bluuebunny/crossref_metadata_2025 huggingface dataset:
Queer Dance in Three Acts
Authors: defrantz thomas f.
Published: May 2017

This chapter considers three dimensions of a queer dance ontology: being, doing, and making. The tri-parte exploration assumes that there is something called queer, and it can be done, and made, as dance. Through exploration of a collaborative queer work “theory-ography 4.5—a we still queer here” created by SLIPPAGE:performance|culture|technology, the chapter demonstrates that dance enhances queer visibility. A consideration of the essential participation of viewing/recognition that defines queer, the chapter concludes that while dance emerges from being and doing, perhaps, its contents are brought into focus by the making of its various audiences who can narrate the queerness at hand.
Aunty Fever
Authors: Khubchandani Kareem
Published: May 2017

This essay attends to origin stories of queerness and dance from the author’s younger years, to suggest that his contemporary manifestations of queer dance emerge from contexts that may not traditionally be labeled as “queer” or “dance.” He describes dance pedagogies offered by his Indian aunties in Ghana, to explain how they inform his queer choreographies and politics as a drag queen performing in the multicultural US nightclub and online. Specifically, he considers how he creates his drag persona, LaWhore Vagistan, blending Bollywood vocabulary and music with drag queen performance in a way that exceeds a colonizing, patriarchal, femme-phobic gaze.
Last Cowboy Standing
Authors: Carpenter Peter
Published: May 2017

Gays and lesbians inaugurated their own country-western dance spaces in the early 1980s, coinciding with the advent of Ronald Reagan’s presidency, which was marked by an anti-queer, cowboy politics. Reagan’s disregard for queers came into devastating relief with his administration’s reckless disregard for the rise and spread of AIDS. The author’s 2007 choreographic work Last Cowboy Standing interrogates Reagan’s rhetoric through a contemporized cowboy choreography that positions his own queer body in an interrogatory relationship to Reagan’s public speeches throughout his political career. Engaging with popular conceptions of the cowboy, the author oscillates between describing knowledge gained in the studio to theorizations of his own work, testing a critical choreographic inquiry as a form of self-reportage.
RMW (A) & RMW from the Inside Out
Authors: Monson Jennifer
Published: May 2017

The essay uses poetic, descriptive, and conceptual writing approaches to articulate how the choreographic strategies of RMW(A) & RMW emerged from their historical and political contexts. The work references the 1990s and the early 2000s as historical moments influenced by the AIDS epidemic and the Internet revolution. It proposes that the notion of a queer object and action might be used to differentiate the kinds of desire that are negotiated between the performers and the audience through these choreographic approaches over time. RMW(A) & RMW is described as a practice that adapts to the unstable notion of what queer dance means for these two differently female bodies as their lives move apart and come together. The essay describes the experience of being inside the work as well as narrates the personal histories that shaped the choreography and practice of RMW(A) & RMW.
Futari Tomo
Authors: Ahlgren Angela K.
Published: May 2017

This essay explores the queer acts and intimacies forged through the practice and performance of taiko, a contemporary form of Japanese drumming widely practiced in North America and, more recently, worldwide. Tracing acts of spectatorship, performance, and the creation of a taiko duet, “Futari Tomo,” this essay ruminates on the space taiko and performance more generally make space for negotiating queer intimacies and lives. It further ruminates on the blurred boundaries and the spaces between two people, music and dance, performer and spectator, and performance and the everyday as it looks at taiko from the space of the backstage, in rehearsal, and in performance.
Choreographing the Chronic
Authors: McKelvey Patrick
Published: May 2017

“Choreographing the Chronic” brings together dance studies, queer disability studies, and performance studies to examine Octavio Campos’s 2007 dance-theater piece, The Bugchasers. The essay considers Campos’s work alongside other representations of bugchasers—people who deliberately pursue HIV—in popular journalism, queer theory, and social media. It argues that Campos’s work illuminates what these other representations obfuscate: that bugchasers stage alternative temporalities of seroconversion and HIV/AIDS more broadly. The bugchasers populating Campos’s piece thwart seroconversion’s prominence as ostensibly the most important event governing queer life. By extension, they challenge dominant understandings of people with HIV and other disabled people deprived of the capacity to represent anything other than disablement.
Superresolution without separation
Authors: Schiebinger Geoffrey , Robeva Elina , Recht Benjamin
Published: May 2017

This article provides a theoretical analysis of diffraction-limited superresolution, demonstrating that arbitrarily close point sources can be resolved in ideal situations. Precisely, we assume that the incoming signal is a linear combination of $M$ shifted copies of a known waveform with unknown shifts and amplitudes, and one only observes a finite collection of evaluations of this signal. We characterize properties of the base waveform such that the exact translations and amplitudes can be recovered from $2M+1$ observations. This recovery can be achieved by solving a weighted version of basis pursuit over a continuous dictionary. Our analysis shows that $\ell_1$-based methods enjoy the same separation-free recovery guarantees as polynomial root finding techniques, such as de Prony’s method or Vetterli’s method for signals of finite rate of innovation. Our proof techniques combine classical polynomial interpolation techniques with contemporary tools from compressed sensing.
The Revolving Door in International Investment Arbitration
Authors: Langford Malcolm , Behn Daniel , Lie Runar Hilleren
Published: May 2017

