bluuebunny/crossref_metadata_2025 huggingface dataset:
Cognitive Linguistics
Authors: Chilton Paul
Published: July 2019

This chapter aims to show the reader how social cognition also includes language. Neither cognitive sociology nor cognitive linguistics can logically ignore one another’s perspectives and empirical findings. The chapter aims to introduce cognitive sociologists to leading strands of research in cognitive linguistics that have a bearing on the structure and processes of society. In explaining the cognitive basis of language, linguists are now beginning to recognize its dialogic nature, the importance of dialogue in language acquisition, and thus the dependence of language on early socialization. This design feature enables the many social uses of the human language faculty that are termed “discourse.” There are many approaches to “discourse” but here the focus is on the recently developed cognitive approaches that are able to handle the complexities of grammatical detail as well as lexical meaning, without ignoring pragmatics. These approaches include cognitive frame theory, which describes lexical meaning and phenomena such as grammatically triggered attention shifts. A widely used approach analyzes conceptual metaphor, where “metaphor” is understood as a mental framing device that works by linking different conceptual domains, including image schemata. A third cognitive approach to socially relevant conceptualization emphasizes the role of spatial cognition, in particular containing spaces and the dimensions of direction and distance. In all cases, this overview relates the social and linguistic aspects to cognitive science and neuroscience.
Class, Cognition, and Cultural Change in Social Class
Authors: Santos Henri C. , Grossmann Igor , Varnum Michael E. W.
Published: July 2019

This chapter discusses how differences in social class affect a variety of psychological processes and outcomes. In particular, it discusses how relatively higher class individuals are more likely to focus on the self—that is, emphasizing personal goals, feelings, and interests—compared to working-class individuals, who pay greater attention to the social context and their relationships with close others. In support of this claim, it discusses evidence of social class differences in values, neural processes, and higher level reasoning. It also explores the dynamic nature of the social class construct, looking at the difficulties people encounter when shifting to a relatively higher class and the historical trends that suggest global shifts in social class structure within societies. Taken together, these findings highlight the importance of understanding social class when looking at various psychological outcomes. At the same time, they challenge researchers to consider the complexity of social class when studying its effects.
Cognitive Dichotomies, Learning Directions, and the Cognitive Architecture
Authors: Sun Ron
Published: July 2019

Within the human mind, are there multiple, qualitatively different systems? Are there different processes of learning and performance that have radically different characteristics? If so, what are these? How do they differ from each other? How do they interact and integrate? There have been various speculations in this regard, often centered on two (or more) interacting systems within the human mind. This chapter reviews arguments in favor of two-system views and discusses the interaction and integration of the two systems in terms of different learning directions going from one system to the other. It also outlines the overall cognitive architecture that encompasses and structures these aspects.
Cognitive Sociology
Authors: Zerubavel Eviatar
Published: July 2019

Following in the rich intellectual footsteps of Emile Durkheim, Karl Mannheim, Alfred Schutz, and Ludwik Fleck, this chapter lays out the foundations for the sociology of thinking, or “cognitive sociology.” Focusing on the impersonal, normative, and conventional dimensions of the way we think (and, as such, on its distinctness from both cognitive individualism and universalism), it highlights the distinctly sociological concern with intersubjectivity as well as epistemic commitment to the study of thought communities, cognitive traditions, cognitive norms, cognitive socialization, cognitive conventions, and the politics of cognition.
Cognitive Sociology and French Psychological Sociology
Authors: Ignatow Gabe
Published: July 2019

This chapter critically reviews work of three representatives of the French tradition of psychologically informed sociology: Marcel Mauss, Pierre Bourdieu, and Loïc Wacquant. It considers both the institutional backgrounds to these scholars’ encounters with psychology and cognitive science and main aspects of the conceptual and methodological evolution that has occurred between Mauss and Wacquant, particularly as regards their use of the habitus concept. Finally, it considers the influence of French psychological sociology on contemporary cognitive sociology, surveying some of the theoretical and methodological innovations that have resulted as well as possible avenues for further development of these interdisciplinary fields.
Fidelity versus Freedom in Miloš Forman’s Film Version of Hair
Authors: Buchman Andrew
Published: July 2019

This chapter looks at the 1979 film version of the stage musical Hair (1968) and the very different political climates in which each appeared. The chapter describes the film as a radical rewrite but also regards it as remaining faithful to the central ideas within the 1968 Broadway show, even returning key elements of the first off-Broadway production, in 1967. Charting the musical’s journey from stage to screen in meticulous detail, the chapter reveals how changing priorities and changing media brought about important shifts in Hair as a work. In particular, the rejection of a draft screenplay by the stage version’s book writers Rado and Ragni in favour of a new text by playwright Michael Weller meant that Hair on the screen was no longer a song cycle, or concept album but instead a completely new rendering by director Miloš Forman, who claimed to have ‘read’ political or social themes already present in the work. In this chapter, Hair becomes a new case study in the fidelity versus freedom debate on musical adaptations.
‘You Will Know That She Is Our Annie’
Authors: Sapiro Ian
Published: July 2019

