bluuebunny/crossref_metadata_2025 huggingface dataset:
WPS and Humanitarian Action
Authors: Martin Sarah , de la Puente Devanna
Published: December 2018

This chapter explores the challenges of addressing the women, peace, and security (WPS) agenda within humanitarian settings by examining experience and knowledge of field practitioners. Often WPS is seen as an issue to address only during post-conflict or development work, even though the same population is affected and there is no clear distinction between humanitarian and development environments. Local women’s organizations are humanitarian first-responders but their role in implementing WPS is neglected. This chapter argues that this artificial divide has limited efforts to promote women’s leadership, secure active participation, and promote the full protection of women’s rights in the humanitarian field. Recently, there has been progress on global commitments to address gender equality, women’s empowerment, and the protection of women and girls in disaster risk reduction and humanitarian response. Yet as this chapter demonstrates, accountability and the establishment of a cohesive link between these commitments remains a significant challenge. Throughout this chapter, the challenges of implementing the “orphan pillar” (relief and recovery) of Resolution 1325 is explored. Moreover, promising practices are highlighted in conflict and natural disaster response in Asia, Syria, and the European refugee crises, and Latin America.
WPS and LGBTI Rights
Authors: Davis Lisa , Stern Jessica
Published: December 2018

This chapter explores current activism and debates on the discourse of gender within the WPS agenda. To do so, the convergence of women’s and LGBTI rights organizing in Iraq is explored. The interpretation of gender under the Women, Peace, and Security (WPS) agenda is outdated, binary, and heteronormative. This narrow approach has overlooked the experiences of lesbians, bisexual women, transgender, and intersex (LBTI) people in conflict and disaster settings, failing to capture threats and/or create tailored responses to meet survivors’ needs. In response, lesbian, gay, bisexual, transgender, and intersex (LGBTI), and women’s rights activists have begun to collaborate, raising awareness about how gender and sexuality are intertwined. This chapter suggests that broadening the WPS agenda’s understanding of gender is in everyone’s interests. It argues that a broader interpretation of gender builds coalitions across the women’s and LGBTI movements which amount to a larger movement committed to ending violence against individuals for defying traditionally ascribed gender roles.
Contested Meanings of Equality
Authors: Moran Rachel F.
Published: December 2018

Many people take for granted that the antidiscrimination principle and an equality norm are one and the same. In fact, there are significant differences that should not be overlooked. Education law offers unique insights into the distinctions because school desegregation cases both concretized demands to be free of discrimination and cultivated aspirations to be equal. In the years since 1954, when the U.S. Supreme Court declared that racially separate schools are inherently unequal in Brown v. Board of Education, the antidiscrimination principle has evolved into a requirement that the government be colorblind; that is, public officials must refrain from all consideration of race in their decision-making. A colorblindness requirement can have perverse consequences for equality. Most notably, local school districts today cannot weigh race in making student assignments to promote voluntary integration. Faced with constraints like these, reformers have sought to capitalize on an antidiscrimination principle without sacrificing their goals for equality. For example, federal civil rights statutes designed to protect children with disabilities and English language learners mandate meaningful access to the curriculum as well as protection from discrimination. In school finance litigation, advocates have moved even further away from an antidiscrimination focus. They have demanded recognition of a right to education, an interest that acknowledges every child’s right to flourish. New strategies that push beyond the antidiscrimination principle to promote equal educational opportunity have not been uniformly successful, but they can deepen our understanding of a fair and inclusive educational system.
Business Organization in American Economic History
Authors: Hilt Eric
Published: December 2018

This chapter presents a history of the organization of American enterprise, from the first corporations to the emergence of large, vertically integrated conglomerates. It begins with a discussion of the monopolistic privileges of early corporations, and efforts to reform the process by which corporations were created. It then presents a discussion of the alternative organizational forms that became available to entrepreneurs. Finally, it analyzes the rise of “big business” in the late nineteenth century, and the legal and institutional context within which those enterprises began to emerge. The discussion of each is focused on the changing nature of the problems faced by entrepreneurs, and the changing legal and institutional environment in which they operated. Among the topics discussed are the evolution of corporation law, the choice of organizational form, recurring problems in corporate governance, the role of financiers in corporate governance, and the emergence of pyramidal holding company structures.
Lying and Certainty
Authors: Marsili Neri
Published: December 2018

In the philosophical literature on the definition of lying, the analysis is generally restricted to cases of flat-out belief. This chapter considers lies involving partial beliefs (beliefs ranging from mere uncertainty to absolute certainty). The first section analyses graded-belief lies: lies uttered while holding a graded belief in the falsity of the assertion. A revised insincerity condition is introduced to deal with these cases, requiring that the liar believes the assertion to be more likely to be false than true. The second section analyses assertions that express graded beliefs, exploring how epistemic modals affect the insincerity conditions of a given utterance. The last section considers the case of lies that attack certainty (knowledge lies), understood as attempts to alter the hearer’s graded beliefs.
Communal Meals
Authors: Ascough Richard S.
Published: December 2018

