Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii)

Rhodococcus defluvii strain Ca11T was isolated from a bioreactor involved in extensive phosphorus removal. We have sequenced the whole genome of this strain and our comparative genomic and phylogenetic analyses confirm its close relatedness with Rhodococcus equi (Rhodococcus hoagii) strains, which share >80% of the gene content. The R. equi virulence plasmid is absent though most of the chromosomal R. equi virulence-associated genes are present in R. defluvii Ca11T. These data suggest that although R. defluvii is an environmental organism, it has the potential to colonise animal hosts

Supporting climate change adaptation using historical climate analysis

Climate change and variability presents a major challenge for rural communities in developing countries. Bridging organisations have a role in helping align top-down and local perspectives, mediating the communication messages that ultimately shape the effectiveness of adaptation responses. We argue that for any coping or adaptation project a first step should be to determine the nature of the climate norms within the project area in order to ascertain the efficacy of current coping strategies. This paper explores the degree to which development organisations in Kenya, Uganda and Tanzania used analysis of local historical climate information in project aims, planning and design. Sixty seven participants, managing 102 community-level climate-related agricultural projects, and three NGO case studies were included. Most projects focused on low-regret options. The majority of respondents’ projects included enhancing farmers’ awareness of climate change and variability as an aim, but only seven percent had used any historical climate information during planning. Instead projects relied on general knowledge or farmers’ perceptions, which can sometimes differ from analysed historical climate information, thus potentially leading to a cycle of reinforcement of perceptions. It is vital that bridging organisations and policy makers be aware of the value of using analysed historical climate information to determine the climate norms (including variability) and to identify what the data shows regarding how the climate is changing. This is essential for planning, consideration with stakeholders, and for example to determine suitability of alternative crops and cultivars or to ensure other relevant environmental factors influencing agricultural production are considered

Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy

Chemotaxonomic methods played an important role in the development of the polyphasic approach to classification of Archaea and Bacteria. However, we here argue that routine application of these methods is unnecessary in an era when genomic data are available and sufficient for species delineation. Thus, authors who choose not to utilize such methods should not be forced to do so during the peer review and editorial handling of manuscripts describing novel species. Instead, we argue that chemotaxonomy will thrive if improved analytical methods are introduced and deployed, primarily by specialist laboratories, in studies at taxonomic levels above the characterisation of novel species

A new improved method for assessing brain deformation after decompressive craniectomy.

BACKGROUND: Decompressive craniectomy (DC) is a surgical intervention used following traumatic brain injury to prevent or alleviate raised intracranial pressure. However the clinical effectiveness of the intervention remains in doubt. The location of the craniectomy (unilateral or bifrontal) might be expected to change the brain deformation associated with the operation and hence the clinical outcome. As existing methods for assessing brain deformation have several limitations, we sought to develop and validate a new improved method. METHODS: Computed tomography (CT) scans were taken from 27 patients who underwent DC (17 bifrontal patients and 10 unilateral patients). Pre-operative and post-operative images were processed and registered to determine the change in brain position associated with the operation. The maximum deformation in the herniated brain, the change in volume and estimates of the craniectomy area were determined from the images. Statistical comparison was made using the Pearson's correlation coefficient r and a Welch's two-tailed T-test, with statistical significance reported at the 5% level. RESULTS: There was a reasonable correlation between the volume increase and the maximum brain displacement (r = 0.64), a low correlation between the volume increase and the craniectomy area (r = 0.30) and no correlation between the maximum displacement and the craniectomy area (r = -0.01). The maximum deformation was significantly lower (P  = 0.023) in the bifrontal patients (mean = 22.5 mm) compared with the unilateral patients (mean = 29.8 mm). Herniation volume was significantly lower (P = 0.023) in bifrontal (mean = 50.0 ml) than unilateral patients (mean = 107.3 ml). Craniectomy area was not significantly different for the two craniectomy locations (P = 0.29). CONCLUSIONS: A method has been developed to quantify changes in brain deformation due to decompressive craniectomy from CT images and allow comparison between different craniectomy locations. Measured displacement is a reasonable way to characterise volume changes.TLF acknowledges funding from the Engineering and Physical Sciences Research Council (EPSRC). AGK is supported by a Royal College of Surgeons of England Research Fellowship (funded by the Freemasons and the Rosetrees Trust), a National Institute of Health Research (NIHR) Academic Clinical Fellowship and a Raymond and Beverly Sackler Studentship. PJH is supported by a NIHR Research Professorship and the NIHR Cambridge Biomedical Research Centre. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the final published version. It is also available from PLOS at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110408

Development of a finite element model of decompressive craniectomy.