It is often claimed that international investment arbitration is marked by a revolving door: individuals act sequentially and even simultaneously as arbitrator, legal counsel, expert witness, or tribunal secretary. If this claim is correct, it has implications for our understanding of which individuals possess power and influence within this community; and ethical debates over conflicts of interests and transparency concerning ‘double hatting’—when individuals simultaneously perform different roles across cases. In this article, we offer the first comprehensive empirical analysis of the individuals that make up the entire investment arbitration community. Drawing on our database of 1039 investment arbitration cases (including ICSID annulments) and the relationships between the 3910 known individuals that form this community, we offer the first use of social network analysis to describe the full investment arbitration community and address key sociological and normative questions in the literature. Our results partly contradict recent empirical scholarship as we identify a different configuration of central ‘power brokers’. Moreover, the normative concerns with double hatting are partly substantiated. A select but significant group of individuals score highly and continually on our double hatting index.
Introduction
Authors: Waldow Anik , DeSouza Nigel
Published: May 2017

This interview explores Charles Taylor’s understanding of philosophical anthropology and its relationship to Herder. Taylor argues that human culture can be properly understood only in a genetic fashion, through hermeneutics and phenomenology, and names Herder as an important precursor here. Taylor illustrates this through the difference between a purely normative political theory and a contextual political philosophy. On the relationship between naturalism and philosophical anthropology, Taylor identifies what he calls a “good naturalism,” associated with Herder, that explains what kind of animal human beings are, and a “bad naturalism” that explains human beings in reductive, natural scientific terms. Finally, Taylor outlines his current work on language, in which a similar opposition arises, between language as necessarily emerging as a rich set of language games/practices and language as pure description. Theories of language that interpret it only in terms of the latter are thus fundamentally flawed and inaccurate.
The Metaphysical and Epistemological Foundations of Herder’s Philosophical Anthropology
Authors: DeSouza Nigel
Published: May 2017

This paper focuses on Herder’s contribution to the development of philosophical anthropology by seeing Herder’s philosophy as a response to recent discoveries in medicine and physiology. The major impulse came from Haller’s discovery of the irritability of muscle and sensibility of nerves, which challenged philosophical and theological dogmas about the existence of an immaterial soul and its ability to cause what the mind perceives as voluntary motion. It blurred the traditional division of labor between the physician investigating the body and the philosopher and theologian studying the soul. The chapter will explore how Herder makes creative use of Haller’s concept of irritability as a way of demonstrating a neo-Aristotelian account of the soul as pervading and informing the entire body.
Human Nature and Human Science
Authors: Gjesdal Kristin
Published: May 2017

It is difficult to accept that Johann Gottfried Herder (1744–1803), an influential philosopher of history, language, and culture, was a prolific preacher and clergyman. His apparent Spinoza connection, his agreement with the pre-critical Kant, and his alleged naturalism seem to contradict his unquestioning acceptance of God. But when the human being is considered as the middle point a reconstruction of Herder devoid of this dichotomy is possible. Herder’s religious anthropology understands human beings both as historical and religious beings, which gives rise to his rejection of Christianity in its actuality as the sole future religion. The church raised itself above the individual and destroyed religions, cultures, and languages, whereas Herder’s notion of human religion—for him a universal concept—allows individual nations, cultures, languages, and religions to remain particular. Central for the argument are Herder’s Christliche Schriften (1793–8), the Ideen (1801–4), and the Adrastea (1801–4).
Herder’s Religious Anthropology in His Later Writings
Authors: Schmidt Johannes
Published: May 2017

Herder uses the image of the spherical shape of the earth as a matrix to evaluate the contrast between plurality and universality: it illustrates the tension between the individuality of diverse peoples and cultures, on the one hand, and the universal identity of the human species, on the other. While Herder’s “globe ontology” implies a rejection of hierarchically structured—and thus normatively laden—theories of history and culture, it does rely on an idea of humanity as a telos embedded in western thinking. Thus at the end of the Ideen Herder praises the glory of Europe, while at the same time acknowledging the value of each individual people. This essay demonstrates that while Herder might think in oppositions, it is precisely this feature of his philosophy that enables him to advance a nuanced and innovative position that goes beyond many historiographical and cultural-theoretical conceptions of the eighteenth century.
Individualism and Universalism in Herder’s Conception of the Philosophy of History
Authors: Bollacher Martin
Published: May 2017

