bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations
Authors: Renzette Nicholas , Pfeifer Susanne P. , Matuszewski Sebastian , Kowalik Timothy F. , Jensen Jeffrey D. 
Published: January 2017

ABSTRACT
Intrahost and interhost assessments of viral diversity are often treated as measures of separate and distinct evolutionary processes, with numerous investigations reporting seemingly incompatible results between the two. For example, in human cytomegalovirus, the nucleotide diversity estimates are 10-fold higher for interhost data, while the number of segregating (i.e., polymorphic) sites is 6-fold lower. These results have been interpreted as demonstrating that sampled intrahost variants are strongly deleterious. In reality, however, these observations are fully consistent with standard population genetic expectations. Here, we analyze published intra- and interhost data sets within this framework, utilizing statistical inference tools to quantify the fitness effects of segregating mutations. Further, we utilize population level simulations to clarify expectations under common evolutionary models. Contrary to common claims in the literature, these results suggest that most observed polymorphisms are likely nearly neutral with regard to fitness and that standard population genetic models in fact well predict observed levels of both intra- and interhost variability.

IMPORTANCE
With the increasing number of evolutionary virology studies examining both intrahost and interhost patterns of genomic variation, a number of seemingly incompatible results have emerged, revolving around the far greater level of observed intrahost than interhost variation. This has led many authors to suggest that the great majority of sampled within-host polymorphisms are strongly deleterious. Here, we demonstrate that there is in fact no incompatibility of these results and, indeed, that the vast majority of sampled within-host variation is likely neutral. These results thus represent a major shift in the current view of observed viral variation.
Channel-Inactivating Mutations and Their Revertant Mutants in the Envelope Protein of Infectious Bronchitis Virus
Authors: To Janet , Surya Wahyu , Fung To Sing , Li Yan , Verdià-Bàguena Carmina , Queralt-Martin Maria , Aguilella Vicente M. , Liu Ding Xiang , Torres Jaume 
Published: January 2017

ABSTRACT

It has been shown previously in the severe acute respiratory syndrome coronavirus (SARS-CoV) that two point mutations, N15A and V25F, in the transmembrane domain (TMD) of the envelope (E) protein abolished channel activity and led to
in vivo
attenuation. Pathogenicity was recovered in mutants that also regained E protein channel activity. In particular, V25F was rapidly compensated by changes at multiple V25F-facing TMD residues located on a neighboring monomer, consistent with a recovery of oligomerization. Here, we show using infected cells that the same mutations, T16A and A26F, in the gamma-CoV infectious bronchitis virus (IBV) lead to, in principle, similar results. However, IBV E A26F did not abolish oligomer formation and was compensated by mutations at N- and C-terminal extramembrane domains (EMDs). The C-terminal EMD mutations clustered along an insertion sequence specific to gamma-CoVs. Nuclear magnetic resonance data are consistent with the presence of only one TMD in IBV E, suggesting that recovery of channel activity and fitness in these IBV E revertant mutants is through an allosteric interaction between EMDs and TMD. The present results are important for the development of IBV live attenuated vaccines when channel-inactivating mutations are introduced in the E protein.

IMPORTANCE
The ion channel activity of SARS-CoV E protein is a determinant of virulence, and abolishment of channel activity leads to viral attenuation. E deletion may be a strategy for generating live attenuated vaccines but can trigger undesirable compensatory mechanisms through modifications of other viral proteins to regain virulence. Therefore, a more suitable approach may be to introduce small but critical attenuating mutations. For this, the stability of attenuating mutations should be examined to understand the mechanisms of reversion. Here, we show that channel-inactivating mutations of the avian infectious bronchitis virus E protein introduced in a recombinant virus system are deficient in viral release and fitness and that revertant mutations also restored channel activity. Unexpectedly, most of the revertant mutations appeared at extramembrane domains, particularly along an insertion specific for gammacoronaviruses. Our structural data propose a single transmembrane domain in IBV E, suggesting an allosteric interaction between extramembrane and transmembrane domains.
Study on sapphire microstructure processing technology based on wet etching
Authors: Shang Ying-Qi , Qi Hong , Ma Yun-Long , Wu Ya-Lin , Zhang Yan , Chen Jing 
Published: January 2017

