Designing the Self-Assembly of Arbitrary Shapes Using Minimal Complexity Building Blocks

The design space for self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. We develop a pipeline to explore the design spaces for a set of structures of various sizes and complexities. To understand the implications of the different solutions, we analyze their assembly dynamics using patchy particle simulations and study the influence of the number of distinct building blocks, and the angular and spatial tolerances on their interactions, on the kinetics and yield of the target assembly. We show that the resource-saving solution with a minimum number of distinct blocks can often assemble just as well (or faster) than designs where each building block is unique. We further use our methods to design multifarious structures, where building blocks are shared between different target structures. Finally, we use coarse-grained DNA simulations to investigate the realization of multicomponent shapes using DNA nanostructures as building blocks.

The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami

This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.

Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation

This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures.

The impact of contracts on outsourcing computed tomography examinations from a Swedish public university hospital to a private radiology unit

INTRODUCTION

After years of outsourcing without detailed contracts from one of Sweden's largest university hospitals to external radiology units, the hospital started to use a specific contract for outsourcing computed tomography (CT) examinations. The purpose of this study was to compare the cost-effectiveness of two outsourcing approaches, where examinations were performed either with a detailed, specific contract (with-contract) or without (no-contract), between a hospital radiology department and private external units.

METHODS

This retrospective study included a group of electively outsourced CT-examinations (n = 132) and a control group of in-house CT-examinations (n = 132), selected from the three different types of CT-examinations referred from the Departments of Oncology and Hematology. These examinations were randomly selected from four different groups over two time periods of one year each, one being outsourcing without a contract (no-contract, during 2013), one time period with a specific contract (with-contract, during 2014) and two control groups of examinations performed in-house within both these time periods. We compared outsourced examinations (both no-contract and with-contract groups) and in-house examinations. The comparison of these groups include five parameters; management-time, patient waiting-time, the quality of the examinations, - image interpretations and costs.

RESULTS

During 2013, management-time for CT-examinations was longer in the outsourced group (no-contract) than in the in-house group, with a statistical significance (P = 0.002). Fewer examinations performed in-house and in the with-contract group needed re-interpretation than in the no-contract group. CT-examinations in the with-contract group were associated with shorter overall management-time, patient waiting time and lower costs compared to the no-contract group.

CONCLUSION

Using a contract with detailed specifications for outsourcing CT-examinations may be an effective way of reducing patient waiting time. Outsourcing based on a well-founded contract can be cost-effective, compared with outsourcing without a detailed plan for the services required.

Prediction of gestational age based on genome-wide differentially methylated regions

Background

We explored the association between gestational age and cord blood DNA methylation at birth and whether DNA methylation could be effective in predicting gestational age due to limitations with the presently used methods. We used data from the Norwegian Mother and Child Birth Cohort study (MoBa) with Illumina HumanMethylation450 data measured for 1753 newborns in two batches: MoBa 1, n = 1068; and MoBa 2, n = 685. Gestational age was computed using both ultrasound and the last menstrual period. We evaluated associations between DNA methylation and gestational age and developed a statistical model for predicting gestational age using MoBa 1 for training and MoBa 2 for predictions. The prediction model was additionally used to compare ultrasound and last menstrual period-based gestational age predictions. Furthermore, both CpGs and associated genes detected in the training models were compared to those detected in a published prediction model for chronological age.

Results

There were 5474 CpGs associated with ultrasound gestational age after adjustment for a set of covariates, including estimated cell type proportions, and Bonferroni-correction for multiple testing. Our model predicted ultrasound gestational age more accurately than it predicted last menstrual period gestational age.

Conclusions

DNA methylation at birth appears to be a good predictor of gestational age. Ultrasound gestational age is more strongly associated with methylation than last menstrual period gestational age. The CpGs linked with our gestational age prediction model, and their associated genes, differed substantially from the corresponding CpGs and genes associated with a chronological age prediction model.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1063-4) contains supplementary material, which is available to authorized users.

25-Hydroxyvitamin D in pregnancy and genome wide cord blood DNA methylation in two pregnancy cohorts (MoBa and ALSPAC)

The aim of the study was to investigate whether maternal mid-pregnancy 25-hydroxyvitamin D concentrations are associated with cord blood DNA methylation. DNA methylation was assessed using the Illumina HumanMethylation450 BeadChip, and maternal plasma 25-hydroxyvitamin D was measured in 819 mothers/newborn pairs participating in the Norwegian Mother and Child Cohort (MoBa) and 597 mothers/newborn pairs participating in the Avon Longitudinal Study of Parents and Children (ALSPAC). Across 473,731CpG DNA methylation sites in cord blood DNA, none were strongly associated with maternal 25-hydroxyvitamin D after adjusting for multiple tests (false discovery rate (FDR)>0.5; 473,731 tests). A meta-analysis of the results from both cohorts, using the Fisher method for combining p-values, also did not strengthen findings (FDR>0.2). Further exploration of a set of CpG sites in the proximity of four a priori defined candidate genes (CYP24A1, CYP27B1, CYP27A1 and CYP2R1) did not result in any associations with FDR<0.05 (56 tests). In this large genome wide assessment of the potential influence of maternal vitamin D status on DNA methylation, we did not find any convincing associations in 1416 newborns. If true associations do exist, their identification might require much larger consortium studies, expanded genomic coverage, investigation of alternative cell types or measurements of 25-hydroxyvitamin D at different gestational time points.