Herder was very familiar with the concept of human rights (in his German, “Menschenrechte”), strongly shared the moral ideals of protecting people at which the concept aims, but tended to avoid using the concept himself. Why this ambivalence? The present article argues that a number of well-founded concerns about the concept underlie, or at least may underlie, his reservation, including concerns about the legal rather than moral nature of the very concept of “rights,” the undue restriction of the focus of “human rights” to protecting people against threats that emanate from their own governments rather than against those from outside (imperialism, colonialism, etc.) as well, and the concept’s dubious restriction of protections to human beings to the exclusion of animals. The article also argues, however, that these concerns are not insurmountable, and that indeed Herder himself has provided some of the most important theoretical tools for surmounting them.
Diagnostic Practices for Suspected Community-Acquired Central Nervous System Infection in the Post–Conjugate Vaccine Era
Authors: Banniettis Natalie , Joshi Saumya , Kaushik Shubhi , Kohlhoff Stephan , Hammerschlag Margaret R.
Published: May 2017

Objective

The aim of this study was to evaluate diagnostic practices for suspected community-acquired central nervous system (CNS) infection in an urban pediatric population.

Methods

This is an observational, retrospective single-center review of cerebrospinal fluid (CSF) studies in children, 1 month to 21 years old, evaluated for suspected CNS infection from 2004 to 2014. Cases of suspected nosocomial meningitis were excluded. The frequency of N-methyl-d-aspartate receptor antibody (NMDAR ab) encephalitis was analyzed from 2010 to 2014.

Results

A total of 940 unique patient visits with CSF studies were included in the final analysis. There were 940 bacterial cultures sent; 4 (0.42%) grew suspected CSF bacterial pathogens, and 18 (1.9%) grew organisms that were suspected contaminants. Bacterial pathogens included late-onset group B Streptococcus in 3 infants younger than 3 months and Streptococcus pneumoniae in an unvaccinated 9-year-old child. Viral CNS infection was 7.5 times more frequent than bacterial infection. Enterovirus was the only virus isolated. Five cases positive for NMDAR ab were identified since 2010.

Conclusions

Bacterial studies were performed more frequently than viral and other studies. Cerebrospinal fluid bacterial culture was nearly 5 times more likely to yield a contaminant than a pathogen. The frequency of viral infection was likely underestimated as only 20% were tested, mainly by culture, which is suboptimal. These data suggest diagnostic practices for the evaluation of suspected community-acquired CNS infections in children need to be modified to reflect current epidemiology and highlight the need for greater accessibility to polymerase chain reaction for viral diagnostics. Furthermore, NMDAR ab–mediated encephalitis should be considered early in children presenting with suggestive symptoms.
Epidemiology of Fractures in Children Younger Than 12 Months
Authors: Rodà Diana , Trenchs Victoria , Curcoy Ana Isabel , Martínez Anibal Dolores , Pou Jordi , Luaces Carles
Published: May 2017

Objectives

The aim of this study is to determine the prevalence and characteristics of fractures in young infants attended at the pediatric emergency department (PED).

Methods

This is a retrospective study for 2 years (2011–2012) of children younger than 12 months attended with a fracture at the PED. Age, sex, site and type of fracture, mechanism of injury, time interval before seeking medical attention, and management were analyzed.

Results

One hundred one patients were included. They represented 0.3% (95% confidence interval, 0.2%–0.4%) of all children younger than 12 months attended at the PED. The median age was 7.7 months (interquartile range, 5.2–10.1 months); 58 (57.4%) were boys. The most common fracture was skull fracture (58, 57.4%), mostly parietal, followed by long bone fractures (27, 26.7%); transverse and torus fractures were the most common types, located at the diaphysis and distal metaphysis, respectively. The principal mechanism reported was falling (83, 82.2%) mainly from furniture. Fifty-one patients (50.1%) were attended in the first 6 hours after injury. Sixty-five patients (64.4%) were admitted at the hospital and the other 9 (8.9%) were controlled in outpatient visits. One of them was injured because of negligence and another was diagnosed with osteoporosis.

Conclusions

Fractures in young infants are uncommon at the PED, the skull fracture being the most common. Pediatricians should alert caretakers of the risks in normal development to prevent these injuries. Fractures caused by child abuse should always be discarded.
A Rare Cause of Shock in an Infant
Authors: Vayngortin Tatyana , Rosenfeld Howard , Mansour Karim
Published: May 2017

Congenital heart disease can be difficult to diagnose in infants because they often present with nonspecific symptoms. Their clinical presentation can resemble that of respiratory infections or sepsis, yet typical treatments for these conditions such as fluid resuscitation may worsen their course. We report a case of an 8-week-old boy who had several weeks of viral symptoms and eventually presented to the emergency department in shock. An echocardiogram revealed the diagnosis of cor triatriatum, a rare congenital heart disease that requires urgent surgical repair. In this article, we review the evaluation and management of such patients and emphasize the importance of considering congenital heart disease in the differential diagnosis for an infant in shock.
Risk of Colorectal Cancer and Associated Mortality in HIV: A Systematic Review and Meta-Analysis
Authors: O'Neill Tyler J. , Nguemo Joseph D. , Tynan Anne-Marie , Burchell Ann N. , Antoniou Tony
Published: May 2017

Background:

As people with HIV live longer, the numbers of colorectal cancer cases are expected to increase. We sought to compare the colorectal cancer incidence and cause-specific mortality among people living with and without HIV.