This chapter begins by briefly discussing the prevalence of communal meals in the Roman world and then turns attention to the form and setting of communal dining. Such meals were framed as semi-public events. While not everyone was invited—indeed, only a small cadre of the especially chosen took part—banquets were often located and structured so that they could be observed. Within the meal setting itself, seating arrangements were such that each participant was also an observer. The bulk of the chapter examines how communal dining rituals model the values of the surrounding culture while also serving to mirror these values back to the banqueters, thus reinforcing and legitimating these values within the group. While meal rituals have the potential to challenge societal norms, in practice, the replication of cultural values reinforce the dominant social order.
Ritual and Texts
Authors: Klostergaard Petersen Anders
Published: December 2018

This chapter focuses on the general problem pertaining to the relationship between ritual and text. What does it mean, when texts include references to ritual or resonate with language that originates in a ritual setting? There are at least three different problems pertinent to this relationship: (1) the relationship between the actual ritual and the text that purports to describe or evoke the ritual to the intended addressees of the text; (2) the question of rhetorical persuasiveness achieved by the evocation of ritual in the minds of the intended recipients; (3) the question of written texts which individually may become objects of ritual as is well known from Judaism, Christianity, and Islam. The chapter discusses all three issues and lays stress on ritual as a bridge that may enhance the plausibility of conveying the text to the recipients. In order to understand this, the chapter makes a detour to Peircian semiotics and argues in the vein of Roy Rappaport that ritual by virtue of its conjunction of indexical and symbolic components is crucial for achieving this effect. Ultimately, an overall Durkheimian view of ritual is espoused in which ritual (and cult) are seen as a prerequisite for creating and preserving culture and obtaining maintaining cultural cohesion.
Ritual and Healing
Authors: Theissen Gerd
Published: December 2018

Pre-modern forms of healing are based on two different cognitive symbolic interpretations: (1) the disease is caused either by a lack of power; or (2) by possession by an evil power. Healings are therefore due to ‘adorcism’ (the good spirits who had previously left the sick person re-enter him) and ‘exorcism’ (the bad spirits who had entered the person are driven out). Early Christianity institutionalized both forms of healing by increasing ritualization. Four theories of pre-modern healings are combined in a theory of effective correspondence: charismatic healing is based on the efficacy of faith (or the placebo effect), social healing on the reduction of social stress, symbolic healing, and ritual healing on the correspondence between internal symbolic and external processes. Embodied rituals are only effective if they are embedded in a social context, with charismatics, cognitive interpretations, and social support.
Early Christian Prayer
Authors: Phillips L. Edward
Published: December 2018

While it is difficult to determine with certainty the habits of daily prayer among the majority of early Christians, we can with care determine some structures of time, gesture, and communal boundaries by examining the written records. The chronological and gestural structures of daily prayer show more stability than the theological interpretations of prayer, which Jeremy Penner calls ‘strategies of legitimation’. This chapter will show how strategies of legitimation are ex post facto explanations of pre-established cultural patterns. Christian authorities drew upon biblical precedents and types to impart theological significance to prayer and to standardize private practices of time and ritual gesture. Distinctive Christian identity was fortified through restrictions such as limiting use of the Lord’s Prayer and the kiss of peace to the baptized. More attention is given to popular practice than to ascetical/monastic practice.
Hymns and Psalmody
Authors: Harkins Angela Kim , Dunkle, SJ Brian P.
Published: December 2018

This chapter examines early Christian hymnody from the point of view of ritual and embodied religious experience. The chapter explores the possible ways that we can recover the ritual experience of songs from antiquity to the post-Constantinian Church, from a study of hymnic collections and references to the performance of these texts in the Latin, Greek, and Syriac traditions.
Wedding Rituals and Episcopal Power
Authors: Hunter David G.
Published: December 2018

This chapter offers a survey of the development of Christian marriage rituals in the first four centuries. It pays special attention to the emerging role of bishops in the ‘consecration’ of Christian marriage through rituals of blessing and veiling. Using categories derived from the ritual theory of Catherine Bell and Pierre Bourdieu, the chapter argues that by displaying ‘ritual mastery’ in this area, the Christian bishops in late antiquity were able to define new symbolic boundaries and thereby enhanced their own authority as ritual agents.
The Cult of Saints
Authors: Eastman David L.
Published: December 2018

Veneration of holy people was a significant feature of early Christian piety. Through a collection of ritualized practices, Christians both received traditions handed down to them and contributed to the expansion of the image of the saints. Thus, ritual was a central factor in the creation of the cult of the saints. This chapter focuses on three of these practices: (1) the telling of stories; (2) pilgrimage; (3) and relic veneration. It then argues that the cult of the saints functioned to create the image of the martyrs as a special class of Christians, to promote the idea that suffering was the mark of true Christianity, to implant a distrust of government officials in Christian collective memory, and to provide opportunities for certain church leaders to control expressions of piety by the populace.
Ancient Sanctuaries
Authors: Raja Rubina
Published: December 2018

