Near surface properties of mixtures of propylammonium nitrate with n-alkanols 1. Nanostructure

In situ amplitude modulated-atomic force microscopy (AM-AFM) has been used to probe the nanostructure of mixtures of propylammonium nitrate (PAN) with n-alkanols near a mica surface. PAN is a protic ionic liquid (IL) which has a bicontinuous sponge-like nanostructure of polar and apolar domains in the bulk, which becomes flatter near a solid surface. Mixtures of PAN with 1-butanol, 1-octanol, and 1-dodecanol at 10–70 vol% n-alkanol have been examined, along with each pure n-alkanol, to reveal the effect of composition and n-alkanol chain length. At low concentrations the butanol simply swells the PAN near-surface nanostructure, but at higher concentrations the nanostructure fragments. Octanol and dodecanol first lower the preferred curvature of the PAN near-surface nanostructure because, unlike n-butanol, their alkyl chains are too long to be accommodated alongside the PAN cations. At higher concentrations, octanol and dodecanol self-assemble into n-alkanol rich aggregates in a PAN rich matrix. The concentration at which aggregation first becomes apparent decreases with n-alkanol chain length

Adsorbed and near surface structure of ionic liquids at a solid interface

The structure of solid–ionic liquid (IL) interfaces has been characterised with unprecedented clarity by employing a range of atomic force microscopy (AFM) imaging techniques and tip pressures appropriate for the system under study. Soft contact and amplitude-modulation (AM) AFM imaging have been used to elucidate the lateral structure of ILs adsorbed onto mica, and in the near surface ion layers. Data is presented for ethylammonium nitrate (EAN) and 1-ethyl-3-methylimidazolium bis(trifluoro-methylsulfonyl)imide (EMIm TFSI). Whereas EAN is a protic IL that forms a nanostructured sponge phase in the bulk, EMIm TFSI is aprotic and has weak (or absent) bulk association structure. Comparison of results obtained for the two liquids elucidates how the strength of bulk liquid morphology effects lateral organisation at the surface, and any effect of IL class, i.e. protic versus aprotic. Imaging reveals EAN self assembles at the solid surface in a worm-like morphology, whereas EMIm cations adsorb in a more isolated fashion, but still in rows templated by the mica surface. To the authors’ knowledge, the wormlike structures present at the EAN–mica interface are the smallest self-assembled aggregates ever imaged on a solid surface

3-Dimensional atomic scale structure of the ionic liquid–graphite interface elucidated by AM-AFM and quantum chemical simulations

In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)–bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL–solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN–graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid–solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition

Development and validation of a simplified score to predict neonatal mortality risk among neonates weighing 2000 g or less (NMR-2000): an analysis using data from the UK and The Gambia.

BACKGROUND: 78% of neonatal deaths occur in sub-Saharan Africa and southern Asia, among which, more than 80% are in low birthweight babies. Existing neonatal mortality risk scores have primarily been developed for high-resource settings. The aim of this study was to develop and validate a score that is practicable for low-income and middle-income countries to predict in-hospital mortality among neonates born weighing 2000 g or less using datasets from the UK and The Gambia. METHODS: This analysis used retrospective data held in the UK National Neonatal Research Database from 187 neonatal units, and data from the Edward Francis Small Teaching Hospital (EFSTH), Banjul, The Gambia. In the UK dataset, neonates were excluded if birthweight was more than 2000 g; if the neonate was admitted aged more than 6 h or following discharge; if the neonate was stillborn; if the neonate died in delivery room; or if they were moribund on admission. The Gambian dataset included all neonates weighing less than 2000 g who were admitted between May 1, 2018, and Sept 30, 2019, who were screened for but not enrolled in the Early Kangaroo Mother Care Trial. 18 studies were reviewed to generate a list of 84 potential parameters. We derived a model to score in-hospital neonatal mortality risk using data from 55 029 admissions to a random sample of neonatal units in England and Wales from Jan 1, 2010, to Dec 31, 2016. All candidate variables were included in a complete multivariable model, which was progressively simplified using reverse stepwise selection. We validated the new score (NMR-2000) on 40 329 admissions to the remaining units between the same dates and 14 818 admissions to all units from Jan 1, to Dec 31, 2017. We also validated the score on 550 neonates admitted to the EFSTH in The Gambia. FINDINGS: 18 candidate variables were selected for inclusion in the modelling process. The final model included three parameters: birthweight, admission oxygen saturation, and highest level of respiratory support within 24 h of birth. NMR-2000 had very good discrimination and goodness-of-fit across the UK samples, with a c-index of 0·8859-0·8930 and a Brier score of 0·0232-0·0271. Among Gambian neonates, the model had a c-index of 0·8170 and a Brier score of 0·1688. Predictive ability of the simplified integer score was similar to the model using regression coefficients, with c-indices of 0·8903 in the UK full validation sample and 0·8082 in the Gambian validation sample. INTERPRETATION: NMR-2000 is a validated mortality risk score for hospitalised neonates weighing 2000 g or less in settings where pulse oximetry is available. The score is accurate and simplified for bedside use. NMR-2000 requires further validation using a larger dataset from low-income and middle-income countries but has the potential to improve individual and population-level neonatal care resource allocation. FUNDING: Bill & Melinda Gates Foundation; Eunice Kennedy Shriver National Institute of Child Health & Human Development; Wellcome Trust; and Joint Global Health Trials scheme of Department of Health and Social Care, Department for International Development, Medical Research Council, and Wellcome Trust

