Uncertainty support in the spectral information System SPECCHIO

The spectral information system SPECCHIO was updated to support the generic handling of uncertainty information in the form of uncertainty tree diagrams. The updates involve changes to the relations database model as well as dedicated methods provided by the SPECCHIO application programming interface. A case study selected from classic field spectroscopy demonstrates the use of the functionality. In conclusion, a database-centric automated uncertainty propagation in combination with measurement protocol standardization will provide a crucial step toward spectroscopy data accompanied by propagated, traceable, uncertainty information

Growth and productivity of New Zealand kauri (Agathis australis (D.Don.) Lindl.) in planted forests

Background: The establishment of even-aged planted stands of New Zealand kauri (Agathis australis (D.Don) Lindl.) for timber has been constrained by a lack of quantitative information on productivity and rotation length on which forest management and investment decisions could be made. Methods: Stand-level models of height and basal area against time were developed (as well as a stand-volume function to calculate volume from height and basal area) based on planted stands that were up to 83-years old and represented planting sites both within and outside the current natural range of the species. Results: Planted kauri was shown to be slow to establish with little height growth for the first five years after planting. Similar trends were observed for basal area and whole-tree volume development. A Schumacher equation with local slope parameter and asymptote bounded at 45 m gave the best fit for height, while a von Bertalanffy-Richards equation in difference form with local slope parameter gave the best fit for basal area. For plantations with an average site index (20.4), height was predicted to be 22.3 m in height at age 60, with a basal area of 78.1 m2 ha−1. Whole-tree volume was predicted to be 702 m3 ha−1. Predicted volume mean annual increment was 11.7 m3 ha−1 yr−1for all stands at age 60. From age 20–60 years, stands with a higher site index had a volume mean annual increment of 18.6 m3 ha−1 yr−1. The best stand exceeded 20 m3 ha−1 yr−1. Conclusions: This study indicates an opportunity to grow kauri in plantations on selected good-quality sites over rotations of 60–80 years or les

Multistate Hepatitis A Outbreak: Vaccination of Food Service Workers as Part of the Kentucky Outbreak Response

Background: In August 2017, a local outbreak of Hepatitis A was identified among homeless individuals in Louisville, Kentucky. This marked the first cases in what has now become recognized as the largest Hepatitis A outbreak in the US. When infection was identified in a Food Service Worker (FSW), vaccination efforts were expanded to target this group. Objective: The purpose of this study was to describe: 1) the processes used to provide access to Hepatitis A vaccine for FSWs, 2) results from the immunization activities, and 3) lessons learned from the outcomes. Methods: Through a partnership between the Louisville Metro Department of Public Health and Wellness (LMDPHW) and the University of Louisville Division of Infectious Diseases, a novel approach to vaccination was implemented. Access to vaccine was provided via on-site immunization in 66 restaurants and subsequent availability in a pop-up vaccination clinic. Data were collected using the LMDPHW data collection form and included demographics, risk factors for Hepatitis A, and vaccine documentation. Results for those vaccinated March-December 2018 were analyzed using descriptive statistics. Results: On-site vaccination was provided to 1337 FSW at 66 restaurants during the seven (7) week period from March 28-May 15, 2018. This process involved a team of 42 including Advanced Practice Registered Nurses, Registered and Licensed Practical Nurses, Physicians, and UL team members. During the 35 weeks the walk-in clinic has been in operation (May 16-December 31, 2018), 3068 additional FSW were vaccinated for a total of 4405 FSWs vaccinated as part of the outbreak response. Critical partners included the Kentucky Restaurant Association and the Kentucky Nurses Association. Conclusions: This study demonstrated a successful model for vaccination of a novel population during an infectious disease outbreak and the importance of expanding partnership networks to ensure success. The outcomes emphasized the importance of the resources available in the academic community for reliable and consistent public health emergency response

Expression capable library for studies of Neisseria gonorrhoeae, version 1.0

Background The sexually transmitted disease, gonorrhea, is a serious health problem in developed as well as in developing countries, for which treatment continues to be a challenge. The recent completion of the genome sequence of the causative agent, Neisseria gonorrhoeae, opens up an entirely new set of approaches for studying this organism and the diseases it causes. Here, we describe the initial phases of the construction of an expression-capable clone set representing the protein-coding ORFs of the gonococcal genome using a recombination-based cloning system. Results The clone set thus far includes 1672 of the 2250 predicted ORFs of the N. gonorrhoeae genome, of which 1393 (83%) are sequence-validated. Included in this set are 48 of the 61 ORFs of the gonococcal genetic island of strain MS11, not present in the sequenced genome of strain FA1090. L-arabinose-inducible glutathione-S-transferase (GST)-fusions were constructed from random clones and each was shown to express a fusion protein of the predicted size following induction, demonstrating the use of the recombination cloning system. PCR amplicons of each ORF used in the cloning reactions were spotted onto glass slides to produce DNA microarrays representing 2035 genes of the gonococcal genome. Pilot experiments indicate that these arrays are suitable for the analysis of global gene expression in gonococci. Conclusion This archived set of Gateway® entry clones will facilitate high-throughput genomic and proteomic studies of gonococcal genes using a variety of expression and analysis systems. In addition, the DNA arrays produced will allow us to generate gene expression profiles of gonococci grown in a wide variety of conditions. Together, the resources produced in this work will facilitate experiments to dissect the molecular mechanisms of gonococcal pathogenesis on a global scale, and ultimately lead to the determination of the functions of unknown genes in the genome

Metabolomics datasets in the Born in Bradford cohort [version 2; peer review: 1 approved, 1 approved with reservations].

