bluuebunny/crossref_metadata_2025 huggingface dataset:
Household and Family
Authors: Dolansky Fanny
Published: December 2018

This chapter provides cultural background for early Christian ritual through an overview of Roman sacra familiae (domestic rites). It offers representative examples from three main areas of domestic religious practice: (1) regular worship of the gods at household shrines; (2) rites de passage or lifecycle rituals, as illustrated by a freeborn boy’s coming of age ceremony; and (3) annual festivals concerned with interactions between freeborn and slave members of the household, and relations between the living and the dead as demonstrated by the commemorative Parentalia festival. These rituals reveal the importance of prayer and sacrifice as key means of communicating with the gods and securing their favour, and the principle of reciprocity which was a cornerstone of Roman religion. Sacra familiae helped to cultivate core social values and unite the household’s diverse membership in a community of worshippers who shared a sense of common identity predicated upon long-standing traditions and beliefs.
Divination
Authors: Nissinen Martti
Published: December 2018

The chapter investigates the ritual aspect of ancient Eastern Mediterranean divination. Divination is defined as acquisition and transmission of allegedly superhuman knowledge by different means and understood as a cognitive process linking human action with its (presumed) preconditions and its (presumed) effects. The emphasis of the divinatory agency is on the preconditions of the action, not on the effect as in magical agency. Examples from ancient Eastern Mediterranean divinatory practices, especially extispicy and prophecy and the Early Christian lot oracle, are used to demonstrate different facets of the ritual aspect in the acquisition and transmission of allegedly divine knowledge. Divinatory acts are often embedded in a ritual setting, and can sometimes as such be characterized as rituals, sharing important characteristics with the so-called special agent rituals.
Rituals of Reintegration
Authors: Roitto Rikard
Published: December 2018

In early Christianity, conflict resolution that involved decisions about exclusion and reintegration of community members was often ritualized as excommunication, penance, confession of sins, and intercession. Mediation of divine forgiveness of sin was central to the rituals that reintegrated transgressing community members and reconciled them with the community. This chapter discusses the experience of ritual forgiveness of sins, the reintegrative shame of penance and confession, confession as costly signalling of commitment, and confession and intercession as social identity maintenance.
Ritual and Emerging Church Hierarchy
Authors: Hylen Susan E.
Published: December 2018

Tradition and scholarship have often assumed that early Christian ritual authority coincided with church office. More recent scholarship raises questions about the uniformity of ancient practices and the extent to which ritual authority was concentrated in the offices of deacon, presbyter, or bishop. This chapter assesses writings of the first and second centuries to discover what kinds of ritual authority they indicate and whether they locate ritual authority in a particular office. Drawing on ritual theory, the chapter argues that language describing baptism, eucharist, and other meal rituals points to the establishment of ritual hierarchies through the enactment of the rites. However, the early texts also leave open the identity and office of the ritual specialists. Many early Christians—male and female, of varying offices or without any office—likely assumed these ritual roles.
Ritual as Action, Performance, and Practice
Authors: Stephenson Barry
Published: December 2018

Throughout the 1970s and the 1980s, scholarly theories of ritual began incorporating the language of ‘action’, ‘performance’, and ‘practice’, partly as a corrective to perceived limitations to existing theory, which was dominated by structuralism and communicative models. Ritual, once conceived as staid and habitual—in the best case, expressive, communicative, and symbolic of already existing ideas, beliefs, and values—was approached freshly in terms of agency and efficacy. In early theory, ritual was said to function as a kind of social glue, binding individuals in groups and confirming social statuses and hierarchies. Performance and action-centred theories variously analyse the socially disruptive and transformative potentials of ritual, questions of aesthetics and embodiment, and the formal, invariant properties of ritual. ‘Action’ is a particularly difficult concept, as it is conceived and used in ritual theory in several different, sometimes antithetical ways.
Christian Initiation
Authors: Bradshaw Paul F.
Published: December 2018

The limited evidence for Christian initiation practices in Syria and North Africa in the third century suggests ritual patterns that differed from each other in some ways but followed the three-stage structure of rites of passage outlined by Arnold van Gennep, even if the first and third of the stages were relatively undeveloped at that time. The fourth century saw the elaboration of these together with the temporal contraction of the middle or liminal phase in the rites of Syria and Milan, as well as in the variant practice of the city of Jerusalem.
Eucharistic Practices
Authors: Larson-Miller Lizette
Published: December 2018

The rapidly changing circumstances of Christianity between the third and fifth centuries are mirrored in the ritual changes of the church’s celebration of the Eucharist. The juxtaposition of continuity of theological expression in an act of thanksgiving, remembrance, and sacrifice with the multiple ecclesial political and cultural shifts throughout the church is reflected in changing interpretations, texts, and patterns. This chapter reviews the extant texts both about and from the liturgy in the three centuries in question before turning to three ritual and theological issues that exemplify the pressures of expressing and creating new ways of believing what is accomplished in the liturgical event. First is the development in understanding eucharistic participation as a ritual of Christian identity, and second, the embodiment of early Christian eucharistic participation in eating and drinking as well as the non-participation of fasting, which both contribute to the importance of cultic leadership in the development of ordained ministry.
Ritualizing Time
Authors: Day Juliette J.
Published: December 2018