This chapter is concerned with ancient sanctuaries and their spaces as places where rituals were performed. It discusses various aspects of sanctuaries and their materiality, and the ways in which reconstructing ritual practice and performance may be approached through archaeological and written sources, which give an insight into sanctuaries and their use. Different types of sanctuaries, primarily from the Roman imperial period (the late first century bce to the fourth century ce) from a variety of locations across the Roman Empire are considered. Furthermore, a number of cults that had specific types of sanctuaries connected to them are presented, such as those of the so-called Mystery cults of, for example, Mithras and Isis. Architectural layouts as well as embellishments, such as decorations and ritual objects, are discussed in brief also, in order to explain ancient sanctuaries as places where ritual experiences occurred. Furthermore, theoretical approaches, among those, the ‘lived ancient religion’ approach, are addressed in order to situate the ways in which such approaches may further our understanding of ancient ritual spaces.
Merleau-Ponty and Psychoanalysis
Authors: Phillips James
Published: December 2018

This chapter traces the trajectory of Maurice Merleau-Ponty’s views on psychoanalysis and the Freudian unconscious. It begins with a discussion of Merleau-Ponty’s first reading of Sigmund Freud by way of The Structure of Behavior, his development of a full description of perceptual consciousness in the Phenomenology of Perception, and his interpretation of the Freudian unconscious as the ambiguity of operative intentionality or perceptual consciousness. The chapter goes on to consider Merleau-Ponty’s lectures as Professor of Psychology at the Sorbonne from 1949 to 1952, the criticisms hurled against his early work, and his relationship with Jacques Lacan. It also examines themes from Merleau-Ponty’s lectures at the Collège de France between 1951 until his death, along with two of his posthumous writings: The Visible and the Invisible, and a Preface to L’Oeuvre de Freud et son Importance pour la Monde, a book on Freud by psychoanalyst Angelo Hesnard.
Ricœur’s Freud
Authors: Bernstein Richard J.
Published: December 2018

Ricœur’s reading of Freud is one of the most comprehensive, perceptive, and judicious explications of Freudianism—one that begins with his early ‘Project’ of 1895 and culminates with the last book that Freud published, Moses and Monotheism. Ricœur is successful in exposing some of the weaknesses in Freud, and even more importantly, in showing why there is a need to move beyond Freud. He also develops the significant idea of a dialectical relationship between a hermeneutics of suspicion and a restorative hermeneutics of meaning—and that they are integral to each other. Ricœur is successful in showing how, if one relentlessly pursues the logic of Freud’s thinking, it leads beyond Freud. But, even though he gives some indications of how such dialectic is to be developed, this remains a task (an Aufgabe) that lies ahead.
Phenomenology and Science: Introduction
Authors: Gipps Richard G.T. , Lacewing Michael
Published: December 2018

This introduction provides an overview of the five chapters in this section, which explores some of the central issues in psychoanalysis as it relates to phenomenology and science. One such issue concerns the scientific status of psychoanalysis (natural or social? bona fide or tendentious?), and more specifically which between the methods of psychoanalysis and its real-life practice may be considered scientific. One of the chapters examines psychoanalysis as a scientific theory of mind, arguing that psychoanalysis fails to test its theories. Another chapter suggests that many of the central tenets of psychoanalytic theory are evidentially supported by recent developments in empirical neuropsychology. Also discussed are the debate between those who view psychoanalysis as science and those who insist that it rather offers a hermeneutic, how psychoanalysis provides a phenomenology in its articulations of unconscious life, and alternative phenomenological schemes for framing the dynamic unconscious.
Aesthetics: Introduction
Authors: Lacewing Michael , Gipps Richard G.T.
Published: December 2018

This introduction provides an overview of the chapters in this section, which explores the role of psychoanalysis in aesthetics. More specifically, the chapters examine some psychoanalytic concepts with which to think more deeply about human creativity and aesthetic sensibility, such as wish and wish fulfilment, the depressive position, projection, containment, and mentalization. The focus is on what Sigmund Freud thinks about art, how we should understand it (the question of criticism), what makes an experience distinctively aesthetic, and how we should understand artistic creativity. One of the chapters deals with film theory, arguing against the cognitive turn in favour of the view that ‘the creation and experience of film is driven by desire and wish fulfilment and functions so as to satisfy certain psychological, protective, expressive needs of both artists and audiences’. Another chapter considers the developmental, transformative nature of art, and the particular importance of its form in this respect.
Psychoanalysis and Religion
Authors: Cottingham John
Published: December 2018

