bluuebunny/crossref_metadata_2025 huggingface dataset:
An Ethical Consideration of Assessment in Music Education through the Lens of Levinas
Authors: Jourdan Kathryn , Finney John
Published: July 2019

This chapter takes as its starting point notions of music making as ethical encounter (Bowman, 2001) and as the exercise of hospitality (Higgins, 2007) in order to explore what ethical practice in music education might look like, through the philosophical writings of Emmanuel Levinas. It puts into question discourses of performativity, which may be understood as constraining and narrowing what we think of as “musical knowing” in the classroom. Thinking tools drawn from Levinas’s first major work, Totality and Infinity (1969), include notions of “practices of facing” and of “putting a world in common.” This conceptual lens enables an investigation of what it might mean for assessment in music education if we embraced Levinas’s radical openness—the breaking in of “infinity” into “totalizing” practices—bringing to light processes of music making, not simply the musical product, as well as the uniqueness of each pupil’s music making in relationship to others and to the Other, and capturing rich learning in the music classroom.
A Case for Integrative Assessment from a Freirian Perspective
Authors: Abrahams Frank
Published: July 2019

This chapter argues for the efficacy of integrative assessment to help teachers know if students have learned what they intended to teach them and how the teaching and learning have changed both student and teacher. Considering teaching and learning as a partnership between students and their teacher, integrative assessment focuses on the teacher, providing both formative and summative opportunities for teachers to be self-reflective and assess their teaching performance and its impact on student learning. Adding this component to the general discussion of assessment links the student/teacher and teacher/student paradigms in positive ways. Integrative assessment is framed by the ideas of Paulo Freire that teaching and learning are a partnership—and that learning takes place only when both teacher and student are changed. This type of assessment is different from the models of teacher evaluation that focus on quantitative analysis of formative and summative data and measures. These models connect outcomes to student grades and performance on standardized tests and are factored into teacher performance. The chapter argues that the most important goals of music education are to promote musical agency among students, empower musicianship, and foster the acquisition of what Freire labeled a critical consciousness. It then discusses four types of validity from the qualitative research tradition and uses them to inform questions teachers might ask themselves about the impact their teaching had on student learning.
Music Teacher Evaluation, Teacher Effectiveness, and Marginalized Populations
Authors: Salvador Karen , Krum Janice
Published: July 2019

While the Every Student Succeeds Act (ESSA) does not explicitly require teacher evaluation, both ESSA and the Higher Education Act (HEA) require states to evaluate teacher quality and effectiveness for reports regarding factors such as educational equity and teacher licensure program evaluation. Moreover, states are heavily invested in evaluating teacher effectiveness, and rhetoric in federal, state, and local governance revolves around eliminating “bad teachers,” so teacher evaluation will continue. Ostensibly, teacher evaluation is intended to increase teacher effectiveness and student achievement. This chapter argues that standardized, high-stakes teacher evaluation reduces music teacher effectiveness, particularly with regard to inclusion and cultural responsiveness. It begins with a brief critical review of the literature on music teacher evaluation, marginalized populations in school music education, and equitable and inclusive practices in the music classroom. It then uses fictionalized vignettes to illustrate an analysis of the cognitive dissonances and perverse incentives inherent in music teacher evaluation and how they manifest in three broad categories: (1) contributing to the gap between theory and practice; (2) misusing measurement tools; and (3) forcing teachers to remain in the status quo, unable to stray from formulaic “markers of effectiveness” to take the risks necessary for the creative, innovative work of inclusion and cultural responsiveness. The chapter concludes with specific suggestions for music teachers who wish to resist these effects of teacher evaluation on their instruction.
Charting the Emergence of the Cultural from the Cognitive with Agent-Based Modeling
Authors: Shaw Lynette
Published: July 2019

This chapter provides an overview of agent-based modeling (ABM), a computational method that allows researchers to simulate how macro-level phenomena spontaneously arise from micro-level interactions, and examines how sociologists might apply it to chart the emergence of cultural phenomena from individual cognitive processing. After providing some historical context for the concepts of “emergence” and the “micro-to-macro” transition in social theory and summarizing contributions ABM has already made in this arena, this work makes a case for how cognitive sociology might employ ABM toward the end of developing new, nonrational microfoundations for social theory and lays out the argument for why it should. The chapter concludes by offering a brief introduction to the basics of ABM design along with an overview of resources available to researchers interested in getting started with it.
Foregrounding and Backgrounding
Authors: Zerubavel Eviatar
Published: July 2019

This chapter examines the sociocognitive act of subverting the conventional semiotic asymmetry between what we culturally mark and what is habitually left unmarked and thereby assumed by default and thus taken for granted. Focusing on the mental processes of foregrounding and backgrounding (both separately and when they are combined), it highlights the politics of cognition as manifested in art, humor, academia, as well as everyday life.
War Widows and Welfare Queens
Authors: Battle Brittany Pearl
Published: July 2019

