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.

Mapping journalism cultures across nations : a comparative study of 18 countries

This article reports key findings from a comparative survey of the role perceptions, epistemological orientations and ethical views of 1800 journalists from 18 countries. The results show that detachment, non-involvement, providing political information and monitoring the government are considered essential journalistic functions around the globe. Impartiality, the reliability and factualness of information, as well as adherence to universal ethical principles are also valued worldwide, though their perceived importance varies across countries. Various aspects of interventionism, objectivism and the importance of separating facts from opinion, on the other hand, seem to play out differently around the globe. Western journalists are generally less supportive of any active promotion of particular values, ideas and social change, and they adhere more to universal principles in their ethical decisions. Journalists from non-western contexts, on the other hand, tend to be more interventionist in their role perceptions and more flexible in their ethical views.

Adolescent men’s pregnancy resolution choices in relation to an unintended pregnancy: A comparative analysis of adolescent men in three countries.

This paper investigates adolescent men's pregnancy resolution choices in Australia, Ireland and Italy. It addresses two main gaps in the literature: the lack of research on (adolescent) men's views on unintended pregnancy and pregnancy resolution; and the lack of international comparative case studies on men and reproductive choices. Consistent with theories of the transformation of intimacies in society and the growth of individualization, the results suggest that adolescent men are interested in the effect of an unintended pregnancy on their individual biographies as well as the effect on their girlfriend's health and well-being. However, Australian male adolescents were much more likely to choose abortion than Italian or Irish adolescents, suggesting adolescent males have also internalized country level debates surrounding abortion. Methodologically, the paper demonstrates an innovative approach to data-collection using a computer-based interactive drama to facilitate participants' deliberation and responses. It was shown to engage a large number of adolescent men and is likely to have wider generalisability in developing international comparative research on the topic, as well as applications for health promotion.

Parallel Time Series Analysis and Income Inequality: A New Approach to Comparative Case Studies

This case study deals with the role of time series analysis in sociology, and its relationship with the wider literature and methodology of comparative case study research. Time series analysis is now well-represented in top-ranked sociology journals, often in the form of ‘pooled time series’ research designs. These studies typically pool multiple countries together into a pooled time series cross-section panel, in order to provide a larger sample for more robust and comprehensive analysis. This approach is well suited to exploring trans-national phenomena, and for elaborating useful macro-level theories specific to social structures, national policies, and long-term historical processes. It is less suited however, to understanding how these global social processes work in different countries. As such, the complexities of individual countries - which often display very different or contradictory dynamics than those suggested in pooled studies – are subsumed. Meanwhile, a robust literature on comparative case-based methods exists in the social sciences, where researchers focus on differences between cases, and the complex ways in which they co-evolve or diverge over time. A good example of this is the inequality literature, where although panel studies suggest a general trend of rising inequality driven by the weakening power of labour, marketisation of welfare, and the rising power of capital, some countries have still managed to remain resilient. This case study takes a closer look at what can be learned by applying the insights of case-based comparative research to the method of time series analysis. Taking international income inequality as its point of departure, it argues that we have much to learn about the viability of different combinations of policy options by examining how they work in different countries over time. By taking representative cases from different welfare systems (liberal, social democratic, corporatist, or antipodean), we can better sharpen our theories of how policies can be more specifically engineered to offset rising inequality. This involves a fundamental realignment of the strategy of time series analysis, grounding it instead in a qualitative appreciation of the historical context of cases, as a basis for comparing effects between different countries.

The Potential of Participedia as a Crowdsourcing Tool for Comparative Analysis of Democratic Innovations

For two reasons, our capacity for systematic comparison of innovative participatory democratic processes remains limited. First, the category of participatory democratic innovations remains relatively vague when compared to more traditional democratic institutions and practices. Second, until recently there existed no large-sample databases that captured relevant variables in the practice of democratic innovation. The lone exception to these patterns is the Participedia database, located online. Participedia is well placed to respond to the two obstacles to systematic comparative research on democratic innovation. First, its crowdsourced data collection strategy means that many of the cases on the platform are not well known and have not been the subject of sustained academic analysis. Second, the data captured in the articles provides the basis for systematic comparative analysis of democratic innovations both within type (e.g., participatory budgeting, mini-publics) and across types. The platform allows for systematic content analysis of text descriptions and/or statistical analysis of the datasets generated from the structured data fields. This article describes the data about innovative participatory democratic processes available from Participedia, and furnishes examples of the kinds of quantitative and qualitative insights about those processes that Participedia enables.