Much valuable work has been done in the last fifty years to establish the historical origins and development of early Christian festivals and commemorations; this chapter extends this work by applying selected approaches from ritual studies to explore the meaning and meaningfulness of rituals of/in time for participants and communities. In the application of mythical or sacred time to chronological or human time, sacramental and calendrical rites assert their efficacy by joining together human and divine or divinized participants. These festivals find their place in the calendar due to a variety of reasons—historical, ideological, and chronological. They establish group identity and boundaries not just in terms of membership, but also foster ideological cohesion, as the debates over the date of Easter demonstrate. Finally, the chapter explores the extent to which the conduct of festivals should correlate to the foundational event or myth, and the effect of participants’ emotional response upon memory and belief.
Women’s Rituals and Women’s Ritualizing
Authors: Day Juliette J.
Published: December 2018

Although women participated in the early Christian rituals described elsewhere in this book, it would not be accurate to presume that their participation was in any way identical to that of men, nor even to the elite men whose evidence forms the basis of scholarly discussions. This chapter focuses on women’s ritualizing in relation to their bodies, the domestic sphere, in women-only religious communities, and in relation to the ecclesial hierarchy. It suggests that in some cases the approaches used by contemporary ritual theorists are insufficiently nuanced to allow for gender difference.
Ritual and Orthodoxy
Authors: Perkins Pheme
Published: December 2018

Study of Christian origins typically separates the development of orthodox doctrines from community rituals of baptism, eucharist, or anointing of the sick and dying. Ritual studies are an appendix to arguments over the truth of teachings about God, the nature of Christ, salvation, and the canon of Scripture. This chapter argues that emerging Christianity was primarily a community that gathered to engage in ritual activities. Its rituals of baptism and eucharist are at the core of community identity in 1 Corinthians and Romans. The energy fuelling intra-Christian disputes reflects anxieties over the effectiveness of ritual celebrations in the pluralistic setting of early Christian assemblies. Both poetic fragments in Christian texts and artistic settings like the baptistery at Dura Europos demonstrate the powers of ritual to reconfigure participants’ vision of the self in the cosmos. Valentinian, Marcionite, and Manichaean authors and their orthodox opponents mirror diverse ritual praxis.
Ritual and the Christianization of Urban Space
Authors: Latham Jacob A.
Published: December 2018

Most studies of the Christianization of cities focus on churches, bishops, or conversion. However, to make cities ‘Christian’ in some way, Christian groups also had to re-frame how the city was conceived and to develop new urban practices. In sermons, Christian preachers attempted to re-conceptualize the city, while some Christian inscriptions attempted to write Christian history into the urban fabric. Newly developed Christian processions as well as Christianized public ceremonies similarly served to transform urban habits. Processional participants claimed to represent the city, even as the procession claimed the city itself. These ritual acts of place-making, whether rhetorical or performed, changed the city as much as church construction even though they did not (physically) change a thing. This ritual Christianization of cities began with Constantine, the first Christian emperor, but it continued for centuries after; if it ever ended.
Ritualization and Ritual Invention
Authors: Stephenson Barry
Published: December 2018

In the lexicon of ritual theory, the notion of ritualization bears a heavy load. The concept aims to account for both the origins and functions of ritual (at both the biological and cultural levels), as well as inform reflection on the meaning and merit of ritual and even ritual theory. Broadly, ritualization refers to modifications in behaviours (or actions) that, when combined, stereotyped, formalized, and repeated eventuate in recognizable rites (or rituals). Ritualization is to ritual as a tree is to a house or a gear to a bike. Since ritualization is especially concerned with processes, the concept is important to discussions of the dynamics of ritual—its origins, changes, adaptations, and developments. Different theorists, however, use the concept in quite specific, sometimes antithetical, ways.
Ritual and Transmission
Authors: Czachesz István
Published: December 2018

This chapter asks the question of how rituals contribute to cultural transmission. Scholars of rituals have taken for granted that rituals somehow preserve traditions; however, how they achieve that has remained an understudied problem. The first section outlines the problem of transmission against the background of religious studies and more traditional approaches to rituals. The second section concentrates on what ritual theories tell us about memory and its involvement in rituals, with special attention to Whitehouse’s theory of the modes of religiosity and insights from the cognitive science of religion. The third section reviews important developments in memory studies that allow for a more nuanced understanding of the role of memory in rituals. The fourth section considers the role of actions, artefacts, and epigenetics in ritual transmission. Finally, the chapter concludes by outlining a model of inheritance systems to study transmission in rituals.
Associations, Guilds, Clubs
Authors: Kloppenborg John S.
Published: December 2018

