bluuebunny/crossref_metadata_2025 huggingface dataset:
Are tetraploids more successful? Floral signals, reproductive success and floral isolation in mixed-ploidy populations of a terrestrial orchid
Authors: Gross Karin , Schiestl Florian P.
Published: February 2015

Background and Aims Polyploidization, the doubling of chromosome sets, is common in angiosperms and has a range of evolutionary consequences. Newly formed polyploid lineages are reproductively isolated from their diploid progenitors due to triploid sterility, but also prone to extinction because compatible mating partners are rare. Models have suggested that assortative mating and increased reproductive fitness play a key role in the successful establishment and persistence of polyploids. However, little is known about these factors in natural mixed-ploidy populations. This study investigated floral traits that can affect pollinator attraction and efficiency, as well as reproductive success in diploid and tetraploid Gymnadenia conopsea (Orchidaceae) plants in two natural, mixed-ploidy populations.

Methods Ploidy levels were determined using flow cytometry, and flowering phenology and herbivory were also assessed. Reproductive success was determined by counting fruits and viable seeds of marked plants. Pollinator-mediated floral isolation was measured using experimental arrays, with pollen flow tracked by means of staining pollinia with histological dye.

Key Results Tetraploids had larger floral displays and different floral scent bouquets than diploids, but cytotypes differed only slightly in floral colour. Significant floral isolation was found between the two cytotypes. Flowering phenology of the two cytotypes greatly overlapped, and herbivory did not differ between cytotypes or was lower in tetraploids. In addition, tetraploids had higher reproductive success compared with diploids.

Conclusions The results suggest that floral isolation and increased reproductive success of polyploids may help to explain their successful persistence in mixed-ploidy populations. These factors might even initiate transformation of populations from pure diploid to pure tetraploid.
Reference-based compression of short-read sequences using path encoding
Authors: Kingsford Carl , Patro Rob
Published: February 2015

Motivation: Storing, transmitting and archiving data produced by next-generation sequencing is a significant computational burden. New compression techniques tailored to short-read sequence data are needed.

Results: We present here an approach to compression that reduces the difficulty of managing large-scale sequencing data. Our novel approach sits between pure reference-based compression and reference-free compression and combines much of the benefit of reference-based approaches with the flexibility of de novo encoding. Our method, called path encoding, draws a connection between storing paths in de Bruijn graphs and context-dependent arithmetic coding. Supporting this method is a system to compactly store sets of kmers that is of independent interest. We are able to encode RNA-seq reads using 3–11% of the space of the sequence in raw FASTA files, which is on average more than 34% smaller than competing approaches. We also show that even if the reference is very poorly matched to the reads that are being encoded, good compression can still be achieved.

Availability and implementation: Source code and binaries freely available for download at http://www.cs.cmu.edu/∼ckingsf/software/pathenc/, implemented in Go and supported on Linux and Mac OS X.

Contact: carlk@cs.cmu.edu.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ethical Issues in Brain Imaging in Psychiatry
Authors: Bluhm Robyn , Raczek Gosia , Broome Matthew , Wall Matthew B.
Published: February 2015

With the increasing use of neuroimaging research in psychiatry and the role imaging plays in society more generally in how mental illness is understood, it is important to consider the myriad ethical issues raised by imaging technologies, for example, for medicine, for law, and for patients. This chapter provides an overview of major ethical questions concerning: imaging of ethical reasoning in psychiatric disorder; forensic psychiatry, criminality, and responsibility; mindblindness and empathy in autism; the use of neuroimaging for screening, prediction, and diagnosis; “mind reading” and the right to privacy of thoughts; and the implications of imaging for the ethics and politics of biological psychiatry.
Ethical Practice of Cognitive Behavior Therapy
Authors: Sookman Debbie
Published: February 2015

Contemporary cognitive behavior therapy (CBT) comprises complex interventions that have demonstrated efficacy and/or are currently the evidence-based psychotherapeutic treatment of choice for many psychiatric disorders. This chapter discusses management of ethical issues that may arise during evidence-based CBT: initial assessment, informed consent, exposure-based therapy, out of office sessions, management of boundaries, homework, and risk management. The patient-therapist relationship and conceptualization of resistance during CBT are discussed. A crucial requirement of ethical mental health care is additional dissemination of CBT expertise. In this current era of specialization, interventions that target disorder specific symptoms and related difficulties (American Psychiatric Association,2013) show special promise. It is the ethical responsibility of clinicians regardless of orientation to be guided by current empirical research and their own specific areas of competence when making treatment recommendations. A priority for clinical research is further examination of the specific therapeutic ingredients that impact outcome and optimize recovery.
Coercive Family Processes and the Development of Child Social Behavior and Self-Regulation
Authors: Snyder James
Published: February 2015