Predictors of knowledge creation performance. A quantitative qualitative comparative study of European doctorandi

Aquesta tesi forma part d'un projecte destinat a predir el rendiment acadèmic dels estudiants de doctorat portat a terme per l'INSOC (International Network on Social Capital and Performance). El grup de recerca INSOC està format per les universitats de Girona (Espanya), Ljubljana (Eslovènia), Giessen (Alemanya) i Ghent (Bèlgica). El primer objectiu d'aquesta tesi és desenvolupar anàlisis quantitatius comparatius sobre el rendiment acadèmic dels estudiants de doctorat entre Espanya, Eslovènia i Alemanya a partir dels resultats individuals del rendiment acadèmic obtinguts de cada una de les universitats. La naturalesa internacional del grup de recerca implica la recerca comparativa. Vam utilitzar variables personal, actitudinals i de xarxa per predir el rendiment. El segon objectiu d'aquesta tesi és entendre de manera qualitativa perquè les variables de xarxa no ajuden quantitativament a predir el rendiment a la universitat de Girona (Espanya). En el capítol 1, definim conceptes relacionats amb el rendiment i donam un llistat de cada una de les variables independents (variables de xarxa, personals i actitudinals), resumint la lliteratura. Finalment, explicam com s'organitzen els estudis de doctorat a cada un dels diferents països. A partir d'aquestes definicions teòriques, en els pròxims capítols, primer presentarem els qüestionaris utilitzats a Espanya, Eslovènia i Alemanya per mesurar aquests diferents tipus de variables. Després, compararem les variables que són relevants per predir el rendiment dels estudiants de doctorat a cada país. Després d'això, fixarem diferents models de regressió per predir el rendiment entre països. En tots aquests models les variables de xarxa fallen a predir el rendiment a la Universitat de Girona. Finalment, utilitzem estudis qualitatius per entendre aquests resultats inesperats. En el capítol 2, expliquem com hem dissenyat i conduït els qüestionaris en els diferents països amb l'objectiu d'explicar el rendiment dels estudiants de doctorat obtinguts a Espanya, Eslovènia i Alemanya. En el capítol 3, cream indicadors comparables però apareixen problemes de comparabilitat en preguntes particulars a Espanya, Eslovènia i Alemanya. En aquest capítol expliquem com utilitzem les variables dels tres països per crear indicadors comparables. Aquest pas és molt important perquè el principal objectiu del grup de recerca INSOC és comparar el rendiment dels estudiants de doctorat entre els diferents països. En el capítol 4 comparem models de regressió obtinguts de predir el rendiment dels estudiants de doctorat a les universitats de Girona (Espanya) i Eslovènia. Les variables són característiques dels grups de recerca dels estudiants de doctorat enteses com una xarxa social egocèntrica, característiques personals i actitudinals dels estudiants de doctorat i algunes carecterístiques dels directors. Vam trobar que les variables de xarxa egocèntriques no predien el rendiment a la Universitat de Girona. En el capítol 5, comparem dades eslovenes, espanyoles i alemnayes, seguint la metodologia del capítol 4. Concluïm que el cas alemany és molt diferent. El poder predictiu de les variables de xarxa no millora. En el capítol 6 el grup de recerca dels estudiants de doctorat és entès com una xarxa duocèntrica (Coromina et al., 2008), amb l'objectiu d'obtendre informació de la relació mútua entre els estudiants i els seus directors i els contactes d'ambdós amb els altres de la xarxa. La inclusió de la xarxa duocèntrica no millora el poder predictiu del model de regressió utilitzant les variales egocèntriques de xarxa. El capítol 7 pretèn entendre perquè les variables de xarxa no predeixen el rendiment a la Universitat de Girona. Utilitzem el mètode mixte, esperant que l'estudi qualitatiu pugui cobrir les raons de perquè la qualitat de la xarxa falla en la qualitat del treball dels estudiants. Per recollir dades per l'estudi qualitatiu utilitzem entrevistes en profunditat.

Process and performance in international collaborative research

Motivated by policy goals to develop international research capability and our experiences of collaborative research, we wanted to learn more about the factors that influence success in collaborative research. This article presents a review of the academic literature on collaborative research, focusing on multinational teams doing international comparative research. We address the question ‘what accounts for variation in process and performance of collaborative research projects?’, through 11 themes: context; vision; reward and commitment; leadership; structure; contract; task capability; sociability; communication; finance; rhythm and pace. We then propose an agenda for future research with an analytic framework and, finally, our conclusions.