Life in the cities and towns of the Hellenistic and Roman periods was organized around two poles: the polis or town, and the family, each with its distinctive structure, organization, membership, and cultic practices. Between these two poles there existed a large number of more or less permanent private associations, guilds, and clubs. A variety of types of ritualized behaviours were common in associations, many of them mimicking political or domestic rituals. Since many associations represented non-elite persons, politically disenfranchised in the cities in which they lived, the mimicry of political rituals functioned both to create social imaginaries that connected them to the polis and to cement affective bonds.
Intellectual Prehistory: Introduction
Authors: Lacewing Michael , Gipps Richard G.T.
Published: December 2018

This section of the Handbook consists of five chapters that focus on how psychoanalysis intersects with the history of philosophy. Three themes are examined: philosophical anticipations of psychoanalytic ideas; the clarification of psychoanalytic ideas by situating them in their intellectual context; and alternative approaches to psychoanalytic material provided by philosophers such as Friedrich Nietzsche and Baruch Spinoza. Also considered in this section is how Nietzsche and Arthur Schopenhauer anticipated aspects of Sigmund Freud’s psychoanalytic theory. The first chapter explores Schopenhauer’s conception of mankind’s motivations and his writings on madness, the second deals with Freud’s thinking on sexuality and the sexual drive, and the third describes an implicit concept of an unconscious first made explicit by Friedrich Wilhelm Joseph von Schelling and later deployed to explicate human motivation by Schopenhauer and Nietzsche. The last two chapters discuss sublimation and the solipsistic aspect of Freud’s systematization.
Imagination and Reason, Method and Mourning in Freudian Psychoanalysis
Authors: Lear Jonathan
Published: December 2018

This chapter begins with a consideration of transience and mourning as a way of thinking about what a failure of imagination might be. It then considers why the ‘fundamental rule’ of psychoanalysis is truly fundamental: not only for psychoanalytic method, but also for understanding why Freudian psychoanalysis is of philosophical significance. The fundamental rule opens up a new meaning of speaking one’s mind. The chapter argues that the psychoanalytic method is a deployment of reason, properly understood. For it is that activity of mind through which reason comes to an understanding of the mental activities—the thinkings—of non-rational and unconscious parts of the human psyche. It thus illuminates Socrates’ claim in the Republic that reason ought to take the lead in organizing human life because it has insight into the whole psyche. The chapter examines what it is for the unconscious to function as a fate.
Literary Form and Mentalization
Authors: Galgut Elisa
Published: December 2018

This chapter argues that literature—or at least certain kinds of literature—facilitates mentalization. Book reading shares some of the same features as mind reading. Psychoanalysis, via the work of Hanna Segal and others, has been interested in the differences between escapist literature and literature that encourages genuine psychological engagement. This chapter engages that issue via the lens of mentalization. It focuses specifically on literary form rather than on content, and examines the ways in which some kinds of literary form facilitate mentalizing capacities. More narrowly, it shows how different kinds of literary techniques—the free indirect discourse employed by Jane Austen, the tight structure of the sonnet form—enable different mentalizing abilities and develop our capacity for self-reflection.
The No-Thing of God: Psychoanalysis of Religion After Lacan
Authors: Boothby Richard
Published: December 2018

This chapter traces some main lines of Jacques Lacan’s interpretation of religion and divinity, which differs significantly from Freud’s critique. Orienting ourselves with respect to what Lacan calls das Ding, the enigmatic desire of the Other, it is possible to sketch a Lacanian analysis of religion parallel to that offered by Kant in Religion Within the Limits of Reason Alone. The difference is that where Kant looked to find in religious representations, especially those of Christianity, the underlying dynamics of pure rationality and of a morality founded upon it, Lacan discerns the very structure of subjectivity and its relation to the unknown Other. New perspectives are thereby opened up on a whole series of problems, including the unconscious dynamics of enjoyment, practices of sacrifice, the structural differences between various religions, and Christian doctrines of incarnation, love, and mystical unknowing.
Epistemic Anxiety
Authors: Rustin Michael
Published: December 2018

This chapter develops a concept of epistemic anxiety and explores its particular relevance to educational settings and to wider contexts in contemporary society. The idea brings into conjunction two significant psychoanalytical ideas. The first is that of the epistemophilic instinct proposed, following Freud’s reflections on anxiety, by Melanie Klein and developed by Wilfred Bion into a theory of thinking and its relations to love and hate. The second is the theory of unconscious social defences against anxiety which first evolved within the Tavistock tradition of psychoanalytic social research in the 1950s and has recently been subject to reappraisal and new applications. Its argument is that epistemic anxiety frequently arises in learning situations, and that learning and thinking can be facilitated if this is understood.
‘In Psychoanalysis Nothing Is True but the Exaggerations’: Freud and the Frankfurt School
Authors: Jay Martin E.
Published: December 2018