Decompressive craniectomy (DC), an operation whereby part of the skull is removed, is used in the management of patients with brain swelling. While the aim of DC is to reduce intracranial pressure, there is the risk that brain deformation and mechanical strain associated with the operation could damage the brain tissue. The nature and extent of the resulting strain regime is poorly understood at present. Finite element (FE) models of DC can provide insight into this applied strain and hence assist in deciding on the best surgical procedures. However there is uncertainty about how well these models match experimental data, which are difficult to obtain clinically. Hence there is a need to validate any modelling approach outside the clinical setting. This paper develops an axisymmetric FE model of an idealised DC to assess the key features of such an FE model which are needed for an accurate simulation of DC. The FE models are compared with an experimental model using gelatin hydrogel, which has similar poro-viscoelastic material property characteristics to brain tissue. Strain on a central plane of the FE model and the front face of the experimental model, deformation and load relaxation curves are compared between experiment and FE. Results show good agreement between the FE and experimental models, providing confidence in applying the proposed FE modelling approach to DC. Such a model should use material properties appropriate for brain tissue and include a more realistic whole head geometry.TLF acknowledges funding from the Engineering and Physical Sciences Research Council (EPSRC). AGK is supported by a Royal College of Surgeons of England Research Fellowship (funded by the Freemasons and the Rosetrees Trust), an NIHR Academic Clinical Fellowship and a Raymond and Beverly Sackler Studentship. PJH is supported by a NIHR Research Professorship and the NIHR Cambridge Biomedical Research Centre. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the final published version, also available from PLOS at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0102131

Modelling of Brain Deformation After Decompressive Craniectomy.

Hyperelastic finite element models, with either an idealized cylindrical geometry or with realistic craniectomy geometries, were used to explore clinical issues relating to decompressive craniectomy. The potential damage in the brain tissue was estimated by calculating the volume of material exceeding a critical shear strain. Results from the idealized model showed how the potentially damaged volume of brain tissue increased with an increasing volume of brain tissue herniating from the skull cavity and with a reduction in craniectomy area. For a given herniated volume, there was a critical craniectomy diameter where the volume exceeding a critical shear strain fell to zero. The effects of details at the craniectomy edge, specifically a fillet radius and a chamfer on the bone margin, were found to be relatively slight, assuming that the dura is retained to provide effective protection. The location in the brain associated with volume expansion and details of the material modeling were found to have a relatively modest effect on the predicted damage volume. The volume of highly sheared material in the realistic models of the craniectomy varied roughly in line with differences in the craniectomy area.TLF acknowledges funding from the Engineering and Physical Sciences Research Council (EPSRC). BW is supported by the Studienstiftung des deutschen Volkes, the Max Weber-Programm and the Stiftung Maximilianeum. AGK is supported by a Royal College of Surgeons of England Research Fellowship (funded by the Freemasons and the Rosetrees Trust), a National Institute of Health Research (NIHR) Academic Clinical Fellowship and a Raymond and Beverly Sackler Studentship. PJH is supported by a NIHR Research Professorship and the NIHR Cambridge Biomedical Research Centre.This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1007/s10439-016-1666-

Factors Influencing the Use of a Mobile App for Reporting Adverse Drug Reactions and Receiving Safety Information:A Qualitative Study

Introduction A mobile app may increase the reporting of adverse drug reactions (ADRs) and improve the communication of new drug safety information. Factors that influence the use of an app for such two-way risk communication need to be considered at the development stage. Objective Our aim was to reveal the factors that may influence healthcare professionals (HCPs) and patients to use an app for two-way risk communication. Methods Focus group discussions and face-to-face interviews were conducted in the Netherlands, Spain and the UK. Patients with type 2 diabetes mellitus, patients with a rare disease or their caregivers and adolescents with health conditions were eligible to participate. HCPs included pharmacists, paediatricians, general practitioners, internists, practice nurses and professionals caring for patients with a rare disease. Patients and HCPs were recruited through various channels. The recorded discussions and interviews were transcribed verbatim. The dataset was analysed using thematic analysis and arranged according to the Unified Theory of Acceptance and Use of Technology. Results Seven focus group discussions and 13 interviews were conducted. In total, 21 HCPs and 50 patients participated. Identified factors that may influence the use of the app were the type of feedback given on reported ADRs, how ADR reports are stored and the type of drug news. Also mentioned were other functions of the app, ease of use, type of language, the source of safety information provided through the app, security of the app, layout, the operating systems on which the app can be used and the costs. Conclusions Further research is needed to assess associations between user characteristics and the direction (positive or negative) of the factors potentially influencing app use