The genus burkholderia: analysis of 56 genomic sequences

The genus Burkholderia consists of a number of very diverse species, both in terms of lifestyle (which varies from category B pathogens to apathogenic soil bacteria and plant colonizers) and their genetic contents. We have used 56 publicly available genomes to explore the genomic diversity within this genus, including genome sequences that are not completely finished, but are available from the NCBI database. Defining the pan- and core genomes of species results in insights in the conserved and variable fraction of genomes, and can verify (or question) historic, taxonomic groupings. We find only several hundred genes that are conserved across all Burkholderia genomes, whilst there are more than 40,000 gene families in the Burkholderia pan-genome. A BLAST matrix visualizes the fraction of conserved genes in pairwise comparisons. A BLAST atlas shows which genes are actually conserved in a number of genomes, located and visualized with reference to a chosen genome. Genomic islands are common in many Burkholderia genomes, and most of these can be readily visualized by DNA structural properties of the chromosome. Trees that are based on relatedness of gene family content yield different results depending on what genes are analyzed. Some of the differences can be explained by errors in incomplete genome sequences, but, as our data illustrate, the outcome of phylogenetic trees depends on the type of genes that are analyzed.

Genome comparison of bacterial pathogens

Bacterial pathogens are being sequenced at an increasing rate. To many microbiologists, it appears that there simply is not enough time to digest all the information suddenly available. In this chapter we present several tools for comparison of sequenced pathogenic genomes, and discuss differences between pathogens and non-pathogens. The presented tools allow comparison of large numbers of genomes in a hypothesis-driven manner. Visualization of the results is very important for clear presentation of the results and various ways of graphical representation are introduced.

Genetic variability of Campylobacter jejuni isolated from fresh and frozen broiler carcasses

AIMS

The aim of this study was to determine the genetic variability of Campylobacter jejuni isolates from poultry before and after freezing treatment in order to identify genotypes that would survive the treatment.

METHODS AND RESULTS

C. jejuni was isolated from both fresh and frozen halves of the same carcass after freezing for 2 or more than 20 days at -20 degrees C. From 36 carcasses, representing five unrelated flocks in Norway, a total of 209 isolates were included in the study. Thirty-two of the isolates were recovered with a qualitative method while the remaining 177 were isolated using a quantitative method. Isolates were genotyped with fluorescent amplified fragment length polymorphism using MfeI and BglII restriction enzymes. Nine different genotypes were identified, however, one genotype was shown to be dominant in three different flocks. This genotype and the dominant genotype of another flock were found among isolates from fresh and frozen broiler halves. They were also shown to be identical to genotypes frequently identified among strains isolated from humans, cattle and poultry flocks in previous years.

CONCLUSIONS

Freezing treatment or isolation method appeared not to select for a particular genotype.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of the present study indicate that the freezing tolerance of strains is not genotype dependent.

Development and maintenance of guideline-based decision support for pharmacological treatment of hypertension

The objective was to build a computer-based decision support system (DSS), which could apply the formal rules embedded in guidelines regarding pharmacological treatment of hypertension. The aim was also to test VISUAL BASIC as a development tool for DSS's in health care. From the Swedish guidelines for treatment of hypertension, the most widely accepted and scientifically best proved treatment strategies were chosen and implemented as rules. A DSS that is capable of applying the evidence-based rules extracted from guidelines regarding drug treatment of hypertension, to any patient's medical profile, was constructed. The output consists of a recommendation regarding preferred generic drug class and also a written report, reflecting decision steps provided by the rule-base and inference engine. We also provide methods for formalising an implementable language of guidelines. A mainstream programming language like VISUAL BASIC can be an alternative when building complicated decision support systems. A logic formal notation can facilitate communication between the expert and the programmer. The program is a stand-alone product independent of computerized medical records and thereby easy to install and maintain.

Evaluation of a computer-based decision support system for treatment of hypertension with drugs: retrospective, nonintervention testing of cost and guideline adherence

OBJECTIVE

To evaluate a computerized decision support system (DSS) for drug treatment of hypertension, regarding quality, safety, and cost compared to actual antihypertensive drug treatment.

DESIGN

The medical profiles of 338 hypertensive patients treated with drugs against hypertension were processed by the DSS. The drug treatment proposed by the system was then compared to actual treatment given by their physician.

SETTING

Four health centres in the county of Västerbotten, in Sweden.

SUBJECTS

A list of hypertensive patients was extracted from the computerized medical records of each health centre and every fifth patient's medical profile was assessed by the system.

INTERVENTIONS

None.

MAIN OUTCOME MEASURES

Drug used, drug used in relation to certain major diseases such as diabetes mellitus, asthma, ischaemic heart disease (IHD), and previous myocardial infarction. Adherence to hypertension guidelines, safety, and cost.

RESULTS

The DSS suggested significantly more thiazides and significantly fewer calcium antagonists than the physicians had prescribed, with a total cost reduction of 33-40%, depending on doses chosen. The DSS drug profile was more adherent to guidelines in patients with major complicating diseases, suggesting an improvement in treatment quality for these patients by the DSS.

CONCLUSION

The DSS which fully implements current guidelines may improve the quality of antihypertensive treatment, concurrently leading to a considerable reduction in drug costs.