Aiming at the problem that sapphire surface roughness is quite large after wet etching in sapphire microstructure processing technology, we optimize the wet etching process parameters, study on the influences of concentration and temperature of etching solution and etching time on the sapphire surface roughness and etching rate, choose different process parameters for the experiment and test and analyze the sapphire results after wet etching. Aiming at test results, we also optimize the process parameters and do experiment. Experimental results show that, after optimizing the parameters of etching solution, surface roughness of etched sapphire is 0.39 nm, effectively with reduced surface roughness, improved light extraction efficiency and meeting the production requirements of high-precision optical pressure sensor.
Depression literacy in women attending university hospital clinics in Riyadh Saudi Arabia
Authors: Siddiqui Amna Rehana , Mahasin Sarah , Alsajjan Roa , Hassounah Marwah , Alhalees Zeinah , AlSaif Norah , Alosaimi Fahad D. , AlQuaiz AlJohara 
Published: January 2017

Background: Depression literacy in general population constitutes an ability to understand depression, with knowledge of disease, its risk factors and symptoms. High levels of depression literacy promote early intervention, potentially reducing related disability. Aim: This study investigated the depression literacy in women visitors to clinics of a tertiary care hospital in Riyadh, Saudi Arabia. Methods: Women of 18 and more years were surveyed during their visit to primary and other healthcare clinics of a public hospital in Riyadh. Knowledge on depression symptoms, causes and management approaches identified depression literate women scoring more than 30 points on a 42-item tool. Results: Of the 409 participants, 65.5% were depression literate, 50% educated as college and above, 64.3% married, 50.7% housewives, 62.4% reported use of multiple information sources (range, 0–8) and had a mean age of 34.9 (standard deviation ( SD), 12.4) years. In a logistic regression model, participants scoring less than 30 for depression literacy were significantly associated with women having less than college-level education, divorced marital status and use of decreasing number of learning resources. Conclusion: Women with low education divorced; using fewer information sources need specific considerations by healthcare providers for assessment of depressive disorders in this setting.
Pathogen Sequence Signature Analysis (PSSA): A software tool for analyzing sequences to identify microorganism genotypes
Authors: Salvatierra Karina , Florez Hector 
Published: January 2017

Introduction The chikungunya virus (CHIKV) is an arbovirus vectored by Aedes mosquitoes that infects humans in tropical and sub-tropical areas of Asia and Africa. Recently, outbreaks have been reported in tropical and sub-tropical areas of countries that were previously unaffected (e.g., Brazil, Colombia). Currently, the following geographical genotypes have been identified through phylogenetic analysis of CHIKV E1 gene sequences: the West African (WAf), East/Central/South African (ECSA), and Asian genotypes. Outbreaks in a geographical area can happen with the same or different genotypes. Determining which genotypes are circulating in an outbreak is important for public health management. Objectives To create a computer-based system available online that is suitable for detecting changes in CHIKV nucleotide and amino acid sequences and identifying their corresponding geographical genotype. Methods We used several computer frameworks, tools, programming languages, algorithms, and infrastructure systems to build a software tool that analyzes changes in nucleotide and amino acid sequences and identifies different geographical genotypes through phylogenetic analysis. Results We have built an online software tool called Pathogen Sequence Signature Analysis (PSSA) that allows researchers to analyze nucleotide and amino acid sequence variations between sample CHIKV sequences taken from infected patients and obtained through conventional Sanger sequencing, to identify their corresponding geographical genotype. Conclusion PSSA is able to analyze sequences in a simple and effective manner, and includes proper documentation (i.e., UML diagrams) and also basic examples that serve to test the algorithm. Furthermore, PSSA provides various ways to visualize the data in order to aid understanding and interpretation of results. Results provided by PSSA will be useful for the identification of circulating CHIKV genotypes and public health surveillance. PSSA is available at: http://pssa.itiud.org.
Optimizing postoperative handover to the intensive care unit at a tertiary centre
Authors: Kumar Shankar , McKean Andrew R , Ramwell Andrew , Johnston Carolyn , Leaver Susannah 
Published: January 2017