This chapter examines the sociocognitive dimensions of cultural categorizations of deservingness. The social issue of poverty has been a persistent source of debate in the American system of policy development, influenced by conceptual distinctions between the “haves” and “have-nots,” “working moms” and “unemployed dads,” and the “deserving poor” and the “undeserving poor.” Although there is a wealth of literature discussing the ideological underpinnings of stratification systems, these discussions often focus on categorical distinctions between the poor and the nonpoor, with much less discussion of distinctions made among the poor. Moreover, while scholars of culture and policy have long referenced the importance of cultural categories of worthiness in policy development, the theoretical significance of these distinctions has been largely understudied. I expand the discourse on the relationship between cultural representations of worth and social welfare policy by exploring how these categories are conceptualized. Drawing on analytical tools from a sociology of perception framework, I create a model that examines deservingness along continuums of morality and eligibility to highlight the taken-for-granted cultural subtleties that shape perceptions of the poor. I focus on social filters created by norms of poverty, welfare, and the family to explore how the deserving are differentiated from the undeserving.
Cognitive Migrations
Authors: DeGloma Thomas , Johnston Erin F.
Published: July 2019

This chapter explores the ways individuals account for cognitive migrations—significant changes of mind and consciousness that are often expressed as powerful discoveries, transformative experiences, and newly embraced worldviews. It outlines three ideal typical forms of cognitive migration: awakenings, self-actualizations, and ongoing quests. Building on prior approaches to such personal transformations, it develops the notion of cognitive migration to argue the following set of interrelated points. First, cognitive migrations take autobiographical form, which is to say they manifest as the narrative identity work of individuals who undergo them. Second, such narrative identity work provides a reflexive foundation for an individual’s understanding of self and identity in relation to other possible selves and identities—for seeing oneself as a relationally situated character. Third, individuals who articulate cognitive migrations use the plot structure and cultural coding at the root of their narratives to express their allegiance to a new sociomental community. They thereby take on new cognitive norms and identity-defining conventions while rejecting potential alternatives, locating themselves within a broader sociomental field. The spatial metaphor of cognitive migrations draws explicit attention to the broader sociomental field in which such radical changes of mind take place. Finally, such narrative identity work links self-understandings to the often-contested meanings of broadly relevant issues, events, and experiences; when individuals account for their cognitive migrations, they also advance claims that reach well-beyond their personal lives.
Silence and Collective Memory
Authors: Vinitzky-Seroussi Vered , Teeger Chana
Published: July 2019

This chapter elaborates on prior work to outline the role of silence not only in forgetting but also in memory. It documents two forms of silence: overt silence and covert silence and discusses how each can be used to enhance either memory or forgetting. In its overt manifestations, silence is characterized by a complete absence of speech. Such silence can foster forgetting by obliterating any mention of particular events or people. Overt silences, however, can also foster memory by demarcating a sacred space for quiet contemplation. Covert silences, on the other hand, inhere in—and are often veiled by—much mnemonic talk. These silences are found in commemorative activities where agents of memory want to recollect the past while minimizing its potentially conflictual elements. They can also be used by agents of forgetting who wish to erase the past while presenting the appearance of commemorating it. The chapter concludes by discussing the various ways in which each of these forms of silence can be broken. In outlining these processes, it highlights the central role played by silence in both collective memory and forgetting.
The Old One-Two
Authors: Vaisey Stephen , Frye Margaret
Published: July 2019

This chapter argues that an important item on the agenda for the ongoing dialogue between cognitive scientists and microsociologists is how to replace Cartesian mind-body dualism. Although it takes the position that strict mind-body dualism should be laid to rest, it argues that replacing this dichotomy with a holistic theory risks making it harder for researchers to see analytic distinctions that make a real difference. It uses examples from Loïc Wacquant’s Body and Soul to illustrate the argument that sociologists should replace the old dualism with a new, improved one that incorporates cognitive science regarding differences between habitual, embodied cognition and intentional, discursive cognition. This will help microsociologists and cognitive scientists be in the best possible position to understand, enrich, and improve each other’s work.
Little Shop of Horrors
Authors: Westover Jonas
Published: July 2019

This chapter examines the movie adaptation of Little Shop of Horrors. The musical was a huge success Off-Broadway and it would have been natural to move it to a larger, Broadway theatre. But David Geffen, who had underwritten the musical’s move from its original, ninety-eight-seat Off-Off-Broadway theatre, the WPA, to the Off-Broadway Orpheum, was now working in the movie industry, developing projects for Warner Bros., thus providing lyricist Howard Ashman and composer Alan Menken with the unusual opportunity to develop a film adaptation of Little Shop. The film reconciles a broad understanding of what made the show work on the stage (by not allowing the landscape of the movie to become too large) with the need to accommodate a different medium (songs were dropped and new ones added). The movie was a huge success, showing how the behind-the-scenes decision to move to film rather than a Broadway theatre (as happened with the Off-Broadway Hair, for example) sustained Little Shop’s commercial and critical success.
Into the Woods from Stage to Screen
Authors: Horowitz Mark Eden
Published: July 2019

