bluuebunny/crossref_metadata_2025 huggingface dataset:
The Reformation of the Household
Authors: Burrow Colin
Published: March 2015

One episode in Edmund Spenser’s Faerie Queene shows a sudden transition of worlds which is paradigmatic of Protestant self-representation. From cannibalistic Catholics to pastoral piety, from a godless outdoors to the small-scale courtesies of the godly household, this shift implies that the act of violent religious Reformation abruptly gives rise to a cultural reformation that profoundly changes the scale and style of social organization. This article argues that Spenser’s Protestant mythology still shapes the understanding of households in the sixteenth century and that it is radically misleading. Royal and magnate households dominate the early part of the century, while representations of small-scale (and sometimes only incidentally Protestant) households richly populate the drama and narrative prose of its end. By focusing on the role played by non-royal households in writing by mid-century Catholics-George Cavendish’s Life and Death of Cardinal Wolsey and William Roper’s The Lyfe of Sir Thomas Moore, Knighte-- this article argues two things: that it is wrong to regard the royal household as the all-encompassing centre of early Tudor writing; and that is incorrect to suggest that the Protestant reformation aided the emergence of smaller-scale domestic institutions. In these mid-century works there is a counter-reformation representation of the household which had a powerful influence on later representations of the household—including even those of Protestants such as Spenser, George Gascoigne and Shakespeare.
Monasticism
Authors: Gillespie Vincent
Published: March 2015

As he faced his own dissolution, Henry VIII repeatedly invoked a religious group who had been absent from his kingdom for seven years: the monks. The 1570s saw an irrevocable change in the nature of English Catholicism as Catholic clergy trained in England died, retired, or conformed. During this period, the first waves of Englishmen trained in the new continental “seminaries” as Catholic secular priests swore allegiance to the universal Church and to the Pope as missionaries for Christ. Moreover, the new orders such as the Theatines, the Capuchins, and the Jesuits eclipsed traditional European and coenobitic monasticism. This article examines the cultural disappearance of monks, monasteries, and monasticism in England during the late medieval period. It also considers how authors such as William Shakespeare, Henry Howard, Earl of Surrey, Thomas Walsingham, Barnabe Googe, John Donne, William Langland, and Geoffrey Chaucer remember the monks in their works.
Revolutionaries, Reactionaries and the Dilemmas of Russian Conservatism
Authors: Martin Alexander M.
Published: March 2015

A peculiarity of the right in imperial Russia was the weakness of conservatism—that portion of the right which equates national identity with the currently dominant cultural values and social hierarchies. Instead, the Russian right was more often palingenetic, that is, it looked to the state to revitalize a nation whose potential was allegedly stifled by the very same cultural values and social hierarchies that conservatives embraced. Russia and its people appeared to lack the rootedness and the matrix of organically evolved local and communal identities that were central to conservatism’s socio-political vision elsewhere. Russians were drawn instead to Utopian schemes resting on palingenetic notions that the nation was capable of, indeed in need of, a ‘regeneration’ that hinged on remaking the collective and individual consciousness. Palingenetic nationalism proved to be a revolutionary force that both destabilized Russia itself and became one of the country’s most explosive exports.
Provincial Russia
Authors: Chulos Chris J.
Published: March 2015

While metropolitan cultural and political elites in the aftermath of the Bolshevik Revolution regarded Voronezh and dozens of provinces like it as backwaters in need of enlightenment, the local perspective (on which this chapter focuses) was different. Despite the problems of pre-revolutionary Russia, educated society in Voronezh considered the province a model of the best the former Empire had to offer: an advancing economy, an accomplished cultural world and a distinctive local identity. In their eyes, the province was not backward, dull or dark, but the soul of what it meant to be Russian at the start of the new revolutionary era.
Buddhaghosa on the Phenomenology of Love and Compassion
Authors: Heim Maria
Published: March 2015

This article argues that Buddhaghosa (fifth century ce), the chief commentator and systematizer of the Pali intellectual tradition, brings a distinctively phenomenological orientation to the study of Buddhist categories. He did not take Buddha’s doctrines, particularly the Abhidhamma, as metaphysical or ontological statements about what exists or does not exist, but rather as analytical methods for exploring and transforming human experience. The article demonstrates how his methods work in his treatment of four meditation topics, called the “sublime abidings” (brahmavihāras): loving kindness, compassion, sympathetic joy, and equanimity. These practices collectively depict Buddhaghosa’s phenomenology and psychology of love. They entail a rigorous therapeutic regime of practical methods aimed at bringing about freedom.
Health
Authors: Grigg Amanda J. , Kirkland Anna
Published: March 2015

