hybridization patterns of 272 representative targets including plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29) and clustered regularly interspaced short palindromic repeats (CRISPR)-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. RCR-, Rep_3-, RepA_N- and Inc18-family plasmids were highly prevalent and with the exception of Rep_3, evenly distributed between the species. There was a considerable difference in the replicon profile, with rep17/pRUM, rep2/pRE25, rep14/EFNP1 and rep20/pLG1 dominating in E. faecium and rep9/pCF10, rep2/pRE25 and rep7 in E. faecalis strains. We observed an overall high correlation between the presence and absence of genes coding for resistance towards antibiotics, metals, biocides and their corresponding MGEs as well as their phenotypic antimicrobial susceptibility pattern. Although most IS families were represented in both E. faecalis and E. faecium, specific IS elements within these families were distributed in only one species. The prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982- and IS4-transposases was significantly higher in E. faecium than E. faecalis, and that of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 that have only been reported in few enterococcal isolates were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented. Conclusions: The targeted MGEs were highly prevalent among the selected STs, underlining their potential importance in the evolution of hospital-adapted lineages of enterococci. Although the propensity of inter-species horizontal gene transfer (HGT) must be emphasized, the considerable species-specificity of these MGEs indicates a separate vertical evolution of MGEs within each species, and for E. faecalis within each ST

Fragmented participation in management of the fishery for small pelagic fish in South Africa – inclusion of small-rights holders is a complex matter

The reasons why most small-rights holders do not participate in management of the fishery for small pelagic fish (‘small pelagics’) in South Africa, despite legislation and policy encouraging their participation, were analysed. Membership of the Small Pelagics Management Working Group (SPMWG), the main participatory governance organ, is limited to representatives of recognised stakeholder associations. Rights holders therefore have to belong to a stakeholder association, which then selects a member or members to represent them on the SPMWG. Small quotas and the difficulties of sourcing capital mean that small-rights holders are not able to invest in infrastructure. Besides, most of the small-rights holders and their companies lack experience and management skills to survive independently in this highly competitive industry, which is based on high volume and low profit margins. As a result, most of the small-rights holders have no option but to enter into complex catching and processing agreements with vessel- and factory owners belonging to the existing recognised stakeholder associations. For the small-rights holders, it does not make sense to join these associations or even to form their own if they cannot actively participate in the industry independently. Greater participation by small-rights holders should start with their genuine integration into the industry through improved ability to invest in infrastructure and through management skills development. Most likely, this will require an interventionist approach by government.Department of HE and Training approved lis

Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland

Publication history: Accepted - 29 July 2021; Published online - 6 August 2021.Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2). As this genotype is highly prevalent in Scotland, transmission through well boat traffic was hypothesized as one possible source of infection. In this study, we performed full-length genome sequencing of SAV2 sampled between 2006 and 2012 in Norway and Scotland, and present the first comprehensive full-length characterization of Norwegian marine SAV2 strains. We analyze their relationship with selected Scottish SAV2 strains and explore the genetic diversity of SAV. Our results show that all Norwegian marine SAV2 share a recent last common ancestor with marine SAV2 circulating in Scotland and a higher level of genomic diversity among the Scottish marine SAV2 strains compared to strains from Norway. These findings support the hypothesis of a single introduction of SAV2 to Norway sometime from 2006–2010, followed by horizontal spread along the coast.This research was funded by Norwegian Seafood Research Fund (FHF) grant 90079

Analysis of free text in electronic health records for identification of cancer patient trajectories

With an aging patient population and increasing complexity in patient disease trajectories, physicians are often met with complex patient histories from which clinical decisions must be made. Due to the increasing rate of adverse events and hospitals facing financial penalties for readmission, there has never been a greater need to enforce evidence-led medical decision-making using available health care data. In the present work, we studied a cohort of 7,741 patients, of whom 4,080 were diagnosed with cancer, surgically treated at a University Hospital in the years 2004–2012. We have developed a methodology that allows disease trajectories of the cancer patients to be estimated from free text in electronic health records (EHRs). By using these disease trajectories, we predict 80% of patient events ahead in time. By control of confounders from 8326 quantified events, we identified 557 events that constitute high subsequent risks (risk > 20%), including six events for cancer and seven events for metastasis. We believe that the presented methodology and findings could be used to improve clinical decision support and personalize trajectories, thereby decreasing adverse events and optimizing cancer treatment

Listening In on the Past: What Can Otolith δ18O Values Really Tell Us about the Environmental History of Fishes?