This chapter addresses the production of the movie adaptation of Into the Woods. It exploits interviews with composer-lyricist Stephen Sondheim, director Rob Marshall, screenwriter James Lapine (also the stage librettist and director), orchestrator Jonathan Tunick, and musical director Paul Gemignani, most of whom were also involved with the original Broadway production, to offer insights into the process of putting the ultimate fairy tale on the big screen. The interviews reveal surprising aspects of the movie’s production, such as the fact that the songs were recorded three different ways: a full orchestra track for the singers to rehearse to, a studio recording with the singers and orchestra together, and live on-set recordings. The final soundtrack includes a mixture of these three options, providing a solution to the age-old problem of how to make singing in film musicals appear natural. The chapter also examines why some of the songs were cut, plus other intriguing and poignant insights into changes made for the film adaptation.
Flamboyance, Exuberance, and Schmaltz
Authors: McQueen Amanda
Published: July 2019

This chapter focuses on the roadshow release of the movie adaptation of Half a Sixpence. The chapter reads the film as a product of its immediate industrial context: it was one of a number of Broadway-Hollywood adaptations that were intended as part of a risk-reduction strategy, it was spectacular and relatively faithful to its stage version, and it had an unusual and markedly contemporary visual style, akin to that found in the low-budget, youth oriented films of the Hollywood Renaissance. Thus, although the movie was no hit, it was not a completely misguided production: the chapter explains that instead it was intended to address the musical genre’s need to adapt to a new industrial climate in order to prolong its marketability into the 1970s.
Cole Porter’s List Songs on Stage and Screen
Authors: Eisen Cliff
Published: July 2019

This chapter focuses on Cole Porter’s list songs on stage and screen. In his private life, Porter liked to make lists of things: the chapter uncovers a list made by Porter of things he required to be provided during the out-of-town tryout of one of his musicals, as well as requests for lists of words and ideas for songs from Can-Can. The list song is a staple of most of Porter’s shows, with key examples including ‘You’re the Top’ and ‘Let’s Do It,’ but their transposition to the screen is not always straightforward. For example, the film adaptation of Kiss Me, Kate moves ‘Brush Up Your Shakespeare’ from a song delivered in front of the curtain to the audience in the theatre (literally a show stop) to a song performed in an alleyway to cheer up Fred. The chapter proposes that this contextual dramatic change from the general to the specific hints at a fundamental aspect of filmed musicals that is inimical to list songs: their separateness and staticness, their drawing of attention to themselves and to words rather than, primarily, visuals or the narrative of the film, and their potential open-endedness may all work against the notion of what a film does.
The Montage Connection between John Heartfield and László Lakner
Authors: Cuevas-Wolf Cristina
Published: July 2019

This article argues that during the 1960s the Hungarian conceptualist and painter László Lakner defined through his works a paradoxical, yet distinctive lineage of a New Leftist visual culture. Based in the tradition of transnational communist, antifascist visual expression, Lakner’s art responded and critiqued the communist regime in Eastern Europe during the 1960s. The German political photomonteur John Heartfield initiated such an alternative leftist visual language in Weimar Germany in his antifascist photomontages, published by the German magazine Arbeiter-Illustrierte Zeitung, to create a politically engaged viewer from within the communist international movement. This essay compares the work of Lakner and Heartfield to show how the montage connection between these two artists stemmed from a transnational cross-pollination between communist visual cultures in the West and East that shared an international and oppositional character informed by radical social movements in the thirties and sixties.
Visions and Visualization of Sustainability
Authors: Karpova Yulia
Published: July 2019

Throughout the 1970s, Soviet designers were increasingly concerned with environments rather than separate objects. By the end of the decade, they came to recognize sustainability as a crucial problem not only of market economies but also of socialist planned economies. This article brings to light an early attempt to practice environmentally affirmative design in the USSR: a design program for nationwide recycling infrastructure, launched in Leningrad in 1979. Drawing on archival sources, it shows how a team of Leningrad designers expressed a distinctly socialist approach to sustainability through a comprehensive visual form: the approach based on citizen responsibility as much as on the role of material objects as agents of social change. This never-implemented design program is considered here not as yet another socialist utopia, but as an original vision of mass mobilization through design, informed by the legacy of Russian avant-garde as much as by current Western design trends.
Critical Factors and Forces Influencing Higher Education in the Twenty-First Century
Authors: Drew Antony , Redding Gordon , Harley Trevor
Published: July 2019

