Ekman veering, internal waves, and turbulence observed under Arctic sea ice

Author Posting. © American Meteorological Society, 2014. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 44 (2014): 1306–1328, doi:10.1175/JPO-D-12-0191.1.The ice–ocean system is investigated on inertial to monthly time scales using winter 2009–10 observations from the first ice-tethered profiler (ITP) equipped with a velocity sensor (ITP-V). Fluctuations in surface winds, ice velocity, and ocean velocity at 7-m depth were correlated. Observed ocean velocity was primarily directed to the right of the ice velocity and spiraled clockwise while decaying with depth through the mixed layer. Inertial and tidal motions of the ice and in the underlying ocean were observed throughout the record. Just below the ice–ocean interface, direct estimates of the turbulent vertical heat, salt, and momentum fluxes and the turbulent dissipation rate were obtained. Periods of elevated internal wave activity were associated with changes to the turbulent heat and salt fluxes as well as stratification primarily within the mixed layer. Turbulent heat and salt fluxes were correlated particularly when the mixed layer was closest to the freezing temperature. Momentum flux is adequately related to velocity shear using a constant ice–ocean drag coefficient, mixing length based on the planetary and geometric scales, or Rossby similarity theory. Ekman viscosity described velocity shear over the mixed layer. The ice–ocean drag coefficient was elevated for certain directions of the ice–ocean shear, implying an ice topography that was characterized by linear ridges. Mixing length was best estimated using the wavenumber of the beginning of the inertial subrange or a variable drag coefficient. Analyses of this and future ITP-V datasets will advance understanding of ice–ocean interactions and their parameterizations in numerical models.Support for this study and the overall ITP program was provided by the National Science Foundation and Woods Hole Oceanographic Institution. Support for S. Cole was partially though the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Devonshire Foundation.2014-11-0

Draft genome sequences of xanthomonas sacchari and two banana-associated xanthomonads reveal insights into the xanthomonas group 1 clade

Original article plus subsequent corrections as described below: Following publication of our article [1], we found errors in analyses performed by the corresponding author (DJS) related to the phylogenetic relationship between Xylella species and the other xanthomonads. These errors do not make any difference to the main findings and conclusions reported in our paper. For example, the phylogenetic positions of NCPPB1131, NCPPB1132 and NCPPB4393 within the Group 1 Xanthomonas species are unaffected. However, we wish to apologize to the authors of a previous work [2] for creating any negative impression on the quality of their phylogenetic analyses and to take this opportunity to rectify the errors. The details of the errors are listed.Freely available on Open AccessNOTE: the published correction is in ORE at http://hdl.handle.net/10871/25734We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in OPEN ACCESSGenes 2011, 2 1051 Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors

Utilising the Integrated Motivational Volitional (IMV) model to guide CBT practitioners in the use of their core skills to assess, formulate and reduce suicide risk factors

Cognitive behavioural therapists based in primary care are not usually expected to provide therapy to acutely suicidal individuals or work directly on suicidal thoughts. However, all practitioners should be vigilant about suicide risk and potentially help to reduce vulnerabilities to future suicide risk as part of their routine work. Many of the risk factors and processes hypothesised to play a role in the development of suicidal thinking and behaviours are likely to be evident within the usual content of standard evidence-based protocols for depression or anxiety disorders. In this paper we are suggesting that even within the current primary care remit, (i) an increased awareness of suicide risk vulnerability factors and (ii) using knowledge of a psychological model of suicidal behaviour to inform clinical care are likely to be extremely helpful in structuring clinical formulation and informing interventions. Key learning aims (1) To understand the IMV model and the factors associated with suicidal thoughts and suicidal behaviour. (2) To understand how core CBT skills and interventions can address these factors. (3) To support CBT practitioners in using their current CBT knowledge and skills in the service of reducing the risk of suicidal behaviour

Genome-Wide Sequencing Reveals Two Major Sub-Lineages in the Genetically Monomorphic Pathogen Xanthomonas campestris Pathovar musacearum

types: ArticleFreely available on Open AccessThe bacterium Xanthomonas campestris pathovar musacearum (Xcm) is the causal agent of banana Xanthomonas wilt (BXW). This disease has devastated economies based on banana and plantain crops (Musa species) in East Africa. Here we use genome-wide sequencing to discover a set of single-nucleotide polymorphisms (SNPs) among East African isolates of Xcm. These SNPs have potential as molecular markers for phylogeographic studies of the epidemiology and spread of the pathogen. Our analysis reveals two major sub-lineages of the pathogen, suggesting that the current outbreaks of BXW on Musa species in the region may have more than one introductory event, perhaps from Ethiopia. Also, based on comparisons of genome-wide sequence data from multiple isolates of Xcm and multiple strains of X. vasicola pathovar vasculorum, we identify genes specific to Xcm that could be used to specifically detect Xcm by PCR-based methods