Acknowledging the layers of the mind below the level of overt consciousness can lead to very divergent accounts of religious belief. One response—taken by Freud himself—argues that religious belief should be abandoned as unavoidably contaminated by unconscious motivations (e.g. an infantile longing for security) that distort our rational judgement. By contrast, Jung maintains that religious thinking is shaped by unconscious structures (the ‘archetypes’), which can play a vital role in the development of an integrated human personality. This chapter examines these contrasting psychoanalytic interpretations of religion, and then explores more recent accounts of the workings of the human psyche and how they affect the status of religious belief. A concluding section discusses some general implications of all this for the epistemology of religious belief and the way in which philosophy of religion should be conducted.
Ethics: Introduction
Authors: Lacewing Michael , Gipps Richard G.T.
Published: December 2018

This introduction provides an overview of the three chapters in this section, which explores central issues in ethics in the context of psychoanalysis, including the nature of virtue, the ground of normativity, moral development, the relation between reason and passion, naturalism and moral motivation. One such issue concerns Sigmund Freud’s theory of the superego, which is said to undermine the ‘authority’ of morality. The first chapter argues that the superego represses conscience, and that our ‘moral-psychological difficulties’ can be understood only in light of repressed love. The second chapter examines the place of psychoanalysis in the relationship between virtue and mental health, and between vice and mental dysfunction. The third chapter discusses the idea of an ‘evolved development niche’ to address object relations and their role in moral development.
Schopenhauer and Freud
Authors: Brook Andrew , Young Chris
Published: December 2018

This chapter engages in a conversation between two seemingly disparate discourses of Hegelian philosophy and psychoanalytic theory. In the work of Jean Hyppolite, the chapter locates the first use of the term intersubjectivity in relation to Hegel’s theory of recognition as found in Phenomenology of Spirit (1977) and argues that Hyppolite pioneered a mode of thinking about Hegel and psychoanalysis. The chapter traces the transmutation initiated by Hyppolite through the work of Paul Ricouer, Jacques Lacan, Judith Butler, Jessica Benjamin, and others to locate the influence of Hegel’s philosophy on a particular line of psychoanalytic thinking. The author’s reading of Hegel incorporated here argues that the majority of attention paid to the concept of recognition, and its translation into terms of intersubjective relating, has confined it to the episode of the Lord and Bondsman and that further attention should be paid to the drama of the Unhappy Consciousness which follows.
From Geschlechtstrieb to Sexualtrieb: the Originality of Freud’s Conception of Sexuality
Authors: Sandford Stella
Published: December 2018

This chapter returns to the 1905 edition of Three Essays on the Theory of Sexuality to argue, against claims to the contrary, for the originality of Freud’s conception of the sexual drive (Sexualtrieb), in relation to his philosophical and psychiatric predecessors. After examining the claims that have been made concerning the relation between Schopenhauer and Freud on the question of sexuality, it lays out the conception of Geschlechtstrieb in Freud’s immediate psychiatric predecessors (particularly Krafft-Ebing and Moll) and its connection to the treatment of the same topic in Kant, Schopenhauer, and Hartmann. It then demonstrates how Freud’s conception of the sexual drive, which is divorced from any reproductive aim, is quite different to the earlier conceptions of the Geschlechtstrieb. The chapter ends by suggesting how Freud’s theory of sexuality can be understood as a contribution to a philosophical anthropology.
Taboos in speaking of sex and sexuality
Authors: Crespo-Fernández Eliecer
Published: December 2018

Sexuality is a driving force of people’s lives; it is beset with powerful taboos that shape human behavior and communication. It is also a multifaceted phenomenon that has many variations and requires many distinct vocabularies. In this regard, this chapter examines the language people use in speaking of sex and sexuality. To this end, it focuses on the types of X-phemistic (i.e., orthophemistic, euphemistic, and dysphemistic) naming in a diversity of sex-related taboo areas, including homosexuality, conventional and unconventional sexual practices, masturbation, prostitution, pornography, and body parts. Because metaphor stands out as a potent source for sexual vocabulary, special attention is paid to the role of figurative language in discussing sex-related matters. This study shows that the sexual taboo is a breeding ground for X-phemistic references that perform different communicative functions, ranging from attenuation to offence, solidarity, or in-group cohesion.
Swearing and the brain
Authors: Finkelstein Shlomit Ritz
Published: December 2018

This chapter explores and summarizes the current knowledge about the neurophysiological substrata of the utterance of expletives—its brain regions, pathways, and neurotransmitters, and its interaction with hormones. The chapter presents clinical data that have been gathered directly from patients of aphasia, Tourette syndrome, Alzheimer’s disease, and brain injuries—all are disorders often accompanied with expletives. It also discusses the possible relations between swearing and aggression, swearing and pain, and swearing and social inhibition in the population at large. Finally, the chapter examines the clinical data and the data gathered from the population at large within one frame, and proposes two hypotheses that can serve as possible directions for future research about the biological substrata of swearing. No previous knowledge of the brain is assumed.
Elimination of Phytoplasmas in Rubus Mother Plants by Tissue Culture Coupled with Heat Therapy
Authors: Linck Holger , Lankes Christa , Krüger Erika , Reineke Annette
Published: December 2018