This chapter acts as a bridge between the previous chapters which focus on education and societal evolution plus the main types of university seen in terms of strategic autonomy; and the following chapters which address the large-scale global changes and their operational implications, the management of universities in the new conditions, and the societal implications of the changing world of higher education. This chapter adopts a strategic management perspective to highlight the critical factors and forces affecting HE now and into the foreseeable future. By examining the external environment in terms of both the macro (external) environment and meso (more immediate) environment, it highlights the key factors and forces of which policy makers, government officials, leaders and managers in universities, industry and civic society need to be cognizant, if they are to ensure HE continues to be relevant to the twenty-first century.
Scholarship in the University
Authors: Barnett Ronald
Published: July 2019

The very idea of scholarship has taken something of a battering over recent years. In parallel, the term ‘scholarship’ itself—in the English language—has also faltered. This chapter explores this phenomenon but also examines the prospects for its re-energizing. Could it be that even if scholarship is becoming invisible at the moment, it might yet become more evident? The idea of scholarship is waning but perhaps it can emerge again as a possibly significant form of academic endeavour. It might even flower anew. That is the possibility that this chapter shall pursue here, and shall do so by advancing an idea of ecological scholarship.
Education and Technological Unemployment in the Fourth Industrial Revolution
Authors: Peters Michael A. , Jandrić Petar
Published: July 2019

This chapter explores the rapidly growing body of research around technological unemployment and asks: What is the role of higher education in the digital age when technological unemployment becomes the rule rather than the exception? It shows that educational solutions based on the concepts of human capital and homo economicus are unable to resolve the problem of technological unemployment, and concludes that contemporary education requires a non-supercessionist approach based on the figure of homo collaborans which fundamentally rethinks the concepts of work, education, and research. Finally, it blends the ‘open model of the digital university’ and the model of ‘creative university as digital public university’ with recent insights into technological unemployment and develops the non-supercessionist ‘model of education for the Fourth Industrial Revolution’ which may serve as a useful point of departure for further discussions in the field.
Educating for the Innovative Society
Authors: Krishna Venni V. , Chandra Nimesh
Published: July 2019

The growth and contribution of the Indian Institutes of Technology (IITs) from the 1950s symbolizes the foresight of a developing nation for educating a special cadre of engineering professionals towards building a modern, industrial society. Drawing inspiration from MIT, these institutes have given top priority to the selection of faculty and as well as students through a nationwide competitive examination. Though IITs constitute a small part of the higher education landscape, they play a very significant part in the knowledge-based society. One sector where IITs have made substantial contribution is information and communication technology (ICT) and related segments. IIT brand image became globally known through its alumni contribution in Silicon Valley. In India, IITs are seen as model institutions to be emulated not only in building a culture of research and innovation, but also in the modes of knowledge technology transfer and university–industry relationships.
Recent Trends in East and West University Governance
Authors: Donleavy Gabriel , Chen Kuan-Cheng
Published: July 2019

The universities in Hong Kong grew to have strong autonomy and academic freedom within the British tradition of the state-contracted university. China is now subtly pressuring them to conform to the Chinese HE ideal of the state-controlled hollow type. Tensions result as the incremental adjustments have been perceived by many scholars as subversive. In China a dual leadership system protects both the academic and the Party interests. In Hong Kong such a formula would appear to be in the making over time. There are different implications for the utilitarian sciences and potentially political humanities. The loss of societal openness in Hong Kong is matched by another form of hollowing in the West, where market-funded consumer-driven ‘skills factories’ now host a contest between traditional scholarship and managerialism.
Cycles of Evolution of Ideal Types of Universities
Authors: Gudkova Svetlana , Pikos Anna , Guminska Valentyna
Published: July 2019

Higher education across the globe is undergoing changes resulting from globalization, demographics, external pressure, and digital transformation. Polish universities are going through a process of transformation as well. They are yet to face significant challenges related to e.g. the increasing demographic low, problems with financing their activity, or the growing competition in the education services market. Universities have to become innovative and entrepreneurial to survive and compete effectively globally. An analysis of selected universities from Poland shows that they appear to be oriented towards e.g. serving the society, entrepreneurship, and establishing relationships with their environment. This suggests that there is a shift towards the entrepreneurial university model. But Polish universities, especially public ones, have little awareness of their strengths, which is a consequence of the model of higher education applied until recently.
Electronic cigarette use and suicidal behaviors among adolescents
Authors: Kim J S , Kim K
Published: June 2019

Background

The aim of this study was to investigate the association of the use of e-cigarettes, which are regarded as alternatives to traditional cigarettes and are easy to purchase, with suicidal behaviors in adolescents.

Methods

Data for 5405 middle and high school students aged 13–18 years who had used e-cigarettes were extracted from the 2016 Korean Youth Risk Behavior Web-Based Survey and analyzed using multiple logistic regression.