This chapter identifies intertextual relationships among different screen adaptations of Annie. The 1982, 1999, and 2014 films not only offer different takes on the material, but they also contain connections to one another as part of the cultural influence of Annie as a larger cultural text stemming back to the 1924 comic strip. This gives rise in the chapter to an exploration of the reinventions of Annie rather than passing judgement on their respective levels of commercial, cultural, or musical merit. The chapter observes how the 1999 Disney version is more influenced by the Broadway original than by the 1982 film, but the 2014 remake combines influences from Broadway and from the 1982 movie, including a chase through Manhattan that closely matches the climactic sequence from 1982; the 1999 version has not had an obvious influence on the 2014 movie, however. In this manner, each film’s reinventions offer just enough of the original narrative and music for a new generation of viewers to recognize and accept it as their Annie.
The Fascinating Moment of Godspell
Authors: Laird Paul R.
Published: July 2019

This chapter delves into contextual issues on the film version of Godspell, focusing on a small religious revival in American popular culture in the early 1970s. Leonard Bernstein’s Mass, Andrew Lloyd Webber’s Jesus Christ Superstar, and Stephen Schwartz’s Godspell appeared on stage within months of one another, and Christianity appeared in other aspects of popular culture at the time, including an image of Jesus on the front of Time magazine in 1971. The producers of Godspell, however, realized that the musical was quickly at the height of its cultural moment and they decided to release it as a movie while the stage production was still in its original run in various cities, thus providing a direct competition between stage and screen versions (normally film adaptations are released after the closing of stage versions). Changes were made to the material for the film version and, like On the Town and Bells Are Ringing, there were challenges related to the location filming in New York City. Reactions to the film were polarized, but it remains an important document of a time when Jesus made more than just a cameo appearance in popular culture.
Li’l Abner from Comic Strip to Hollywood
Authors: Lovensheimer Jim
Published: July 2019

This chapter examines the curiously overlooked film adaptation of Li’l Abner. The chapter points out that rarely has a Broadway musical been adapted for film that looked like that original stage version as the 1959 Paramount Pictures version of Li’l Abner. The film’s sets and costumes reproduced the artificiality of the Broadway sets, which in turn recalled Al Capp’s imaginatively grotesque comic strip on which both were based, and the staging of the film’s musical numbers was unapologetically theatrical and presentational. Yet the chapter also reveals that by 1959, Capp’s comic strip had moved away from the overt political satire for which it had become famous. Thus the film contains a much deeper social satire than the strip was at that time providing.
‘A Great American Service’
Authors: Titrington Craft Elizabeth
Published: July 2019

This chapter looks at the musical biopic Yankee Doodle Dandy. George M. Cohan was still alive when the movie about his life was made and his influence is seen on how it depicts aspects of his life to suit his own account of it. But the chapter also explores how the movie is a self-reflexive backstage musical and how its attention to theatrical authenticity served to deflect scrutiny from the lack of veracity in Cohan’s biography. Examples include the changing of details in scenes from the stage musicals George Washington, Jr and I’d Rather Be Right to serve the movie’s hagiographic depiction of Cohan’s life, as memorably played by James Cagney. But on the whole, the chapter reveals that fidelity was the byword in the treatment of Cohan’s musical oeuvre and the staging of musical numbers. James Cagney also took great care to capture Cohan’s renowned, distinctive dancing style; his instructor Johnny Boyle had even performed in Cohan shows and staged dances for Cohan.
Loud, Pretty, Strong, White [Repeat]
Authors: Decker Todd
Published: July 2019

This chapter focuses on the series of operettas made by MGM for Jeanette MacDonald and Nelson Eddy in the 1930s and early 1940s. Describing the series as a sustained exercise in nostalgia and prestige product, the chapter examines the films’ legacy as nostalgic romantic film operettas, richly realized in visual and musical terms and shaped entirely around the two stars’ distinct voices and personas. The movies are marked by lavish production values and the recurrent grafting onto these musical films of narrative tropes from more prestige-oriented genres, such as historical epics and period-setting melodramas. The films featured consistent elements—regular plot devices, the use of a legitimate singing style, similar character types, approaches to key and tonality in the arrangement of the songs, the preservation of racial whiteness— a formula that was facilitated by a liberal approach to the source material in all but Bitter Sweet.
‘Is This the Right Material, Girl?’
Authors: Allen Richard J.
Published: July 2019

