How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

Over the past decade the mitochondrial (mt) genome has become the most widely used genomic resource available for systematic entomology. While the availability of other types of ‘–omics’ data – in particular transcriptomes – is increasing rapidly, mt genomes are still vastly cheaper to sequence and are far less demanding of high quality templates. Furthermore, almost all other ‘–omics’ approaches also sequence the mt genome, and so it can form a bridge between legacy and contemporary datasets. Mitochondrial genomes have now been sequenced for all insect orders, and in many instances representatives of each major lineage within orders (suborders, series or superfamilies depending on the group). They have also been applied to systematic questions at all taxonomic scales from resolving interordinal relationships (e.g. Cameron et al., 2009; Wan et al., 2012; Wang et al., 2012), through many intraordinal (e.g. Dowton et al., 2009; Timmermans et al., 2010; Zhao et al. 2013a) and family-level studies (e.g. Nelson et al., 2012; Zhao et al., 2013b) to population/biogeographic studies (e.g. Ma et al., 2012). Methodological issues around the use of mt genomes in insect phylogenetic analyses and the empirical results found to date have recently been reviewed by Cameron (2014), yet the technical aspects of sequencing and annotating mt genomes were not covered. Most papers which generate new mt genome report their methods in a simplified form which can be difficult to replicate without specific knowledge of the field. Published studies utilize a sufficiently wide range of approaches, usually without justification for the one chosen, that confusion about commonly used jargon such as ‘long PCR’ and ‘primer walking’ could be a serious barrier to entry. Furthermore, sequenced mt genomes have been annotated (gene locations defined) to wildly varying standards and improving data quality through consistent annotation procedures will benefit all downstream users of these datasets. The aims of this review are therefore to: 1. Describe in detail the various sequencing methods used on insect mt genomes; 2. Explore the strengths/weakness of different approaches; 3. Outline the procedures and software used for insect mt genome annotation, and; 4. Highlight quality control steps used for new annotations, and to improve the re-annotation of previously sequenced mt genomes used in systematic or comparative research.

Gene electrotransfer into murine skeletal muscle: A systematic analysis of parameters for long-term gene expression

Skeletal muscle is an attractive target tissue for delivery of therapeutic genes, since it is well vascularized, easily accessible, and has a high capacity for protein synthesis. For efficient transfection in skeletal muscle, several protocols have been described, including delivery of low voltage electric pulses and a combination of high and low voltage electric pulses. The aim of this study was to determine the influence of different parameters of electrotransfection on short-term and long-term transfection efficiency in murine skeletal muscle, and to evaluate histological changes in the treated tissue. Different parameters of electric pulses, different time lags between plasmid DNA injection and application of electric pulses, and different doses of plasmid DNA were tested for electrotransfection of tibialis cranialis muscle of C57BI/6 mice using DNA plasmid encoding green fluorescent protein (GFP). Transfection efficiency was assessed on frozen tissue sections one week after electrotransfection using a fluorescence microscope and also noninvasively, followed by an in vivo imaging system using a fluorescence stereo microscope over a period of several months. Histological changes in muscle were evaluated immediately or several months after electrotransfection by determining infiltration of inflammatory mononuclear cells and presence of necrotic muscle fibers. The most efficient electrotransfection into skeletal muscle of C57BI/6 mice in our experiments was achieved when one high voltage (HV) and four low voltage (LV) electric pulses were applied 5 seconds after the injection of 30 μg of plasmid DNA. This protocol resulted in the highest short-term as well as long-term transfection. The fluorescence intensity of the transfected area declined after 2-3 weeks, but GFP fluorescence was still detectable 18 months after electrotransfection. Extensive inflammatory mononuclear cell infiltration was observed immediately after the electrotransfection procedure using the described parameters, but no necrosis or late tissue damage was observed. This study showed that electric pulse parameters, time lag between the injection of DNA and application of electric pulses, and dose of plasmid DNA affected the duration of transgene expression in murine skeletal muscle. Therefore, transgene expression in muscle can be controlled by appropriate selection of electrotransfection protocol.

Wellness programs at firefighter and police workplaces : a systematic review

Objectives This systematic review summarizes the literature on the health effects of wellness programs at police and firefighter workplaces. The review also considers process outcomes and economic evaluations of such programs. Methods A systematic search of articles published from January 1, 2000 through September 1, 2012 in 13 databases was conducted. Data on 7 studies from 9 articles were extracted. An assessment of the methodological quality of the studies was conducted. Results Studies showed acceptable completion rates and high satisfaction with programs, but mixed results for changes in individual outcomes. Conclusion Empirical evidence for effective health and wellness programs in police and firefighter populations is scarce. Better evaluation and documentation of such programs is needed to advance this field of research.