Background: Comprehensive handover of patients transferred from operating theatre to the intensive care unit is crucial in ensuring ongoing quality and safety of care. Handover in this setting poses unique challenges, yet few studies have considered or tested approaches to improve the process. A quality improvement project was undertaken to assess and improve the quality of information transfer during the handover of postoperative patients to the general intensive care unit at a tertiary centre. Methods: This quality improvement project considered all postoperative patients aged 18 years and over, using the plan-do-study-act (PDSA) approach, over a 3-month period in 2015. Baseline audit encompassing intraoperative details (allergies, grade of intubation, estimated blood loss, difficulties and complications) and the postoperative plan (analgesia, thromboprophylaxis, antibiotics and their proposed duration and nutrition) was undertaken to define the extent of the clinical problem. Changes were implemented over two cycles, centred around a novel checklist, and the transfer of information was re-audited after each cycle. Results: Baseline audit (n=30) revealed a need for improvement across all domains. In PDSA cycle 1, a novel checklist was introduced which led to global improvement across all areas with performance exceeding 70% in all but three out of nine domains (n=33). Engaging key stakeholders (PDSA cycle 2) resulted in overall improvement from baseline but decreased performance in just under half of domains in comparison to PDSA cycle 1 (n=31). Conclusions: Successful implementation of a series of simple interventions resulted in more effective handover of postoperative patients admitted to an intensive care unit. Sustained long-term improvement is a major challenge and can only be achieved with the global engagement of all staff and incorporation of changes into routine clinical practice.
Real men: Representations of masculinity in Iranian cinema
Authors: Gow Christopher 
Published: January 2017

Abstract
The article examines different representations of masculinity in Iranian cinema, using Shahin Gerami’s essay ‘Mullahs, martyrs, and men: Conceptualizing masculinity in the Islamic Republic of Iran’ as the basis for its analysis. The article looks at examples of post-revolutionary Iranian cinema – in particular Rakhshan Bani-Etemad’s Nargess (1992) and Kamal Tabrizi’s The Lizard (2002) – featuring male characters that can be considered in light of the masculine archetypes that Gerami identifies. This analysis is prefaced by a brief consideration of representations of masculinity in post-revolutionary Iranian cinema, in particular Masud Kimiai’s Dash Akol (1971) as an example of the luti or ‘tough guy’ genre. By considering these different representations of masculinity, the article aims to address the gender imbalance in recent studies of Iranian cinema, most of which focus predominantly or indeed exclusively on the representation of women, as well as challenge stereotypes of Iranian and/or Middle Eastern masculinity more generally.
A Self that hides in Others: The cosmopolitan vision of Abbas Kiarostami
Authors: Khatami Nojang 
Published: January 2017

Abstract
Given his immense influence on cinema in his homeland, much has been said about Abbas Kiarostami as a quintessentially Iranian director and artist. Yet his most recent films – Shirin (2008), Certified Copy (2010) and Like Someone in Love (2012) – offer interesting terrain for exploring how he deals with love and empathy beyond borders. This article examines these recent films to argue that Kiarostami’s growing cosmopolitan vision encompasses one way of going beyond the notion of the gaze as a mode of objectification and domination. Relying heavily on the power of the image, his is an aesthetic that invites care and empowerment, transcending violence and objectification by teaching the audience to look in new ways.
Performing Lampedusa in Miraculi: Thoughts on theatre and research in a saturated field-site
Authors: Zagaria Valentina 
Published: January 2017