Over its long history, the Frankfurt School attempted to enrich its critique of modern society, largely rooted in its imaginative rereading of the Marxist tradition, by drawing on insights from psychoanalysis. Although the specific insights informing the work of Erich Fromm, Max Horkheimer, Herbert Marcuse, and Theodor W. Adorno may have been different, all supported the productive integration of Marx and Freud. In particular, the Frankfurt School used Freudian theory to explain the failure of the working class to assume its putative revolutionary mission, the unexpected rise of fascism, and the possible ways in which utopia might be envisaged. In addition, most explicitly in the work of Adorno, they pitted the materialist impulses of psychoanalysis against the consciousness philosophy they identified with the Idealist tradition.
The psychology of expressing and interpreting linguistic taboos
Authors: Jay Timothy B.
Published: December 2018

This chapter describes from a psychological point of view two aspects of taboo word use in American English: the ways people use taboo words to express themselves and the ways people comprehend taboo word expressions. Expression topics selected here include: spoken frequency, verbal fluency, personality traits, emotion expression, anger and frustration, name calling, humor, and coping with pain. Interpretation topics selected include: connotation and denotation, word offensiveness, frequency judgments, fighting words, sexual harassment, and pragmatic contextual variables. The production of expressions with taboo words, as well as the interpretation of them, depends on contextual variables encompassing the expressions including: the speaker–listener relationship and their ages, the social and physical context, and the intended meaning and emotional valence of the expression. Universal statements cannot be made about the production or interpretation of taboo word expressions due to the influence of contextual variables.
Taboo terms and their grammar
Authors: Hoeksema Jack
Published: December 2018

Taboo terms are used for far more than verbal abuse and linguistic mayhem. They may serve to strengthen questions and negative statements, they express high degree, and add negative connotations to otherwise neutral words. They may appear as negative polarity items, but also as positive polarity items. The variety of ways in which they may be employed is quite remarkable, and deserves to be studied from a cross-linguistic perspective. This chapter presents an overview of the main uses of taboo terms and the syntactic constructions they give rise to, and illustrates with material taken largely from English and Dutch, but in addition German, Estonian, Polish, and modern Hebrew.
Bone maturation of MRI residual developmental dysplasia of the hip with discrepancy between osseous and cartilaginous acetabular index
Authors: Walbron Paul , Müller Florence , Mainard-Simard Laurence , Luc Amandine , Journeau Pierre
Published: December 2018

Quality of spontaneous amelioration of residual developmental dysplasia of the hip (DDH) is nowadays not possible to predict. Normal age-related values of the osseous acetabular index (OAI), cartilaginous acetabular index and labral acetabular index have been established on MRI. In this study, MRI of dysplastic hips has been evaluated, and further osseous acetabular maturation was followed-up over time on pelvic radiography to find a correlation between MRI findings and radiological evolution. This is a retrospective single-centre study. Children with DDH who had a pelvic MRI between February 2007 and June 2014 were included. AI was measured for osseous (OAI), cartilaginous (cartilaginous acetabular index) and labral (labral acetabular index) values on MRI. OAI was thereafter recorded on each available radiograph during follow-up. A total of 20 hips were included. The mean age at MRI diagnosis was 3.55 years. Two types of DDH were observed: harmonious dysplasia, associated with an osseous and cartilaginous defect (group A, n = 14), and divergent dysplasia, associated with an osseous defect but with sufficient cartilaginous coverage (group B, n = 6). The mean age at final radiological follow-up was 7.6 and 8.3 years (P = 0.7408), respectively. In group A, four (28.6%) children older than 6 years had an OAI of less than 18°, whereas only two (33.3%) children older than 6 years had an OAI less than 18° in group B (P = 0.0117). This study shows that, in one-third of cases, divergent dysplasia leads to a spontaneous recovery. MRI should be used early to accurately diagnose and follow-up DDH cases and allow surgeons to justify the required surgical treatment. Level of Evidence: IV.
Participation in a population-based screening for colorectal cancer using the faecal immunochemical test decreases mortality in 5 years
Authors: Idigoras Rubio Isabel , Arana-Arri Eunate , Portillo Villares Isabel , Bilbao Iturribarrria Isabel , Martínez-Indart Lorea , Imaz-Ayo Natale , de la Cruz Marta , de Castro Visitación , López de Munain Arantza , Torrejón Perez Idoia , Gutiérrez-Ibarluzea Iñaki
Published: December 2018

Background

The steady increase in colorectal cancer (CRC) could be reversed through timely secondary prevention (screening) as a main strategy. The aims of this study were to determine the main features of CRC, survival rate and related factors for different types of identified CRCs in a population-based screening programme using the faecal immunochemical test (FIT).

Materials and methods

The CRCs in the susceptible population to be screened between 2009 and 2014 were identified and classified into four groups: (a) nonscreening-detected CRC (diagnosed before first screening invitation and nonparticipants), (b) screening-detected CRC, (c) interval cancer (IC) FIT (diagnosed between screening rounds after a negative FIT) and (d) IC colonoscopy (diagnosed before the colonoscopy surveillance, which is recommended after the screening colonoscopy). Patient demographics and epidemiological characteristics, tumour characteristics and survival were compared between the four groups.