The impact of nurse practitioner services on cost, quality of care, satisfaction and wait times in the emergency department: A systematic review

Aims To provide the best available evidence to determine the impact of nurse practitioner services on cost, quality of care, satisfaction and waiting times in the emergency department for adult patients. Background The delivery of quality care in the emergency department is one of the most important service indicators in health delivery. Increasing service pressures in the emergency department have resulted in the adoption of service innovation models: the most common and rapidly expanding of these is emergency nurse practitioner services. The rapid uptake of emergency nurse practitioner service in Australia has outpaced the capacity to evaluate this service model in terms of outcomes related to safety and quality of patient care. Previous research is now outdated and not commensurate with the changing domain of delivering emergency care with nurse practitioner services. Data A comprehensive search of four electronic databases from 2006-­‐2013 was conducted to identify research evaluating nurse practitioner service impact in the emergency department. English language articles were sought using MEDLINE, CINAHL, Embase and Cochrane and included two previous systematic reviews completed five and seven years ago. Methods A three step approach was used. Following a comprehensive search, two reviewers assessed identified studies against the inclusion criteria. From the original 1013 studies, 14 papers were retained for critical appraisal on methodological quality by two independent reviewers and data extracted using standardised tools. Results Narrative synthesis was conducted to summarise and report the findings as insufficient data was available for meta-­‐analysis of results. This systematic review has shown that emergency nurse practitioner service has a positive impact on quality of care, patient satisfaction and waiting times. There was insufficient evidence to draw conclusions regarding impact on costs. Conclusion Synthesis of the available research attempts to provide an evidence base for emergency nurse practitioner service to guide healthcare leaders, policy makers and clinicians in reforming emergency department service provision. The findings suggest that further quality research is required for comparative measures of clinical and service effectiveness of emergency nurse practitioner service. In the context of increased health service demand and the need to provide timely and effective care to patients, such measures will assist in delivering quality patient care.

Robust control scheme for a microgrid with PFC capacitor connected

Capacitors are widely used for power-factor correction (PFC) in power systems. When a PFC capacitor is installed with a certain load in a microgrid, it may be in parallel with the filter capacitor of the inverter interfacing the utility grid and the local distributed-generation unit and, thus, change the effective filter capacitance. Another complication is the possibility of occurrence of resonance in the microgrid. This paper conducts an in-depth investigation of the effective shunt-filter-capacitance variation and resonance phenomena in a microgrid due to a connection of a PFC capacitor. To compensate the capacitance-parameter variation, an Hinfin controller is designed for the voltage-source- inverter voltage control. By properly choosing the weighting functions, the synthesized Hinfin controller would exhibit high gains at the vicinity of the line frequency, similar to traditional high- performance P+ resonant controller and, thus, would possess nearly zero steady-state error. However, with the robust Hinfin controller, it will be possible to explicitly specify the degree of robustness in face of parameter variations. Furthermore, a thorough investigation is carried out to study the performance of inner current-loop feedback variables under resonance conditions. It reveals that filter-inductor current feedback is more effective in damping the resonance. This resonance can be further attenuated by employing the dual-inverter microgrid conditioner and controlling the series inverter as a virtual resistor affecting only harmonic components without interference with the fundamental power flow. And finally, the study in this paper has been tested experimentally using an experimental microgrid prototype.

The benefits and challenges of conducting an overview of systematic reviews in public health: a focus on physical activity

Introduction The ultimate aim of Cochrane systematic reviews is to inform policy and practice decisions for better health outcomes. However, due to the increasing numbers of scientific publications, wading through the available evidence of both individual studies and systematic reviews can be challenging and overwhelming even for avid authors and readers. This paper briefly describes the first overview (a systematic review of reviews) of the Cochrane Public Health Group (CPHG) in development and proposes a way forward for the methodologies under consideration.

Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging

Cryo-electron tomography together with averaging of sub-tomograms containing identical particles can reveal the structure of proteins or protein complexes in their native environment. The resolution of this technique is limited by the contrast transfer function (CTF) of the microscope. The CTF is not routinely corrected in cryo-electron tomography because of difficulties including CTF detection, due to the low signal to noise ratio, and CTF correction, since images are characterised by a spatially variant CTF. Here we simulate the effects of the CTF on the resolution of the final reconstruction, before and after CTF correction, and consider the effect of errors and approximations in defocus determination. We show that errors in defocus determination are well tolerated when correcting a series of tomograms collected at a range of defocus values. We apply methods for determining the CTF parameters in low signal to noise images of tilted specimens, for monitoring defocus changes using observed magnification changes, and for correcting the CTF prior to reconstruction. Using bacteriophage PRDI as a test sample, we demonstrate that this approach gives an improvement in the structure obtained by sub-tomogram averaging from cryo-electron tomograms.

Systematic Review Protocol : "Are community-based interventions effective in identifying and responding to emerging zoonotic infectious diseases?"

Review question/objective The objective of this review is to identify the effectiveness of surveillance systems and community-based interventions in identifying and responding to emerging and re-emerging zoonotic infections in Southeast Asia (SE Asia). More specifically the research questions are: 1. What is the effectiveness of community-based surveillance interventions designed to identify emerging zoonotic infectious diseases? 2. What is the effectiveness of non-pharmaceutical community-based interventions designed to prevent transmission of emerging zoonotic infectious diseases? 3. How do factors related to the emergence and management of emerging zoonotic infectious diseases impact the effectiveness of interventions designed to identify and respond to them?