Phytoplasmas are plant-pathogenic bacteria that cause a disease in Rubus species which is referred to as Rubus stunt. As phytoplasmas can be spread by vegetative propagation and latency periods of Rubus stunt can be up to one year, the use of pathogen-free Rubus propagation material in plant nurseries is important in order to stop the spread of this disease. Even though heat therapy has been commonly applied against viruses in many plants, its potential for phytoplasma eradication has been much less explored. Here, the efficacy of heat therapy with subsequent tissue culture to eliminate phytoplasmas from infected raspberry and blackberry plants is evaluated. Heat therapy was performed on 25 phytoplasma-infected raspberry and 33 infected blackberry plants, out of which 100 raspberry and 65 blackberry plants were regenerated via subsequent tissue culture. All plants were negative for the presence of phytoplasma DNA by qPCR at the end of cultivation periods of 481 to 565 days for the treated raspberry plants and 231 to 337 days for the treated blackberry plants. These results show the suitability of heat therapy combined with tissue culture as a routine tool to ensure the presence of phytoplasma-free Rubus mother plants in nurseries.
Assessment of fatty infiltration of the multifidus muscle in patients with adolescent idiopathic scoliosis through evaluation by magnetic resonance imaging compared with histological analysis: a diagnostic accuracy study
Authors: Wajchenberg Marcelo , Astur Nelson , Fernandes Eloy A. , Paredes-Gamero Edgar J. , Luciano Rafael P. , Schmidt Beny , Oliveira Acary S.B. , Martins Delio E.
Published: December 2018

To evaluate fat infiltration in the multifidus muscle close to the scoliotic curve as seen in MRI compared with the histological evaluation in patients with adolescent idiopathic scoliosis (AIS). The evaluation of fatty infiltration in the multifidus muscle of patients with AIS by MRI was compared with biopsy. Fatty infiltration was greater in concave side than in the convex side in both MRI (P=0.005) and biopsy evaluation (P=0.026). There was no correlation between the fatty infiltration findings evaluated through MRI and biopsy. The MRI measurements do not express accurately the tissue changes observed in the biopsy.
Isolation and characterization of rare circulating autoantibody-producing cells from patients with muscle-specific kinase myasthenia gravis
Authors: Takata Kazushiro , Stathopoulos Panos , Cao Michelangelo , Mane-Damas Marina , Fichtner Miriam , Benotti Erik S. , Jacobson Leslie , Waters Patrick , Irani Sarosh R. , Martinez-Martinez Pilar , Beeson David , Losen Mario , Vincent Angela , Nowak Richard J. , O'Connor Kevin C.
Published: December 2018

Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by muscle weakness and caused by autoantibodies that bind to functional membrane proteins at the neuromuscular junction. Most patients have autoantibodies to the acetylcholine receptor (AChR), but a subset of patients instead have autoantibodies to muscle specific tyrosine kinase (MuSK). MuSK is an essential component of the Agrin/Lipoprotein receptor-related protein 4(LRP4)/MuSK/downstream of tyrosine kinase 7 (DOK7) pathway that is responsible for synaptic differentiation, including clustering of AChRs at the neuromuscular junction, both during development and in adult muscle. Nerve-released Agrin binds to LRP4 which then binds to MuSK, stimulating autophosphorylation and recruitment of DOK7 to complete the membrane component of the pathway. Serum-derived IgG4 subclass MuSK autoantibodies prevent the binding of LRP4 to MuSK, subsequently impairing autophosphorylation, resulting in the loss of Agrin-induced AChR clustering in the mouse myotube-forming C2C12 line. Although this autoimmune mechanism appears well understood, MuSK autoantibodies from patients are polyclonal. Most are IgG4 but IgG1, 2 and 3 are also present and can achieve similar results on AChR clustering. In addition, most bind the first Ig-like domain in MuSK, however some patients harbor serum autoantibodies that recognize other domains in MuSK. We sought to establish individual MuSK IgG clones so that the disease mechanisms could be better understood. We isolated MuSK autoantibody-expressing B cells from MuSK MG patients with a fluorescent-tagged MuSK antigen multimer and generated a panel of human monoclonal autoantibodies (mAbs) from these cells. We produced 77 mAbs from single B cells collected from six MuSK MG patients. Here we focused on three highly specific mAbs that bound quantitatively to MuSK in solution, to MuSK-expressing HEK cells and at mouse neuromuscular junctions where they co-localized with AChRs. These three IgG isotype mAbs (two IgG4 and one IgG3 subclass) recognized the Ig-like domain 2 of MuSK. The three MuSK mAbs inhibited Agrin induced-AChR clustering in C2C12 myotubes, but intriguingly, they enhanced rather than inhibited MuSK phosphorylation. This approach for ex vivo isolation of MuSK MG autoantibody-producing cells and production of human recombinant mAbs has identified distinct autoantibody specificities and likely divergent effector mechanisms. Collectively, these findings will enable a better understanding of MuSK autoantibody-mediated pathology.
Is Anopheles gambiae a natural host of Wolbachia?
Authors: Chrostek Ewa , Gerth Michael
Published: December 2018