Results

5909 individuals were diagnosed with a CRC. The median follow-up of survival was 4.6 years (range: 0–9 years). The study highlights a significant difference (P<0.0001) in the 5-year survival in the screening-detected CRC group compared with those who had nonscreening-detected CRCs (90.1 vs. 66.7%). Although ICs are not desirable events, the 5-year survival rate is significantly higher with respect to nonparticipants (P<0.0001) (76.3 vs. 60.5%), this being the group with the lowest survival rate.

Conclusion

The significantly higher 5-year survival rate of 23.4% of the participants in the screening programme suggests that incidence and mortality rates of CRC will decrease in the near future for participants in screening programmes. A high participation rate is essential to achieve health benefits, irrespective of the type of participation.
Characterization of Triniti virus supports its reclassification in the family Peribunyaviridae
Authors: Lima Juliana Abreu , Nunes Neto Joaquim Pinto , Castro Karoline Silva , Travassos da Rosa Amélia Paes de Andrade , Tesh Robert , Nunes Márcio Roberto Teixeira , Popov Vsevolod Leonidovich , Vasilakis Nikos , Guzman Hilda , Widen Steven , Silva Sandro Patroca da , Medeiros Daniele Barbosa de Almeida , Cardoso Jedson Ferreira , Martins Lívia Carício , Azevedo Raimunda do Socorro da Silva , Vasconcelos Pedro Fernando da Costa , Chiang Jannifer Oliveira
Published: December 2018

Triniti virus (TNTV) has been isolated in Trinidad and Tobago and in Brazil. To date little is known about this virus, which is classified as an ungrouped virus within the family Togaviridae. Here, three isolates of TNTV were characterized both genetically and antigenically. The genome was shown to contain three RNA segments: small (S), medium (M) and large (L). Genome organization, protein sizes and protein motifs were similar to those of viruses in the genus Orthobunyavirus, family Peribunyaviridae. Antigenic reactivity revealed the three TNTV isolates to be closely related, but no serologic cross-reaction with other orthobunyaviruses. Morphological observation by transmission electron microscopy indicated that virus size and symmetry were compatible with those of viruses in the family Peribunyaviridae. Our serological, morphological and molecular results support the taxonomic reclassification of TNTV as a member of the genus Orthobunyavirus, family Peribunyaviridae.
Drought frequency predicts life history strategies in Heliophila
Authors: Monroe J. Grey , Gill Brian , Turner Kathryn , McKay John K
Published: December 2018

Explaining variation in life history strategies is a long-standing goal of evolutionary biology. For plants, annual and perennial life histories are thought to reflect adaptation to environments that differ in the frequency of stress events such as drought. Here we test this hypothesis in Heliophila (Brassicaceae), a diverse genus of flowering plants native to Africa, by integrating 34 years of satellite-based drought measurements with 2192 herbaria occurrence records. Consistent with predictions from classic life history theory, we find that perennial Heliophila species occur in environments where droughts are significantly less frequent compared to annuals. These associations are predictive while controlling for phylogeny, lending support to the hypothesis that drought related natural selection has influenced the distributions of these strategies. Additionally, the collection dates of annual and perennial species indicate that annuals escape drought prone seasons during the seed phase of their life cycle. Together, these findings provide empirical support for classic hypotheses about the drivers of life history strategy in plants - that perennials out compete annuals in environments with less frequent drought and that annuals are adapted to environments with more frequent drought by escaping drought prone seasons as seeds.
Rare variants imputation in admixed populations: Comparison across reference panels and bioinformatics tools
Authors: Sariya Sanjeev , Lee Joseph , Mayeux Richard , Vardarajan Badri N. , Reyes-Dumeyer Dolly , Manly Jennifer , Brickman Adam , Lantigua Rafael , Medrano Martin , Jimenez-Velazquez Ivonne Z. , Tosto Giuseppe
Published: December 2018

Background

Imputation has become a standard approach in genome-wide association studies (GWAS) to infer in silico untyped markers. Although feasibility for common variants imputation is well established, we aimed to assess rare and ultra-rare variants’ imputation in an admixed Caribbean Hispanic population (CH).

Methods

We evaluated imputation accuracy in CH (N = 1,000), focusing on rare (0.1% ≤minor allele frequency (MAF) ≤ 1%) and ultra-rare (MAF < 0.1%) variants. We used two reference panels, the Haplotype Reference Consortium (HRC; N = 27,165) and 1000 Genome Project (1000G phase 3; N = 2,504) and multiple phasing (SHAPEIT, Eagle2) and imputation algorithms (IMPUTE2, MACH-Admix). To assess imputation quality, we reported: a) high-quality variant counts according to imputation tools’ internal indexes (e.g. IMPUTE2 “Info”≥80%). b) Wilcoxon Signed-Rank Test comparing imputation quality for genotyped variants that were masked and imputed; c) Cohen’s kappa coefficient to test agreement between imputed and whole-exome sequencing (WES) variants; d) imputation of G206A mutation in the PSEN1 (ultra-rare in the general population an more frequent in CH) followed by confirmation genotyping. We also tested ancestry proportion (European, African and Native American) against WES-imputation mismatches in a Poisson regression fashion.