Oxygen isotope ratios from fish otoliths are used to discriminate marine stocks and reconstruct past climate, assuming that variations in otolith δ18O values closely reflect differences in temperature history of fish when accounting for salinity induced variability in water δ18O. To investigate this, we exploited the environmental and migratory data gathered from a decade using archival tags to study the behaviour of adult plaice (Pleuronectes platessa L.) in the North Sea. Based on the tag-derived monthly distributions of the fish and corresponding temperature and salinity estimates modelled across three consecutive years, we first predicted annual otolith δ18O values for three geographically discrete offshore sub-stocks, using three alternative plausible scenarios for otolith growth. Comparison of predicted vs. measured annual δ18O values demonstrated >96% correct prediction of sub-stock membership, irrespective of the otolith growth scenario. Pronounced inter-stock differences in δ18O values, notably in summer, provide a robust marker for reconstructing broad-scale plaice distribution in the North Sea. However, although largely congruent, measured and predicted annual δ18O values of did not fully match. Small, but consistent, offsets were also observed between individual high-resolution otolith δ18O values measured during tag recording time and corresponding δ18O predictions using concomitant tag-recorded temperatures and location-specific salinity estimates. The nature of the shifts differed among sub-stocks, suggesting specific vital effects linked to variation in physiological response to temperature. Therefore, although otolith δ18O in free-ranging fish largely reflects environmental temperature and salinity, we counsel prudence when interpreting otolith δ18O data for stock discrimination or temperature reconstruction until the mechanisms underpinning otolith δ18O signature acquisition, and associated variation, are clarified

Influence of Dietary Supplementation of Probiotic Pediococcus acidilactici MA18/5M During the Transition From Freshwater to Seawater on Intestinal Health and Microbiota of Atlantic Salmon (Salmo salar L.)

publishedVersio

Halogenase Genes in Nonribosomal Peptide Synthetase Gene Clusters of Microcystis (Cyanobacteria): Sporadic Distribution and Evolution

Cyanobacteria of the genus Microcystis are known to produce secondary metabolites of large structural diversity by nonribosomal peptide synthetase (NRPS) pathways. For a number of such compounds, halogenated congeners have been reported along with nonhalogenated ones. In the present study, chlorinated cyanopeptolin- and/or aeruginosin-type peptides were detected by mass spectrometry in 17 out of 28 axenic strains of Microcystis. In these strains, a halogenase gene was identified between 2 genes coding for NRPS modules in respective gene clusters, whereas it was consistently absent when the strains produced only nonchlorinated corresponding congeners. Nucleotide sequences were obtained for 12 complete halogenase genes and 14 intermodule regions of gene clusters lacking a halogenase gene or containing only fragments of it. When a halogenase gene was found absent, a specific, identical excision pattern was observed for both synthetase gene clusters in most strains. A phylogenetic analysis including other bacterial halogenases showed that the NRPS-related halogenases of Microcystis form a monophyletic group divided into 2 subgroups, corresponding to either the cyanopeptolin or the aeruginosin peptide synthetases. The distribution of these peptide synthetase gene clusters, among the tested Microcystis strains, was found in relative agreement with their phylogeny reconstructed from 16S–23S rDNA intergenic spacer sequences, whereas the distribution of the associated halogenase genes appears to be sporadic. The presented data suggest that in cyanobacteria these prevalent halogenase genes originated from an ancient horizontal gene transfer followed by duplication in the cyanobacterial lineage. We propose an evolutionary scenario implying repeated gene losses to explain the distribution of halogenase genes in 2 NRPS gene clusters that subsequently defines the seemingly erratic production of halogenated and nonhalogenated aeruginosins and cyanopeptolins among Microcystis strains