The putative drug efflux systems of the Bacillus cereus group

The Bacillus cereus group of bacteria includes seven closely related species, three of which, B. anthracis, B. cereus and B. thuringiensis, are pathogens of humans, animals and/or insects. Preliminary investigations into the transport capabilities of different bacterial lineages suggested that genes encoding putative efflux systems were unusually abundant in the B. cereus group compared to other bacteria. To explore the drug efflux potential of the B. cereus group all putative efflux systems were identified in the genomes of prototypical strains of B. cereus, B. anthracis and B. thuringiensis using our Transporter Automated Annotation Pipeline. More than 90 putative drug efflux systems were found within each of these strains, accounting for up to 2.7% of their protein coding potential. Comparative analyses demonstrated that the efflux systems are highly conserved between these species; 70-80% of the putative efflux pumps were shared between all three strains studied. Furthermore, 82% of the putative efflux system proteins encoded by the prototypical B. cereus strain ATCC 14579 (type strain) were found to be conserved in at least 80% of 169 B. cereus group strains that have high quality genome sequences available. However, only a handful of these efflux pumps have been functionally characterized. Deletion of individual efflux pump genes from B. cereus typically had little impact to drug resistance phenotypes or the general fitness of the strains, possibly because of the large numbers of alternative efflux systems that may have overlapping substrate specificities. Therefore, to gain insight into the possible transport functions of efflux systems in B. cereus, we undertook large-scale qRT-PCR analyses of efflux pump gene expression following drug shocks and other stress treatments. Clustering of gene expression changes identified several groups of similarly regulated systems that may have overlapping drug resistance functions. In this article we review current knowledge of the small molecule efflux pumps encoded by the B. cereus group and suggest the likely functions of numerous uncharacterised pumps

Recruitment to randomised trials : Strategies for Trial Enrolment and Participation Study. The STEPS study