This chapter (1) examines the multiple ways in which coercive processes may be manifested during family interaction in addition to their more blatant, aversive forms, including emotion dismissing, invalidating, intrusive/controlling social actions; (2) assesses the role of higher cognitive processing and control in coercive social interaction in the context of previous assumptions that coercive processes are primarily overlearned and automatic; (3) examines the utility of extensions of environmental main effects models of coercive processes by explicitly focusing on synergistic models that involve child temperamental self-regulatory capacities (reflecting underlying molecular genetic and neurobiological mechanisms); and (4) assesses the role of coercive family processes in relation to borderline features and trauma/PTSD.
Metacognitive Aspects of Source Monitoring
Authors: Kuhlmann Beatrice G. , Bayen Ute J.
Published: February 2015

Source monitoring involves attributing remembered information to a source, such as determining who told you something. Source-monitoring is a highly inferential process, involving the evaluation of memory for contextual features but also drawing onto more general knowledge and beliefs (Johnson, Hashtroudi, and Lindsay, 1993). After an introduction to the typical laboratory paradigm of source monitoring and the measurement of the cognitive states involved through multinomial modeling, we review research on metacognitive influences on this inferential source-monitoring process. We also consider means of metacognitive control over source encoding through encoding strategies. Moving on to metacognitive monitoring processes, we review research on predictions of later source memory (judgments of source) and on the monitoring of source-attribution accuracy at test. The chapter concludes with questions for future research.
Work, Family, and Community
Authors: Minnotte Krista Lynn
Published: February 2015

This chapter explores scholarship on work, family, and community, suggesting ways to move it forward in new and exciting directions. Different ways of conceptualizing community are described, along with issues surrounding the lack of conceptual clarity in the treatment of community in the work–family literature. The main theories that are used to guide the study of community, work, and family are outlined, including ecological theory, life-course theory, and the demands and resources perspective. The existing work–family and community scholarship is described, with a focus on how community is related to family, work–family, and individual outcomes. Emerging scholarship on family supportive communities is explored, along with scholarship on the impact of contemporary work–family trends on community involvement. Lastly, promising areas for future research are proposed, with an eye toward identifying solutions at the community level for working families.
A Retrospective Timeline of the Evolution of Work–Family Research
Authors: French Kimberly A. , Johnson Ryan C.
Published: February 2015

This chapter provides a historic overview of the work–family field from the 1970s through today. Several reviews and timelines are compiled to identify themes throughout each time period. To supplement published resources, interviews with prominent work–family scholars were conducted to identify key trends and issues, and to obtain a more personal view into the lives of some of work–family’s most influential minds. The review covers a broad range of topics across time, including the evolution of societal trends and legislation, key organizations and foundations, popular topics, theoretical developments, and methodological techniques. The chapter concludes with the interviewed work–family scholars’ future visions for the work–family field.
What Can Allies Do?
Authors: Ashburn-Nardo Leslie
Published: February 2015

Allies are individuals who espouse egalitarian ideals and who are motivated not only to avoid responding with prejudice themselves but also to confront others’ prejudicial remarks and discriminatory behavior and to be a source of support for targets of discrimination. This chapter discusses the role that allies can play in the reduction of employment discrimination, with particular emphasis on self-regulation strategies that enable allies to recognize and regulate their own biases, confrontation strategies to point out and convey disapproval of others’ biases, and social strategies that help allies be more supportive and understanding of the discrimination targets face. The chapter summarizes theory and empirical findings regarding these strategies and offers practical suggestions for increasing the likelihood and effectiveness of these prejudice-reduction tools as well as future directions for researchers. By being more than passive egalitarians, allies can be key parts of the solution to this organizational and societal problem.
Individual Differences
Authors: Donlan Chris
Published: February 2015

This article discusses the results of three studies that have attempted to identify the factors underlying individual differences in mathematics. Holloway and Ansari (2009), explored the relation between basic number processing and attainment in primary school mathematics. Mazzocco et al. (2011) used a non-symbolic comparison task as an indicator of a preschool child’s Approximate Number System (ANS). Goebel et al. (2014), who tested the number knowledge of 173 six-year olds using a number identification task. All three studies tested specific hypotheses by making use of individual differences and associations between them. They also strongly validate two fundamental principles: that correlational models are limited by the measurements they contain, and that evidence consistent with a particular hypothesis does not necessarily constitute strong evidence in its favour. This article concludes by providing an overview of the topics covered in this book concerning individual differences in mathematics.
Choral Singers’ Perceptions of Musical Leadership
Authors: Jansson Dag
Published: February 2015

The conductor role has only been researched to a limited degree. Even less attention has been given to the impact view: how choral singers perceive the conductor's role and how musical leadership is experienced by those who produce the sounding music. This chapter investigates these questions with a qualitative approach to understanding the lived experience of choral singers. Three conceptualizations of choral leadership are proposed: (1) the legitimacy model—the why; (2) the enactment model—the how; and (3) the notion of elusive perfection—the balancing acts that conductors are continuously faced with. The holistic view of the singer viewpoint sheds new light on several ideals and conceptions about choral conducting that are often taken for granted.
Gender and the American State
Authors: McDonagh Eileen , Nackenoff Carol
Published: February 2015