Results

SHAPEIT2 retrieved higher percentage of imputed high-quality variants than Eagle2 (rare: 51.02% vs. 48.60%; ultra-rare 0.66% vs 0.65%, Wilcoxon p-value < 0.001). SHAPEIT-IMPUTE2 employing HRC outperformed 1000G (64.50% vs. 59.17%; 1.69% vs 0.75% for high-quality rare and ultra-rare variants, respectively; Wilcoxon p-value < 0.001). SHAPEIT-IMPUTE2 outperformed MaCH-Admix. Compared to 1000G, HRC-imputation retrieved a higher number of high-quality rare and ultra-rare variants, despite showing lower agreement between imputed and WES variants (e.g. rare: 98.86% for HRC vs. 99.02% for 1000G). High Kappa (K = 0.99) was observed for both reference panels. Twelve G206A mutation carriers were imputed and all validated by confirmation genotyping. African ancestry was associated with higher imputation errors for uncommon and rare variants (p-value < 1e-05).

Conclusion

Reference panels with larger numbers of haplotypes can improve imputation quality for rare and ultra-rare variants in admixed populations such as CH. Ethnic composition is an important predictor of imputation accuracy, with higher African ancestry associated with poorer imputation accuracy.
Bone-Inspired Microarchitectured Materials with Enhanced Fatigue Life
Authors: Torres Ashley M. , Trikanad Adwait A. , Aubin Cameron A. , Lambers Floor M. , Luna Marysol , Rimnac Clare M. , Zavattieri Pablo , Hernandez Christopher J.
Published: December 2018

Microarchitectured materials achieve superior mechanical properties through geometry rather than composition1-4. Although lightweight, high-porosity microarchitectured materials can have high stiffness and strength, stress concentrations within the microstructure can cause flaw intolerance under cyclic loading5,6, limiting fatigue life. However, it is not known how microarchitecture contributes to fatigue life. Naturally occurring materials can display exceptional mechanical performance and are useful models for the design of microarchitectured materials7,8. Cancellous bone is a naturally occurring microarchitectured material that often survives decades of habitual cyclic loading without failure. Here we show that resistance to fatigue failure in cancellous bone is sensitive to the proportion of material oriented transverse to applied loads – a 30% increase in density caused by thickening transversely oriented struts increases fatigue life by 10-100 times. This finding is surprising in that transversely oriented struts have negligible effects on axial stiffness, strength and energy absorption. The effects of transversely oriented material on fatigue life are also present in synthetic lattice microstructures. In both cancellous bone and synthetic microarchitectures, the fatigue life can be predicted using the applied cyclic stress after adjustment for apparent stiffness and the proportion of the microstructure oriented transverse to applied loading. In the design of microarchitectured materials, stiffness, strength and energy absorption is often enhanced by aligning the microstructure in a preferred direction. Our findings show that introduction of such anisotropy, by reducing the amount of material oriented transverse to loading, comes at the cost of reduced fatigue life. Fatigue failure of durable devices and components generates substantial economic costs associated with repair and replacement. As advancements in additive manufacturing expand the use of microarchitectured materials to reusable devices including aerospace applications, it is increasingly necessary to balance the need for fatigue life with those of strength and density.
Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads
Authors: De La Harpe Marylaure , Paris Margot , Hess Jaqueline , Barfuss Michael H. J. , Serrano-Serrano Martha L. , Ghatak Arindam , Chaturvedi Palak , Weckwerth Wolfram , Till Walter , Salamin Nicolas , Wai Ching Man , Ming Ray , Lexer Christian
Published: December 2018

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by several ‘key innovations’ including the transition from C3 to CAM photosynthesis. We used a phylogenomic approach complemented by differential gene expression (RNA-seq) and targeted metabolite profiling to address the patterns and mechanisms of C3/CAM evolution in the extremely species-rich bromeliad genus Tillandsia and related taxa. Evolutionary analyses at a range of different levels (selection on protein-coding genes, gene duplication and loss, regulatory evolution) revealed three common themes driving the evolution of CAM: response to heat and drought, alterations to basic carbohydrate metabolism, and regulation of organic acid storage. At the level of genes and their products, CAM/C3 shifts were accompanied by gene expansion of a circadian regulator, re-programming of ABA-related gene expression, and adaptive sequence evolution of an enolase, effectively linking carbohydrate metabolism to ABA-mediated stress response. These changes include several pleiotropic regulators, which facilitated the evolution of correlated adaptive traits during a textbook adaptive radiation.
Tissue distribution and tumor concentrations of hydroxychloroquine and quinacrine analogs in mice
Authors: Solitro Abigail R. , MacKeigan Jeffrey P.
Published: December 2018