Alan Parker’s film version of Lloyd Webber and Rice’s Evita (1996) provides a case study of how a star’s agency can affect a film musical’s narrative. This chapter on the movie reveals how adjustments made to the piece for its movie incarnation result in a change of presentation of the title character, played by Madonna. Whereas the stage show depicts Eva as a figure of moral ambiguity, the film turns her into a probably well-meaning, mostly sympathetic, inherently romantic heroine. A series of newly created flashbacks, scenes, lyrics, and entire songs were crafted for the purpose of gaining insight into and empathy for Eva. For example, Eva, rather than Peron’s mistress, now sings ‘Another Suitcase in Another Hall,’ one of the hit songs from the score, and the ‘Waltz for Evita and Che’ is staged as a romantic duet, without conveying the cynicism of the lyrics. The addition of ‘You Must Love Me’ adds a new insight into her realization that if Peron can still show her such attention and affection when she is dying and no longer of any use to him, then he must love her after all. In these and many other ways, Eva is humanized in a way that is not the case in the Broadway original.
The Many Faces of Rio Rita
Authors: Graziano John
Published: July 2019

This chapter focuses on the adaptations of Rio Rita. The first adaptation was released in 1929 and rereleased, due to its enormous popularity, in 1932; though largely faithful to the stage version, it contained numerous changes to the script and score, including the addition of a new number. In 1942, MGM bought the screen rights in order to readapt it into a vehicle for the celebrated comic team of Abbott and Costello. This was a much more liberal adaptation: only two of the original songs made it into the film, with a miscellany of other numbers being added, including a new song by Harburg and Arlen and a performance by Kathryn Grayson of the ‘Shadow Song’ from Meyerbeer’s Dinorah. As with The Desert Song, Nazi characters were added to the film from this era. On its own patriotic terms, the 1942 version served its purpose; audiences would be entertained by the antics of its stars but also be made aware of the secret foreign intruders who were threatening to overthrow the American way of life.
‘An Elegant Legacy?’
Authors: Birkett Danielle
Published: July 2019

Different issues challenged the screen adaptation of Finian’s Rainbow, which was one of the most successful Broadway musicals of the 1940s but took more than twenty years to be released as a film. Using archival research, this chapter reveals the frustrated early attempts to make Finian’s into an animated film musical, partly blighted by the blacklisting of lyricist E. Y. Harburg in 1951. Ex-Disney animator John Hubley was hired to work on the film and created more than 400 storyboard sketches, designs, and character drafts for the movie. By 1954, ten key songs had been recorded by leading artists such as Frank Sinatra, Ella Fitzgerald, and Louis Armstrong; indeed, in an attempt to make the project as commercial as possible, Sinatra was assigned a part in nearly all the songs. A new prologue was added and changes were made to the story to soften its vigorous political message, but for a mixture of political and financial reasons the production was abruptly closed down; Finian’s Rainbow would not reach the screen until late the following decade.
‘I’m Once Again the Previous Me’
Authors: McHugh Dominic
Published: July 2019

This chapter on Barbra Streisand’s first three film musicals considers how her star text affects the adaptation of the three Broadway musicals on which they are based. Although Streisand starred in Funny Girl on the stage, the screen version made significant changes to the musical, relating the story as a flashback so that it could be telescoped through her perspective. Most of the other characters’ songs were cut, a ploy that was also used in On a Clear Day You Can See Forever to emphasize Streisand as the star. In both films, as well as in Hello, Dolly!, Streisand was cast opposite men with weak singing voices, empowering her performance musically in each case. A good example of how this works is in the title song of On a Clear Day, where Yves Montand performs the number complete with a simple orchestration and staging, followed by Streisand’s much grander performance. Meanwhile, in Dolly! it was necessary to make changes to the title character in order to draw attention away from the fact that Streisand was much too young for the role; thus she is depicted as a general busybody in ‘Just Leave Everything to Me,’ which replaced ‘I Put My Hand In,’ which focuses on Dolly as a matchmaker.
Listening between the Images
Authors: Dovey Lindiwe
Published: July 2019

This article explores the relationships between African filmmakers and communism during the Cold War period, with a particular focus on those African filmmakers who were trained in the Soviet Union, such as Sarah Maldoror, Ousmane Sembene, and Abderrahmane Sissako. The essay argues that, while affinities can be found between the work of African and Soviet filmmakers, these relationships were often compromised by utopian assumptions of “brotherhood” or racism—an issue frequently critiqued by African filmmakers in their films through creating tension between images and soundtrack. The analysis thus foregrounds the aural language of film, the sonic contexts in which films are made and viewed, and the language(s) in which research is conducted, to emphasize how the aural is an important aspect of the visual even in its absence, and to sound a note of caution against overly celebratory accounts of transnational film relationships.
Beauty and Quality for All
Authors: Cabrera Arús María A.
Published: July 2019