Key insights for the future of urban ecosystem services research

Understanding the dynamics of urban ecosystem services is a necessary requirement for adequate planning, management, and governance of urban green infrastructure. Through the three-year Urban Biodiversity and Ecosystem Services (URBES) research project, we conducted case study and comparative research on urban biodiversity and ecosystem services across seven cities in Europe and the United States. Reviewing > 50 peer-reviewed publications from the project, we present and discuss seven key insights that reflect cumulative findings from the project as well as the state-of-the-art knowledge in urban ecosystem services research. The insights from our review indicate that cross-sectoral, multiscale, interdisciplinary research is beginning to provide a solid scientific foundation for applying the ecosystem services framework in urban areas and land management. Our review offers a foundation for seeking novel, nature-based solutions to emerging urban challenges such as wicked environmental change issues.

Researching and writing in law (3rd ed.)

The revolution in legal research provides exciting challenges for those exploring and writing about the legal landscape. Cumbersome paper sources have largely been replaced by electronic files and a new range of skills and sources are required to successfully conduct legal research.--------- Researching and Writing in Law, 3rd Edition is an updated research guide, mapping the developments that have taken place and providing the keys to the fundamental electronic sources of legal research, especially those now available on the web, as well as exploring traditional doctrinal methodologies. Included in this edition are extensive checklists for locating and validating the law in Australia, England, Canada, the United States, New Zealand, India and the European Union.-------- This third edition includes expanded discussion of the process of formulating a research proposal, writing project abstracts and undertaking a literature review (Chapter 7). Research methodologies are also extensively examined, focusing on the process of doctrinal methodology as well as discussing other useful methodologies, such as Comparative Research and Content Analysis (Chapter 5). Further highlighted are issues surrounding research ethics, including plagiarism and originality, the importance of developing skills in critique, and the influence of current university research environments on postgraduate legal research.-------- Law students and members of the practising profession aiming to update their research, knowledge and skills will find Researching and Writing in Law, 3rd Edition invaluable.

Cultural Science and Methodological Challenge!

The processes of digitization and deregulation have transformed the production, distribution and consumption of information and entertainment media over the past three decades. Today, researchers are confronted with profoundly different landscapes of domestic and personal media than the pioneers of qualitative audience research that came to form much of the conceptual basis of Cultural Studies first in Britain and North America and subsequently across all global regions. The process of media convergence, as a consequence of the dual forces of digitisation and deregulation, thus constitutes a central concept in the analysis of popular mass media. From the study of the internationalisation and globalisation of media content, changing regimes of media production, via the social shaping and communication technologies and conversely the impact of communication technology on social, cultural and political realities, to the emergence of transmedia storytelling, the interplay of intertextuality and genre and the formation of mediated social networks, convergence informs and shapes contemporary conceptual debates in the field of popular communication and beyond. However, media convergence challenges not only the conceptual canon of (popular) communication research, but poses profound methodological challenges. As boundaries between producers and consumers are increasingly fluent, formerly stable fields and categories of research such as industries, texts and audiences intersect and overlap, requiring combined and new research strategies. This preconference aims to offer a forum to present and discuss methodological innovations in the study of contemporary media and the analysis of the social, cultural,and political impact and challenges arising through media convergence. The preconference thus aims to focus on the following methodological questions and challenges: *New strategies of audience research responding to the increasing individualisation of popular media consumption. *Methods of data triangulation in and through the integrated study of media production, distribution and consumption. *Bridging the methodological and often associated conceptual gap between qualitative and quantitative research in the study of popular media. *The future of ethnographic audience and production research in light of blurring boundaries between media producers and consumers. *A critical re-examination of which textual configurations can be meaningfully described and studied as text. *Methodological innovations aimed at assessing the macro social, cultural and political impact of mediatization (including, but not limited to, "creative methods"). *Methodological responses to the globalisation of popular media and practicalities of international and transnational comparative research. *An exploration of new methods required in the study of media flow and intertextuality.

Optimism about safety and group-serving interpretations of safety among pedestrians and cyclists in relation to road use in general and under low light conditions

Drivers are known to be optimistic about their risk of crash involvement, believing that they are less likely to be involved in a crash than other drivers. However, little comparative research has been conducted among other road users. In addition, optimism about crash risk is conceptualised as applying only to an individual’s assessment of his or her personal risk of crash involvement. The possibility that the self-serving nature of optimism about safety might be generalised to the group-level as a cyclist or a pedestrian, i.e., becoming group-serving rather than self-serving, has been overlooked in relation to road safety. This study analysed a subset of data collected as part of a larger research project on the visibility of pedestrians, cyclists and road workers, focusing on a set of questionnaire items administered to 406 pedestrians, 838 cyclists and 622 drivers. The items related to safety in various scenarios involving drivers, pedestrians and cyclists, allowing predictions to be derived about group differences in agreement with items based on the assumption that the results would exhibit group-serving bias. Analysis of the responses indicated that specific hypotheses about group-serving interpretations of safety and responsibility were supported in 22 of the 26 comparisons. When the nine comparisons relevant to low lighting conditions were considered separately, seven were found to be supported. The findings of the research have implications for public education and for the likely acceptance of messages which are inconsistent with current assumptions and expectations of pedestrians and cyclists. They also suggest that research into group-serving interpretations of safety, even for temporary roles rather than enduring groups, could be fruitful. Further, there is an implication that gains in safety can be made by better educating road users about the limitations of their visibility and the ramifications of this for their own road safety, particularly in low light.