Advance Care Planning in palliative care : a systematic literature review of the contextual factors influencing its uptake 2008-2012

Background: Advance Care Planning is an iterative process of discussion, decision-making and documentation about end-of-life care. Advance Care Planning is highly relevant in palliative care due to intersecting clinical needs. To enhance the implementation of Advance Care Planning, the contextual factors influencing its uptake need to be better understood. Aim: To identify the contextual factors influencing the uptake of Advance Care Planning in palliative care as published between January 2008 and December 2012. Methods: Databases were systematically searched for studies about Advance Care Planning in palliative care published between January 2008 and December 2012. This yielded 27 eligible studies, which were appraised using National Institute of Health and Care Excellence Quality Appraisal Checklists. Iterative thematic synthesis was used to group results. Results: Factors associated with greater uptake included older age, a college degree, a diagnosis of cancer, greater functional impairment, being white, greater understanding of poor prognosis and receiving or working in specialist palliative care. Barriers included having non-malignant diagnoses, having dependent children, being African American, and uncertainty about Advance Care Planning and its legal status. Individuals’ previous illness experiences, preferences and attitudes also influenced their participation. Conclusion: Factors influencing the uptake of Advance Care Planning in palliative care are complex and multifaceted reflecting the diverse and often competing needs of patients, health professionals, legislature and health systems. Large population-based studies of palliative care patients are required to develop the sound theoretical and empirical foundation needed to improve uptake of Advance Care Planning in this setting.

An experimental approach to air gap optimisation for a correction-less small field diode

Aim A recent Monte Carlo based study has shown that it is possible to design a diode that measures small field output factors equivalent to that in water. This is accomplished by placing an appropriate sized air gap above the silicon chip (1) with experimental results subsequently confirming that a particular Monte Carlo design was accurate (2). The aim of this work was to test if a new correction-less diode could be designed using an entirely experimental methodology. Method: All measurements were performed on a Varian iX at a depth of 5 cm, SSD of 95 cm and field sizes of 5, 6, 8, 10, 20 and 30 mm. Firstly, the experimental transfer of kq,clin,kq,msr from a commonly used diode detector (IBA, stereotactic field diode (SFD)) to another diode detector (Sun Nuclear, unshielded diode, (EDGEe)) was tested. These results were compared to Monte Carlo calculated values of the EDGEe. Secondly, the air gap above the EDGEe silicon chip was optimised empirically. Nine different air gap “tops” were placed above the EDGEe (air depth = 0.3, 0.6, 0.9 mm; air width = 3.06, 4.59, 6.13 mm). The sensitivity of the EDGEe was plotted as a function of air gap thickness for the field sizes measured. Results: The transfer of kq,clin,kq,msr from the SFD to the EDGEe was correct to within the simulation and measurement uncertainties. The EDGEe detector can be made “correction-less” for field sizes of 5 and 6 mm, but was ∼2% from being “correction-less” at field sizes of 8 and 10 mm. Conclusion Different materials will perturb small fields in different ways. A detector is only “correction-less” if all these perturbations happen to cancel out. Designing a “correction-less” diode is a complicated process, thus it is reasonable to expect that Monte Carlo simulations should play an important role.

Integrated chronic disease management in primary-secondary care : a systematic literature review of the evidence

Introduction: Diabetes has traditionally been managed as a single chronic disease state, but it exists with co-morbidities such as depression and metabolic syndrome. Treatment is multifaceted, requiring both primary and secondary care, however, the delivery of diabetes care is often fragmented. Integrated chronic disease management is a growing model of interest, and is underpinned by the chronic care model (CCM), devised as a guide for primary care management of patients with chronic conditions. The model identifies six key elements for effective care, and has shown promise in improving the management of diabetes. Aim: To find empirical evidence of integrated care interventions targeted at co-morbidities including diabetes, across primary/secondary care. Method: A systematic review of peer reviewed literature from PubMed, CINAHL, Embase, Cochrane Library and Joanna Briggs was performed. Studies were reviewed according to inclusion criteria- studies published in English, between 2004-2014, empirical studies, studies with evidence of primary/secondary implementation, and those dealing with chronic co-morbid disease states. Results: 51 studies met the inclusion criteria. Included studies were mostly from the US (38), with five from Australia, UK (2), Canada (2), Netherlands (1), Norway (1), Ireland (1), and one multi-country study. It was found that all interventions adopted at least one (average 3-4) of the chronic care model, with the majority implementing delivery system redesign activities within the primary care practice/s. We found evidence of interventions which significantly reduced emergency department and hospital admissions, improved processes of care, patient health outcomes such as HbA1c, improved patient satisfaction, and reduced costs. Conclusion/Implications for practice: Diabetes exists as a co-morbid disease, requiring both primary and secondary care. We found that integrated care interventions adopting elements of the chronic care model positively impacted on patient outcomes, service utilisation, as well as costs. This review has highlighted that it may not be necessary to adopt all CCM elements to improve clinical outcomes, patient satisfaction and costs.