Results

Among those who used e-cigarettes for 1–30 days in the past 30 days, suicidal ideation (odds ratio [OR] = 1.58, 95% CI, 1.31–1.89), suicidal plans (OR = 2.44, 95% CI, 1.94–3.08), suicidal attempts (OR = 2.44, 95% CI, 1.85–3.22) and serious attempts (OR = 3.09, 95% CI, 1.51–6.32) were higher compared to those who did not use an e-cigarette in the past 30 days.

Conclusions

Suicidal behaviors are significantly higher among current adolescent e-cigarette smokers than adolescents who have not used an e-cigarette in the past 30 days. Therefore, comprehensive intervention is needed to protect adolescents’ mental health.
Depth and location influence prokaryotic and eukaryotic microbial community structure in New Zealand fjords
Authors: Tobias-Hünefeldt Sven P. , Wing Stephen R. , Espinel-Velasco Nadjejda , Baltar Federico , Morales Sergio E.
Published: June 2019

Systems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from inner to outer regions, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.
Genetic and functional diversification of chemosensory pathway receptors in mosquito-borne filarial nematodes
Authors: Wheeler Nicolas J , Heimark Zachary W , Airs Paul M , Mann Alexis , Bartholomay Lyric C , Zamanian Mostafa
Published: June 2019

Lymphatic filariasis (LF) afflicts over 60 million people worldwide and leads to severe pathological outcomes in chronic cases. The nematode parasites (Nematoda: Filarioidea) that cause LF require both arthropod (mosquito) intermediate hosts and mammalian definitive hosts for their propagation. The invasion and migration of filarial worms through host tissues are complex and critical to survival, yet little is known about the receptors and signaling pathways that mediate directed migration in these medically important species. In order to better understand the role of chemosensory signaling in filarial worm taxis, we employ comparative genomics, transcriptomics, reverse genetics, and chemical approaches to identify putative chemosensory receptor proteins and perturb chemotaxis phenotypes in filarial worms. We find that chemoreceptor family size is correlated with the presence of environmental (extra-host) stages in nematode life cycles, and that filarial worms contain a compact and highly-diverged chemoreceptor complement and lineage-specific ion channels that are predicted to operate downstream of chemoreceptor activation. InBrugia malayi, an etiological agent of LF, chemoreceptor expression patterns correspond to distinct parasite migration events across the life cycle. To interrogate the role of chemosensation in the migration of larval worms, arthropod infectious stage (microfilariae) and mammalian infectious stage (L3)Brugiaparasites were incubated in nicotinamide, an agonist of the nematode transient receptor potential (TRP) channel OSM-9. Exposure of microfilariae to nicotinamide alters intra-mosquito migration while exposure of L3s reduces chemotaxis towards host-associated cuesin vitro. Nicotinamide also potently modulates thermosensory responses in L3s, suggesting a polymodal sensory role forBrugia osm-9. Reverse genetic studies implicate bothBrugia osm-9and the cyclic nucleotide-gated (CNG) channel subunittax-4in larval chemotaxis towards host serum, and these ion channel subunits rescue sensory defects inC. elegans osm-9andtax-4knock-out strains. Together, these data reveal genetic and functional diversification of chemosensory signaling proteins in filarial worms, and encourage a more thorough investigation of clade and parasite-specific facets of nematode sensory receptor biology.
A MALDI-MS biotyping-like method to address honey bee health status through computational modelling
Authors: Arafah Karim , Voisin Sébastien Nicolas , Masson Victor , Alaux Cédric , Le Conte Yves , Bocquet Michel , Bulet Philippe
Published: July 2019

Among pollinator insects, bees undoubtedly account for the most important species. They play a critical role in boosting reproduction of wild and commercial plants and therefore contribute to the maintenance of plant biodiversity and sustainability of food webs. In the last few decades, domesticated and wild bees have been subjected to biotic and abiotic threats, alone or in combination, causing various health disorders. Therefore, monitoring solutions to improve bee health are increasingly necessary. MALDI mass spectrometry has emerged within this decade as a powerful technology to biotype micro-organisms. This method is currently and routinely used in clinical diagnosis where molecular mass fingerprints corresponding to major protein signatures are matched against databases for real-time identification. Based on this strategy, we developed MALDI BeeTyping as a proof of concept to monitor significant hemolymph molecular changes in honey bees upon infection with a series of entomopathogenic Gram-positive and -negative bacteria. ASerratia marcescensstrain isolated from one “naturally” infected honey bee collected from the field was also considered. We performed a series of individually recorded hemolymph molecular mass fingerprints and built, to our knowledge, the first computational model made of nine molecular signatures with a predictive score of 97.92%. Hence, we challenged our model by classifying a training set of individual bees’ hemolymph and obtained overall recognition of 91.93%. Through this work, we aimed at introducing a novel, realistic, and time-saving high-throughput biotyping-like strategy that addresses honey bee health in infectious conditions and on an individual scale through direct “blood tests”.