This article focuses on sartorial visions put forth by institutions and representatives of the Cuban regime throughout the 1960s to the 1980s, in particular the visions of modernity produced by and circulated through the institutions of fashion and clothing production of the Cuban state. It presents these visions as oriented to put forth a figured world of power aimed at persuading individuals to participate in the construction of the communist future by catering to the aspirational dreams of the middle class. The article concludes that such an imaginary helped in the short term to consolidate and legitimize the Cuban state socialist regime, allowing the new socialist middle classes to reinvent themselves as consumers, while participating in the construction of socialism. Yet, at the same time, for many people these visions were mostly a mirage, as fashionable clothes were not for sale.
Futures Remembered
Authors: Hodgin Nick
Published: July 2019

This article seeks to understand and speculate on the significance of certain visual features of the communist past after communism. Focusing in particular on East Germany, it considers the interplay of futures remembered and pasts experienced and the relevance of that interaction to our understanding of the GDR. It looks at the enduring appeal of cosmic culture and especially the figure of the cosmonaut as referenced across a range of media. Surveying its representation in both historical and contemporary culture, it traces the evolution of the cosmonaut as symbol, which was originally representative of socialist achievement and progressive humanism, and examines the ways in which it has come to be represented in visual and popular culture at a time when “the pendulums of the public mindset and mentality,” as Zygmunt Bauman has argued, have performed “a U-turn: from investing public hopes of improvement in the uncertain and ever too obviously un-trustworthy future, to re-investing them in the vaguely remembered past, valued for its assumed stability and so trustworthiness.”
Red Stars, Biorhythms, and Circuit Boards
Authors: Švelch Jaroslav
Published: July 2019

This article traces the intersections of Western computer technology and everyday life in communist-era Czechoslovakia. It follows computer professionals and hobbyists who participated in bottom-up computing practices, and it discusses the improvised, do-it-yourself aesthetics of the artifacts they created. It focuses on three key examples: the printing of biorhythm charts, which provided the first personal encounters with computing to many ordinary citizens in the 1970s; hardware tinkering, which remedied the scarcity of computer equipment by salvaging and repurposing local resources; and production of local computer games, which built on Western templates but engaged with local themes, sometimes even subverting the authority of the communist party and ironically appropriating its propaganda. It concludes that computer enthusiasts were ahead of party officials in realizing that computers are not just data processing machines but also tools for making and dissemination of culture.
Who Doesn’t Like Aleksander Kobzdej?
Authors: Moskalewicz Magdalena
Published: July 2019

This article looks into the extraordinary Cold War–era career of the Polish artist Aleksander Kobzdej in order to provide insight into the complexity of the emergence and demise of socialist realism in the People’s Republic of Poland and its repercussions for today’s discourses. The author reconstructs Kobzdej’s smooth shift from a much-awarded socialist realist artist into an internationally recognized modernist abstract painter through the analysis of his artworks, travels, and participation in major art exhibitions, and discusses them in the context of the larger changes that took place in the official state policies and cultural diplomacy as Stalinism was giving way to the cultural Thaw in the mid-1950s. This case study serves to argue that not just socialist realism but also much of the later modernist art produced in Poland should be seen as de facto communist, that is, as art that emerged as a product of the delicate but stable, and mutually beneficial, consensus between artists and the communist state.
Educating for the Cooperative Society
Authors: Mayhew Ken
Published: July 2019

The role of government in fostering HE’s contribution to societal cooperativeness is, in present conditions of high demand, contested both politically and ideologically. Although devolution of decision taking to universities is widely apparent, four types of strong influence remain in government use: mandates, funding incentives, investment in capacity-building, and overall system adjustment. These have fostered changes in the HE policy agenda from the outcomes espoused in the foundational Robbins Report namely: skilling (not prioritized), general powers of the mind, the advancement of learning, and a shared culture of citizenship. Over-skilling now grows, and leaves difficult policy questions such as: occupational filtering down, student debt and loan servicing, bureaucratic drift with related transaction costs, and decline in education standards. Considering what a university is good for, as opposed to good at, is a challenge for many policy makers.
The Collegial Tradition in English Higher Education
Authors: Palfreyman David , Tapper Ted
Published: July 2019

The basic structure of the Oxbridge type evolved historically as a federal set of multi-disciplinary and largely self-governing colleges. Each set was balanced between competition and cooperation. A distinct feature is that teaching is divided between the university role of organizing and examining taught courses, and the college role of organizing the attendant processes of student learning, especially via the system of tutorials/supervisions, a form of apprenticeship in critical thinking. University policy is strongly influenced by faculty assemblies. This formula is now under pressure from greater dependence on government research funding, and from new performance criteria in evaluation. There are fears that new forms of state control will result in a decline of autonomy, and so the capacity for academic initiative, as universities as a whole become more market-driven.
Managing a University in Turbulent Times
Authors: Redding Gordon , Drew Antony , Harley Trevor
Published: July 2019