Objectives: To identify factors associated with good and poor recruitment to multicentre trials. Data sources: Part A: database of trials started in or after 1994 and were due to end before 2003 held by the Medical Research Council and Health Technology Assessment Programmes. Part B: interviews with people playing a wide range of roles within four trials that their funders identified as ‘exemplars’. Part C: a large multicentre trial (the CRASH trial) of treatment for head injury. Review methods: The study used a number of different perspectives (‘multiple lenses’), and three components. Part A: an epidemiological review of a cohort of trials. Part B: case studies of trials that appeared to have particularly interesting lessons for recruitment. Part C: a single, in-depth case study to examine the feasibility of applying a businessorientated analytical framework as a reference model in future trials. Results: In the 114 trials found in Part A, less than one-third recruited their original target within the time originally specified, and around one-third had extensions. Factors observed more often in trials that recruited successfully were: having a dedicated trial manager, being a cancer or drug trial, and having interventions only available inside the trial. The most commonly reported strategies to improve recruitment were newsletters and mailshots, but it was not possible to assess whether they were causally linked to changes in recruitment. The analyses in Part B suggested that successful trials were those addressing clinically important questions at a timely point. The investigators were held in high esteem by the interviewees, and the trials were firmly grounded in existing clinical practices, so that the trial processes were not alien to clinical collaborators, and the results could be easily applicable to future practice. The interviewees considered that the needs of patients were well served by participation in the trials. Clinical collaborators particularly appreciated clear delineation of roles, which released them from much of the workload associated with trial participation. There was a strong feeling from interviewees that they were proud to be part of a successful team. This pride fed into further success. Good groundwork and excellent communications across many levels of complex trial structures were considered to be extremely important, including training components for learning about trial interventions and processes, and team building. All four trials had faced recruitment problems, and extra insights into the working of trials were afforded by strategies invoked to address them. The process of the case study in Part C was able to draw attention to a body of research and practice in a different discipline (academic business studies). It generated a reference model derived from a combination of business theory and work within CRASH. This enabled identification of weaker managerial components within CRASH, and initiatives to strengthen them. Although it is not clear, even within CRASH, whether the initiatives that follow from developing and applying the model will be effective in increasing recruitment or other aspects of the success of the trial, the reference model could provide a template, with potential for those managing other trials to use or adapt it, especially at foundation stages. The model derived from this project could also be used as a diagnostic tool if trials have difficulties and hence as a basis for deciding what type of remedial action to take. It may also be useful for auditing the progress of trials, such as during external review. Conclusions: While not producing sufficiently definitive results to make strong recommendations, the work here suggests that future trials should consider the different needs at different phases in the life of trials, and place greater emphasis on ‘conduct’ (the process of actually doing trials). This implies learning lessons from successful trialists and trial managers, with better training for issues relating to trial conduct. The complexity of large trials means that unanticipated difficulties are highly likely at some time in every trial. Part B suggested that successful trials were those flexible and robust enough to adapt to unexpected issues. Arguably, the trialists should also expect agility from funders within a proactive approach to monitoring ongoing trials. Further research into different recruitment patterns (including ‘failures’) may help to clarify whether the patterns seen in the ‘exemplar’ trials differ or are similar. The reference model from Part C needs to be further considered in other similar and different trials to assess its robustness. These and other strategies aimed at increasing recruitment and making trials more successful need to be formally evaluated for their effectiveness in a range of trials.Not peer reviewedPublisher PD

Intracluster correlation coefficients in cluster randomized trials: empirical insights into how should they be reported

BACKGROUND: Increasingly, researchers are recognizing that there are many situations where the use of a cluster randomized trial may be more appropriate than an individually randomized trial. Similarly, the need for appropriate standards of reporting of cluster trials is more widely acknowledged. METHODS: In this paper, we describe the results of a survey to inform the appropriate reporting of the intracluster correlation coefficient (ICC) – the statistical measure of the clustering effect associated with a cluster randomized trial. RESULTS: We identified three dimensions that should be considered when reporting an ICC – a description of the dataset (including characteristics of the outcome and the intervention), information on how the ICC was calculated, and information on the precision of the ICC. CONCLUSIONS: This paper demonstrates the development of a framework for the reporting of ICCs. If adopted into routine practice, it has the potential to facilitate the interpretation of the cluster trial being reported and should help the development of new trials in the area

Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102

Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting biological outcome of this experiment is the indication of the extent to which the phosphorus regulatory system of this cyanobacterium affects the expression of multiple genes beyond those strictly involved in phosphorus acquisition

What influences recruitment to randomised controlled trials? A review of trials funded by two UK funding agencies.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: A commonly reported problem with the conduct of multicentre randomised controlled trials (RCTs) is that recruitment is often slower or more difficult than expected, with many trials failing to reach their planned sample size within the timescale and funding originally envisaged. The aim of this study was to explore factors that may have been associated with good and poor recruitment in a cohort of multicentre trials funded by two public bodies: the UK Medical Research Council (MRC) and the Health Technology Assessment (HTA) Programme. METHODS: The cohort of trials was identified from the administrative databases held by the two funding bodies. 114 trials that recruited participants between 1994 and 2002 met the inclusion criteria. The full scientific applications and subsequent trial reports submitted by the trial teams to the funders provided the principal data sources. Associations between trial characteristics and recruitment success were tested using the Chi-squared test, or Fisher's exact test where appropriate. RESULTS: Less than a third (31%) of the trials achieved their original recruitment target and half (53%) were awarded an extension. The proportion achieving targets did not appear to improve over time. The overall start to recruitment was delayed in 47 (41%) trials and early recruitment problems were identified in 77 (63%) trials. The inter-relationship between trial features and recruitment success was complex. A variety of strategies were employed to try to increase recruitment, but their success could not be assessed. CONCLUSION: Recruitment problems are complex and challenging. Many of the trials in the cohort experienced recruitment difficulties. Trials often required extended recruitment periods (sometimes supported by additional funds). While this is of continuing concern, success in addressing the trial question may be more important than recruitment alone.Published versio