Design:

Systematic review and meta-analysis.

Methods:

We searched 5 electronic databases up to June 28, 2016, for primary studies reporting standardized incidence ratios (SIRs), standardized mortality ratios (SMRs)/hazard ratios or data sufficient for estimating these summary measures. We performed a random effects pooled analysis to estimate SIR and SMR of colorectal cancer in HIV.

Results:

Of 8110 articles, we included 27 studies from North America (n = 18), Europe (n = 7), the Pacific region (n = 4), and South America (n = 1). Overall, 1660 cases of colorectal cancer and colon cancer (excluding rectal cancer) occurred among 1,696,070 persons with HIV. In pooled analysis, we found no summary risk of malignancy among those with HIV relative to an uninfected population (SIR 1.00; 95% confidence interval 0.82 to 1.22; I2 = 89.2%). Colorectal cancer–specific mortality was higher among people with HIV but did not reach statistical significance (SMR 2.09; 95% confidence interval: 1.00 to 4.40; I2 = 85.0%).

Conclusions:

Rates of colorectal cancer are similar between people with and without HIV. Existing screening guidelines are likely adequate for people with HIV.
Measuring Fatigue in Triage
Authors: McMahon Bryn , Hudson John , Prewitt Judy , Carman Margaret J. , Engleson Monica
Published: May 2017

Given the critical nature of triage in facilitating emergency department (ED) functions, an understanding of the factors that impact triage nurses' ability to accurately assign triage scores and the ways in which these factors may affect various patient outcomes is extremely important; yet, there exists a paucity of such research in the literature. To further develop this knowledge base, an investigation of triage nurse fatigue and the role it may play in the ability to accurately assign triage scores was developed. The purpose of this pilot study was to determine how the length of a triage shift affects perceived fatigue levels among triage nurses. This pilot study was conducted using a prospective, descriptive cohort design with 28 registered nurses at a university-affiliated community hospital in the southeastern United States. Fatigue data were collected every 2 hr while the subject was in triage over the course of eighteen 24-hr periods between November 2015 and April 2016. Fatigue was measured using a self-reported fatigue questionnaire that included 2 validated fatigue scales: Karolinska Sleepiness Scale and Samn–Perelli Seven-Point Fatigue Scale. Data were analyzed using SPSS and Microsoft Excel. Results indicate a strong correlation between the amount of time spent in triage and fatigue scores, with average fatigue scores increasing by 64.4%–75.2% over the course of a 12-hr shift. Findings suggest that there was a positive correlation between the length of a triage shift and perceived fatigue levels among triage nurses in the ED. The biggest percent increase in fatigue scores is between hours 4 and 8. Further studies are needed to determine optimal triage shift length as well as the effect of nursing fatigue on triage accuracy.
Industry 1.61803: the transition to an industry with reduced material demand fit for a low carbon future
Authors: Allwood Julian M. , Gutowski Timothy G. , Serrenho André C. , Skelton Alexandra C. H. , Worrell Ernst
Published: May 2017

Arising from a discussion meeting in September 2016, this editorial introduces a special issue on the transition to a future industrial system with greatly reduced demand for material production and attempts to synthesize the main findings. The motivation for such a transition is to reduce industrial greenhouse gas emissions, but unlike previous industrial transformations, there are no major stakeholders who will pursue the change for their own immediate benefit. The special issue, therefore, explores the means by which such a transition could be brought about. The editorial presents an overview of the opportunities identified in the papers of the volume, presents examples of actions that can be taken today to begin the process of change and concludes with an agenda for research that might support a rapid acceleration in the rate of change.

This article is part of the themed issue ‘Material demand reduction’.
Exploring demand reduction through design, durability and ‘usership’ of fashion clothes
Authors: Fletcher Kate
Published: May 2017

Global planetary boundaries confer limits to production and consumption of material goods. They also confer an obligation to experiment, as individuals and collectively as society, with less-materially-intensive, but no less exuberant, ways of living. This paper takes up this mantle and explores materials demand reduction through a focus on design, fashion garments and the universal, everyday activity of wearing clothes. It takes as its starting point the design of longer-lasting products, a widely favoured strategy for increasing materials efficiency and reducing materials demand in many sectors, including fashion. Drawing on scholarship in the field of design for sustainability and ethnographic research conducted in 16 locations in nine countries about already-existing practices of intensive use and maintenance of clothing, this paper critiques the effectiveness of durability strategies to reduce the amount of materials used. It argues for an update in the familiar preference within sustainability debates for the ‘techno-fix’ to explore instead resourceful use of materials as emerging from human actions and relationships with material goods. It suggests that, while facilitated by design, technology and engineering, opportunities to reduce materials demand begin in individual and collective practices, which, in turn, have dynamic implications for use of materials.