Universities are a distinct organizational type, evolved for a particular set of purposes and resting essentially on the allocation of influence to scholars, within a supporting administrative system. This traditional structure is now threatened by forces that have risen on a wave of global demand never before experienced. University management is now under severe pressure to reconcile the earlier rationale with the recent pressures. This is an under-researched managerial challenge. To address it lessons are drawn from a general theory of executive duty in large complex organizations undergoing change. At the core of this is the problem of retaining willing cooperation with the organization’s purposes by its key members. A current partial response to this challenge is reported. Certain more universal lessons about moral legitimacy and executive authority within strategic management are also drawn.
Christology
Authors: Bauckham Richard
Published: July 2019

Christology is concerned with the identity of Jesus Christ. This essay explores Paul’s Christology with the help of the various categories that make up a concept of personal identity: name, narrative, character, relationships, and roles. In the case of Jesus Christ, however, the issue of identity is complicated by the fact that Paul not only understands Jesus to be a human individual, but also, in some sense, includes him in the divine identity of the one and only God. This essay explains this puzzle in terms of a Christology of divine identity.
Going Back to Kahlbaum’s Psychomotor (and GABAergic) Origins: Is Catatonia More Than Just a Motor and Dopaminergic Syndrome?
Authors: Hirjak Dusan , Kubera Katharina M , Wolf R Christian , Northoff Georg
Published: July 2019

In 1874, Karl Kahlbaum described catatonia as an independent syndrome characterized by motor, affective, and behavioral anomalies. In the following years, various catatonia concepts were established with all sharing the prime focus on motor and behavioral symptoms while largely neglecting affective changes. In 21st century, catatonia is a well-characterized clinical syndrome. Yet, its neurobiological origin is still not clear because methodological shortcomings of hitherto studies had hampered this challenging effort. To fully capture the clinical picture of catatonia as emphasized by Karl Kahlbaum, 2 decades ago a new catatonia scale was developed (Northoff Catatonia Rating Scale [NCRS]). Since then, studies have used NCRS to allow for a more mechanistic insight of catatonia. Here, we undertook a systematic review searching for neuroimaging studies using motor/behavioral catatonia rating scales/criteria and NCRS published up to March 31, 2019. We included 19 neuroimaging studies. Studies using motor/behavioral catatonia rating scales/criteria depict cortical and subcortical motor regions mediated by dopamine as neuronal and biochemical substrates of catatonia. In contrast, studies relying on NCRS found rather aberrant higher-order frontoparietal networks which, biochemically, are insufficiently modulated by gamma-aminobutyric acid (GABA)-ergic and glutamatergic transmission. This is further supported by the high therapeutic efficacy of GABAergic agents in acute catatonia. In sum, this systematic review points out the difference between motor/behavioral and NCRS-based classification of catatonia on both neuronal and biochemical grounds. That highlights the importance of Kahlbaum’s original truly psychomotor concept of catatonia for guiding both research and clinical diagnosis and therapy.
Differences in isoprenoid-mediated energy dissipation pathways between coastal and interior Douglas-fir seedlings in response to drought
Authors: Junker-Frohn Laura Verena , Kleiber Anita , Jansen Kirstin , Gessler Arthur , Kreuzwieser Jürgen , Ensminger Ingo
Published: July 2019

Plants have evolved energy dissipation pathways to reduce photooxidative damage under drought when photosynthesis is hampered. Non-volatile and volatile isoprenoids are involved in non-photochemical quenching of excess light energy and scavenging of reactive oxygen species. A better understanding of trees’ ability to cope with and withstand drought stress will contribute to mitigate the negative effects of prolonged drought periods expected under future climate conditions. Therefore we investigated if Douglas-fir (Pseudotsuga menziesii(Mirb.)) provenances from habitats with contrasting water availability reveal intraspecific variation in isoprenoid-mediated energy dissipation pathways. In a controlled drought experiment with 1-year-old seedlings of an interior and a coastal Douglas-fir provenance, we assessed the photosynthetic capacity, pool sizes of non-volatile isoprenoids associated with the photosynthetic apparatus, as well as pool sizes and emission of volatile isoprenoids. We observed variation in the amount and composition of non-volatile and volatile isoprenoids among provenances, which could be linked to variation in photosynthetic capacity under drought. The coastal provenance exhibited an enhanced biosynthesis and emission of volatile isoprenoids, which is likely sustained by generally higher assimilation rates under drought. In contrast, the interior provenance showed an enhanced photoprotection of the photosynthetic apparatus by generally higher amounts of non-volatile isoprenoids and increased amounts of xanthophyll cycle pigments under drought. Our results demonstrate that there is intraspecific variation in isoprenoid-mediated energy dissipation pathways among Douglas-fir provenances, which may be important traits when selecting provenances suitable to grow under future climate conditions.
XV American Literature to 1900
Authors: McGettigan Katie , Hughes Tomos , Salway Matthew , White Rebecca
Published: July 2019