The study of gender in American political development (APD) challenges the efficacy for advancing women’s political inclusion of a liberal tradition valorizing principles of individual equality and positing a separation of the family and the state. Masked are ways in which gender roles and the family are integral to governance and state-building. Gender is both a dependent and an independent variable in APD. Shaped by institutions and policies of the state, it also shapes institutions and policies that promote women’s political citizenship and expand the state’s capacity for social provision—by asserting not only liberal claims of women’s equality with men, but also by invoking maternalist claims based on women’s difference from men, thereby challenging and altering relationships between public and private spheres.
The Shape of Political Communication
Authors: Blumler Jay G.
Published: February 2015

This chapter stresses the importance of trying to understand the political communication process in the round (i.e., its shape), in addition to its specific workings and effects, and explains what this can involve. For this purpose, the concept of a “political communication system” is proposed, the key components of which are identified. Four ways in which this concept has been applied in analysis and research are then outlined (including especially for comparative research). Finally, the chapter considers whether the concept of a political communication system can be accommodated to the onset of recent transforming trends, such as increased communication abundance and the Internet.
Improvisation Technology as Mode of Redesigning the Urban
Authors: Dell Christopher , Matton Ton
Published: February 2015

This chapter elaborates on the notion of improvisation in urban design from a specific perspective, not as an informal, non-planning endeavor but as a way to re-use planning from a Situationist perspective. Design modulates to redesign. The aim is not to follow the ideology of creativity and its teleological imperative of creating something new but to work constructively with the “as found” in community to reassemble and draw relationships between actors and actants. Representational modes of design unveil their structural potential from an improvisational perspective: from a non-altering identity form to a performative (re)presentation of structure and relationship as open notation. The city is to be read as a performative process in which we all take part, whether we want to or not—externalization is over! It is about finding ways to internalize spatial relations, make them public, and act from there.
Lively Cities
Authors: Owens Marcus , Wolch Jennifer
Published: February 2015

The study of nonhuman animals in urban ecosystems is a recent but expanding field. This chapter explores the ways in which human-animal relationships in cities have historically been framed and argues that a consideration of nonhuman animals is vital to a robust urban theory in the age of ecology. The places of animals within the urban planning and design professions that shape cities are elucidated, along with contemporary developments in ecology that increasingly inform city planning, design, and management. The chapter then highlights four global dynamics that promise to radically reshape urban animal ecologies, and concludes with a call for lively cities characterized by the coexistence of people and animals.
The Modern Endeavor to Interpret Early Chinese Religions
Authors: Brashier K.E.
Published: February 2015

Early Chinese religions consist of individual religious components, on one hand, and the systems uniting those components, on the other, but the systems get lost over time. Hence, when we study early Chinese religions, we tend to superimpose our own templates on the surviving components. To better navigate these religions, we must analyze our situatedness relative to theirs, be wary of how we play “dot-to-dot” with the components, and ultimately adopt a polythetic approach to defining religion. Part one addresses both the scope of individual religious components (i.e. their temporal longevity, geographic spread and degree of representativeness among the people) and their significance (i.e. from influential belief to banal flourish). Part two considers how we interconnect those components within a “religion” as well as connect them to non-religious components such as contemporaneous social and political forces. Part three discusses our projection of modern religious categories and theories onto early China.
Baroque Catholic Theologies of Christ and Mary
Authors: Pomplun Trent
Published: February 2015

This essay provides an historical account of the simultaneous development of Mariology and Christology in the early modern period. The main Thomist and Scotist arguments regarding the Incarnation and Immaculate Conception are discussed, together with the many “strict” and “mitigated” variants propounded by major theologians of religious orders, including the Jesuits, Dominicans, Franciscans, Mercedarians, and others; and the increasing trend toward the theological position of Duns Scotus is shown. Several of these now-forgotten theologies on the absolute primacy of Christ and Mary integrated the rather scattered Mariological reflections of the medieval world into the various baroque syntheses that shaped much of nineteenth-century theological debate, one result of which was the declaration of the dogma of the Immaculate Conception in 1854.
Early Modern Jansenism
Authors: Radner Ephraim
Published: February 2015

This chapter presents Jansenism as an originally seventeenth-century Counter-Reformation movement with a key commitment to a certain theology of grace. This had several pastoral consequences that were broadly influential among both Catholics and Protestants, especially in the areas of scriptural study and devotion. Jansenist interest in the Augustinian tradition, however, proved a losing cause within the evolving modern church. Three papal bulls condemned certain Jansenist ideas and provided the impetus for the conflict with Rome, the French monarchy, and other institutions. The major political aspects associated with the movement in the eighteenth century eventually overwhelmed its theology and hopes. By the nineteenth century, the movement’s final political phase was seen as an amalgam of anti-papalism, anti-Jesuitism, conciliarism, republicanism, and nationalism.
Dōgen on the Language of Creative Textual Hermeneutics
Authors: Heine Steven
Published: February 2015