This chapter explores how health has simultaneously been a significant focus of feminist activism and also an underexplored topic in feminist theory. We trace both the theoretical challenges to traditional notions of health that came out of the decades of women’s health activism in the United States, as well as note the points within feminist scholarly work at which health makes an appearance. We conclude that feminist theorizing about health has failed to keep pace with its proliferation as a dominant cultural concept, and that feminist thinkers are only just now finding ways to recover some of the lost critical edge of an earlier era.
Training for Decision Making under the Stress of Emergency Conditions
Authors: Kleespies Phillip M.
Published: March 2015

When under time or procedure pressure, people change their decision-making strategies. They may accelerate information processing and filter the information they will process. In this chapter, the author presents several models for decision making under pressure and compares them to more traditional models. The naturalistic decision-making models are proposed as more appropriate for decision making when working with high-risk patients under emergency conditions. Given that it is often stressful for clinicians to evaluate and manage patients or clients who are considered at acute risk to themselves or others, the author presents a model for training to reduce stress that is based on Meichenbaum’s stress inoculation training. The chapter concludes with a discussion of the training for skill development and competence in dealing with behavioral emergencies that is consistent with the recommendations of the APA Task Force on the Assessment of Competence in Professional Psychology.
Pragmatics
Authors: Potts Christopher
Published: March 2015

This chapter reviews core empirical phenomena and technical concepts from linguistic pragmatics, including context dependence, common ground, indexicality, conversational implicature, presupposition, and speech acts. It seeks to identify unifying themes among these concepts, provide a high-level guide to the primary literature, and relate the phenomena to issues in computational linguistics.
Recognition of Music Therapy in Europe
Authors: Nöcker-Ribaupierre Monika
Published: March 2015

The development of formal systems of professional recognition for music therapy within Europe has taken many decades and is still not complete. The European Music Therapy Confederation (EMTC) was established in 1990 with a primary goal being the pursuit of recognition for the profession. This ambition is complicated by the fact that there are so many associations across Europe and not all are in the EMTC. In this chapter the quest for formal professional recognition is outlined. The process by which some countries have achieved recognition, that is in Latvia, UK, and Netherlands, is presented.
Religious Peacebuilding
Authors: Omer Atalia
Published: March 2015

The emphasis of the field of religious peacebuilding on the potentially constructive role of religion in transforming conflicts should not preclude considering how the field might, and even should, also challenge religious traditions and political ideologies. Exploration of religious traditions’ peace-promoting resources and the very field of religious peacebuilding are largely grounded in Scott Appleby’s The Ambivalence of the Sacred: Religion, Violence, and Reconciliation. However, Appleby’s insight is misapplied if a preoccupation with theological retrieval impedes an examination of how interpretations of events from multiple perspectives may challenge and transform religious and political systems. Cultivating religious peacebuilding as a rigorous academic enterprise will entail questioning the field’s reliance on secularist presumptions about religion, which facilitate complicity with religion’s contribution to injustices. It also requires reconsidering the presumed unidirectionality of religion and historical change and connecting the field to broader conversations about religion in public life.
Religious Violence
Authors: Appleby R. Scott
Published: March 2015

Although the literature on religious violence is contested to such a degree that one is uncertain what to call the field of study, this chapter argues that there is such a thing as religion and that under certain circumstances religions incite or legitimate deadly violence. Yet the relationship between religions, religious actors, and violence is much more complex than that. This chapter surveys the main trends of a vast literature on that relationship and sorts it into three categories and several sub-categories. Each category explicates a different conceptualization and evaluation of religion and religious agency. In the concluding section this chapter suggests that sufficient work of high quality exists to make possible the integration of the seminal insights of these literatures into a coherent theory of religion and violence.
Structural and Cultural Violence in Religion and Peacebuilding
Authors: Springs Jason A.
Published: March 2015