This chapter has two sections: 1. Journals; 2. Monographs and Edited Collections. Section 1 is by Katie McGettigan; section 2 is by Tomos Hughes, Katie McGettigan, Matthew Salway, and Rebecca White.
Flooding-Associated Soft Rot of Sweetpotato Storage Roots Caused by Distinct Clostridium Isolates
Authors: da Silva Washington L. , Yang Kuei-Ting , Pettis Gregg S. , Soares Natasha R. , Giorno Rebecca , Clark Christopher A.
Published: July 2019

Flooding of sweetpotatoes in the field leads to development of soft rot on the storage roots while they remain submerged or on subsequent harvest and storage. Incidences of flooding after periods of intense rainy weather are on the rise in the southeastern United States, which is home to the majority of sweetpotato production in the nation. In an effort to characterize the causative agent(s) of this devastating disease, here we describe two distinct bacterial strains isolated from soft-rotted sweetpotato storage roots retrieved from an intentionally flooded field. Both of these anaerobic spore-forming isolates were identified as members of the genus Clostridium based on sequence similarity of multiple housekeeping genes, and both were confirmed to cause soft rot disease on sweetpotato and other vegetable crops. Despite these common features, the isolates were distinguishable by several phenotypic and biochemical properties, and phylogenetic analysis placed them in separate well-supported clades within the genus. Overall, our results demonstrate that multiple plant-pathogenic Clostridium species can cause soft rot disease on sweetpotato and suggest that a variety of other plant hosts may also be susceptible.
Jointly inferring the dynamics of population size and sampling intensity from molecular sequences
Authors: Parag KV , du Plessis L , Pybus OG
Published: July 2019

Estimating past population dynamics from molecular sequences that have been sampled longitudinally through time is an important problem in infectious disease epidemiology, molecular ecology and macroevolution. Popular solutions, such as the skyline and skygrid methods, infer past effective population sizes from the coalescent event times of phylogenies reconstructed from sampled sequences, but assume that sequence sampling times are uninformative about population size changes. Recent work has started to question this assumption by exploring how sampling time information can aid coalescent inference. Here we develop, investigate, and implement a new skyline method, termed the epoch sampling skyline plot (ESP), to jointly estimate the dynamics of population size and sampling rate through time. The ESP is inspired by real-world data collection practices and comprises a flexible model in which the sequence sampling rate is proportional to the population size within an epoch but can change discontinuously between epochs. We show that the ESP is accurate under several realistic sampling protocols and we prove analytically that it can at least double the best precision achievable by standard approaches. We generalise the ESP to incorporate phylogenetic uncertainty in a new Bayesian package (BESP) in BEAST2. We re-examine two well-studied empirical datasets from virus epidemiology and molecular evolution and find that the BESP improves upon previous coalescent estimators and generates new, biologically-useful insights into the sampling protocols underpinning these datasets. Sequence sampling times provide a rich source of information for coalescent inference that will become increasingly important as sequence collection intensifies and becomes more formalised.
notum1, acting downstream of pitx2, is essential for proper eye and craniofacial development
Authors: Hendee Kathryn E. , Sorokina Elena A. , Muheisen Sanaa S. , Collery Ross F. , Semina Elena V.
Published: July 2019

Axenfeld-Rieger syndrome (ARS) is a rare autosomal dominant developmental disorder characterized by ocular anterior chamber anomalies with an increased risk of glaucoma and systemic defects. Mutations in the transcription factorPITX2were the first identified genetic cause of ARS. Despite the developmental importance ofPITX2and its role in ARS, the pathways downstream of PITX2 have yet to be fully characterized. Comparative transcriptome analyses involvingpitx2-enriched cell populations isolated via fluorescence activated cell sorting of tissues expressing (Tg(-2.6pitx2-CE4:GFP))reporter in wild-type andpitx2M64*mutant zebrafish embryos identified the highly down-regulated targetnotum1b, an ortholog of humanNOTUMencoding a secreted carboxylesterase that cleaves a necessary palmitoleate moiety from WNT proteins. Further experiments confirmed a decrease innotum1band identified down-regulation of another NOTUM ortholog,notum1a, in the developing mutant eye. CRISPR-generated permanent double knockout zebrafish lines ofnotum1bandnotum1a, notum1−/−,displayed defects in craniofacial and ocular development, including corneal defects, small lenses, increased sizes of the anterior and posterior chambers, and anomalies in teeth development. Analysis of head transcriptome ofnotum1−/−zebrafish in comparison to wild-type predicted an up-regulation of the WNT pathway. We presentNOTUM/notum1as an important factor in ocular and craniofacial development and a novel downstream member of the PITX2/pitx2 pathway.
Reckless driving: Improved phosphorous availability is a most likely important driver and species killer in angiosperm evolution
Authors: Olsson Stefan
Published: July 2019