The chapter first discusses the intellectual historical context of Chan/Zen Buddhist debates regarding appropriate uses of language that took place in twelfth- and thirteenth-century China and Japan and helped shape the formation of Dōgen’s philosophy of language as textual hermeneutics. In particular, this examination demonstrates that Dōgen was greatly influenced by the expansive manner of viewing language in the famous kōan collection, the Biyanlu by Yuanwu, as a matter of unraveling entangling vines (kattō) of discourse while rejecting the minimalist view of using catchphrases (watō) endorsed by Yuanwu’s contentious but equally prominent disciple Dahui, who is said to have burned the xylographs of his mentor’s collection. The chapter next focuses on a case study of Dōgen’s innovative way of applying creative hermeneutics in dealing with the so-called Mu Kōan, in which master Zhaozhou responds to a query about whether a dog possesses the universal spirituality of Buddha-nature.
Japanese Neo-Confucian Philosophy
Authors: Tucker John A.
Published: February 2015

This study explores Neo-Confucianism as a set of philosophical teachings that developed in distinctive ways in Japan. The study suggests that virtually all expressions of Confucian philosophy from Song times forward, in the wake of centuries of Buddhist domination of China and most of East Asia, were expressions of Neo-Confucianism. The study emphasizes differences between Japanese Neo-Confucianism and Chinese and Korean Neo-Confucianism by highlighting the distinctive relationships between Japanese Neo-Confucianism, Christianity, and Shinto, noting how, on the one hand, Japanese Neo-Confucians generally opposed Christianity as a foreign heterodoxy but, on the other, often embraced Shinto as a comparable expression of many of its own ideas, especially those found in the Book of Changes. The study also examines Neo-Confucian ideas in Meiji Japan, noting how they contributed to the Freedom and People’s Rights Movement of the mid-Meiji, but also to late-Meiji conservatism and the subsequent rise of nationalist ideological expressions.
Ancient Learning
Authors: Tucker John A.
Published: February 2015

This chapter examines the claim that the Ancient Learning School (kogakuha) presided over a revival of classical Confucian learning during the early-modern period of Japanese history, otherwise known as the Edo period (1600–1868). While questioning the claim’s validity, the study seeks to salvage the notion of kogaku by interpreting it as another expression of Neo-Confucianism. Kogaku thinkers criticized Zhu Xi and other Neo-Confucians, but doing so arguably reflected their involvement in the learning of Neo-Confucianism rather than something divorcing them from it. The study cites methodological, terminological, and philosophical similarities between the major kogaku thinkers and Neo-Confucian followers of Zhu Xi. The chapter concludes with a brief survey of subsequent, late-Tokugawa critiques of Sokō, Jinsai, and Sorai, prior to their revival in the late-Meiji by Inoue Tetsujirō in his efforts to define a philosophical tradition for modern Japan.
Comparative Philosophy in Japan
Authors: Krummel John W.M.
Published: February 2015

This chapter discusses the comparative philosophies of two premier comparativists of postwar Japan, Nakamura Hajime and Izutsu Toshihiko. Both were known as accomplished scholars within their respective fields—Buddhist studies and Indology for Nakamura, and Islamic studies for Izutsu—when they initiated their comparative projects. Each had a distinct vision of what comparison entails and the sort of philosophy it would produce. Nakamura’s project was a world history of ideas that uncovers basic patterns in the unfolding of human thought. Izutsu aims to reconstruct Oriental philosophy on the basis of certain key concepts common to the traditions. The chapter covers the aims, methods, and philosophical achievements of their comparative projects. In their juxtaposition, it makes evident significant differences in their projects, methods, and results.
Raichō: Zen and the Female Body in the Development of Japanese Feminist Philosophy
Authors: Yusa Michiko , Kalmanson Leah
Published: February 2015

Hiratsuka Raichō (1886–1971) was a pioneer feminist philosopher and activist. This chapter discusses the development of Raichō’a thinking on questions of gender, embodiment, and women’s liberation, highlighting the influence of Zen practice on her life and work. In her early years, Raichō conceives of women’s liberation abstractly, based on her interpretation of Buddhist teachings on equality. However, after encountering the work of Swedish feminist Ellen Key, she comes to understand liberation not for an abstract, unsexed subject, but in terms of the “sexed body” and the uniqueness of women’s experiences. Her considerations of gender and sexuality remain relevant to feminism today, especially to debates within care ethics and feminist moral theory over the meaning of liberal values such as autonomy and individualism. Raichō’s commitment to both spiritual and political liberation brings added perspective to these debates and speaks to the breadth and depth of her philosophy.
National Learning
Authors: Flueckiger Peter
Published: February 2015

