BGS Groundhog® desktop Geoscientific Information System external user manual

BGS Groundhog is a software platform developed by the British Geological Survey (BGS) for the management and display of subsurface geological information. There are two main components; 1. BGS Groundhog Web 2. BGS Groundhog Desktop GSIS This user manual relates specifically to the Desktop GSIS component of the platform. The software is available under the UK’s Open Government Licence, which means the software is free to use, exploit and re-distribute for academic, personal, research or commercial purposes, subject to the terms of the UK’s Open Government Licence. Groundhog Desktop is intended as a basic GeoScientific Information System (GSIS*) – a software tool which facilitates the collation, display, filtering and editing of a range of data relevant to subsurface interpretation and modelling. It has been developed by the Modelling Systems software development team, with help and advice being provided by Holger Kessler, Steve Mathers and Ricky Terrington. This manual provides information on the use of the software for external clients

Potential clinical efficacy of the 10-valent pneumococcal-Protein D conjugate vaccine in children with chronic suppurative lung diseases: A double-blind randomised controlled trial

Background • Chronic suppurative lung diseases (CSLD) in children are important causes of morbidity and recurrent acute exacerbations are associated with long term lung function decline. • Non-­‐typeable H. influenzae (NTHi) and S. pneumoniae are commonly isolated from the lower airways of both children and adults with CSLD. • The potential clinical impact of a non-­‐typeable Haemophilus influenzae (NTHi) vaccine in children with CSLD has not been investigated. • We aimed to determine the clinical efficacy of the 10-­‐valent pneumococcal-­‐Protein D conjugate vaccine (10vPHiD-­‐CV) in children aged 18-­‐months to <18-­‐years with CSLD (Immunogenicity data are presented in Poster xxx). Primary clinical objective. • Determine the efficacy of 10vPHiD-­‐CV in reducing the incidence of acute exacerbations in the 12-­‐months following the 2nd dose of study vaccine. Secondary clinical objectives. • Determine the efficacy of 10vPHiD-­‐CV in reducing the incidence of any parent/carer-­‐reported respiratory symptoms in the 12 months following the second dose of study vaccine. • Determine the efficacy of 10vPHiD-­‐CV in reducing antibiotic use in the 12 months following the second dose of study vaccine

The clinical, immunological and microbiological impact of the 10-valent pneumococcal-Protein D conjugate vaccine in children with recurrent protracted bacterial bronchitis, chronic suppurative lung disease and bronchiectasis: A multi-centre, double-blind, randomised controlled trial.

We aimed to determine the efficacy of the 10-valent pneumococcal-Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) in children aged 18-months to <18-years with recurrent protracted bacterial bronchitis (rPBB), chronic suppurative lung disease (CSLD) or bronchiectasis. In a multi-centre, double-blind randomised controlled trial, children received two doses, 2-months apart of the 10vPHiD-CV or quadrivalent meningococcal-ACYW135 conjugate vaccine. Active surveillance for acute exacerbations, respiratory symptoms and antibiotic use was undertaken through to 12-months after the second vaccine dose (clinical cohort only). Serum, saliva and nasopharyngeal swabs were collected to measure immunological and microbiological effects (immunology cohort). Between December 2012 and August 2015, 62 children were enrolled onto the clinical protocol (1 excluded from clinical analyses due to unblinding), while 74 contributed to the immunology cohort (overall mean age = 6.8-years (standard deviation = 3.7), 42 (56.8%) male). The absolute risk difference comparing the 10vPHiD-CV group (n = 31 children) to the MenACYW135 group (n = 30 children) for acute exacerbations was -0.5 exacerbations/100-weeks at risk (95% confidence interval (CI) -2.0, 0.9). Compared to the MenACYW135 group, children who received the 10vPHiD-CV were less likely to have respiratory symptoms in each fortnight of surveillance (incidence density ratio (IDR) 0.82, 95%CI 0.61, 1.10) and required fewer short-course (<14-days duration) antibiotics (IDR 0.81, 95% CI 0.61, 1.09). The vaccine was immunogenic and no serious adverse events related to the vaccine were reported. In conclusion, 10vPHiD-CV might have a future role in managing children with rPBB, CSLD and bronchiectasis, but larger multicentre trials are needed to confirm or refute findings from this preliminary study

HPV.edu study protocol: a cluster randomised controlled evaluation of education, decisional support and logistical strategies in school-based human papillomavirus (HPV) vaccination of adolescents