Abstract
In the summer of 2011 I carried out ethnographic research on the island of Lampedusa on the ways in which those who lose their lives on their journeys to Europe are buried and cared for by Lampedusans. In September 2013 I returned to the island with seven theatre makers from the devised theatre school Jacques Lecoq to carry out a month of collaborative fieldwork research. The main idea of the project was to employ anthropological methods, observation and immersion in people’s daily routines to develop a performance about life on this frontier island. By focusing on people’s memories and on understanding what the everyday involves at the edges of Europe, we wished to address bigger questions of belonging and responsibility. Our group fieldwork developed into a theatre show, Miraculi. This article explores the different stages of the project and examines the ethical questions and methods, both theatrical and anthropological, employed along the way, in the hope of contributing to thinking through the significance of artistic projects and collaborative research in over-mediatized and saturated field-sites.
Tales of Journeys
Authors: Mohamad Ali Zakaria , Yimer Dagmawi , Aman Mahamed , Ghermandi Gabriella 
Published: January 2017

Abstract
Extract from an unpublished travel diary
(translated from Italian by Valentina Zagaria)

Names and bodies: Tales from across the sea

Return to Lampedusa
(translated from Italian by Rose Campbell)

Melkam Amlak
(translated from Italian by Rose Campbell)
Glamour labour in the Age of Kardashian
Authors: Wissinger Elizabeth 
Published: January 2017

Abstract
Viewed through the lens of the Kardashians as glamour labourers, this article examines the Kardashian phenomenon as it unfurls in a changing labour market, where glamour is becoming a common aspiration, no longer the domain of a privileged few. My analysis reveals how Kim Kardashian exemplifies the process by which the fashionably cool’s ever-morphing ideal seduces publics into chasing it, pulling publics into a highstakes game in which few realize exactly what they are losing. I argue that practices of no-holds-barred sharing and giving up privacy online are normalized, and presented as the ticket to achieving glamour, visibility and social acceptance.
How do we talk about fashion in Italy? The big players and independent publishers from 2000 to today: Transformations and orientations
Authors: Martina Marta 
Published: January 2017

Abstract
The article wants to shine a light on new orientations in contemporary fashion media in order to begin to understand the new playing field for the journalistic system from the point of view of the publishing economy. In the face of a global redefinition of the language, which has changed thanks to the entry into the press and publishing market of new subjectivity and communication platforms, the media shifts lead fashion journalism and publishing increasingly towards hybridization with contemporary audio-visual languages. The examples we will set out concern publishing projects that are being reconfigured as multimedia systems that hybridize the language of cinema, television, advertising, video games and interactive platforms. This article will begin by analysing how fashion, commerce and consumption have changed, acknowledging the transformation and evolution of the concept of Made in Italy since the mid-1990s to today and will focus on large and small players, independent publishing, praiseworthy online-only projects and the recent Italian experimentation of shoppable magazines, sponsored platforms and the return of house organs, which lead large and small publishers and brands to increasingly define themselves as media companies.
Sancaklar Mosque: Displacing the Familiar
Authors: Gür Berin F. 
Published: January 2017

Abstract
Studying contemporary mosque architecture necessitates dealing concurrently with both the past and the present. Burdens of the past cause a crisis at a point when architects attempt to design prayer spaces that avoid historicist references while attending to the religion’s liturgical requirements. This crisis indicates the moment at which architects are forced to become critical of what is preceding, and thus creates a challenging situation in the evolution of mosque architecture. This article takes the Sancaklar Mosque, designed by Emre Arolat Architecture (EAA), as its main object of research in order to assess this challenge. The Sancaklar Mosque presents a significant attempt to free mosque design from the prevailing formal practices observed in the majority of current mosques, by rejecting any clear reference to the historical mosque type and the use of any conventional mosque elements. However, I argue that while Sancaklar Mosque displays a clear break with the past, it is not ahistorical. The mosque suggests both a suspension of discussions on mosque architecture reduced to formal significations and historical prototypes, but also a different way of dealing with the past, which is, in this article, conceptualized as ‘defamiliarization’. The Sancaklar Mosque provides a significant example for a project in which familiar codified formal elements are displaced as a particular response to the challenge that architects face when designing religious buildings.
Subverting authority in illustrations of Dante’s Commedia
Authors: Collins Matthew 
Published: January 2017