Followers of the Tokugawa intellectual and literary movement known as “National Learning” (kokugaku 国学) sought to recover native forms of Japanese culture free from the influence of Confucianism and other foreign ideologies, which they claimed had corrupted the original harmony of ancient Japan. Ancient Japanese poetry played a central role for them because they believed it to be a repository of purely Japanese values and language. This chapter explores the role of poetry in National Learning scholars’ philosophical conceptions of human nature and interpersonal relations, arguing that these figures put emotional connections at the core of their conception of community and saw poetry as uniting people through its capacity to express and communicate emotions. It discusses how these scholars used Japanese poetry in their philology, seeing it as a means for learning both the ancient Japanese language and the underlying mindset from which ancient texts were produced.
Kūkai’s Shingon
Authors: Krummel John W.M.
Published: February 2015

This chapter explicates the philosophy of the body of sixth-century Buddhist thinker Kūkai. Kūkai brings together what initially seem to be opposing concepts: body and emptiness. He does this in the context of formulating a system of cosmology inseparable from religious practice. We interact with the rest of the cosmos through our body. Kūkai characterizes the cosmos in turn as the body of the Buddha, who personifies the embodiment of the dharma. This cosmic body is comprised of myriad bodies through their interactivities, in which we ourselves partake. The interdependence obtains both horizontally (among microcosmic bodies) and vertically (between macrocosm and microcosm). But this interdependent nature of bodies also means emptiness. All bodies are empty of substantiality. Enlightenment is to realize this emptiness of all. An additional factor is language because Kūkai conceives the body as the linguistic medium for communicating that dharma of emptiness.
Narrative Readings, Contextualized Readers, and Matthew’s Gospel
Authors: Carter Warren
Published: February 2015

This chapter begins by identifying and evaluating five central emphases evident in narrative criticism as it involves work on Matthew’s Gospel: attention to a unified coherent narrative, the linear reading experience, examination of dimensions of the narrative (plot, characters, settings, etc.), attention to reading as an implied reader, and the relationship between narrative and history. It argues that claims of some narrative exponents to produce the expected reading of an ideal implied reader is an illusion. It proposes instead that the way ahead lies in an acknowledgment of and attention to the constructive roles of real readers and an alliance with ideological and cultural criticisms to value multiple voices, locations, and readings from real readers.
Characterizing God in His/Our Own Image
Authors: Lasine Stuart
Published: February 2015

According to some scholars, the God of the Hebrew Bible has a “dark side.” Since this God is sometimes described as a parent, husband, king, or warrior, we must therefore ask, What kind of father is Yahweh shown to be? What kind of husband and king? The way in which the deity is presented also depends upon who is doing the presenting—and to which readers. Who does Yahweh say he is? Who do other characters say he is? Who do the narrators show him to be? And, who do (and should) we
readers say that Yahweh is? After addressing these questions, the chapter concludes by considering whether the various characterizations of Yahweh in his various roles constitute a coherent representation of a “round” character, and why this character has so many problematic features.
The Story of Exodus and Its Literary Kinships
Authors: Ngwa Kenneth
Published: February 2015

The chapter examines Exodus as a story of adoption, counteradoption, and readoption, fueled by multiple consciousnesses about kinship relations at the crevices of political, ethnic, religious, and regional identities and transitions. Political transition defines Israel’s relation to Egypt; ethnic consciousness distinguishes between the Hebrews and other subgroups; religious consciousness straddles ancestral worship and allegiance to Yahweh; and regional consciousness transitions liberated/expulsed Israel toward an extraterritorial land by way of the wilderness. Because these consciousnesses do not exist as disjointed narrative tropes but as a cluster of identity and social markers, Exodus repeatedly constructs, deconstructs, and reconstructs narrative kinships that are familiar and alien. Read through the motifs of adoption, counteradoption, and readoption organized across institutional and geographical spaces, the exodus story develops a rich sense of layered consciousnesses, ranging from safety, belonging, and purpose to vulnerability, exposure, and alienation to reconstructions and reimaginations of fractured memories.
Cell Death Triggered by a Putative Amphipathic Helix ofRadish mosaic virusHelicase Protein Is Tightly Correlated With Host Membrane Modification
Authors: Hashimoto Masayoshi , Komatsu Ken , Iwai Ryo , Keima Takuya , Maejima Kensaku , Shiraishi Takuya , Ishikawa Kazuya , Yoshida Tetsuya , Kitazawa Yugo , Okano Yukari , Yamaji Yasuyuki , Namba Shigetou
Published: February 2015