This article is part of the themed issue ‘Material demand reduction’.
Living both well and sustainably: a review of the literature, with some reflections on future research, interventions and policy
Authors: Kasser Tim
Published: May 2017

The idea that human well-being (WB) can be supported and even enhanced by using, producing, buying, selling and consuming less ‘stuff’ is anathema to many living under consumer capitalism. Yet a growing research literature actually finds that frequent engagement in pro-ecological behaviours (PEBs) is positively correlated with personal WB. This paper reviews data relevant to three possible explanations for the apparent compatibility of PEBs and WB: (i) engaging in PEBs leads to psychological need satisfaction, which in turn causes WB; (ii) being in a good mood causes people to engage in more prosocial behaviours, including PEBs; and (iii) personal characteristics and lifestyles such as intrinsic values, mindfulness and voluntary simplicity cause both PEBs and WB. Because each explanation has some empirical support, I close by reflecting on some relevant interventions and policies that could strengthen each of these three pathways and thereby promote living both well and sustainably.

This article is part of the themed issue ‘Material demand reduction’.
Frugal innovation: doing more with less for more
Authors: Prabhu Jaideep
Published: May 2017

The global economy will face significant challenges over the next few decades. On the one hand, it must meet the needs of 7 billion consumers (growing to 9 billion by 2050), including the currently unmet basic needs of large numbers in developing countries in areas such as food, energy, housing and health. On the other hand, it must achieve this growth without exceeding the resources available on the planet or causing environmental devastation. This paper argues that such change is possible through a systemic shift to a frugal economy that involves radical, frugal innovation across sectors. Such a transformation will involve the participation of large and small firms, consumers and governments alike. The paper introduces the notion of frugal innovation—the creation of faster, better and cheaper solutions for more people that employ minimal resources—and discusses strategies and examples of such change already taking place in core sectors like manufacturing, food, automotive and energy in developing and developed economies. It also outlines the role of the interaction between large and small firms as well as between firms and consumers in making change possible, as well as the role of governments in driving change where market mechanisms alone will not suffice.

This article is part of the themed issue ‘Material demand reduction’.
Why on earth did I buy that? A study of regretted appliance purchases
Authors: Roberts T. , Hope A. , Skelton A.
Published: May 2017

If targets to reduce greenhouse gas emissions and thereby tackle climate change are to be achieved, it will be necessary to reduce both embodied energy costs (e.g. in terms of producing and manufacturing the products and services that society consumes) and operational energy costs. Reducing the number of purchases that people regret could be a first step in changing the overall dynamic of consumption patterns. This research looks at some potentially adverse effects of consumption on well-being (e.g. negative emotions), applying social practice theory to give insights into why people make purchases that they feel negatively about. This paper draws from: (i) findings of a national survey of over 2000 respondents which found that 53% of adults had reported regretting purchasing an electrical device at some point, and that 23% regretted making such a purchase within the past year; and (ii) a series of walking interviews around people's homes that provide detailed insights into the nature and extent of regretted purchases of electrical goods (e.g. resentment at built-in obsolescence, frustration at the pace of technological change). By combining the qualitative and quantitative data, we develop a typology of regretted consumption and explore the underlying factors that lead to such purchases. The paper concludes with a discussion of the policy implications of this research.

This article is part of the themed issue ‘Material demand reduction’.
The carbon price: a toothless tool for material efficiency?
Authors: Skelton Alexandra C. H. , Allwood Julian M.
Published: May 2017

This article explores whether a carbon price will effectively encourage the more efficient use of greenhouse gas intensive materials such as steel. The article identifies a range of distortions that arise when some of the restrictive assumptions of neoclassical economics are relaxed. Distortions occur due to the sequential nature of decision-making along supply chains, due to imperfect competition and due to government intervention to reduce the risk of carbon leakage. If upstream sectors do not pass on carbon costs, downstream sectors do not have the opportunity to react. Of the distortions identified, compensation mechanisms that reduce the risk of carbon leakage are likely to act as the greatest hinderance to appropriate incentives for the more efficient use of steel in the UK: as things currently stand, unless upstream companies are encouraged to make windfall profits, incentives downstream are weakened. The article concludes by exploring policy options to address the distortions identified, including efforts to reinstate the carbon price downstream and efforts to remove other distortive taxes.