Significance Statement

Domesticated and wild bees worldwide represent the most active and valuable pollinators that ensure plant biodiversity and the success of many crops. These pollinators and others are exposed to deleterious pathogens and environmental stressors. Despite efforts to better understand how these threats affect honey bee health status, solutions are still crucially needed to help beekeepers, scientists and stakeholders in obtaining either a prognosis, an early diagnosis or a diagnosis of the health status of the apiaries. In this study, we describe a new method to investigate honey bee health by a simple “blood test” using fingerprints of some peptides/proteins as health status signatures. By computer modelling, we automated the identification of infected bees with a predictive score of 97.92%.
Alterations in brain network organization in adults with obesity as compared to healthy-weight individuals and seniors
Authors: Ottino-González J. , Baggio H.C. , Jurado M.A. , Segura B. , Caldú X. , Prats-Soteras X. , Tor C. , Sender-Palacios M.J. , Miró N. , Sánchez-Garre C. , Dadar M. , Dagher A. , García-García I. , Garolera M
Published: June 2019

Life expectancy and obesity rates have drastically increased in recent years. An unhealthy weight is related to long-lasting biological deregulations that might compromise the normal course of aging. The aim of the current study was to test whether the network composition of young adults with obesity would show signs of premature aging. To this end, subjects with obesity (N = 30, mean age 32.8 ± 5.68), healthy-weight controls (N = 33, mean age 30.9 ± 6.24) as well as non-demented seniors (N = 30, mean age 67.1 ± 6.65) all underwent a resting-state MRI acquisition. Functional connectivity was studied by means of graph-theory measurements (i.e., small-world index, clustering coefficient, characteristic path length, and mean degree). Contrary to what expected, obesity in adults was related to disruptions in small-world properties driven by increases in network segregation (i.e., clustering coefficient) as compared to elders. Also, this group showed alterations in global and regional centrality metrics (i.e., degree) relative to controls and seniors. Despite not mimicking what was here shown by seniors, the topological organization linked to an obesity status may represent a flaw for cognitive functions depending on the rapid combination between different modular communities.
Ensemble-level organization of human kinetochores and evidence for distinct tension and attachment sensors
Authors: Roscioli Emanuele , Germanova Tsvetelina E. , Smith Christopher A. , Embacher Peter A. , Erent Muriel , Thompson Amelia I. , Burroughs Nigel J. , McAinsh Andrew D.
Published: June 2019

Kinetochores are multi-protein machines that form dynamic attachments to microtubules and generate the forces for chromosome segregation. High-fidelity is ensured because kinetochores can monitor attachment status and tension, using this information to activate checkpoints and error correction mechanisms. To explore how kinetochores achieve this we used two and three colour subpixel fluorescence localisation to define how six protein subunits from the major kinetochore complexes CCAN, MIS12, NDC80, KNL1, RZZ and the checkpoint proteins Bub1 and Mad2 are organised in the human kinetochore. This reveals how the kinetochore outer plate is a liquid crystal-like system with high nematic order and largely invariant to loss of attachment or tension except for two mechanical sensors. Firstly, Knl1 unravelling relays tension and secondly NDC80 jack-knifes under microtubule detachment, with only the latter wired up to the checkpoint signalling system. This provides insight into how kinetochores integrate mechanical signals to promote error-free chromosome segregation.
Endless Conflicts: Detecting Molecular Arms Races in Mammalian Genomes
Authors: Cooper Jacob C. , Leonard Christopher J. , Pedersen Brent S. , Carey Clayton M. , Quinlan Aaron R. , Elde Nels C. , Phadnis Nitin
Published: June 2019

Recurrent positive selection at the codon level is often a sign that a gene is engaged in a molecular arms race – a conflict between the genome of its host and the genome of another species over mutually exclusive access to a resource that has a direct effect on the fitness of both individuals. Detecting molecular arms races has led to a better understanding of how evolution changes the molecular interfaces of proteins when organisms compete over time, especially in the realm of host-pathogen interactions. Here, we present a method for detection of gene-level recurrent positive selection across entire genomes for a given phylogenetic group. We deploy this method on five mammalian clades – primates, mice, deer mice, dogs, and bats – to both detect novel instances of recurrent positive selection and to compare the prevalence of recurrent positive selection between clades. We analyze the frequency at which individual genes are targets of recurrent positive selection in multiple clades. We find that coincidence of selection occurs far more frequently than expected by chance, indicating that all clades experience shared selective pressures. Additionally, we highlight Polymeric Immunoglobulin Receptor (PIGR) as a gene which shares specific amino acids under recurrent positive selection in multiple clades, indicating that it has been locked in a molecular arms race for ∼100My. These data provide an in-depth comparison of recurrent positive selection across the mammalian phylogeny, and highlights of the power of comparative evolutionary approaches to generate specific hypotheses about the molecular interactions of rapidly evolving genes.
The origin of the Gravettians: genomic evidence from a 36,000-year-old Eastern European
Authors: Bennett E. Andrew , Prat Sandrine , Péan Stéphane , Crépin Laurent , Yanevich Alexandr , Puaud Simon , Grange Thierry , Geigl Eva-Maria
Published: June 2019