Wolbachia (Alphaproteobacteria, Rickettsiales) is an intraovarially-transmitted symbiont of insects able to exert striking phenotypes, including reproductive manipulations and pathogen blocking. These phenotypes make Wolbachia a promising tool to combat mosquito-borne diseases. Although Wolbachia is present in the majority of terrestrial arthropods, including many disease vectors, it was considered absent from Anopheles gambiae mosquitos, the main vectors of malaria in sub-Saharan Africa. In 2014, Wolbachia sequences were detected in A. gambiae samples collected in Burkina Faso. Subsequently, similar evidence came from collections all over Africa, revealing a high Wolbachia 16S sequence diversity, low abundance, and a lack of congruence between host and symbiont phylogenies. Here, we reanalyze and discuss recent evidence on the presence of Wolbachia sequences in A. gambiae. We find that although detected at increasing frequencies, the unusual properties of these Wolbachia sequences render them insufficient to diagnose natural infections in A. gambiae. Future studies should focus on uncovering the origin of Wolbachia sequence variants in Anopheles and seeking sequence-independent evidence for this new symbiosis. Understanding the ecology of Anopheles mosquitos and their interactions with Wolbachia will be key in designing successful, integrative approaches to limit malaria spread. Although the prospect of using Wolbachia to fight malaria is intriguing, the newly discovered strains do not bring it closer to realization.

Significance

Anopheles gambiae mosquitos are the main vectors of malaria, threatening around half of the world’s population. The bacterial symbiont Wolbachia can interfere with disease transmission by other important insect vectors, but until recently it was thought to be absent from natural A. gambiae populations. Here, we critically analyze the genomic, metagenomic, PCR, imaging and phenotypic data presented in support of the presence of natural Wolbachia infections in A. gambiae. We find that they are insufficient to diagnose Wolbachia infections and argue for the need of obtaining robust data confirming basic Wolbachia characteristics in this system. Determining Wolbachia infection status of Anopheles is critical due to its potential to influence Anopheles population structure and Plasmodium transmission.
CaptureSeq: Hybridization-based enrichment of cpn60 gene fragments reveals the community structures of synthetic and natural microbial ecosystems
Authors: Links Matthew G. , Dumonceaux Tim J. , McCarthy Luke , Hemmingsen Sean M. , Topp Edward , Town Jennifer R.
Published: December 2018

Background

Molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with universal PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics.

Methods

We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir.

Results

The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three Domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health.
The dynamic emergence of musical pitch structure in human cortex
Authors: Sankaran Narayan , Carlson Thomas A , Thompson William Forde
Published: December 2018

Tonal music the world over is characterized by a hierarchical structuring of pitch, whereby certain tones appear stable and others unstable within their musical context. Despite its prevalence, the cortical mechanisms supporting such a percept remain poorly understood. The current study probed the neural processing dynamics underlying the representation of pitch in Western Tonal Music. Listeners were presented with tones comprising all twelve pitch-classes embedded within a musical context whilst having their magnetoencephalographic (MEG) activity recorded. Using multivariate pattern analysis (MVPA), decoders attempted to classify the identity of tones from their corresponding MEG activity at each peristimulus time sample, providing a dynamic measure of their cortical dissimilarity. Time-evolving dissimilarities between tones were then compared with the predictions of several acoustic and perceptual models. Following tone onset, we observed a temporal evolution in the neural representation. Dissimilarities between tones initially reflected their fundamental frequency separation, but beyond 200 ms reflected their status within the tonal hierarchy of perceived stability. Furthermore, when the dissimilarities corresponding to this latter period were transposed into different keys, cortical relations between keys correlated with the well-known circle of fifths. Convergent with fundamental principles of music-theory and perception, current results detail the dynamics with which the complex perceptual structure of Western tonal music emerges in human cortex within the timescale of an individual tone.
Low acetylcholine during early sleep is important for motor memory consolidation
Authors: Inayat Samsoon , Qandeel  , Nazariahangarkolaee Mojtaba , Singh Surjeet , McNaughton Bruce L. , Whishaw Ian Q. , Mohajerani Majid H.
Published: December 2018