Hydroxychloroquine (HCQ) is a 4-aminoquinoline molecule used for the treatment of malaria, and more recently to treat rheumatoid arthritis, systemic lupus erythematosus, and cancer. In cancer, HCQ is being used in multiple cancer clinical trials as an inhibitor of autophagy, a cytosolic degradation process employing the lysosome. Importantly, more potent lysosomotropic agents are being developed as autophagy inhibitors. Additional studies revealed that acridine-based compounds such as quinacrine (QN) increased potency over the 4-aminoquinoline HCQ. In line with these initial discoveries, we performed chemical synthesis of acridine-based compounds and screened for potent autophagy inhibition. The novel compound VATG-027 increased potency and cytotoxicity over HCQ in osteosarcoma and melanoma cell lines, supporting further investigation in vivo. Here, we developed a liquid chromatography tandem mass spectrometry (LC-MS/MS) method to investigate HCQ, QN, and VATG-027 compound concentrations across various tissue types in mice. This method detected compound concentrations in whole blood, lung, liver, kidney, and subcutaneous tumor tissues. Concentrations of HCQ, QN, and VATG-027 varied within and between tissue types, suggesting unique tissue distribution profiles for 4-aminoquinoline and acridine compounds.
TDAG8 (GPR65) Inhibits Intestinal Inflammation in the DSS-Induced Experimental Colitis Mouse Model
Authors: Sanderlin Edward J , Satturwar Swati , Hong Heng , Lertpiriyapong Kvin , Marie Mona , Yang Li V
Published: December 2018

T cell death-associated gene 8 (TDAG8, also known as GPR65) is a proton-sensing G protein-coupled receptor (GPCR) predominantly expressed in immune cells. Genome-wide association studies identify TDAG8 as a susceptibility candidate gene linked to several human inflammatory diseases including inflammatory bowel disease (IBD), asthma, spondyloarthritis, and multiple sclerosis. In this study, our results demonstrate that mice deficient of TDAG8 exhibited more severe inflammatory phenotypes than wild-type mice in a chronic dextran sulfate sodium (DSS)-induced colitis mouse model. Several disease parameters, such as diarrhea, colon shortening, fibrosis, histopathological score, and mesenteric lymph node enlargement were aggravated in TDAG8-null mice in comparison to wild-type mice treated with DSS. Increased leukocyte infiltration and myofibroblast expansion were observed in colonic tissues of DSS-treated TDAG8-null mice. These changes may represent a cellular basis of the observed exacerbation of intestinal inflammation and fibrosis in these mice. In line with high expression of TDAG8 in infiltrated leukocytes, real-time RT-PCR revealed that TDAG8 mRNA expression was increased in inflamed intestinal tissue samples of IBD patients when compared to normal intestinal tissues. Altogether, our data demonstrate that TDAG8 suppresses intestinal inflammation and fibrosis in the chronic DSS-induced colitis mouse model, suggesting potentiation of TDAG8 with agonists may have anti-inflammatory therapeutic effects in IBD.
Spatiotemporal Variability in Dengue Transmission Intensity in Jakarta, Indonesia
Authors: O’Driscoll Megan , Imai Natsuko , Ferguson Neil M. , Hadinegoro Sri Rezeki , Satari Hindra Irawan , Tam Clarence C. , Dorigatti Ilaria
Published: December 2018

Background

Approximately 70% of the global burden of dengue disease occurs on the Asian continent, where many large urban centres provide optimal environments for sustained endemic transmission and periodic epidemic cycles. Jakarta, the capital of Indonesia, is a densely populated megacity with hyperendemic dengue transmission. Characterization of the spatiotemporal distribution of dengue transmission intensity is of key importance for optimal implementation of novel control and prevention programmes, including vaccination. In this paper we use mathematical models to provide the first detailed description of spatial and temporal variability in dengue transmission in Jakarta.

Methodology/Principal Findings

We applied catalytic models in a Bayesian framework to age-stratified dengue case notification data to estimate dengue force of infection and reporting probabilities in 42 subdistricts of Jakarta. The model was fit to yearly and average annual data covering a 10- year period between 2008 and 2017. We estimated a long-term average annual transmission intensity of 13.0% (95%CrI: 12.9-13.1%) per year in Jakarta province, ranging from 9.0% (95%CrI: 7.7-10.3%) to 16.4% (95%CrI: 15.3-17.4%) across subdistricts. Annual average transmission intensity in Jakarta province during the 10-year period ranged from 1.2% (95%CrI: 1.1-1.3%) in 2017 to 12.4% (95%CrI: 12.1-12.8%) in 2016.