This article is part of the themed issue ‘Material demand reduction’.
Who is reducing their material consumption and why? A cross-cultural analysis of dematerialization behaviours
Authors: Whitmarsh Lorraine , Capstick Stuart , Nash Nicholas
Published: May 2017

The environmental and economic imperatives to dematerialize economies, or ‘do more with less’, have been established for some years. Yet, to date, little is known about the personal drivers associated with dematerializing. This paper explores the prevalence and profile of those who are taking action to reduce consumption in different cultural contexts (UK and Brazil) and considers influences on dematerialization behaviours. We find that exemplar behaviours (avoiding buying new things and avoiding packaging) are far less common than archetypal environmental behaviours (e.g. recycling), but also that cultural context is important (Brazilians are more likely to reduce their material consumption than people in the UK). We also find that the two dematerialization behaviours are associated with different pro-environmental actions (more radical action versus green consumption, respectively); and have distinct, but overlapping, psychological (e.g. identity) and socio-demographic (e.g. education) predictors. Comparing a more traditional value-identity model of pro-environmental behaviour with a motivation-based (self-determination) model, we find that the latter explains somewhat more variance than the former. However, overall, little variance is explained, suggesting that additional factors at the personal and structural levels are important for determining these consumption behaviours. We conclude by outlining policy implications and avenues for further research.

This article is part of the themed issue ‘Material demand reduction’.
Streptococcus suis serotype 9 endocarditis and subsequent severe meningitis in a growing pig despite specific bactericidal humoral immunity
Authors: Rieckmann Karoline , Müller Kristin , Moter Annette , Baums Christoph G , Seydel Anna
Published: May 2017

Introduction. Meningitis and endocarditis are common pathologies of Streptococcus
suis infections in pigs and humans. S. suis serotype 9 strains contribute substantially to health problems in European pig production, and immune prophylaxis against this serotype is very difficult.

Case presentation. We report the clinical course and histopathological picture of a 10-week-old growing pig following experimental intravenous infection with S. suis serotype 9. The piglet showed rapid onset of severe clinical signs of meningitis 11 days post-intravenous challenge following prime-booster vaccination. Histopathological findings revealed a diffuse fibrinosuppurative leptomeningitis. Additionally, a polyphasic endocarditis valvularis thromboticans with numerous bacterial colonies was diagnosed. Bacteriological culture of the brain and the mitral valve confirmed association with the challenge strain. However, virulent serotype 2 and 9 strains were killed in the blood of this piglet ex vivo prior experimental infection.

Conclusion. Endocarditis induced by S. suis infection might develop and persist despite the presence of high specific bactericidal activity in the blood. Severe leptomeningitis is a putative sequela of such an endocarditis.
Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil
Authors: Everall Izzy , Nogueira Christiane Lourenço , Bryant Josephine M , Sánchez-Busó Leonor , Chimara Erica , Duarte Rafael da Silva , Ramos Jesus Pais , Lima Karla Valéria Batista , Lopes Maria Luíza , Palaci Moises , Kipnis Andre , Monego Fernanda , Floto R. Andres , Parkhill Julian , Leão Sylvia Cardoso , Harris Simon R
Published: May 2017

An epidemic of post-surgical wound infections, caused by a non-tuberculous mycobacterium, has been on-going in Brazil. It has been unclear whether one or multiple lineages are responsible and whether their wide geographical distribution across Brazil is due to spread from a single point source or is the result of human-mediated transmission. 188 isolates, collected from nine Brazilian states, were whole genome sequenced and analysed using phylogenetic and comparative genomic approaches. The isolates from Brazil formed a single clade, which was estimated to have emerged in 2003. We observed temporal and geographic structure within the lineage that enabled us to infer the movement of sub-lineages across Brazil. The genome size of the Brazilian lineage was reduced relative to most strains in the three subspecies of Mycobacterium abscessus and contained a novel plasmid, pMAB02, in addition to the previously described pMAB01 plasmid. One lineage, which emerged just prior to the initial outbreak, is responsible for the epidemic of post-surgical wound infections in Brazil. Phylogenetic analysis indicates that multiple transmission events led to its spread. The presence of a novel plasmid and the reduced genome size suggest that the lineage has undergone adaptation to the surgical niche.
Structure of the Cpf1 endonuclease R-Loop complex after target DNA cleavage
Authors: Stella Stefano , Alcón Pablo , Montoya Guillermo
Published: April 2017