Systemic necrosis is one of the most severe symptoms caused by plant RNA viruses. Recently, systemic necrosis has been suggested to have similar features to a defense response referred to as the hypersensitive response (HR), a form of programmed cell death. In virus-infected plant cells, host intracellular membrane structures are changed dramatically for more efficient viral replication. However, little is known about whether this replication-associated membrane modification is the cause of the symptoms. In this study, we identified an amino-terminal amphipathic helix of the helicase encoded by Radish mosaic virus (RaMV) (genus Comovirus) as an elicitor of cell death in RaMV-infected plants. Cell death caused by the amphipathic helix had features similar to HR, such as SGT1-dependence. Mutational analyses and inhibitor assays using cerulenin demonstrated that the amphipathic helix–induced cell death was tightly correlated with dramatic alterations in endoplasmic reticulum (ER) membrane structures. Furthermore, the cell death–inducing activity of the amphipathic helix was conserved in Cowpea mosaic virus (genus Comovirus) and Tobacco ringspot virus (genus Nepovirus), both of which are classified in the family Secoviridae. Together, these results indicate that ER membrane modification associated with viral intracellular replication may be recognized to prime defense responses against plant viruses.
Evaluation of Dormant-Stage Inoculum Sanitation as a Component of a Fire Blight Management Program for Fresh-Market Bartlett Pear
Authors: Elkins Rachel B. , Temple Todd N. , Shaffer Carolyn A. , Ingels Chuck A. , Lindow Steven B. , Zoller Broc G. , Johnson Kenneth B.
Published: February 2015

From 2010 to 2013, the efficacy of copper-based inoculum sanitation as a component of fire blight management programs was evaluated in commercial pear orchards located in northern California. Forty-one 4-ha sections of orchard were split into two equal-sized plots, with the orchardist applying horticultural oil alone to one plot and horticultural oil plus a fixed copper bactericide to the other plot. These treatments were timed to begin just prior to and finish at the “green tip” phenological stage, which occurs about 5 weeks before full bloom. During bloom, flower samples were collected from the plots and subjected to a loop-mediated isothermal DNA amplification (LAMP) assay for specific detection of Erwinia amylovora. Overall, epiphytic populations of E. amylovora on flowers were detected rarely at midbloom (6% of samples) but commonly at petal fall (44% of samples). In three of four seasons, E. amylovora detection in flower samples at a given bloom stage was significantly suppressed in copper-plus-oil-treated plots compared with oil-only plots. All orchards also received antibiotic treatments during the bloom period and, perhaps as a consequence, the development of fire blight was sporadic and not affected significantly by the copper treatment in any season. The pathogen detection data indicate that copper sanitation may add value to a fire blight management program by delaying the increase of epiphytic populations of E. amylovora in flowers to the late stages of the bloom period, at which time the number of susceptible flowers declines rapidly.
Trichothecene Genotype Composition of Fusarium graminearum Not Differentiated Among Isolates from Maize Stubble, Maize Ears, Wheat Spikes, and the Atmosphere in New York
Authors: Kuhnem Paulo R. , Spolti Pierri , Del Ponte Emerson M. , Cummings Jaime A. , Bergstrom Gary C.
Published: February 2015

In order to test the hypothesis that the trichothecene genotype composition of local populations of Fusarium graminearum is structured by specific habitats, a collection of 1,407 isolates was obtained from overwintered maize stubble, mature maize ears and wheat spikes, and the atmosphere 1.5 m aboveground during the flowering stage of these crops. These isolates were sampled at three diverse agricultural locations in New York State: namely, Aurora (sampled in 2012 and 2013) in central New York, Belmont (sampled in 2013) in southwestern New York, and Willsboro (sampled in 2013) in northeastern New York. Approximately 100 isolates of F. graminearum from each habitat were collected within a 10-mile2 area in each location. Polymerase chain reaction assays were used to identify three main B-trichothecene genotypes—3-acetyldeoxynivalenol (3-ADON), 15-ADON, or nivalenol (NIV)—based on amplification of portions of Tri3 and Tri12 genes. All but the NIV genotype were detected. The 15-ADON genotype predominated in most locations; frequencies were 92% (652/709) at Aurora, 78% (332/379) at Belmont, and 53% (167/319) at Willsboro. Frequencies of any genotype did not differ in general among the four habits in each location. An exception was in Aurora 2012, where only 5 in 24 3-ADON isolates were found in samplings from the air and grains of both crops. As viewed by the composition of trichothecene genotypes, local populations of F. graminearum appear not to be structured by these four habitats inclusive of pathogenic and saprophytic phases of the fungus life cycle. The similar frequency of 3-ADON and 15-ADON in eastern New York (Willsboro), which is less than 400 km away from the Aurora sampling location in the central area of the state, suggests that regional populations may be differentiated based on selection associated with climatic or landscape features not currently identified.
Better than fish on land? Hearing across metamorphosis in salamanders
Authors: Christensen Christian Bech , Lauridsen Henrik , Christensen-Dalsgaard Jakob , Pedersen Michael , Madsen Peter Teglberg
Published: February 2015