Abstract
In this article, illustrations of Dante’s Commedia are viewed from the particular angle of textual subversion, which increased in degree over time. After beginning with a consideration of Dante’s own subversive habits in the context of the medieval literary world in order to highlight the fact that illustrators who visually undermined the letter of the text were in ironic harmony with the spirit of this work, the article turns to instances of late medieval and early modern illuminators and illustrators who, in these earlier stages, more subtly punctured the authoritative status which Dante’s text obtained almost immediately following its completion. The article moves on to show that by Dante’s renaissance in the eighteenth and nineteenth centuries illustrators felt far freer to blatantly meld their own imaginations with that of the original author, and by the mid-twentieth century, certain Commedia illustrations subjected text to image in varying ways.
Book Reviews
Authors: Vasek Cheri , Lynch Julie , Bartlett Djurdja 
Published: January 2017

Abstract

Fashioning Bollywood: The Making and Meaning of Hindi Film Costume, Clare M. Wilkinson-Weber (2014) London, New Delhi, New York and Sydney: Bloomsbury, 212 pp., 978-1-847-88697-2, p/bk

Shakespeare and Costume, Patricia Lennox and Bella Mirabella (2015) London and New York: Bloomsbury Arden Shakespeare, Bloomsbury Publishing, 291 pp., ISBN: 978-1-472-52507-9, h/bk

Modernism on Stage: The Ballets Russes and the Parisian Avant-garde, Juliet Bellow (2013) Surrey and Burlington: Ashgate Publishing, 280 pp., 67 b&w and 18 colour illustrations, ISBN: 978-1-409-40911-3, h/bk, ISBN: 978-1-138-24736-9, p/bk
Big possibility: Moscow, and musical theatre’s subjunctive dramaturgy
Authors: Dorsey Zachary A. 
Published: January 2017

Abstract
Grammatically speaking, many, many key songs and moments in musical theatre rely on the subjunctive, a grammatical mood that is used variously to express openness, hopefulness, wishfulness and possibility, as well as doubts, opinions, judgements and fears. Tevye’s ‘If I Were a Rich Man’ from Fiddler on the Roof is such a prime example of the subjunctive that it is often invoked in grammar guides and textbooks that seek to teach the proper use of this mood. This article explores the phenomenon that I describe as ‘subjunctive dramaturgy’ – the way that the spirit of the subjunctive mood underpins and crackles through the musical genre. I argue that particularly when amplified by speech, song and dance, the subjunctive mood helps to join character, actor and audience in a shared affective experience. One big intervention that subjunctive dramaturgy makes is that it encourages practitioners, audiences and musical theatre scholars to look beyond always pursuing temporal enquiries, such as with the musical’s often investigated nostalgic impulses or utopic drives. The subjunctive sits adjacent to time, and its study reveals the large meaning-making possibility and untapped potential in understanding the expansive, contradictory, messy and multi-directional nature and energies of the musical form. In this article, I analyse subjunctive moments from a number of classic American musicals, and I examine as case study Nick Salamone and Maury R. McIntyre’s Moscow, a seldom-produced musical from 1998 that I contend both reveals and teaches to its audience the merits of seeing and singing the subjunctive.
Book Reviews
Authors: Everett William A. , Karantonis Pamela , Laird Paul 
Published: January 2017

Abstract
SAVOY CURTAIN-RAISERS (MUSICA BRITANICA XCIX), CHRISTOPHER O’BRIEN (ED.) (2015) London: Stainer and Bell, 204 pp., ISBN: 978 0 85249 943 6, h/bk, £100
POSTOPERA: REINVENTING THE VOICE-BODY, JELENA NOVAK (2015) London: Ashgate Interdisciplinary Studies in Opera, 173 pp., ISBN: 9781472441034, h/bk, £60
AMERICAN MUSICAL THEATER, JAMES LEVE (2016) New York and Oxford: Oxford University Press, 426 pp., ISBN: 9780195379600, p/bk, $59.95