This chapter makes the case for the necessity of a multi-focal conception of violence in religion and peacebuilding. It first traces the emergence and development of the analytical concepts of structural and cultural violence in peace studies, demonstrating how these lenses draw central insights from, but also differ from and improve upon, critical theory and reflexive sociology. It argues that addressing structural and cultural forms of violence—perhaps especially in non-deadly manifestations—are concerns as central as addressing direct (explicit, personal) and deadly forms of violence for building just and sustainable peace. It argues, further, that religiously informed and/or motivated peacebuilders are especially well-appointed and equipped to identify and address violence in its structural and cultural manifestations. The chapter then examines how concepts of structural and cultural violence centrally inform the efforts of Martin Luther King Jr. and Cornel West to cultivate just and sustainable peace in a context as putatively peaceful and prosperous as the United States.
Violent and Nonviolent Religious Militancy
Authors: Mason Patrick Q.
Published: March 2015

This chapter explores religious militancy as a multivalent phenomenon that includes both violent and nonviolent expressions. Religious militancy has too frequently been equated with violence in popular opinion and scholarly writing alike, a trend that has both marginalized and delegitimized the contributions of nonviolent religious actors. A brief examination of the civil rights movement in the mid-twentieth-century United States illustrates how religion motivated activists on both sides of the debate, moving them toward either extreme violence or radical peace. Religiously militant peacebuilders can build upon the notion of “justpeace” to develop a comprehensive approach to addressing the multiple forms of violence, seeking not only to counter the influence of violent religious extremists but ultimately to win the internal argument within each host religious tradition.
Negotiating Secular and Religious Contributions to Social Change and Peacebuilding
Authors: Gopin Marc
Published: March 2015

This chapter challenges the alleged differences between liberal peace and religious peacebuilding. The seeming division between the two arises in part from the lack of acknowledgment of religious conflict analysis and conflict resolution, both in and out of government, which has harmed the global capacity to respond constructively to destructive conflicts. It is also due to historical and personal Western tendencies to see secularity and religiosity as bifurcated realities. Some practitioners and analysts of conflict resolution can remedy this problem by examining their own experience with combinations of secular and religious motivations and practices, and the challenges they have faced as a result. This chapter examines in particular the attempts of one practitioner to engage in a creative tension of critiquing religion, advocating attention to it, and experimenting with forms of conflict resolution that draw on both religious and secular Western legacies.
The Possibilities and Limits of Inter-Religious Dialogue
Authors: Ochs Peter
Published: March 2015

This chapter reports on a twenty-year experiment in “scriptural reasoning,” a type of inter-religious dialogue that emerges from places of maximal warmth and potential fire—“hearths”—within each participating religious community. It also explores how this dialogue is being adapted for peacebuilding efforts in regions of inter-religious violence. The goal of scriptural reasoning (SR) is to nurture “hearth-to-hearth” dialogue that summons the warmth of each hearth as a resource for conflict reduction, without at the same time stoking the fire. This is potentially the most dangerous form of inter-religious dialogue. This chapter argues, however, that it is also the one that, when handled properly, is most likely to contribute to long-term conflict transformation.
The Intersection of Christian Theology and Peacebuilding
Authors: DuBois Heather M. , Hunter-Bowman Janna
Published: March 2015

This chapter argues that without explicit, theoretically robust, and practically grounded theological reflection, scholarship and practice tend to neglect significant dimensions of existing—and potential—peacebuilding. First, it explicates how theological method can help peacebuilders to counter positivist and secularist assumptions that often eclipse religious, spiritual, existential, psychic, and emotional experiences that are relevant to naming and healing violence. Second, it uses theological analysis to explore ways in which the Mennonite sociolinguistic community of peacebuilder John Paul Lederach contributes to social theory he developed in contradistinction to the liberal peace. Specifically, the chapter identifies eschatological influences in Lederach’s signature notions of “expansive time” and the “beckoning horizon.” Harnessing the strategic peacebuilding paradigm’s inclusion of multiple sociolinguistic communities, the chapter encourages more extensive conversation between peacebuilding and the discipline of theology.
Deaths and Silences
Authors: Attinello Paul
Published: March 2015

This chapter examines censorship in relation to music and the AIDS crisis and the social or political timidity that seems to characterize such music. It argues that music about AIDS reflects a combination of caution and defiance, provocation and obscurity, and tends to foreground implicit feelings of transgression. The chapter supports its arguments by presenting musical works that represent most of the major genres on sale in record stores, including classical, avant-garde, musicals, and film scores. It also cites the work of Frank Zappa and how it underwent a process that mirrors the problems of popular and avant-garde music.
Economic Job Search and Decision-Making Models
Authors: van den Berg Gerard J. , Uhlendorff Arne
Published: March 2015

