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.

Paratransit demand of disabled people

This paper estimates the demand for transportation systems that are used primarily by disabled individuals. These systems are known as paratransit systems and have experienced large increases in number and average size over the past 15 years. We first use a national database and standard time series techniques to model aggregate demand. We then use a unique data set of administrative records from a paratransit system in central Virginia to estimate standard and nonstandard count models of individual demand. We conclude that most of the demand growth is from new passengers, but that predicting the growth of new passengers is very difficult. Our results also highlight the importance of incorporating autocorrelation and possible sample attrition into standard count models.

New estimates for CRNA vacancies

A national survey to estimate vacancy rates of Certified Registered Nurse Anesthetists (CRNAs) in hospitals and ambulatory surgical centers was conducted in 2007. Poisson regression methods were used to improve the precision of the estimates. A significant increase in the estimated vacancy rate was reported for hospitals relative to an earlier study from 2002, although it is important to note that there were some methodological differences between the 2 surveys explaining part of the increase. Results from this study found the vacancy rate was higher in rural hospitals than in nonrural hospitals, and it was lower in ambulatory surgical centers. A number of simulations were run to predict the effects of relevant changes in the market for surgeries and number of CRNAs, which were compared to the predictions from the previous survey. The remarkable factor since the last survey was the unusually large rate of new CRNAs entering the market, yet the vacancy rates remain relatively high.

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.

Methods for sociological inquiry on emotion in educational settings

Sociological approaches to inquiry on emotion in educational settings are growing. Despite a long tradition of research and theory in disciplines such as psychology and sociology, the methods and approaches for naturalistic investigation of emotion are in a developmental phase in educational settings. In this article, recent empirical studies on emotion in educational contexts are canvassed. The discussion focuses on the use of multiple methods within research conducted in high school and university classrooms highlighting recent methodological progress. The methods discussed include facial expression analysis, verbal and non-verbal conduct, and self-report methods. Analyses drawn from different studies, informed by perspectives from microsociology, highlight the strengths and limitations of any one method. The power and limitations of multi-method approaches is discussed.

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.

Theorizing in design science research : an abstraction layers framework

For Design Science Research (DSR) to gain wide credence as a research paradigm in Information Systems (IS), it must contribute to theory. “Theory cannot be improved until we improve the theorizing process, and we cannot improve the theorizing process until we describe it more explicitly, operate it more self-consciously, and decouple it from validation more deliberately” (Weick 1989, p. 516). With the aim of improved design science theorizing, we propose a DSR abstraction-layers framework that integrates, interlates, and harmonizes key methodological notions, primary of which are: 1) the Design Science (DS), Design Research (DR), and Routine Design (RD) distinction (Winter 2008); 2) Multi Grounding in IS Design Theory (ISDT) (Goldkuhl & Lind 2010); 3) the Idealized Model for Theory Development (IM4TD) (Fischer & Gregor 2011); and 4) the DSR Theorizing Framework (Lee et al. 2011). Though theorizing, or the abstraction process, has been the subject of healthy discussion in DSR, important questions remain. With most attention to date having focused on theorizing for Design Research (DR), a key stimulus of the layered view was the realization that Design Science (DS) produces abstract knowledge at a higher level of generality. The resultant framework includes four abstraction layers: (i) Design Research (DR) 1st Abstract Layer, (ii) Design Science (DS) 2nd Abstract Layer, (iii) DSR Incubation 3rd Layer, and (iv) Routine Design 4th Layer. Differentiating and inter-relating these layers will aid DSR researchers to discover, position, and amplify their DSR contributions. Additionally, consideration of the four layers can trigger creative perspectives that suggest unplanned outputs. The first abstraction layer, including its alternative patterns of activity, is well recognized in the literature. The other layers, however, are less well recognized; and the integrated representation of layers is novel.

Reconceptualizing digital service quality : a call-to-action and research approach

The nature of services and service delivery has been changing rapidly since the 1980’s when many seminal papers in services research were published. Services are increasingly digital, or have a digital component. Further, a large and heterogeneous literature, with competing and overlapping definitions, many of which are dated and inappropriate to contemporary digital services offerings is impeding progress in digital services research. In this conceptual paper, we offer a critical review of some existing conceptualizations of services and digital services. We argue that an inductive approach to understanding cognition about digital services is required to develop a taxonomy of digital services and a new vocabulary. We argue that this is a pre-requisite to theorizing about digital services, including understanding quality drivers, value propositions, and quality determinants for different digital service types. We propose a research approach for reconceptualising digital services and service quality, and outline methodological approaches and outcomes.

Troubling dissemination : experimentations with the salon as conference event

Salons became popular in Europe in 17th Century as sites of philosophic and literary conversation. A group of female academics interested in Deleuzian theories experimented with the salon to challenge presentation and dissemination norms that hierarchize and centralize the human. For Deleuze and Guattari (1987), assemblages are shifting and decentering, so how might assemblages of chairs, tables, bodies, lights, space, help to trouble thinking about the methodological conventions around academic disseminations? The authors discuss the salon as a critical-cultural site: Cumming presents Deleuze and play-dough, an exploration of how the playful dissemination format of the salon prompted a re-reading of a methodological vignette from earlier research. Knight, an arts-based researcher, uses video art as a creative methodology to examine conceptualizations of rhizomes and assemblages at the salon as a dissemination site. The authors conclude that the salon, as a critical, cultural site disrupts hierarchized ways of approaching and presenting research.