The synaptic homeostasis theory of sleep proposes that low neurotransmitter activity in sleep is optimal for memory consolidation. We tested this theory by asking whether increasing acetylcholine levels during early sleep would disrupt motor memory consolidation. We trained separate groups of adult mice on the rotarod walking and skilled reaching for food tasks, and after training, administered physostigmine, an acetylcholinesterase inhibitor, to increase cholinergic tone in subsequent sleep. Post-sleep testing suggested that physostigmine impaired motor skill acquisition. Home-cage video monitoring and electrophysiology revealed that physostigmine disrupted sleep structure, delayed non-rapid-eye-movement sleep onset, and reduced slow-wave power in the hippocampus and cortex. The impaired motor performance with physostigmine, however, was not solely due to its effects on sleep structure, as one hour of sleep deprivation after training did not impair rotarod performance. A reduction in cholinergic tone by inactivation of cholinergic neurons during early sleep also affected rotarod performance. Administration of agonists and antagonists of muscarinic and nicotinic acetylcholine receptors revealed that activation of muscarinic receptors during early sleep impaired rotarod performance. The experiments suggest that the increased slow wave activity and inactivation of muscarinic receptors during early sleep due to reduced acetylcholine contribute to motor memory consolidation.
Bioinformatic screening of genes present only in well regenerating vertebrates reveals novel FGF and purinergic signaling modulator - c-Answer
Authors: Korotkova Daria D , Lyubetsky Vassily A , Ivanova Anastasia S , Rubanov Lev I , Seliverstov Alexander V , Zverkov Oleg A , Martynova Natalia Yu , Nesterenko Alexey M , Tereshina Maria B , Peshkin Leonid , Zaraisky Andrey G
Published: December 2018

The genetic basis of higher regenerative capacity of fishes, amphibians and reptiles compared to birds and mammals is still poorly understood. Though it is thought to be a result of restructuring in the regulatory network of a static set of genes, we argued that it could be due to the loss of genes essential for regeneration. In the present work, we formulate a bioinformatic approach to systematic search for the such genes. Having identified them, we further investigated one we dubbed c-Answer, which encodes a membrane protein, regulating the regeneration of body appendages and the telencephalic development through binding to FGFR and P2Y1 receptors and promoting MAPK/ERK and purinergic signaling. The obtained data suggest that elimination of c-Answer in the ancestors of warm-blooded animals conditioned the decreased activity of at least two signaling pathways, which in turn could contribute to changes in mechanisms that regulate the forebrain development and regeneration.
The Goldilocks Window of Personalized Chemotherapy: An Immune Perspective
Authors: Park Derek S. , Robertson-Tessi Mark , Maini Philip , Bonsall Michael B , Gatenby Robert A , Anderson Alexander RA
Published: December 2018

The immune system is increasingly being recognized for its untapped potential in being recruited to attack tumors in cancer therapy. The main challenge, however, is that most tumors exist in a state of immune tolerance where the patient's immune system has become insensitive to the cancer cells. In order to investigate the ability to use chemotherapy to break immune tolerance, we created a mathematical modeling framework for tumor-immune dynamics. Our results suggest that optimal chemotherapy scheduling must balance two opposing objectives: maximal tumor reduction and preserving patient immune function. Successful treatment requires therapy to operate in a "Goldilocks Window" where patient immune health is not overly compromised. By keeping therapy "just right", we show that the synergistic effects of immune activation and chemotherapy can maximize tumor reduction and control.
CHANging Consciousness Epistemically (CHANCE): An empirical method to convert the subjective content of consciousness into scientific data
Authors: Tanaka Daisuke H. , Tanabe Tsutomu
Published: December 2018

The content of consciousness (cC) constitutes an essential part of human life and is at the very heart of the hard problem of consciousness. The cC of a person (e.g., study participant) has been examined indirectly by evaluating the person’s behavioral reports, bodily signs, or neural signals. However, the measures do not reflect the full spectrum of the person’s cC. In this paper, we define a method, called “CHANging Consciousness Epistemically” (CHANCE), to consciously experience a cC that would be identical to that experienced by another person, and thus directly know the entire spectrum of the other’s cC. In addition, the ontologically subjective knowledge about a person’s cC may be considered epistemically objective and scientific data. The CHANCE method comprises two empirical steps: (1) identifying the minimally sufficient, content-specific neural correlates of consciousness (mscNCC) and (2) reproducing a specific mscNCC in different brains.
Separate Compartments for Chromosome Entrapment and DNA Binding during SMC translocation
Authors: Nunez Roberto Vazquez , Avila Laura B. Ruiz , Gruber Stephan
Published: December 2018

