Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle

Single nucleotide polymorphisms have been the DNA variant of choice for genomic prediction, largely because of the ease of single nucleotide polymorphism genotype collection. In contrast, structural variants (SV), which include copy number variants (CNV), translocations, insertions, and inversions, have eluded easy detection and characterization, particularly in nonhuman species. However, evidence increasingly shows that SV not only contribute a substantial proportion of genetic variation but also have significant influence on phenotypes. Here we present the discovery of CNV in a prominent New Zealand dairy bull using long-read PacBio (Pacific Biosciences, Menlo Park, CA) sequencing technology and the Sniffles SV discovery tool (version 0.0.1; https://github.com/fritzsedlazeck/Sniffles). The CNV identified from long reads were compared with CNV discovered in the same bull from Illumina sequencing using CNVnator (read depth-based tool; Illumina Inc., San Diego, CA) as a means of validation. Subsequently, further validation was undertaken using whole-genome Illumina sequencing of 556 cattle representing the wider New Zealand dairy cattle population. Very limited overlap was observed in CNV discovered from the 2 sequencing platforms, in part because of the differences in size of CNV detected. Only a few CNV were therefore able to be validated using this approach. However, the ability to use CNVnator to genotype the 557 cattle for copy number across all regions identified as putative CNV allowed a genome-wide assessment of transmission level of copy number based on pedigree. The more highly transmissible a putative CNV region was observed to be, the more likely the distribution of copy number was multimodal across the 557 sequenced animals. Furthermore, visual assessment of highly transmissible CNV regions provided evidence supporting the presence of CNV across the sequenced animals. This transmission-based approach was able to confirm a subset of CNV that segregates in the New Zealand dairy cattle population. Genome-wide identification and validation of CNV is an important step toward their inclusion in genomic selection strategies.

Development of a video-based education and process change intervention to improve advance cardiopulmonary resuscitation decision-making

BACKGROUND

Advance cardiopulmonary resuscitation (CPR) decision-making and escalation of care discussions are variable in routine clinical practice. We aimed to explore physician barriers to advance CPR decision-making in an inpatient hospital setting and develop a pragmatic intervention to support clinicians to undertake and document routine advance care planning discussions.

METHODS

Two focus groups, which involved eight consultants and ten junior doctors, were conducted following a review of the current literature. A subsequent iterative consensus process developed two intervention elements: (i) an updated 'Goals of Patient Care' (GOPC) form and process; (ii) an education video and resources for teaching advance CPR decision-making and communication. A multidisciplinary group of health professionals and policy-makers with experience in systems development, education and research provided critical feedback.

RESULTS

Three key themes emerged from the focus groups and the literature, which identified a structure for the intervention: (i) knowing what to say; (ii) knowing how to say it; (iii) wanting to say it. The themes informed the development of a video to provide education about advance CPR decision-making framework, improving communication and contextualising relevant clinical issues. Critical feedback assisted in refining the video and further guided development and evolution of a medical GOPC approach to discussing and recording medical treatment and advance care plans.

CONCLUSION

Through an iterative process of consultation and review, video-based education and an expanded GOPC form and approach were developed to address physician and systemic barriers to advance CPR decision-making and documentation. Implementation and evaluation across hospital settings is required to examine utility and determine effect on quality of care.

The effect of antenatal magnesium sulfate on left ventricular afterload and myocardial function measured using deformation and rotational mechanics imaging

OBJECTIVE

Assess the effect of antenatal magnesium sulfate (MgSO4) on left ventricular function measured using deformation and rotational mechanics imaging.

STUDY DESIGN

Infants who received MgSO4 were matched for gestation, birth weight and mode of delivery with controls. Echocardiography was carried out on days 1 and 2 to measure left ventricle longitudinal strain (LV LS), twist, untwist rate, ejection fraction (EF), and systemic vascular resistance (SVR).

RESULTS

Thirty-eight infants with a median gestation and birth weight of 27.1 weeks and 923 g were included. On day 1, the MgSO4 group (n=19) had a lower SVR and higher LV LS, EF, twist and untwist rate than the Control group (n=19) (all P<0.05). There were no differences between the groups on day 2.

CONCLUSION

Antenatal MgSO4 administration is associated with a lower SVR and higher myocardial function on day 1 in preterm infants <29 weeks gestation.

The Goals of Patient Care project: implementing a proactive approach to patient-centred decision-making

BACKGROUND

Patients in the later stages of their lives risk being harmed by futile or unwanted interventions if realistic care goals and patient values are not recognised. Doctors have difficulty discussing and informing patients' healthcare goals.

AIMS

To review implementation of a Goals of Patient Care (GOPC) summary in medical inpatients and its applicability in emergency medical response (EMR) situations.