Background The National Human Papillomavirus (HPV) Vaccination Program in Australia commenced in 2007 for females and in 2013 for males, using the quadrivalent HPV vaccine (HPV 6,11,16,18). Thus far, we have demonstrated very substantial reductions in genital warts and in the prevalence of HPV among young Australian women, providing early evidence for the success of this public health initiative. Australia has a long history of school-based vaccination programs for adolescents, with comparatively high coverage. However, it is not clear what factors promote success in a school vaccination program. The HPV.edu study aims to examine: 1) student knowledge about HPV vaccination; 2) psycho-social outcomes and 3) vaccination uptake. Methods/Design HPV.edu is a cluster randomised trial of a complex intervention in schools aiming to recruit 40 schools with year-8 enrolments above 100 students (approximately 4400 students). The schools will be stratified by Government, Catholic, and Independent sectors and geographical location, with up to 20 schools recruited in each of two states, Western Australia (WA) and South Australia (SA), and randomly allocated to intervention or control (usual practice). Intervention schools will receive the complex intervention which includes an adolescent intervention (education and distraction); a decisional support tool for parents and adolescents and logistical strategies (consent form returns strategies, in-school mop-up vaccination and vaccination-day guidelines). Careful process evaluation including an embedded qualitative evaluation will be undertaken to explore in depth possible mechanisms for any observed effect of the intervention on primary and secondary outcomes. Discussion This study is the first to evaluate the relative effectiveness of various strategies to promote best practice in school-based vaccination against HPV. The study aims to improve vaccination-related psychosocial outcomes, including adolescent knowledge and attitudes, decision-making involvement, self-efficacy, and to reduce fear and anxiety. The study also aims to improve school vaccination program logistics including reduction in time spent vaccinating adolescents and increased number of consent forms returned (regardless of decision). Less anxiety in adolescents will likely promote more efficient vaccination, which will be more acceptable to teachers, nurses and parents. Through these interventions, it is hoped that vaccination uptake will be increased. Trial registration Australian and New Zealand Clinical Trials Registry, ACTRN12614000404628, 14.04.2014. Electronic supplementary material The online version of this article (doi:10.1186/s12889-015-2168-5) contains supplementary material, which is available to authorized users

From protest to progress through partnership with students: Being human in STEM (HSTEM)

In Fall 2015, Amherst College students held a four-day sit-in in unity with student protests occurring all over the United States highlighting barriers to inclusion of underrepresented and marginalized students.Following appeals for action, students partnered with faculty and staff in science, technology, engineering, and mathematics (STEM) to develop the Being Human in STEM (HSTEM) Initiative. HSTEM involves exploring past diversity and inclusion efforts in STEM, sharing one’s own experiences in STEM with others, and developing student-driven projects to improve belonging in STEM. In this student, faculty, and staff co-authored paper, we describe the origin of HSTEM; share student, faculty and staff reflections on our experiences with HSTEM; and present two inquiry projects examining HSTEM impact. We discuss lessons learned and recommendations for diversity and inclusion efforts in higher education, both in and beyond STEM, emphasizing the power of an initiative that was originated by and remains driven by student partners

XYalign: Inferring and Correcting for Sex Chromosome Ploidy in Next-Generation Sequencing Data

Sex chromosome aneuploidies are currently estimated to be as common as 1/400 in humans. Atypical ploidy will affect variant calling and measures of genomic variation that are central to most clinical genomic studies. Further, the high degree of similarity between gametologous sequences on the X and Y chromosomes can lead to the misalignment of sequencing reads and substantially affect variant calling. Here we present XYalign, a new tool that (1) quickly infers sex chromosome ploidy in NGS data (DNA and RNA), (2) remaps reads based on the inferred sex chromosome complement of the individual, and (3) outputs quality, depth, and allele-balance metrics across the sex chromosomes

Three-Year Antibody Persistence and Safety following a Single Dose of Combined Haemophilus influenzae Type b-Neisseria meningitidis Serogroup C-Tetanus Toxoid Conjugate Vaccine in Hib-Primed Toddlers

BACKGROUND: Persistence of seroprotective bactericidal antibody titers is important for long-term protection against meningococcal serogroup C disease in young children. Antibody persistence values were determined in children up to 3 years after vaccination with a single dose of the combined Haemophilus influenzae type b (Hib)-Neisseria meningitidis serogroup C (MenC)-tetanus toxoid (TT) conjugate vaccine (Hib-MenC-TT; www.ClinicalTrials.gov: NCT00326118). METHODS: The children had been randomized at ages 12-18 months to receive either 1 dose of Hib-MenC-TT (Hib-MenC group) or separately administered Hib-TT conjugate vaccine and MenC-CRM197 (MCC) vaccine (Hib plus MCC group). All children had been primed in infancy with a Hib vaccine. Antibodies against MenC were measured by a serum bactericidal assay using rabbit complement (rSBA-MenC) and antibodies against Hib polyribosylribitol phosphate were assessed by enzyme-linked immunosorbent assay. RESULTS: The rSBA-MenC titers ≥1:8 were demonstrated 3 years after vaccination in 64.2% and 53.2% of participants in the Hib-MenC group and in the Hib plus MCC group, respectively. Antipolyribosylribitol phosphate concentrations ≥0.15 μg/mL persisted in >98% of participants in both groups. The rSBA-MenC geometric mean titers and antipolyribosylribitol phosphate geometric mean concentrations remained higher 3 years after vaccination than before vaccination. No serious adverse events assessed by the investigator as being related to vaccination were reported. CONCLUSION: In this antibody persistence study of Hib-primed but MenC-naïve toddlers who received a single dose of Hib-MenC-TT, protective antibody levels against Hib and MenC were maintained in the majority of children 3 years after vaccination