Multi-subunit SMC ATPase complexes translocate on chromosomal DNA. They control chromosome structure and DNA topology, presumably by acting as DNA extrusion motors. The SMC-kleisin ring entraps chromosomal DNA. The ring lumen is strongly reduced in size by alignment of the SMC arms and upon ATP binding is divided in two by engagement of SMC head domains. Here, we provide evidence for DNA binding in the SMC compartment and chromosome entrapment in the Kleisin compartment of B. subtilis Smc/ScpAB. We show that DNA binding at the Smc hinge is dispensable and identify an essential DNA binding site at engaged heads which faces the S compartment. Mutations interfering with DNA binding do not prevent ATP hydrolysis but block DNA translocation by Smc/ScpAB. Our findings are consistent with the notion that Smc/DNA contacts stabilize looped DNA segments in the S compartment, while the base of a chromosomal DNA loop is enclosed in the K compartment. Transfer of DNA double helices between S and K compartments may support DNA translocation.
Predicting phenotype using morphological cell responses to nanotopography
Authors: Cutiongco Marie F.A. , Jensen Bjørn S. , Reynolds Paul M. , Gadegaard Nikolaj
Published: December 2018

Cells respond in complex ways to topographies, making it challenging to identify a direct relationship between surface topography and cell response. A key problem is the lack of informative representations of topographical parameters that translate directly into biological properties. Here, we present a platform to relate the effects of nanotopography on morphology to function. This platform utilizes the ‘morphome’, a multivariate dataset containing single cell measures of focal adhesions, the cytoskeleton, and chromatin. We demonstrate that nanotopography-induced changes in cell phenotype are uniquely encoded by the morphome. The morphome was used to create a Bayesian linear regression model that robustly predicted changes in bone, cartilage, muscle and fibrous tissue gene expression induced by nanotopography. Furthermore, the morphome effectively predicted nanotopography-induced phenotype within a complex co-culture microenvironment. Thus, the morphome enables the cell function-oriented exploration of new topographies, with potential applications in the development of novel surface-patterned biomaterials for tissue implants.
An integrated model of population genetics and community ecology
Authors: Overcast Isaac , Emerson Brent C. , Hickerson Michael J.
Published: December 2018

Aim

Quantifying abundance distributions is critical for understanding both how communities assemble, and how community structure varies through time and space, yet estimating abundances requires considerable investment in field work. Community-level population genetic data potentially offer a powerful way to indirectly infer richness, abundance, and the history of accumulation of biodiversity within a community. Here we introduce a joint model linking neutral community assembly and comparative phylogeography to generate both community-level richness, abundance and genetic variation under a neutral model, capturing both equilibrium and non-equilibrium dynamics.

Location

Global.

Methods

Our model combines a forward-time individual-based community assembly process with a rescaled backward-time neutral coalescent model of multi-taxa population genetics. We explore general dynamics of genetic and abundance-based summary statistics and use approximate Bayesian computation (ABC) to estimate parameters underlying the model of island community assembly. Finally, we demonstrate two applications of the model using community-scale mtDNA sequence data and densely sampled abundances of an arachnid community on La Réunion. First, we use genetic data alone to estimate a summary of the abundance distribution, ground-truthing this against the observed abundances. Then we jointly use the observed genetic data and abundances to estimate the proximity of the community to equilibrium.

Results

Simulation experiments of our ABC procedure demonstrate that coupling abundance with genetic data leads to improved accuracy and precision of model parameter estimates compared with using abundance-only data. We further demonstrate reasonable precision and accuracy in estimating a metric underlying the shape of the abundance distribution, temporal progress toward local equilibrium, and several key parameters of the community assembly process. For the insular arachnid assemblage, we find the joint distribution of genetic diversity and abundance approaches equilibrium expectations, and that the Shannon entropy of the observed abundances can be estimated using genetic data alone.

Main Conclusions

The framework that we present unifies neutral community assembly and comparative phylogeography to characterize the community-level distribution of both abundance and genetic variation through time, providing a resource that should greatly enhance understanding of both the processes structuring ecological communities and the associated aggregate demographic histories.
Stable Genetic Transformation and Heterologous Expression in the Nitrogen-fixing Plant Endosymbiont Frankia alni ACN14a
Authors: Gifford Isaac , Vance Summer , Nguyen Giang , Berry Alison M
Published: December 2018

Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes, which are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. However the corresponding endosymbionts, Frankia and the rhizobia, are distantly related groups of bacteria, leading to questions of their symbiotic mechanisms and evolutionary history. To date, a stable system of genetic transformation has been lacking in Frankia. Here, we report the successful electrotransformation of Frankia alni ACN14a, by means of replicating plasmids expressing chloramphenicol-resistance for selection, and the use of GFP as a marker of gene expression. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation and circumvented this barrier by using unmethylated plasmids, which allowed the transformation of F. alni as well as the maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the plasmid transformation system was used with expression of egfp under the control of the nif gene cluster promoter, it was possible to demonstrate by fluorescence imaging the expression of nitrogen fixation in vesicles but not hyphae in nitrogen-limited culture.