Strategic issues for the Not-for-profit sector

Bringing together some of Australia’s leading and emerging researchers studying different aspects of the not-for-profit (NFP) sector, Strategic Issues in the Not-for-Profit Sector draws on original Australian and comparative research to provide a spirited exploration of strategic issues facing NFP organisations. A diverse, vital and ever-growing sector in Australia, the NFP sector provides the organisational framework through which many of the most disadvantaged in the community receive access to services and support. However, pressures such as a changing composition, an erosion of financial sustainability, the need to professionalise, and demographic trends affecting patterns of volunteering have put pressure on the NFP sector to innovate and grow in new directions. Strategic Issues in the Not-for-Profit Sector considers the local and global drivers of change, as well as the industry, policy and community imperatives impacting upon NFP sustainability, providing a unique insight into not only the strategic issues, but also strategic responses emerging within the sector.

Quantitative approaches to comparing communication patterns on Twitter

To date, the available literature mainly discusses Twitter activity patterns in the context of individual case studies, while comparative research on a large number of communicative events and their dynamics and patterns is missing. By conducting a comparative study of more than 40 different cases (covering topics such as elections, natural disasters, corporate crises, and televised events) we identify a number of distinct types of discussion that can be observed on Twitter. Drawing on a range of communicative metrics, we show that thematic and contextual factors influence the usage of different communicative tools available to Twitter users, such as original tweets, @replies, retweets, and URLs. Based on this first analysis of the overall metrics of Twitter discussions, we also demonstrate stable patterns in the use of Twitter in the context of major topics and events.

Child sexual abuse prevention education : A review of school policy and curriculum provision in Australia

The past four decades have seen increasing public and professional awareness of child sexual abuse. Congruent with public health approaches to prevention, efforts to eliminate child sexual abuse have inspired the emergence of prevention initiatives which can be provided to all children as part of their standard school curriculum. However, relatively little is known about the scope and nature of child sexual abuse prevention efforts in government school systems internationally. This paper assesses and compares the policies and curriculum initiatives for child sexual abuse prevention education in primary (elementary) schools across state and territory Departments of Education in Australia. Using publicly available electronic data, a deductive qualitative content analysis of policy and curriculum documents was undertaken to examine the characteristics of child sexual abuse prevention education in these school systems. It was found that the system-level provision of child sexual abuse prevention education occurs unevenly across state and territory jurisdictions. This results in the potential for substantial inequity in Australian children’s access to learning opportunities in child abuse prevention education as a part of their standard school curriculum. In this research, we have developed a strategy for generating a set of theoretically-sound empirical criteria that may be more extensively applied in comparative research about prevention initiatives internationally.

An examination of the factorial invariance and refinement of the multidimensional school anger inventory for five Pacific Rim countries

The validity of the Multidimensional School Anger Inventory (MSAI) was examined with adolescents from 5 Pacific Rim countries (N ¼ 3,181 adolescents; age, M ¼ 14.8 years; 52% females). Confirmatory factor analyses examined configural invariance for the MSAI’s anger experience, hostility, destructive expression, and anger coping subscales. The model did not converge for Peruvian students. Using the top 4 loaded items for anger experience, hostility, and destructive expression configural invariance and partial metric and scalar invariances were found. Latent means analysis compared mean responses on each subscale to the U.S. sample. Students from other countries showed higher mean responses on the anger experience subscale (ds ¼ .37–.73). Australian (d ¼ .40) and Japanese students (d ¼ .21) had significantly higher mean hostility subscale scores. Australian students had higher mean scores on the destructive expression subscale (d ¼ .30), whereas Japanese students had lower mean scores (d ¼ 2.17). The largest latent mean gender differences (females lower than males) were for destructive expression among Australian (d ¼ 2.67), Guatemalan (d ¼ 2.42), and U.S. (d ¼ 2.66) students. This study supported an abbreviated, 12-item MSAI with partial invariance. Implications for the use of the MSAI in comparative research are discussed.