METHODS

Single-centre cross-sectional study of adult medical inpatients and adult inpatients requiring EMR at a Victorian general hospital.

MEASURES

presence and content of GOPC summary, secondary review of decision-making and discussion documentation, patient characteristics; EMR precipitants and outcomes.

RESULTS

GOPC were documented for 82 of 101 patients. One had an existing advance directive, and six had records of a patient-appointed substitute decision-maker. For patients with GOPC, 80 had life-prolonging treatment aims, with a varying degree of treatment limitation in 48. Discussion with patient or substitute decision-maker was evident in 43 cases. GOPC were documented prior to nine of 23 EMR. The EMR triggered a GOPC modification in three instances.

CONCLUSIONS

Introduction of a routine GOPC summary encourages consideration of goals of care for most medical inpatients. Few have pre-existing records of their wishes, and there are opportunities for improvement in this regard. Doctors may still have difficulty determining goals of care, and discussion of GOPC with patients and families may not be clearly documented. Most patients requiring EMR do not have prior GOPC review, and the role of the summary in these situations remains unclear.

Attitudes of Hospital Healthcare Workers towards Influenza Vaccination in a Tertiary Hospital Setting

The rate of uptake of seasonal influenza vaccination worldwide by healthcare workers (HCWs) has been suboptimal. Nationally, uptake among hospital HCWs was less than 20% prior to 2014. Indeed in our hospital following the 2010/2011 influenza season, a significant number of staff chose to have their vaccinations after the usual campaign period. The Occupational Health Department (OHD) undertook a questionnaire survey to determine the reason(s) for their late presentation. This was not anonymised, with a 21.7% participation rate (119 replied out of 548). We found 86(72.3%) HCWs believed influenza to be a serious illness, 84(70.6%) wanted to protect their family members and friends, and 64(53.8%) their patients from the infection. Nevertheless, 77(64.7%) were influenced by the recent media attention on the H1N1 influenza pandemic. We conclude external factors such as the arrival of the H1N1 pandemic continue to play an important role in influencing HCWs' attitudes towards receiving the vaccine.

Sharps injuries in a teaching hospital: changes over a decade

BACKGROUND

Sharps injuries create a high volume of occupational health (OH) workload in the health care setting. The deadline for implementation of the European Sharps Directive was 11 May 2013.

AIMS

To compare the epidemiology of sharps injuries reported in a large Irish teaching hospital in 2008-10 with those reported between 1998 and 2000.

METHODS

We compared data from electronic and paper OH records of sharps injuries reported between 1 January 2008 and 31 December 2010 with those from a previous study of sharps injuries reported between 1 January 1998 and 31 December 2000.

RESULTS

A total of 325 sharps injuries were reported in 2008-10, compared with 332 in 1998-2000 (P = 0.568). Hepatitis B immunity in sharps injury recipients in 2008-10 was 87% compared to 86% in 1998-2000 (P = 0.32). Glove use was reported in 80% of reported injuries in 2008-10 compared with 74% in 1998-2000 (P = 0.32). In 2008-10, 49% of injuries occurred during disposal or following improper disposal of sharps, compared with 42% in 1998-2000.

CONCLUSIONS

There was no significant change in the epidemiology of sharps injuries reported between 2008 and 2010 compared with 1998-2000. Further education in standard precautions, safe disposal of sharps, the use of safety-engineered devices and the benefits of hepatitis B immunization is needed.

Evaluation of spinosad for the oral treatment and control of flea infestations on cats in Europe

METHODS

An ectoparasiticide containing spinosad was evaluated as an oral formulation for cats. Two European laboratory studies and a European multicentre field efficacy and safety study assessed the use of a chewable tablet formulation of spinosad at a dose range of 50-75 mg/kg for treatment and control of flea infestations on cats.

RESULTS

The studies with experimentally infested cats consistently demonstrated persistent activity against Ctenocephalides felis with >98 per cent efficacy at four weeks post-treatment. In the field study with naturally infested client-owned cats from 18 clinics across Germany and Italy, two monthly doses of spinosad were administered; selamectin was the comparator product. Safety was evaluated in 226 cats, each receiving at least one dose of spinosad or selamectin; both products were well tolerated. 113 spinosad-treated cats and 71 selamectin-treated cats showed >97 per cent reductions in geometric mean flea counts within 14 days post-treatment and at 60 days post-treatment efficacy was >98 per cent in both groups. Analysis of success rates showed 96 per cent in spinosad-treated cats compared with 90.9 per cent in selamectin-treated cats at day 60. The spinosad tablets were successfully administered to over 98 percent of cats. These studies indicate that this formulation of spinosad is safe and efficacious for treatment and prevention of flea infestations in cats.