Introductory summarizing paragraph

Plants show a large range of genome sizes with a more than thousand fold difference between the largest and the smallest genomes (Bennett, M. D., 1972; Bennett, 2005; Knight, 2005; Gregory et al., 2007; Bai et al., 2012; Kelly et al., 2015). Since, 1. DNA phosphorous is a phosphorous pool not possible to recycle within the cell. 2. Carnivorous plants with very small genomes living in low phosphorous environments uses carnivory to supply phosphorous (Leushkin et al., 2013). 3. The genus Fritillaria with very large genomes is dependent on mycorrhiza (Wang & Qiu, 2006; Kelly et al., 2015) probably mainly for supply of P, I decided to investigate if lifestyles connected with releases from P-limitation correlate with 1C-genome sizes. For the investigation I used available lifestyle data from several websites and articles (Wang & Qiu, 2006; Lysak et al., 2008) together with the Angiosperm C-values available at Kew http://data.kew.org/cvalues/. Based on this analysis I suggest the following order of P restriction for genome size expansions, from the least restricted to the most restricted, for the different lifestyles: Myco-heterotrophs<Parasitic plants<Mycorrhizal plants<Non-Mycorrhizal plants<Carnivorous plants. The data further suggest that a general improved P status most likely precedes whole genome duplication events and that uneven ploidy increases are more punishing than even ploidy most probably since uneven ploidy increases cannot be followed by adaptive recombination/selection. Thus P-limitation is a likely main restraint for angiosperm evolution and genome-expansion. However, relaxing this restraint leads plants into an evolutionary dead end with large nuclei (Bennetzen & Kellogg, 1997) and high P demand.
To find better neural network models of human vision, find better neural network models of primate vision
Authors: Jozwik Kamila Maria , Schrimpf Martin , Kanwisher Nancy , DiCarlo James J.
Published: July 2019

Specific deep artificial neural networks (ANNs) are the current best models of ventral visual processing and object recognition behavior in monkeys. We here explore whether models of non-human primate vision generalize to visual processing in the human primate brain. Specifically, we asked if model match to monkey IT is a predictor of model match to human IT, even when scoring those matches on different images. We found that the model match to monkey IT is a positive predictor of the model match to human IT (R = 0.36), and that this approach outperforms the current standard predictor of model accuracy on ImageNet. This suggests a more powerful approach for pre-selecting models as hypotheses of human brain processing.
Organic farming expansion drives natural enemy abundance not diversity in agricultural landscapes
Authors: Muneret Lucile , Auriol Arthur , Bonnard Olivier , Richart-Cervera Sylvie , Thiéry Denis , Rusch Adrien
Published: July 2019

Organic farming is seen as a prototype of ecological intensification able to conciliate crop productivity and biodiversity conservation in agricultural landscapes. However, how natural enemies, an important functional group supporting pest control services, respond to organic farming at different scales and in different landscape contexts remain unclear.

Using a hierarchical design within a vineyard-dominated region located in southwestern France, we examine the independent effects of organic farming and semi-natural habitats at the local and landscape scales on natural enemies.

We show that the proportion of organic farming is a stronger driver of species abundance than the proportion of semi-natural habitats and is an important facet of landscape heterogeneity shaping natural enemy assemblages. Although our study highlight a strong taxonomic group-dependency about the effect of organic farming, organic farming benefits to dominant species while rare species occur at the same frequency in the two farming systems.

Independently of farming systems, enhancing field age, reducing crop productivity, soil tillage intensity and pesticide use are key management options to increase natural enemy biodiversity.

Synthesis and Applications. Our study indicates that policies promoting the expansion of organic farming will benefit more to ecological intensification strategies seeking to enhance ecosystem services than to biodiversity conservation.
Precision of auditory responses deteriorates on the way to frontal cortical areas
Authors: López-Jury Luciana , Mannel Adrian , Garcia-Rosales Francisco , Hechavarria Julio C.
Published: July 2019

Frontal areas of the mammalian cortex are thought to be important for cognitive control and complex behaviour. These areas have been studied mostly in humans, non-human primates and rodents. In this article, we present a quantitative characterization of response properties of a frontal auditory area responsive to sound in the bat brain, the frontal auditory field (FAF). Bats are highly vocal animals and they constitute an important experimental model for studying the auditory system. At present, little is known about neuronal sound processing in the bat FAF. We combined electrophysiology experiments and computational simulations to compare the response properties of auditory neurons found in the bat FAF and auditory cortex (AC) to simple sounds (pure tones). Anatomical studies have shown that the latter provide feedforward inputs to the former. Our results show that bat FAF neurons are responsive to sounds, however, when compared to AC neurons, they presented sparser, less precise spiking and longer-lasting responses. Based on the results of an integrate-and-fire neuronal model, we speculate that slow, low-threshold, synaptic dynamics could contribute to the changes in activity pattern that occur as information travels through cortico-cortical projections from the AC to the FAF.
A bibliometric analysis of Soil remediation Based on Massive research literature data During 1988-2018
Authors: Hu Ya , Han Jichang , Sun Zenghui , Wang Huanyuan , Liu Xiang , Kong Hui
Published: July 2019