Life story work and social work practice : a case study with ex-prisoners labelled as having an intellectual disability

In common with other professions social workers have the power to articulate certain ‘‘truths’’ about the people who use their services (Hare Mustin, 1994). These knowledge statements about people, often situated in case files may become the only background information of the lived experience for people with disability (Gillman, Swain, & Heyman, 1997). Social workers need to develop interviewing, assessment and recording practices that give precedent to the worldview of service users, if they are to truly understand and respond effectively to people's lives (Bigby, 2007). One such way of doing this is by adopting a life story approach to working with vulnerable people, which can provide a holistic stance to a person's social reality (Ortiz, 1985). This article outlines the use of this approach in research with Queensland ex-prisoners who were labelled as having an intellectual disability. By explaining the process used by the first author (hereafter known as the researcher), the methodological findings of this study illustrate how life story work can contribute to social work practice.

1000 voices: reflective online multimodal narrative inquiry as a research methodology for disability research

This article outlines the research approach used in the international 1000 Voices Project. The 1000 Voices project is an interdisciplinary research and public awareness project that uses a customised online multimodal storytelling platform to explore the lives of people with disability internationally. Through the project, researchers and partners have encouraged diverse participants to select the modes of storytelling (e.g. images, text, videos and combinations thereof) that suit them best and to self-define what both ‘disability’ and ‘life story’ mean to them. The online reflective component of the approach encourages participants to organically and reflectively develop story events and revisions over time in ways that suit them and their emerging lives. This article provides a detailed summary of the project's theoretical and methodological development alongside suggestions for future development in social work and qualitative research.

Australian Environmental Law : Norms, Principles & Rules, 3rd Edition

Australian Environmental Law: Norms, Principles and Rules, 3rd Edition provides a detailed examination of the fundamental concepts and principles of the environmental legal system in Australia. This new edition updates relevant State, Territory and Commonwealth legislation and case law and expands on the themes set out in the 2nd edition, namely:the origins and contexts of environmental governance; the movement toward ecologically sustainable development; the relevance and function of ecologically sustainable development today in the legal system; and the range of instrumental rules supporting environmental governance. The 3rd edition in particular expands upon the range of instrumental rules by analysing through the case law the emerging sets of rules of competence and limitation on the one hand and the emerging sets of purposive, deliberative, methodological, strategic, liability and market rules on the other hand. This thematic and principled approach adopted in Australian Environmental Law: Norms, Principles and Rules, 3rd Edition presents the reader with coverage of the important issues surrounding this area of the law in a clear and concise way.

Information Experience : Contemporary Perspectives

The purpose of this book is to open a conversation on the idea of information experience, which we understand to be a complex, multidimensional engagement with information. In developing the book we invited colleagues to propose a chapter on any aspect of information experience, for example conceptual, methodological or empirical. We invited them to express their interpretation of information experience, to contribute to the development of this concept. The book has thus become a vehicle for interested researchers and practitioners to explore their thinking around information experience, including relationships between information experience, learning experience, user experience and similar constructs. It represents a collective awareness of information experience in contemporary research and practice. Through this sharing of multiple perspectives, our insights into possible ways of interpreting information experience, and its relationship to other concepts in information research and practice, is enhanced. In this chapter, we introduce the idea of information experience. We also outline the book and its chapters, and bring together some emerging alternative views and approaches to this important idea.

The relationship between N2O, NO, and N2 fluxes from fertilized and irrigated dryland soils of the Aral Sea Basin, Uzbekistan

Microbial respiratory reduction of nitrous oxide (N2O) to dinitrogen (N2) via denitrification plays a key role within the global N-cycle since it is the most important process for converting reactive nitrogen back into inert molecular N2. However, due to methodological constraints, we still lack a comprehensive, quantitative understanding of denitrification rates and controlling factors across various ecosystems. We investigated N2, N2O and NO emissions from irrigated cotton fields within the Aral Sera Basin using the He/O2 atmosphere gas flow soil core technique and an incubation assay. NH4NO3 fertilizer, equivalent to 75 kg ha−1 and irrigation water, adjusting the water holding capacity to 70, 100 and 130% were applied to the incubation vessels to assess its influence on gaseous N emissions. Under soil conditions as they are naturally found after concomitant irrigation and fertilization, denitrification was the dominant process and N2 the main end product of denitrification. The mean ratios of N2/N2O emissions increased with increasing soil moisture content. N2 emissions exceeded N2O emissions by a factor of 5 ± 2 at 70% soil water holding capacity (WHC) and a factor of 55 ± 27 at 130% WHC. The mean ratios of N2O/NO emissions varied between 1.5 ± 0.4 (70% WHC) and 644 ± 108 (130% WHC). The magnitude of N2 emissions for irrigated cotton was estimated to be in the range of 24 ± 9 to 175 ± 65 kg-N ha−1season−1, while emissions of NO were only of minor importance (between 0.1 to 0.7 kg-N ha−1 season−1). The findings demonstrate that for irrigated dryland soils in the Aral Sera Basin, denitrification is a major pathway of N-loss and that substantial amounts of N-fertilizer are lost as N2 to the atmosphere for irrigated dryland soils.

Productivity measures and effects from subsidies and trade : an empirical analysis for Japan's forestry

Several techniques have been proposed in the literature to measure productivity. While allowing for inefficiency of the production unit, we provide a methodological comparison of alternative approaches to measure total factor productivity. This article evaluates the effects of unintended policy outcomes such as government subsidies and foreign trade. Empirically, we analyse the forest productivity of timber in Japan by using panel data on 46 regions. The results suggest substantial variation in productivity between these two techniques although average trends are similar. We find that subsidies impede competition since the government is ready to rescue a loss-making firm with subsidies rather than allow it to close. In contrast, trade is shown to have positive effects on productivity.