Yarning/Aboriginal storytelling: towards an understanding of an Indigenous perspective and its implications for research practice

There is increasing recognition of Indigenous perspectives from various parts of the world in relation to storytelling, research and its effects on practice. The recent emergence of storytelling or yarning as a research method in Australian Aboriginal and Torres Strait Island studies and other Indigenous peoples of the world is gaining momentum. Narratives, stories, storytelling and yarning are emerging methods in research and has wide ranging potential to shape conventional research discourse making research more meaningful and accessible for researchers. In this paper we argue for the importance of Indigenous research methods and Indigenous method(ology), within collaborative respectful partnerships with non-Indigenous researchers. It is imperative to take these challenging steps together towards better outcomes for Indigenous people and their communities. In the Australian context we as researchers cannot afford to allow the gap between Aboriginal and Torres Strait Islanders and mainstream Australia health outcomes to grow even wider. One such pathway is the inclusion of Aboriginal storytelling or yarning from an Aboriginal and Torres Strait perspective within Indigenous and non-Indigenous research paradigms. Utilising Aboriginal storytelling or yarning will provide deeper understanding; complementing a two-way research paradigm for collaborative research. Furthermore, it has significant social implications for research and clinical practice amongst Indigenous populations; thus complementing the biomedical medical paradigm.

Building Indigenous Australian research capacity

OBJECTIVES

To build individual Indigenous research capacity and strengthen the capability of health research programmes to be culturally and ethically inclusive of Indigenous Australians in public health research.

METHODS

In order to facilitate optimal participation and in recognition of the differing levels of research experience and knowledge held within this community of practice, an inclusive and culturally appropriate mixed methods approach with influences from action research and Indigenous research principles was undertaken.

RESULTS

Over the duration of the project, participants improved their research outcomes as measured by a range of factors including publications, completion of degrees and retention of project members.

CONCLUSIONS

Provision of an Indigenous led, culturally appropriate system of infrastructure and support centred on capacity building is effective in strengthen the inclusion of Indigenous Australians in research.

Clinical model for ethical cardiopulmonary resuscitation decision-making

BACKGROUND

Decisions to withhold cardiopulmonary resuscitation (CPR) for future cardiac arrest continue to be problematic, with a lack of consistency in how doctors approach this decision.

AIMS

To develop a clinical model that can be used in education to improve consistency in CPR decision-making.

METHODS

A qualitative study, using semistructured interviews with a total of 33 senior doctors, junior doctors and nurses from two Melbourne hospitals explored how decisions to withhold CPR are made. Interviews explored: issues arising; how doctors learn to make these decisions; how they deal with disagreement and their experiences of performing CPR. The transcripts were coded and analysed thematically.

RESULTS

Three major themes were identified: CPR as a life-and-death decision; good and bad dying; and trust. The research also defined the two elements to a CPR decision: (i) technical and (ii) ethical.

CONCLUSIONS

Applying ethical principles commonly used in medicine, a model for ethical CPR decision-making has been developed that identifies four patient groups, each with a different discussion aim. This approach simplifies the complexities of the CPR decision, providing a structured way to teach CPR decision-making to doctors and thereby achieve greater consistency in the decisions made.

The Houdini effect--an unusual case of blunt abdominal trauma resulting in perforative appendicitis

We present a unique case of perforative appendicitis that occurred in an adult following blunt abdominal trauma. This case represents the first such reported case from Ireland. It also represents a modern practical example of Laplace's theory of the effect of increased pressure on colonic wall tension leading to localized perforation, and serves to highlight not only the importance in preoperative imaging for blunt abdominal trauma, but also the importance of considering appendiceal perforation.

Evaluation of spinosad for the oral treatment and control of flea infestations on dogs in Europe

The novel ectoparasiticide spinosad is a naturally occurring mixture of spinosyns A and D formed during a fermentation process. The spinosyns are tetracyclic macrolides with a unique ring system. Their mode of action differs from that of other commercially available insecticides. Laboratory and field trials were conducted to evaluate the use of spinosad in a chewable tablet at a dose range of 45 to 70 mg/kg for the treatment and control of flea infestations on dogs in Europe. Laboratory studies with artificially infested dogs confirmed persistent activity against Ctenocephalides felis of higher than 99 per cent at three weeks post-treatment with values of 96.5 to 97.8 per cent at four weeks. Two multicentric field trials with naturally infected client-owned animals in five European countries used selamectin as comparator. Monthly doses were given during the summer when many homes were heavily infested. Households with spinosad-treated dogs showed cumulative benefits with flea burdens reduced by about 97 per cent at 14 and 30 days and by 99.6 per cent at 60 and 90 days. Corresponding figures for selamectin were significantly lower (P<0.05) at all time points: between 88.5 and 91 per cent at 14 and 30 days, then 97.8 and 98.2 per cent at 60 and 90 days. Thus, the performance of spinosad compared favourably with that of the established reference product.