The Gravettian technocomplex was present in Europe from more than 30,000 years ago until the Last Glacial Maximum, but the source of this industry and the people who manufactured it remain unsettled. We use genome-wide analysis of a ~36,000-year-old Eastern European individual (BuranKaya3A) from Buran-Kaya III in Crimea, the earliest documented occurrence of the Gravettian, to investigate relationships between population structures of Upper Palaeolithic Europe and the origin and spread of the culture. We show BuranKaya3A to be genetically close to both contemporary occupants of the Eastern European plain and the producers of the classical Gravettian of Central Europe 6,000 years later. These results support an Eastern European origin of an Early Gravettian industry practiced by members of a distinct population, who contributed ancestry to individuals from much later Gravettian sites to the west.
Enlarging the Scope of Randomization and Permutation Tests in Neuroimaging and Neuroscience
Authors: Maris Eric
Published: June 2019

Especially for the high-dimensional data collected in neuroscience, nonparametric statistical tests are an excellent alternative for parametric statistical tests. Because of the freedom to use any function of the data as a test statistic, nonparametric tests have the potential for a drastic increase in sensitivity by making a biologically-informed choice for a test statistic. In a companion paper (Geerligs & Maris, 2020), we demonstrate that such a drastic increase is actually possible. This increase in sensitivity is only useful if, at the same time, the false alarm (FA) rate can be controlled. However, for some study types (e.g., within-participant studies), nonparametric tests do not control the FA rate (see Eklund, Nichols, & Knutsson, 2016). In the present paper, we present a family of nonparametric randomization and permutation tests of which we prove exact FA rate control. Crucially, these proofs hold for a much larger family of study types than before, and they include both within-participant studies and studies in which the explanatory variable is not under experimental control. The crucial element of this statistical innovation is the adoption of a novel but highly relevant null hypothesis: statistical independence between the biological and the explanatory variable.
In vitroprototyping and rapid optimization of biosynthetic enzymes for cellular design
Authors: Karim Ashty S. , Dudley Quentin M. , Juminaga Alex , Yuan Yongbo , Crowe Samantha A. , Heggestad Jacob T. , Abdalla Tanus , Grubbe William , Rasor Blake , Coar Dave , Torculas Maria , Krein Michael , Liew FungMin (Eric) , Quattlebaum Amy , Jensen Rasmus O. , Stuart Jeff , Simpson Sean D. , Köpke Michael , Jewett Michael C.
Published: June 2019

Microbial cell factories offer an attractive approach for production of biobased products. Unfortunately, designing, building, and optimizing biosynthetic pathways remains a complex challenge, especially for industrially-relevant, non-model organisms. To address this challenge, we describe a platform forin vitroPrototyping andRapidOptimization ofBiosyntheticEnzymes (iPROBE). In iPROBE, cell lysates are enriched with biosynthetic enzymes by cell-free protein synthesis and then metabolic pathways are assembled in a mix-and-match fashion to assess pathway performance. We demonstrate iPROBE with two examples. First, we tested and ranked 54 different pathways for 3-hydroxybutyrate production, improvingin vivoproduction inClostridiumby 20-fold to 14.63 ± 0.48 g/L and identifying a new biosynthetic route to(S)-(+)-1,3-butanediol. Second, we used iPROBE and data-driven design to optimize a 6-stepn-butanol pathway, increasing titers 4-fold across 205 pathways, and showed strong correlation between cell-free and cellular performance. We expect iPROBE to accelerate design-build-test cycles for industrial biotechnology.
The SUMO Protease SENP3 regulates Mitochondrial Autophagy mediated by Fis1
Authors: Waters Emily , Wilkinson Kevin A. , Carmichael Ruth E. , Guo Chun
Published: June 2019

