Assembly complexity of prokaryotic genomes using short reads

<p>Abstract</p> <p>Background</p> <p>De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes.</p> <p>Results</p> <p>We provide the first survey of the repeat structure of a large number of genomes. The analysis gives an upper-bound on the performance of genome assemblers for <it>de novo </it>reconstruction of genomes across a wide range of read lengths. Further, we demonstrate that the majority of genes in prokaryotic genomes can be reconstructed uniquely using very short reads even if the genomes themselves cannot. The non-reconstructible genes are overwhelmingly related to mobile elements (transposons, IS elements, and prophages).</p> <p>Conclusions</p> <p>Our results improve upon previous studies on the feasibility of assembly with short reads and provide a comprehensive benchmark against which to compare the performance of the short-read assemblers currently being developed.</p

Innovation, low energy buildings and intermediaries in Europe: systematic case study review

As buildings throughout their lifecycle account for circa 40% of total energy use in Europe, reducing energy use of the building stock is a key task. This task is, however, complicated by a range of factors, including slow renewal and renovation rates of buildings, multiple non- coordinated actors, conservative building practices, and limited competence to innovate. Drawing from academic literature published during 2005-2015, this article carries out a systematic review of case studies on low energy innovations in the European residential building sector, analysing their drivers. Specific attention is paid to intermediary actors in facilitating innovation processes and creating new opportunities. The study finds that qualitative case study literature on low energy building innovation has been limited, particularly regarding the existing building stock. Environmental concerns, EU, national and local policies have been the key drivers; financial, knowledge and social sustainability and equity drivers have been of modest importance; while design, health and comfort, and market drivers have played a minor role. Intermediary organisations and individuals have been important through five processes: (1) facilitating individual building projects, (2) creating niche markets, (3) implementing new practices in social housing stock, (4) supporting new business model creation, and (5) facilitating building use post construction. The intermediaries have included both public and private actors, while local authority agents have acted as intermediaries in several cases

Determination of electron density and energy influx in a hollow cathode glow discharge used for powder modification

The electron density and energy influx in an argon hollow cathode glow discharge were determined to obtain adequate parameters for subsequent surface modification of low density polyethylene (LDPE) powder to change the wettability. The electron density was studied by Langmuir probe measurement in dependence on process gas pressure and hollow cathode material. Besides the determination of the rate of increasing electron density with input power an optimal experimental pressure was determined. The energy influx was studied by thermal probe measurements in dependence on process gas pressure, bias voltage, axial position and hollow cathode material. Inside the hollow cathode the energy influx is nearly constant along the whole cathode length. With increasing pressure the energy influx decreased. At biased thermal probe the energy influx was observed to decrease up to the floating potential and beyond it increases with increasing voltage. Using different hollow cathode materials the electron density as well as the energy influx reach higher values for aluminum than for copper and stainless steel

Effect of atazanavir versus other protease inhibitor-containing antiretroviral therapy on endothelial function in HIV-infected persons: randomized controlled trial

OBJECTIVE: Impaired endothelial function was demonstrated in HIV-infected persons on protease-inhibitor (PI)-containing antiretroviral therapy, probably due to altered lipid metabolism. Atazanavir is a PI causing less atherogenic lipoprotein changes. We studied whether endothelial function improves after switching from other PI to atazanavir. DESIGN: Randomized, observer-blind, treatment-controlled trial. SETTING: Three university-based outpatient clinics. PATIENTS: 39 HIV-infected persons with suppressed viral replication on PI-containing regimens and fasting LDL-cholesterol >3mmol/L. INTERVENTION: Patients were randomized either to continue the current PI or change to unboosted atazanavir. MAIN OUTCOME MEASURES: Endpoints at week 24 were endothelial function assessed by flow-mediated vasodilation (FMD) of the brachial artery, lipid profiles, high sensitive C-reactive protein, malondyaldehyde, total antioxidative capacity and oxidized LDL. RESULTS: Baseline characteristics and mean FMD values of the two treatment groups were comparable (3.9+/-1.8% on atazanavir vs. 4.0+/-1.5% in controls). After 24 weeks' treatment, FMD decreased to 3.3+/-1.4% and 3.4+/-1.7%, respectively (all p=n.s.). Total cholesterol improved in both groups (p=<0.0001 and p=0.01, respectively) but changes were more pronounced on atazanavir (p=0.05, changes between groups). HDL and triglyceride levels improved on atazanavir (p=0.03 and p=0.003, respectively) but not in the control group. Serum inflammatory and oxidative stress parameters did not change; oxidized LDL improved significantly in the atazanavir group. CONCLUSIONS: The switch from another PI to atazanavir among treatment experienced patients did not result in improvement of endothelial function despite significantly improved serum lipids. Not only atherogenic lipid profiles but also direct effects of reverse transcriptase inhibitor plus PI-containing combination on the endothelium may affect vascular function. ClinicalTrials.gov Identifier: NCT00447070

Dabigatran after Short Heparin Anticoagulation for Acute Intermediate-Risk Pulmonary Embolism: Rationale and Design of the Single-Arm PEITHO-2 Study

Patients with intermediate-risk pulmonary embolism (PE) may, depending on the method and cut-off values used for definition, account for up to 60% of all patients with PE and have an 8% or higher risk of short-term adverse outcome. Although four non-vitamin K-dependent direct oral anticoagulants (NOACs) have been approved for the treatment of venous thromboembolism, their safety and efficacy as well as the optimal anticoagulation regimen using these drugs have not been systematically investigated in intermediate-risk PE. Moreover, it remains unknown how many patients with intermediate-high-risk and intermediate-low-risk PE were included in most of the phase III NOAC trials. The ongoing Pulmonary Embolism International Thrombolysis 2 (PEITHO-2) study is a prospective, multicentre, multinational, single-arm trial investigating whether treatment of acute intermediate-risk PE with parenteral heparin anticoagulation over the first 72 hours, followed by the direct oral thrombin inhibitor dabigatran over 6 months, is effective and safe. The primary efficacy outcome is recurrent symptomatic venous thromboembolism or death related to PE within the first 6 months. The primary safety outcome is major bleeding as defined by the International Society on Thrombosis and Haemostasis. Secondary outcomes include all-cause mortality, the overall duration of hospital stay (index event and repeated hospitalizations) and the temporal pattern of recovery of right ventricular function over the 6-month follow-up period. By applying and evaluating a contemporary risk-tailored treatment strategy for acute PE, PEITHO-2 will implement the recommendations of current guidelines and contribute to their further evolution