Metabolomics is the quantification of small molecules, commonly known as metabolites. Collectively, these metabolites and their interactions within a biological system are known as the metabolome. The metabolome is a unique area of study, capturing influences from both genotype and environment. The availability of high-throughput technologies for quantifying large numbers of metabolites, as well as lipids and lipoprotein particles, has enabled detailed investigation of human metabolism in large-scale epidemiological studies. The Born in Bradford (BiB) cohort includes 12,453 women who experienced 13,776 pregnancies recruited between 2007-2011, their partners and their offspring. In this data note, we describe the metabolomic data available in BiB, profiled during pregnancy, in cord blood and during early life in the offspring. These include two platforms of metabolomic profiling: nuclear magnetic resonance and mass spectrometry. The maternal measures, taken at 26-28 weeks’ gestation, can provide insight into the metabolome during pregnancy and how it relates to maternal and offspring health. The offspring cord blood measurements provide information on the fetal metabolome. These measures, alongside maternal pregnancy measures, can be used to explore how they may influence outcomes. The infant measures (taken around ages 12 and 24 months) provide a snapshot of the early life metabolome during a key phase of nutrition, environmental exposures, growth, and development. These metabolomic data can be examined alongside the BiB cohorts’ extensive phenotype data from questionnaires, medical, educational and social record linkage, and other ‘omics data

A New System for Profiling Drug-Induced Calcium Signal Perturbation in Human Embryonic Stem Cell–Derived Cardiomyocytes

The emergence of human stem cell–derived cardiomyocyte (hSCCM)–based assays in the cardiovascular (CV) drug discovery sphere requires the development of improved systems for interrogating the rich information that these cell models have the potential to yield. We developed a new analytical framework termed SALVO (synchronization, amplitude, length, and variability of oscillation) to profile the amplitude and temporal patterning of intra- and intercellular calcium signals in hSCCM. SALVO quantified drug-induced perturbations in the calcium signaling “fingerprint” in spontaneously contractile hSCCM. Multiparametric SALVO outputs were integrated into a single index of in vitro cytotoxicity that confirmed the rank order of perturbation as astemizole > thioridazine > cisapride > flecainide > valdecoxib > sotalol > nadolol ≈ control. This rank order of drug-induced Ca2+ signal disruption is in close agreement with the known arrhythmogenic liabilities of these compounds in humans. Validation of the system using a second set of compounds and hierarchical cluster analysis demonstrated the utility of SALVO to discriminate drugs based on their mechanisms of action. We discuss the utility of this new mechanistically agnostic system for the evaluation of in vitro drug cytotoxicity in hSCCM syncytia and the potential placement of SALVO in the early stage drug screening framework

The Good Behaviour Game intervention to improve behavioural and other outcomes for children aged 7-8 years: A cluster RCT