Exploring the impact on primary care mental health practitioners of the death of a patient by suicide: An IPA study

Objectives There have been numerous qualitative studies into the impact of the death of a patient by suicide on clinicians, but the majority of studies have focussed on psychiatrists and psychologists, primarily in inpatient or secondary care settings. To date, little has been done to explore the impact of such deaths on other mental health practitioners working in primary care, such as those working in Improving Access to Psychological Therapies (IAPT) services. Design This qualitative study used purposive sampling and adopted an interpretative phenomenological analysis (IPA) methodology. Method All participants had experienced the death of a patient in their role as a practitioner in an IAPT service. Seven practitioners were recruited from services across the North of England. Semi-structured, one-hour telephone interviews were audio recorded and then transcribed verbatim. Results Analysis of the transcripts identified a number of themes, which were represented in the majority of cases. Specifically, the analyses yielded four superordinate themes: (1) feeling shocked and upset about the death of a patient; (2) attempting to understand the causes of the suicide; (3) learning from the tragic event; and (4) reflections on what helped in coping with the tragic event. The emotional responses of shock, upset, guilt and fear of blame by IAPT practitioners following the death of a patient through suicide is consistent with that found in studies of other mental health practitioners. Conclusions It is hoped that the current study will help raise awareness amongst primary care mental health practitioners, services and training centres, of the impact of losing a patient to suicide and will encourage them to consider how best to prepare and support practitioners in this eventuality. Recommendations include raising awareness of the potential for patient suicide in primary care services, providing clarity on the individualised support available and on the requirements of investigations. Practitioner points Be aware of the likelihood of experiencing a patient suicide. (i.e. the ‘career prevalence’ of such an event). Have regular training in risk assessment, formulation and safety planning, including recognition of the poor predictive power of risk assessment tools and the importance of the therapeutic encounter to enable open discussion of risk. Receive clear guidance on self-care and support available in the event of a patient death and have an understanding of the service and statutory procedures following a suicide. Benefit from a clear procedure for communicating to the practitioner in the event of a patient death (by those with direct management or clinical responsibility for that person) in a caring and supportive manner

The adaptation of a measure of confidence in assessing, formulating, and managing suicide risk

Background: To date little has been done to evaluate the effectiveness of suicide risk formulation training. Aims: We aimed to investigate the psychometric properties of a new scale measuring clinicians' confidence in assessing, formulating, and managing suicide risk. Method: A total of 128 mental health practitioners from an UK National Health Service Trust completed the scale. Of them, 85 from an Improving Access to Psychological Therapies service did so before and after training in Risk Assessment, Formulation, and Management (RAFM); 28 practitioners from the Older Adults service also completed the measure. For test–retest analysis, a further 15 completed the scale again 1 week after baseline without attending any training. Of the training group, 52 (61%) completed the measure at the 6-month follow-up. Results: Analysis indicated a single-factor structure, good test–retest reliability, and statistically significant increases in confidence between pre- and posttraining and between pretraining and 6 month follow-up. Cohen's effect size values suggest a moderate-to-large effect. Limitations: The relatively small sample sizes indicate that this study should be considered a preliminary investigation of a new measure, which warrants further replication. Conclusion: This measure could be useful in gauging practitioners' confidence in the RAFM approach and in evaluating and developing training

An investigation into the factor structure of the Attitudes to Suicide Prevention Scale

Aim: The aim of this study was to investigate the factor structure of the Attitudes to Suicide Prevention Scale (ASPS). Method: The ASPS was distributed to all staff in a UK National Health Service Trust (N = 957). We conducted an exploratory factor analysis followed by a confirmatory factor analysis by splitting the data 60/40 into training and testing subsets. A multiple regression analysis was carried out to investigate whether the overall scale score varied as a function of professional role, age, and gender and whether respondents had completed suicide prevention training or not. Results: Two items displaying poor item-scale correlation were excluded from the factor analysis and a further item was excluded as it was based on different anchor points. For the remaining 11 items, no adequate factor structure emerged. The scale total demonstrated statistically significant differences in attitudes between staff groups (defined by attendance at suicide awareness or prevention training, by gender, and by level of patient contact), but not between groups defined by age range. Generally, however, there were positive attitudes across all Trust staff. Limitations: This study had a low response rate (24%) and was cross-sectional which limits the conclusions that could be drawn. Furthermore, other areas such as convergent validity and test–retest reliability were not examined. Conclusion: Our findings found no satisfactory factor structure for the ASPS. Further scale development would be beneficial