ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes

This is the final version of the article. Available from the publisher via the DOI in this record.Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl.MWJvP is funded by the Netherlands Organization for Scientific Research (NWO) via a VENI grant. TtB and MAvD are funded by the BioAssist/BRS programme of the Netherlands Bioinformatics Centre, which is supported by the Netherlands Genomics Initiative. This work is part of the programme of BiG Grid, the Dutch e-Science Grid, which is financially supported by the NWO. MV is supported by investment from the European Regional Development Fund and the European Social Fund Convergence Programme for Cornwall and the Isles of Scilly to the European Centre for the Environment and Human Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Ever Green: An Enduring System of Parks and Greenways in Detroit

http://deepblue.lib.umich.edu/bitstream/2027.42/110956/1/ever_green.pd

Trade-off between angular and spatial resolutions in in vivo fiber tractography

Tractography is becoming an increasingly popular method to reconstruct white matter connections in vivo. The diffusion MRI data that tractography is based on requires a high angular resolution to resolve crossing fibers whereas high spatial resolution is required to distinguish kissing from crossing fibers. However, scan time increases with increasing spatial and angular resolutions, which can become infeasible in clinical settings. Here we investigated the trade-off between spatial and angular resolutions to determine which of these factors is most worth investing scan time in. We created a unique diffusion MRI dataset with 1.0mm isotropic resolution and a high angular resolution (100 directions) using an advanced 3D diffusion-weighted multi-slab EPI acquisition. This dataset was reconstructed to create subsets of lower angular (75, 50, and 25 directions) and lower spatial (1.5, 2.0, and 2.5mm) resolution. Using all subsets, we investigated the effects of angular and spatial resolutions in three fiber bundles-the corticospinal tract, arcuate fasciculus and corpus callosum-by analyzing the volumetric bundle overlap and anatomical correspondence between tracts. Our results indicate that the subsets of 25 and 50 directions provided inferior tract reconstructions compared with the datasets with 75 and 100 directions. Datasets with spatial resolutions of 1.0, 1.5, and 2.0mm were comparable, while the lowest resolution (2.5mm) datasets had discernible inferior quality. In conclusion, we found that angular resolution appeared to be more influential than spatial resolution in improving tractography results. Spatial resolutions higher than 2.0mm only appear to benefit multi-fiber tractography methods if this is not at the cost of decreased angular resolution

Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis

<p>Abstract</p> <p>Background</p> <p><it>Lactobacillus reuteri </it>harbors the genes responsible for glycerol utilization and vitamin B₁₂synthesis within a genetic island phylogenetically related to gamma-Proteobacteria. Within this island, resides a gene (<it>lreu_1750</it>) that based on its genomic context has been suggested to encode the regulatory protein PocR and presumably control the expression of the neighboring loci. However, this functional assignment is not fully supported by sequence homology, and hitherto, completely lacks experimental confirmation.</p> <p>Results</p> <p>In this contribution, we have overexpressed and inactivated the gene encoding the putative PocR in <it>L. reuteri</it>. The comparison of these strains provided metabolic and transcriptional evidence that this regulatory protein controls the expression of the operons encoding glycerol utilization and vitamin B₁₂synthesis.</p> <p>Conclusions</p> <p>We provide clear experimental evidence for assigning Lreu_1750 as PocR in <it>Lactobacillus reuteri</it>. Our genome-wide transcriptional analysis further identifies the loci contained in the PocR regulon. The findings reported here could be used to improve the production-yield of vitamin B₁₂, 1,3-propanediol and reuterin, all industrially relevant compounds.</p

Micro-coagulation effects on direct ultrafiltration of challenging raw river water

Background The feasibility and competitiveness of substituting the conventional pre-treatment of drinking water treatment plants (dioxichlorination, coagulation/flocculation, settling, sand filtration) by raw river water direct ultrafiltration (UF) was addressed. Results A full scale UF module was operated continuously for 2 years, treating highly variable surface water. The sustainable hydraulic conditions leading to a greater water yield from the direct UF treatment scheme under different scenarios were defined. Summer periods enabled the attainment of higher filtration fluxes, although raw river water showed greater turbidity and total suspended solids content. Winter periods presented higher dissolved organic carbon concentration, with greater biopolymers content, which have been claimed as main membrane foulants. A preliminary micro-coagulation of FeCl3 (<1.5 mg Fe(III) L-1) enabled supporting harsher hydraulic conditions and thus, implementing similar conditions throughout the year. Impacts of micro-coagulation were more pronounced on filtration, particularly in winter, but a positive effect was also noticed in hydraulic and chemical cleaning stages, increasing the efficiency of the former and decreasing by half the frequency of the latter. Conclusion Direct UF proved to be competitive with the current conventional pre-treatment, leading to a significant reduction in reagents needs and sludge production and an increased and more stable product water quality. © 2016 Society of Chemical IndustryPeer ReviewedPostprint (author's final draft

Automated multiple trajectory planning algorithm for the placement of stereo-electroencephalography (SEEG) electrodes in epilepsy treatment.