Background. Universal, school-based behaviour management interventions can produce meaningful improvements in children’s behaviour and other outcomes. However, the UK evidence base for these remains limited. Objective. The objective of this trial was to investigate the impact, value for money and longer-term outcomes of the Good Behaviour Game. Study hypotheses centred on immediate impact (hypothesis 1); subgroup effects (at-risk boys, hypothesis 2); implementation effects (dosage, hypothesis 3); maintenance/sleeper effects (12- and 24-month post-intervention follow-ups, hypothesis 4); the temporal association between mental health and academic attainment (hypothesis 5); and the health economic impact of the Good Behaviour Game (hypothesis 6). Design. This was a two-group, parallel, cluster-randomised controlled trial. Primary schools (n = 77) were randomly assigned to implement the Good Behaviour Game for 2 years or continue their usual practice, after which there was a 2-year follow-up period. Setting. The trial was set in primary schools across 23 local authorities in England. Participants. Participants were children (n = 3084) aged 7–8 years attending participating schools. Intervention. The Good Behaviour Game is a universal behaviour management intervention. Its core components are classroom rules, team membership, monitoring behaviour and positive reinforcement. It is played alongside a normal classroom activity for a set time, during which children work in teams to win the game to access the agreed rewards. The Good Behaviour Game is a manualised intervention delivered by teachers who receive initial training and ongoing coaching. Main outcome measures. The measures were conduct problems (primary outcome; teacher-rated Strengths and Difficulties Questionnaire scores); emotional symptoms (teacher-rated Strengths and Difficulties Questionnaire scores); psychological well-being, peer and social support, bullying (i.e. social acceptance) and school environment (self-report Kidscreen survey results); and school absence and exclusion from school (measured using National Pupil Database records). Measures of academic attainment (reading, standardised tests), disruptive behaviour, concentration problems and prosocial behaviour (Teacher Observation of Child Adaptation Checklist scores) were also collected during the 2-year follow-up period. Results. There was no evidence that the Good Behaviour Game improved any outcomes (hypothesis 1). The only significant subgroup moderator effect identified was contrary to expectations: at-risk boys in Good Behaviour Game schools reported higher rates of bullying (hypothesis 2). The moderating effect of the amount of time spent playing the Good Behaviour Game was unclear; in the context of both moderate (≥ 1030 minutes over 2 years) and high (≥ 1348 minutes over 2 years) intervention compliance, there were significant reductions in children’s psychological well-being, but also significant reductions in their school absence (hypothesis 3). The only medium-term intervention effect was for peer and social support at 24 months, but this was in a negative direction (hypothesis 4). After disaggregating within- and between-individual effects, we found no temporal within-individual associations between children’s mental health and their academic attainment (hypothesis 5). Last, our cost–consequences analysis indicated that the Good Behaviour Game does not provide value for money (hypothesis 6). Limitations. Limitations included the post-test-only design for several secondary outcomes; suboptimal implementation dosage (mitigated by complier-average causal effect estimation); and moderate child-level attrition (18.5% for the primary outcome analysis), particularly in the post-trial follow-up period (mitigated by the use of full information maximum likelihood procedures). Future work. Questions remain regarding programme differentiation (e.g. how distinct is the Good Behaviour Game from existing behaviour management practices, and does this makes a difference in terms of its impact?) and if the Good Behaviour Game is impactful when combined with a complementary preventative intervention (as has been the case in several earlier trials). Conclusion. The Good Behaviour Game cannot be recommended based on the findings reported here

Implementing street triage: a qualitative study of collaboration between police and mental health services.

BACKGROUND: Street Triage is a collaborative service between mental health workers and police which aims to improve the emergency response to individuals experiencing crisis, but peer reviewed evidence of the effectiveness of these services is limited. We examined the design and potential impact of two services, along with factors that hindered and facilitated the implementation of the services. METHODS: We conducted 14 semi-structured interviews with mental health and police stakeholders with experience of a Street Triage service in two locations of the UK. Framework analysis identified themes related to key aspects of the Street Triage service, perceived benefits of Street Triage, and ways in which the service could be developed in the future. RESULTS: Stakeholders endorsed the Street Triage services which utilised different operating models. These models had several components including a joint response vehicle or a mental health worker in a police control room. Operating models were developed with consideration of the local geographical and population density. The ability to make referrals to the existing mental health service was perceived as key to the success of the service yet there was evidence to suggest Street Triage had the potential to increase pressure on already stretched mental health and police services. Identifying staff with skills and experience for Street Triage work was important, and their joint response resulted in shared decision making which was less risk averse for the police and regarded as in the interest of patient care by mental health professionals. Collaboration during Street Triage improved the understanding of roles and responsibilities in the 'other' agency and led to the development of local information sharing agreements. Views about the future direction of the service focused on expansion of Street Triage to address other shared priorities such as frequent users of police and mental health services, and a reduction in the police involvement in crisis response. CONCLUSION: The Street Triage service received strong support from stakeholders involved in it. Referral to existing health services is a key function of Street Triage, and its impact on referral behaviour requires rigorous evaluation. Street Triage may result in improvement to collaborative working but competing demands for resources within mental health and police services presented challenges for implementation

The Genetic Links to anxiety and depression (GLAD) study: Online recruitment into the largest recontactable study of depression and anxiety

Background: Anxiety and depression are common, debilitating and costly. These disorders are influenced by multiple risk factors, from genes to psychological vulnerabilities and environmental stressors, but research is hampered by a lack of sufficiently large comprehensive studies. We are recruiting 40,000 individuals with lifetime depression or anxiety and broad assessment of risks to facilitate future research. Methods: The Genetic Links to Anxiety and Depression (GLAD) Study (www.gladstudy.org.uk) recruits individuals with depression or anxiety into the NIHR Mental Health BioResource. Participants invited to join the study (via media campaigns) provide demographic, environmental and genetic data, and consent for medical record linkage and recontact. Results: Online recruitment was effective; 42,531 participants consented and 27,776 completed the questionnaire by end of July 2019. Participants’ questionnaire data identified very high rates of recurrent depression, severe anxiety, and comorbidity. Participants reported high rates of treatment receipt. The age profile of the sample is biased toward young adults, with higher recruitment of females and the more educated, especially at younger ages. Discussion: This paper describes the study methodology and descriptive data for GLAD, which represents a large, recontactable resource that will enable future research into risks, outcomes, and treatment for anxiety and depression