Early tetrapods faced an auditory challenge from the impedance mismatch between air and tissue in the transition from aquatic to terrestrial lifestyles during the Early Carboniferous (350 Ma). Consequently, tetrapods may have been deaf to airborne sounds for up to 100 Myr until tympanic middle ears evolved during the Triassic. The middle ear morphology of recent urodeles is similar to that of early ‘lepospondyl’ microsaur tetrapods, and experimental studies on their hearing capabilities are therefore useful to understand the evolutionary and functional drivers behind the shift from aquatic to aerial hearing in early tetrapods. Here, we combine imaging techniques with neurophysiological measurements to resolve how the change from aquatic larvae to terrestrial adult affects the ear morphology and sensory capabilities of salamanders. We show that air-induced pressure detection enhances underwater hearing sensitivity of salamanders at frequencies above 120 Hz, and that both terrestrial adults and fully aquatic juvenile salamanders can detect airborne sound. Collectively, these findings suggest that early atympanic tetrapods may have been pre-equipped to aerial hearing and are able to hear airborne sound better than fish on land. When selected for, this rudimentary hearing could have led to the evolution of tympanic middle ears.
Odourant dominance in olfactory mixture processing: what makes a strong odourant?
Authors: Schubert Marco , Sandoz Jean-Christophe , Galizia Giovanni , Giurfa Martin
Published: February 2015

The question of how animals process stimulus mixtures remains controversial as opposing views propose that mixtures are processed analytically, as the sum of their elements, or holistically, as unique entities different from their elements. Overshadowing is a widespread phenomenon that can help decide between these alternatives. In overshadowing, an individual trained with a binary mixture learns one element better at the expense of the other. Although element salience (learning success) has been suggested as a main explanation for overshadowing, the mechanisms underlying this phenomenon remain unclear. We studied olfactory overshadowing in honeybees to uncover the mechanisms underlying olfactory-mixture processing. We provide, to our knowledge, the most comprehensive dataset on overshadowing to date based on 90 experimental groups involving more than 2700 bees trained either with six odourants or with their resulting 15 binary mixtures. We found that bees process olfactory mixtures analytically and that salience alone cannot predict overshadowing. After normalizing learning success, we found that an unexpected feature, the generalization profile of an odourant, was determinant for overshadowing. Odourants that induced less generalization enhanced their distinctiveness and became dominant in the mixture. Our study thus uncovers features that determine odourant dominance within olfactory mixtures and allows the referring of this phenomenon to differences in neural activity both at the receptor and the central level in the insect nervous system.
Speed and accuracy in nest-mate recognition: a hover wasp prioritizes face recognition over colony odour cues to minimize intrusion by outsiders
Authors: Baracchi D. , Petrocelli I. , Chittka L. , Ricciardi G. , Turillazzi S.
Published: February 2015

Social insects have evolved sophisticated recognition systems enabling them to accept nest-mates but reject alien conspecifics. In the social wasp,
Liostenogaster flavolineata
(Stenogastrinae), individuals differ in their cuticular hydrocarbon profiles according to colony membership; each female also possesses a unique (visual) facial pattern. This species represents a unique model to understand how vision and olfaction are integrated and the extent to which wasps prioritize one channel over the other to discriminate aliens and nest-mates.
Liostenogaster flavolineata
females are able to discriminate between alien and nest-mate females using facial patterns or chemical cues in isolation. However, the two sensory modalities are not equally efficient in the discrimination of ‘friend’ from ‘foe’. Visual cues induce an increased number of erroneous attacks on nest-mates (false alarms), but such attacks are quickly aborted and never result in serious injury. Odour cues, presented in isolation, result in an increased number of misses: erroneous acceptances of outsiders. Interestingly, wasps take the relative efficiencies of the two sensory modalities into account when making rapid decisions about colony membership of an individual: chemical profiles are entirely ignored when the visual and chemical stimuli are presented together. Thus, wasps adopt a strategy to ‘err on the safe side’ by memorizing individual faces to recognize colony members, and disregarding odour cues to minimize the risk of intrusion from colony outsiders.
Fulminant psittacosis in a traveller
Authors: Waidyasekara Pasan , Ramanathan Kollengode
Published: February 2015

Introduction:

Psittacosis is a rare cause of pneumonia, caused by Chlamydia psittaci. The disease is transmitted to humans via inhalation of dried bird faeces, feather dust, urine or respiratory secretions. The disease can range from a mild form with non‐specific symptoms to severe systemic disease with prominent respiratory symptoms. Psittacosis causing severe respiratory failure requiring mechanical ventilation is uncommon.

Case presentation:

A 64‐year‐old male tourist from Hong Kong presented to the emergency department with a 5 day history of headache, myalgia and fever. He had a productive cough and was short of breath. The patient developed septic shock with multiorgan failure requiring intensive care support. We received information from the Centre for Health Diseases in Hong Kong about a psittacosis outbreak in an animal management centre where our patient had been working with recent occupational exposure to dead parrots. Despite a significant increased mortality rate associated with respiratory and renal involvement in psittacosis, our patient survived the sepsis and multiorgan failure and was repatriated back for further rehabilitation.