PURPOSE: About one-third of individuals with focal epilepsy continue to have seizures despite optimal medical management. These patients are potentially curable with neurosurgery if the epileptogenic zone (EZ) can be identified and resected. Stereo-electroencephalography (SEEG) to record epileptic activity with intracranial depth electrodes may be required to identify the EZ. Each SEEG electrode trajectory, the path between the entry on the skull and the cerebral target, must be planned carefully to avoid trauma to blood vessels and conflicts between electrodes. In current clinical practice trajectories are determined manually, typically taking 2-3 h per patient (15 min per electrode). Manual planning (MP) aims to achieve an implantation plan with good coverage of the putative EZ, an optimal spatial resolution, and 3D distribution of electrodes. Computer-assisted planning tools can reduce planning time by quantifying trajectory suitability. METHODS: We present an automated multiple trajectory planning (MTP) algorithm to compute implantation plans. MTP uses dynamic programming to determine a set of plans. From this set a depth-first search algorithm finds a suitable plan. We compared our MTP algorithm to (a) MP and (b) an automated single trajectory planning (STP) algorithm on 18 patient plans containing 165 electrodes. RESULTS: MTP changed all 165 trajectories compared to MP. Changes resulted in lower risk (122), increased grey matter sampling (99), shorter length (92), and surgically preferred entry angles (113). MTP changed 42 % (69/165) trajectories compared to STP. Every plan had between 1 to 8 (median 3.5) trajectories changed to resolve electrode conflicts, resulting in surgically preferred plans. CONCLUSION: MTP is computationally efficient, determining implantation plans containing 7-12 electrodes within 1 min, compared to 2-3 h for MP

Trends in hospital admissions and surgical procedures for degenerative lumbar spine disease in England: a 15-year time-series study.

OBJECTIVES: Low back pain (LBP), from degenerative lumbar spine disease, represents a significant burden on healthcare resources. Studies worldwide report trends attributable to their country's specific demographics and healthcare system. Considering England's specific medico-socioeconomic conditions, we investigate recent trends in hospital admissions and procedures for LBP, and discuss the implications for the allocation of healthcare resources. DESIGN: Retrospective cohort study using Hospital Episode Statistics data relating to degenerative lumbar spine disease in England, between 1999 and 2013. Regression models were used to analyse trends. OUTCOME MEASURES: Trends in the number of admissions and procedures for LBP, mean patient age, gender and length of stay. RESULTS: Hospital admissions and procedures have increased significantly over the study period, from 127.09 to 216.16 and from 24.5 to 48.83 per 100 000, respectively, (p<0.001). The increase was most marked in the oldest age groups with a 1.9 and 2.33-fold increase in admissions for patients aged 60-74 and ≥75 years, respectively, and a 2.8-fold increase in procedures for those aged ≥60 years. Trends in hospital admissions were characterised by a widening gender gap, increasing mean patient age, and decreasing mean hospital stay (p<0.001). Trends in procedures were characterised by a narrowing gender gap, increasing mean patient age (p=0.014) and decreasing mean hospital stay (p<0.001). Linear regression models estimate that each hospital admission translates to 0.27 procedures, per 100 000 (95% CI 0.25 to 0.30, r 0.99, p<0.001; r, Pearson's correlation coefficient). Hospital admissions are increasing at 3.5 times the rate of surgical procedures (regression gradient 7.63 vs 2.18 per 100 000/year). CONCLUSIONS: LBP represents a significant and increasing workload for hospitals in England. These trends demonstrate an increasing demand for specialists involved in the surgical and non-surgical management of this disease, and highlight the need for services capable of dealing with the increased comorbidity burden associated with an ageing patient group

Plan for promoting the demonstrated systems and technologies for further development – D6.4

This report is the output of the task 6.4 to approach a Plan for promoting the  demonstrated systems and technologies for further deployment. The goal of this task was divided into four specific objectives: 1. To assess the role of the demonstrated new or improved machinery for the sustainable and reliable supply of forest biomass to the facilities, with special focus on cost reduction and/or additional biomass supply that can be achieved by the demonstrated innovative technology; 2. To make proposals to promote the innovation and subsequent technology transfer and to present suggestions on how the inventions that have been developed in this project can overcome the obstacles encountered and reach commercialization; 3. To develop scenarios for the potential markets of lignocellulosic forestry residues for biorefineries and energy use; 4. To perform a risk assessment to estimate the side‐effects of not putting interesting inventions into practice. In the first part, there is a summary of the assessment of the machinery demonstrated in the framework of the INFRES project. Some of the main advantages of the innovations are the cost reduction in comparison with conventional systems, in addition to improved productivity and increased supply. Besides this, a couple of innovations showed fuel savings compared to previous supply chains. Moreover, other improvements have been observed, but without a quantitative assessment. Finally, as a conclusion, certain innovations are successful only when they are used in the conditions they were designed for. In the second part, a plan for overcoming the previously identified barriers was elaborated, and the plan was then submitted for assessment by several experts. The application of the most important measures to overcome the barriers that manufacturers face when developing an innovation is mainly in the hands of the manufacturers themselves, and partly in the hands of policy makers who may contribute through the development of appropriate financing instruments or compensations for high‐risk investments in SME’s. In the case of measures proposed to overcome the barriers that manufacturers face during the implementation or use phase, the application of the measures is in the hands of a balanced mix of the main stakeholders, including forest companies and manufacturers. It means that both have to work, sometimes together, to overcome the detected barriers. In the third part, any of the future scenarios anticipates an increase in woody biomass demand. The growth of the biorefinery sector will change the landscape of the forest biomass requirements by 2030. Indeed, feedstocks such as forest residues and stumps can be easily used by this sector. Besides this, the increase and improvement of the machinery used in the forest biomass supply chains, together with the optimization of the whole chains, take some time. As a consequence, it is a challenge for Europe to reach high enough competitiveness and innovation levels so as to cover the demand needs in the best way, with its own resources, seeking a positive impact on all EU regions and on European machinery manufacturers. Finally, the fourth part concludes that if technological and logistical innovations are not implemented in forest biomass supply chains, then energy and environmental targets in the EU will not be reached. Sustainability and cost efficiency gains in the biomass supply chains will not be achieved either. The introduction of innovative solutions as those presented by INFRES will be made possible by implementing the measures that were identified in the third part for overcoming the barriers in the development, implementation and use phases of the innovations.201