Conclusions/Significance

While the absolute number of dengue case notifications cannot be relied upon as a measure of endemicity, the age-distribution of reported dengue cases provides valuable insights into the underlying nature of transmission. Our estimates from yearly and average annual case notification data represent the first detailed estimates of dengue transmission intensity in Jakarta’s subdistricts, which will be important to consider when assessing the population-level impact and cost-effectiveness of potential control and prevention programmes in Jakarta province, such as the controlled release of Wolbachia-carrying mosquitoes and vaccination.
Integrated single-cell potency and expression landscape in mammary epithelium reveals novel bipotent-like cells associated with breast cancer risk
Authors: Teschendorff Andrew E. , Morabito Samuel J , Kessenbrock Kai , Meyer Kerstin
Published: December 2018

The identification of progenitor and stem like cells in epithelial tissues, as well as those that may serve as the cell of origin for epithelial cancers, is an outstanding challenge. Here we present a novel algorithm, called LandSCENT, which constructs a 3-dimensional integrated landscape of cell-states, encompassing cell-potency and expression subtypes, to facilitate the identification of progenitor and stem-like cells. Application to thousands of single-cell RNA-Seq profiles from the normal mammary epithelium reveals a rare 5% subpopulation of highly potent single-cells. The integrated landscape naturally predicts that these cells define a bi-potent-like state, a result not obtainable via standard methods or without invoking prior assumptions. The bi-potent-like cells are overrepresented within the basal compartment but also overlap with an immature luminal phenotype. We characterize the transcriptome of these cells and show that is enriched for a mammary stem-cell module. We further identifyYBX1, a regulator of breast cancer risk identified from GWAS, as the key transcription factor defining this candidate bi-potent cellular phenotype. We validate the putative bi-potency ofYBX1-marked cells using independent FACS-sorted bulk expression data. In addition,YBX1is overexpressed in basal breast cancer and correlates with clinical outcome. In summary, we here provide a novel computational framework which may serve to identify and prioritize candidate normal or cancer progenitor/stem-like single-cell phenotypes, for subsequent functional studies.
Collection development procedure adopted for acquisition of EIRs across agricultural libraries of northern India
Authors: Bhat Nazir Ahmad , Ganaie Shabir Ahmad
Published: December 2018

Purpose

The purpose of this paper is to explore the change(s) brought about by the advent of electronic information resources in the overall collection development process across agricultural libraries of northern India.

Design/methodology/approach

A survey was conducted in 2015 by using a questionnaire as a data collection tool. The investigator also interacted with the librarians through telephone and also availed the e-mail service for required correspondence.

Findings

There is a major change in the identification, selection and acquisition procedures across agricultural libraries of northern India, as the majority of these libraries are seen to adhere to an onsite demo of products and services, as the publishers/vendors to set online trial for ample of time before any decision is taken. The libraries are also seen to take advantage of e-mail correspondence to identify, select and acquire best possible information products against utmost economical costs. The responsibility of identifying and selecting the required items devolves mainly with scientists/subject experts, whereas the requisitions of students and suggestions of library staff are comparatively taken as lesser cognisance, while executing this job Library advisory committee is the most prominent authority responsible for final approval of the purchase of e-resources, while “Heads of Divisions” also play a considerable role in this regard.

Research limitations/implications

Only seven agricultural libraries have been taken as a sample. Moreover, the work is confined to only four aspects, i.e. the identification, selection and acquisition procedures adopted and the authorities responsible for carrying out the job. Other aspects like that of adoption of proper collection development; policy and the criteria used for selection; and acquisition of information also need to be studied. Similar studies need to be conducted in other parts of India and also across libraries of other domains of knowledge.

Originality/value

This is a first work of its nature in northern India with its domain as agricultural libraries. The findings will help the librarians and the library advisory committees to decide on logical grounds about the identification, selection and acquisition procedures adopted at present and look forward for bringing about the uniformity and improvement in the process and make changes in the policy to make room for efficient acquisition of information resources.
Can’t take the heat? Climate and foreign subsidiary locations
Authors: Budde-Sung Amanda , Peacock Tanya A.
Published: December 2018

Purpose

This paper aims to build upon climato-economic theory to investigate the issue of climate’s effect on foreign expansion and location choice.

Design/methodology/approach

This empirical paper looks at foreign subsidiary location through the lens of the climato-economic theory. To do this, the study uses a balanced data set, looking at foreign expansion before, during and after the global financial crisis of US multinational firms. A multilevel step-wise regression is used to look at climate, culture and economic effects on foreign location choice.

Findings

The findings suggest that US multinational enterprises tend to have fewer foreign subsidiaries in countries with extreme climates, and they prefer locations with warmer climates, avoiding locations with colder climates, although they gravitate toward locations with less sunshine. Climate emerges as an important factor in location choice, with greater weighting than other factors, including economic and cultural factors in times of economic calm, but the weightings of the factors change during times of economic crisis.

Originality/value

This paper contributes to the global business literature by extending the climate-economic theory to macro levels affecting the firm. The paper is the first to look specifically at how climate affects foreign subsidiary location.