Conclusion:

The case illustrates the importance of exploring a patient’s occupational history to establish an infection exposure. The respiratory symptoms, myalgia and fever warranted consideration of an atypical pneumonia. The patient had bilateral pulmonary infiltrates contrary to the unilateral involvement in the majority of the patients with chest X‐ray abnormalities. Despite a high mortality rate associated with respiratory and renal involvement, our patient survived the severe sepsis.
Gastrointestinal anthrax in coastal south India: a critical alert on a fatal masquerader
Authors: Iqbal Nayyar , Basheer Aneesh , Ramesh Ayil Nagarajan , Vimal Joseph , Mookkappan Sudhagar , Kanungo Reba , Anandhalakshmi  , Princess Isabella
Published: February 2015

Introduction:

Anthrax remains endemic to some parts of southern India including Pondicherry. Among various forms of the infection, gastrointestinal anthrax appears to be the least common. Cases of inhalational anthrax causing sepsis and disseminated intravascular coagulation have been reported in the literature.

Case presentation:

We report the first case, to the best of our knowledge, of gastrointestinal anthrax with sepsis and disseminated intravascular coagulation from India. The patient ate raw meat under the influence of alcohol, following which he developed fever and gastrointestinal bleeding. Later, he presented with ascites, intracerebral haemorrhage, haematuria and a deranged coagulation profile. Culture of his blood yielded Bacillus anthracis. He succumbed to the infection after 18 h of admission in the intensive care unit. The case was reported to the public health authorities for the necessary follow‐up and preventive measures.

Conclusion:

Gastrointestinal anthrax can have various non‐specific clinical manifestations, making diagnosis difficult. Meticulous history taking, a high index of suspicion and prompt institution of antibiotics with or without surgical intervention is likely to improve outcomes.
Methylomic trajectories across human fetal brain development
Authors: Spiers Helen , Hannon Eilis , Schalkwyk Leonard C. , Smith Rebecca , Wong Chloe C.Y. , O’Donovan Michael C. , Bray Nicholas J. , Mill Jonathan
Published: February 2015

Epigenetic processes play a key role in orchestrating transcriptional regulation during development. The importance of DNA methylation in fetal brain development is highlighted by the dynamic expression of de novo DNA methyltransferases during the perinatal period and neurodevelopmental deficits associated with mutations in the methyl-CpG binding protein 2 (MECP2) gene. However, our knowledge about the temporal changes to the epigenome during fetal brain development has, to date, been limited. We quantified genome-wide patterns of DNA methylation at ∼400,000 sites in 179 human fetal brain samples (100 male, 79 female) spanning 23 to 184 d post-conception. We identified highly significant changes in DNA methylation across fetal brain development at >7% of sites, with an enrichment of loci becoming hypomethylated with fetal age. Sites associated with developmental changes in DNA methylation during fetal brain development were significantly underrepresented in promoter regulatory regions but significantly overrepresented in regions flanking CpG islands (shores and shelves) and gene bodies. Highly significant differences in DNA methylation were observed between males and females at a number of autosomal sites, with a small number of regions showing sex-specific DNA methylation trajectories across brain development. Weighted gene comethylation network analysis (WGCNA) revealed discrete modules of comethylated loci associated with fetal age that are significantly enriched for genes involved in neurodevelopmental processes. This is, to our knowledge, the most extensive study of DNA methylation across human fetal brain development to date, confirming the prenatal period as a time of considerable epigenomic plasticity.
Towards RIP using free-electron laser SFX data
Authors: Galli Lorenzo , Son Sang-Kil , White Thomas A. , Santra Robin , Chapman Henry N. , Nanao Max H.
Published: February 2015

Here, it is shown that simulated native serial femtosecond crystallography (SFX) cathepsin B data can be phased by rapid ionization of sulfur atoms. Utilizing standard software adopted for radiation-damage-induced phasing (RIP), the effects on both substructure determination and phasing of the number of collected patterns and fluences are explored for experimental conditions already available at current free-electron laser facilities.
Satisfaction and continuance with a learning management system
Authors: Islam A.K.M. Najmul , Azad Nasreen
Published: February 2015

Purpose

– The purpose of this paper is to compare the perceptions of educators and students with a learning management system (LMS). The comparison is based on survey data collected from 185 educators and 249 students in a Finnish university who use a popular LMS, Moodle.

Design/methodology/approach

– The analysis of the survey data follows a two-phase strategy. In the first phase, perceptions of educators and students regarding ease of use, result demonstrability, usefulness, access, reliability, compatibility, satisfaction, and continuance intention were compared using one way analysis of variance (ANOVA). In the second phase, partial least squares (PLS) technique is employed to compare the path values and explained variances of satisfaction, and continuance intention by putting relevant variables as predictors.

Findings

– The ANOVA results suggest that students have higher positive perceptions regarding ease of use, usefulness, access, reliability, and compatibility of the LMS than the educators. The PLS analysis results revealed that the amount of variance of students’ satisfaction explained by its predictors was 9 percentage points lower than that of educators. It also revealed that the variance of students’ continuance intention explained by satisfaction and usefulness was 12 percentage points lower than that of educators.

Practical implications

– The study concludes with both theoretical and managerial implications.

Originality/value

– While prior research has investigated either educators’ or students’ perspective, the authors have investigated both and presented a comparison. The authors have reported several differences that help practitioners make customized intervention plan.