Cpf1 is a single RNA-guided endonuclease of class 2 type V CRISPR-Cas system, emerging as a powerful genome editing tool1,2. To provide insight into its DNA targeting mechanism, we have determined the crystal structure ofFrancisella novicidaCpf1 (FnCpf1) in complex with the triple strand R-loop formed after target DNA cleavage. The structure reveals a unique machinery for target DNA unwinding to form a crRNA-DNA hybrid and a displaced DNA strand inside FnCpf1. The protospacer adjacent motif (PAM) is recognised by the PAM interacting (PI) domain. In this domain, the conserved K667, K671 and K677 are arranged in a dentate manner in a loop-lysine helix-loop motif (LKL). The helix is inserted at a 45° angle to the dsDNA longitudinal axis. Unzipping of the dsDNA in a cleft arranged by acidic and hydrophobic residues facilitates the hybridization of the target DNA strand with crRNA. K667 initiates unwinding by pushing away the guanine after the PAM sequence of the dsDNA. The PAM ssDNA is funnelled towards the nuclease site, which is located 70 Å away, through a hydrophobic protein cavity with basic patches that interact with the phosphate backbone. In this catalytically active conformation the PI and the helix-loop-helix (HLH) motif in the REC1 domain adopt a “rail shape” and “flap-on” conformations, channelling the PAM strand into the cavity. A steric barrier between the RuvC-II and REC1 domains forms a “septum” that separates the displaced PAM strand and the crRNA-DNA hybrid, avoiding re-annealing of the DNA. Mutations in key residues reveal a novel mechanism to determine the DNA product length, thereby linking the PAM and DNAase sites. Our study reveals a singular working model of RNA-guided DNA cleavage by Cpf1, opening up new avenues for engineering this genome modification system2-4.
Perceptual Expectations do not Modulate Image Repetition Effects as Measured by Event-Related Potentials
Authors: Feuerriegel Daniel , Churches Owen , Coussens Scott , Keage Hannah A. D.
Published: May 2017

Repeated stimulus presentation leads to complex changes in cortical neuron response properties, commonly known as repetition suppression or stimulus-specific adaptation. Circuit-based models of repetition suppression provide a framework for investigating patterns of repetition effects that propagate through cortical hierarchies. To further develop such models it is critical to determine whether (and if so, when) repetition effects are modulated by top-down influences, such as those related to perceptual expectation. We investigated this by presenting pairs of repeated and alternating face images, and orthogonally manipulating expectations regarding the likelihood of stimulus repetition. Event-related potentials (ERPs) were recorded from n=39 healthy adults, to map the spatiotemporal progression of stimulus repetition and expectation effects, and interactions between these factors, using mass univariate analyses. We also tested whether the ability to predict unrepeated (compared to repeated) face identities could influence the magnitude of observed repetition effects, by presenting separate blocks with predictable and unpredictable alternating faces. Multiple repetition and expectation effects were identified between 99-800ms from stimulus onset, which did not statistically interact at any point. Repetition effects in blocks with predictable alternating faces were smaller than in unpredictable alternating face blocks between 117-179ms and 506-652ms, and larger between 246-428ms. ERP repetition effects appear not to be modulated by perceptual expectations, supporting separate mechanisms for repetition and expectation suppression. However, previous studies that aimed to test for repetition effects, in which the repeated (but not unrepeated) stimulus was predictable, are likely to have conflated repetition and stimulus predictability effects.

Highlights

- ERP face image repetition effects were apparent between 99-800ms from stimulus onset

- Expectations of stimulus image properties did not modulate face repetition effects

- The predictability of unrepeated stimuli influenced repetition effect magnitudes
An anisotropic attraction model for the diversity and robustness of cell arrangement in nematodes
Authors: Yamamoto Kazunori , Kimura Akatsuki
Published: May 2017

In early embryogenesis stages in animals, cells are arranged into a species-specific pattern in a robust manner. The cell arrangement patterns are diverse, even among close relatives. We evaluated how the diversity and robustness are achieved in developing embryos. We succeeded in reproducing different patterns of cell arrangements observed in various nematode species usingCaenorhabditis elegansembryos by changing the eggshell shapes. This implies that the diversity of cell arrangements can be explained by differences in a shape parameter. Additionally, we found that the cell arrangement was robust against eggshell deformation. Computational modeling revealed that, in addition to repulsion forces, attraction forces are sufficient for this robustness. Genetic perturbation experiments demonstrated that attraction forces derived from cell adhesion are necessary for the robustness. The proposed model accounts for both diversity and robustness of cell arrangements and contributes to our understanding of how diversity and robustness are achieved in developing embryos.
A high resolution atlas of gene expression in the domestic sheep (Ovis aries)
Authors: Clark EL , Bush SJ , McCulloch MEB , Farquhar IL , Young R , Lefevre L , Pridans C , Tsang HG , Wu C , Afrasiabi C , Watson M , Whitelaw CB , Freeman TC , Summers KM , Archibald AL , Hume DA
Published: May 2017

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. TheOvis ariesreference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.