Mitochondria are unavoidably subject to organellar stress resulting from exposure to a range of reactive molecular species. Consequently, cells operate a poorly understood quality control programme of mitophagy to facilitate elimination of dysfunctional mitochondria. Here we use a model stressor, deferiprone (DFP), to investigate the molecular basis for stress-induced mitophagy. We show that mitochondrial fission 1 protein (Fis1) is required for DFP-induced mitophagy and that Fis1 is SUMOylated at K149, an amino acid residue critical for Fis1 mitochondrial localization. We find that DFP treatment leads to the stabilisation of the SUMO protease SENP3, which is mediated by downregulation of the E3 ubiquitin (Ub) ligase CHIP. SENP3 is responsible for Fis1 deSUMOylation and depletion of SENP3 abolishes DFP-induced mitochondrial mitophagy. Furthermore, preventing Fis1 SUMOylation by conservative K149R mutation enhances Fis1 mitochondrial localization. Critically, expressing a Fis1 K149R mutant restores DFP-induced mitophagy in SENP3 depleted cells. Thus, we propose a model in which SENP3-mediated deSUMOylation facilitates Fis1 mitochondrial localization to underpin stress-induced mitophagy.
Evolutionary implementation of Bayesian computations
Authors: Czégel Dániel , Giaffar Hamza , Zachar István , Tenenbaum Joshua B. , Szathmáry Eörs
Published: June 2019

The Bayesian framework offers a flexible language for the consistent modular assembly of statistical models used by both minds and machines. Another algorithmic domain capable of adaptation in potentially high-dimensional and uncertain environments is Darwinian evolution. The equivalence of their fundamental dynamical equations, replicator dynamics and Bayesian update, hints at a deeper algorithmic analogy. Here we show, based on a unified mathematical discussion of evolutionary dynamics and statistical learning in terms of Bayesian graphical models, that this is indeed the case. Building blocks of Bayesian computations, such as inference in hierarchical models, filtering in hidden Markov models, gradient likelihood optimization, and expectation-maximization dynamics of mixture models, map naturally to fundamental concepts of evolution: multilevel selection, quasispecies dynamics, phenotypic adaptation and ecological competition, respectively. We believe that these correspondences point towards a more comprehensive understanding of flavors of adaptive computation observed in Nature, as well as suggesting new ways to combine insights from the two domains in engineering applications.
De novo protein design enables precise induction of functional antibodies in vivo
Authors: Sesterhenn Fabian , Yang Che , Bonet Jaume , Cramer Johannes T , Wen Xiaolin , Wang Yimeng , Chiang Chi-I , Abriata Luciano A , Kucharska Iga , Castoro Giacomo , Vollers Sabrina S , Galloux Marie , Dheilly Elie , Rosset Stéphane , Corthésy Patricia , Georgeon Sandrine , Villard Mélanie , Richard Charles-Adrien , Descamps Delphyne , Delgado Teresa , Oricchio Elisa , Rameix-Welti Marie-Anne , Más Vicente , Ervin Sean , Eléouët Jean-François , Riffault Sabine , Bates John T , Julien Jean-Phillipe , Li Yuxing , Jardetzky Theodore , Krey Thomas , Correia Bruno E
Published: June 2019

De novo protein design has been successful in expanding the natural protein repertoire. However, most de novo proteins lack biological function, presenting a major methodological challenge. In vaccinology, the induction of precise antibody responses remains a cornerstone for next-generation vaccines. Here, we present a novel protein design algorithm, termed TopoBuilder, with which we engineered epitope-focused immunogens displaying complex structural motifs. Both in mice and non-human primates, cocktails of three de novo designed immunogens induced robust neutralizing responses against the respiratory syncytial virus. Furthermore, the immunogens refocused pre-existing antibody responses towards defined neutralization epitopes. Overall, our de novo design approach opens the possibility of targeting specific epitopes for vaccine and therapeutic antibody development, and more generally will be applicable to design de novo proteins displaying complex functional motifs.
Diverse cell junctions with unique molecular composition in tissues of a sponge (Porifera)
Authors: Mitchell Jennyfer M. , Nichols Scott A.
Published: June 2019

The integrity and organization of animal tissues depends upon specialized protein complexes that mediate adhesion between cells with each other (cadherin-based adherens junctions), and with the extracellular matrix (integrin-based focal adhesions). Reconstructing how and when these cell junctions evolved is central to understanding early tissue evolution in animals. We examined focal adhesion protein homologs in tissues of the freshwater sponge,Ephydatia muelleri(phylum Porifera). We found that sponge homologs of focal adhesion proteins co-precipitate as a complex and localize to cell junctions in sponge tissues. These data support that the adhesion roles of these proteins evolved early, prior to the divergence of sponges and other animals. However, in contrast to the spatially partitioned distribution of cell junctions in epithelia of other animals, focal adhesion proteins were found to be co-distributed with the adherens junction protein Emβ-catenin in sponge tissues; both at certain cell-cell and cell-extracellular matrix (ECM) adhesions. Sponge adhesion structures were found to be unique in other ways, too. The basopinacoderm (substrate-attachment epithelium) lacks typical polarity in that cell-ECM adhesions form on both basal and apical surfaces, and compositionally unique cell junctions form at the interface between cells with spicules (siliceous skeletal elements) and between cells and environmental bacteria. These results clarify the diversity, distribution and molecular composition of cell junctions in tissues ofE. muelleri, but raise new questions about their function and homology with cell junctions in other animals.