Soil is an important part of the ecosystem with significant roles that help human population sustain. Research on prevention and remediation of soil pollution has been carried out when 1985. This study analyzed the 1988–2018 soil remediation dataset in the Web of Science database by bibliometric methods to illustrate the current research trends and hot topics of quantitative analysis and soil remediation in the world. To further identify the major soil contamination topics, we employed social network analysis. The results indicate that the field of soil remediation has entered a stage of rapid progress. The United States has a strong overall strength with the largest number of published articles and larger impact. China ranks second. We identified Journal of hazardous materials as the most influential journal and Chinese academy of sciences as the most influential institution. Academic cooperation showed an increasing trend at the author, institutional, and national levels with an average level of cooperation of 3.57, 1.66, and 1.16, respectively. However, the growth rate of cooperation at the national level is relatively low. In addition, the frequency and co-word analyses of keywords revealed the important research topics. “heavy metals”, “PAH”, “bioremediation”, “Phytoremediation” and “Electrokinetic remediation” were identified as the hot topics. The findings of this study will help researchers understand the status of soil remediation as well as provide guidance for future research.
Highly Efficient, Massively-Parallel Single-Cell RNA-Seq Reveals Cellular States and Molecular Features of Human Skin Pathology
Authors: Hughes Travis K , Wadsworth Marc H , Gierahn Todd M , Do Tran , Weiss David , Andrade Priscilla R. , Ma Feiyang , de Andrade Silva Bruno J. , Shao Shuai , Tsoi Lam C , Ordovas-Montanes Jose , Gudjonsson Johann E , Modlin Robert L , Love J Christopher , Shalek Alex K
Published: July 2019

The development of high-throughput single-cell RNA-sequencing (scRNA-Seq) methodologies has empowered the characterization of complex biological samples by dramatically increasing the number of constituent cells that can be examined concurrently. Nevertheless, these approaches typically recover substantially less information per-cell as compared to lower-throughput microtiter plate-based strategies. To uncover critical phenotypic differences among cells and effectively link scRNA-Seq observations to legacy datasets, reliable detection of phenotype-defining transcripts – such as transcription factors, affinity receptors, and signaling molecules – by these methods is essential. Here, we describe a substantially improved massively-parallel scRNA-Seq protocol we term Seq-Well S^3 (“Second-Strand Synthesis”) that increases the efficiency of transcript capture and gene detection by up to 10- and 5-fold, respectively, relative to previous iterations, surpassing best-in-class commercial analogs. We first characterized the performance of Seq-Well S^3 in cell lines and PBMCs, and then examined five different inflammatory skin diseases, illustrative of distinct types of inflammation, to explore the breadth of potential immune and parenchymal cell states. Our work presents an essential methodological advance as well as a valuable resource for studying the cellular and molecular features that inform human skin inflammation.
Reduction in voluntary activation of elbow and wrist muscles in individuals with chronic hemiparetic stroke
Authors: Garmirian Lindsay R. P. , Dewald Julius P. A. , Acosta Ana Maria
Published: July 2019

After a stroke, descending drive is impaired due to the loss of corticospinal and corticobulbar projections which causes a reduction in voluntary activation or an inability of the nervous system to activate muscles to their full capacity, which in turn contributes to weakness of the upper extremity. Voluntary activation has not been quantified at specific joints in the upper extremity, in part because directly assessing changes descending drive is difficult. In this study, voluntary activation of elbow and wrist flexors and extensors was assessed in participants with chronic hemiparetic stroke using twitch interpolation. Twitch interpolation uses electrical stimulation to estimate voluntary activation and relies on the principle that there is an inverse relationship between the amplitude of a twitch evoked by a stimulus and the voluntary force output during stimulation (Taylor, 2009). We measured voluntary activation using twitch interpolation as well as maximum voluntary torque (MVT) of the elbow and wrist flexors and extensors in the paretic and non-paretic limb of ten participants post stroke and the dominant and non-dominant limb of 2 control participants. Results show, MVT interlimb differences were significantly greater for stroke participants compared to control, across muscle groups (p≤0.005). For stroke participants, MVT interlimb differences were significantly greater at the wrist compared to the elbow (P=0.003). Voluntary activation was significantly less in the paretic limb compared to the non-paretic, dominant and non-dominant limbs, across participants and muscle groups (p<0.005 for all four muscle groups). For the stroke participants, the voluntary activation interlimb difference was significantly greater for the wrist muscles compared to the elbow muscles (p<0.005). There was a significant positive correlation (r = 0.39, P = .022) between each participant’s impairment level, as measured by a hand specific subscore of the Fugl-Meyer Assessment, and the wrist extensor voluntary activation in the paretic limb but the relationship was not significant for the other muscle groups.