Author Summary

Sheep are ruminant mammals kept as livestock for the production of meat, milk and wool in agricultural industries across the globe. Genetic and genomic information can be used to improve production traits such as disease resiliance. The sheep genome is however missing important information relating to gene function and many genes, which may be important for productivity, have no informative gene name. This can be remedied using RNA-Sequencing to generate a global expression profile of all protein-coding genes, across multiple organ systems and developmental stages. Clustering genes based on their expression profile across tissues and cells allows us to assign function to those genes. If for example a gene with no informative gene name is expressed in macrophages and is found within a cluster of known macrophage related genes it is likely to be involved in macrophage function and play a role in innate immunity. This information improves the quality of the reference genome and provides insight into biological processes underlying the complex traits that influence the productivity of sheep and other livestock species.
In uterodiffusion tensor imaging of the fetal brain: a reproducibility study
Authors: Jakab András , Tuura Ruth O`Gorman , Kellenberger Christian , Scheer Ianina
Published: May 2017

Our purpose was to evaluate the within-subject reproducibility of in uterodiffusion tensor imaging (DTI) metrics and the visibility of major white matter structures.

Images for 30 fetuses (20-33. postmenstrual weeks, normal neurodevelopment: 6 cases, cerebral pathology: 24 cases) were acquired on 1.5T or 3.0T MRI. DTI with 15 diffusion-weighting directions was repeated three times for each case, TR/TE: 2200/63 ms, voxel size: 1*1 mm, slice thickness: 3-5 mm, b-factor: 700 s/mm2. Reproducibility was evaluated from structure detectability, variability of DTI measures using the coefficient of variation (CV), image correlation and structural similarity across repeated scans for six selected structures. The effect of age, scanner type, presence of pathology was determined using Wilcoxon rank sum test.

White matter structures were detectable in the following percentage of fetuses in at least two of the three repeated scans: corpus callosum genu 76%, splenium 64%, internal capsule, posterior limb 60%, brainstem fibers 40% and temporooccipital association pathways 60%. The mean CV of DTI metrics ranged between 3% and 14.6% and we measured higher reproducibility in fetuses with normal brain development. Head motion was negatively correlated with reproducibility, this effect was partially ameliorated by motion-correction algorithm using image registration. Structures on 3.0 T had higher variability both with- and without motion correction.

Fetal DTI is reproducible for projection and commissural bundles during mid-gestation, however, in 16-30% of the cases, data were corrupted by artifacts, resulting in impaired detection of white matter structures. To achieve robust results for the quantitative analysis of diffusivity and anisotropy values, fetal-specific image processing is recommended and repeated DTI is needed to ensure the detectability of fiber pathways.

Abbreviations

AD

axial diffusivity;

CCA

corpus callosum agenesis;

CV

coefficient of variation,

DTI

diffusion tensor imaging;

FA

fractional anisotropy;

GW

gestational week;

MD

mean diffusivity;

RD

radial diffusivity;

ROI

region of interest;

SSIM

structural similarity index
Identifying differential isoform abundance with RATs: a universal tool and a warning
Authors: Froussios Kimon , Mourão Kira , Simpson Gordon G. , Barton Geoffrey J. , Schurch Nick J.
Published: May 2017

Motivation

The biological importance of changes in gene and transcript expression is well recognised and is reflected by the wide variety of tools available to characterise these changes. Regulation via Differential Transcript Usage (DTU) is emerging as an important phenomenon. Several tools exist for the detection of DTU from read alignment or assembly data, but options for detection of DTU from alignment-free quantifications are limited.

Results

We present an R package named RATs – (Relative Abundance of Transcripts) – that identifies DTU transcriptome-wide directly from transcript abundance estimations. RATs is agnostic to quantification methods and exploits bootstrapped quantifications, if available, to inform the significance of detected DTU events. RATs contextualises the DTU results and shows good False Discovery performance (median FDR ≤0.05) at all replication levels. We applied RATs to a human RNA-seq dataset associated with idiopathic pulmonary fibrosis with three DTU events validated by qRT-PCR. RATs found all three genes exhibited statistically significant changes in isoform proportions based on Ensembl v60 annotations, but the DTU for two were not reliably reproduced across bootstrapped quantifications. RATs also identified 500 novel DTU events that are enriched for eleven GO terms related to regulation of the response to stimulus, regulation of immune system processes, and symbiosis/parasitism. Repeating this analysis with the Ensembl v87 annotation showed the isoform abundance profiles of two of the three validated DTU genes changed radically. RATs identified 414 novel DTU events that are enriched for five GO terms, none of which are in common with those previously identified. Only 141 of the DTU evens are common between the two analyses, and only 8 are among the 248 reported by the original study. Furthermore, the original qRT-PCR probes no longer match uniquely to their original transcripts, calling into question the interpretation of these data. We suggest parallel full-length isoform sequencing, annotation pre-filtering and sequencing of the transcripts captured by qRT-PCR primers as possible ways to improve the validation of RNA-seq results in future experiments.

Availability

The package is available through Github at https://github.com/bartongroup/Rats.