The economic job search theory is based on the assumption that individuals have imperfect information about jobs and wages. It takes time to find an acceptable job and individuals have to make decisions about their job search behavior. The optimal job search behavior is characterized by the reservation wage, that is, the wage above which job offers are accepted, and by the search effort. Both components depend on factors such as the income during job search and the probability of receiving a job offer. Search effort can be described by the amount of resources used for finding a job, which includes time but can also include the type of search channels. We present the basic models of economic job search theory and selected empirical findings, in which we focus on the job search behavior of unemployed individuals.
Acquired Alexias: Mechanisms of Reading
Authors: Riley Ellyn A. , Brookshire C. Elizabeth , Kendall Diane L.
Published: March 2015

Reading is one of the most important cognitive skills an individual can acquire and the process of reading has been debated much in the psycholinguistic, neurolinguistic, and educational literature for many years now. Much of this literature has discussed the process of reading, proposed theoretical models to describe its components, and identification of neuroanatomic underpinnings. In this chapter we have attempted to provide a review of both dual-route and connectionist models of alexia, outline specific types of peripheral and central alexias, provide a brief overview of the neural substrates linked with reading processes, and finally offer diagnostic and treatment strategies.
Biological Markers of Aphasia Recovery after Stroke
Authors: Meinzer Marcus , Ulm Lena , Lindenberg Robert
Published: March 2015

Language recovery after stroke is often incomplete and residual symptoms may persist for many years. However, there is ample evidence for structural and functional reorganization of language networks after stroke that mediate recovery. This chapter reviews studies that investigated biological markers of language recovery by means of functional and structural imaging techniques. In particular, we discuss neural signatures associated with spontaneous and treatment-induced language recovery across the first year poststroke and in the chronic stage of aphasia, studies that aimed at predicting recovery and treatment outcome as well as recent developments in brain stimulation that may be suited to enhance the potential for functional recovery.
Semantic Processing in Transcortical Sensory Aphasia
Authors: Reilly Jamie , Martin Nadine
Published: March 2015

Transcortical sensory aphasia (TCSA) has historically been regarded as a disconnection syndrome characterized by impaired access between words and otherwise intact core object knowledge. Yet, an extensive body of research has also demonstrated a range of associated nonverbal semantic deficits in TCSA, suggestive of a multimodal semantic impairment that transcends representational modality (i.e., language). Here we delineate the semantic impairment incurred in TCSA within a neurologically constrained model of semantic memory premised upon dynamic interactivity between stored knowledge (e.g., semantic features) and integrative processes that serve to bind this knowledge into cohesive object representations. We discuss practical implications for clinical aphasiology and outline considerations for the broader fields of cognitive neuropsychology and neurolinguistics.
The Problem with Zoos
Authors: Malamud Randy
Published: March 2015

Zoos and aquariums have been traditionally and commonly regarded as august civic institutions that save animals from the immediate perils of a besieged wilderness and from extinction. Zookeepers say that their institutions inspire audiences to work to make our planet a place that is respectful of all living beings. But a more ecologically and ethically critical reading of zoos suggests that they are prisons for kidnapped, alienated, tortured specimens who are forced to live their lives in vastly unsuitable compounds for the titillation of ignorant crowds brought in by marketing and advertising campaigns that promise highbrow ecological experiences but actually pander to audiences’ less noble cravings for amusement parks, or even freakshows. Zoos’ efforts at ecological education fail because patrons show no inclination to improve their records as plunderers of natural resources or to acknowledge the pain inherent in the forced displacement and captivity of other animals.
Victimization and Help-Seeking Among Survivors of Intimate Partner Violence
Authors: Gover Angela R. , Tomsich Elizabeth A. , Richards Tara N.
Published: March 2015

Intimate partner violence (IPV) occurs at high rates in US society and has numerous negative physical, psychological, and economic consequences for victims and survivors. Given the high rates and deleterious consequences of IPV, research has focused added attention on behaviors survivors engage in as a response to the violence. This article discusses help seeking behaviors among victims and survivors of IPV by reviewing the incidence of help-seeking behavior and formal and informal outlets of assistance. The article presents theoretical explanations of help-seeking behaviors and reviews factors associated with the decision to seek help, as well as positive and negative outcomes of help-seeking. Although most victims seek assistance, they are more likely to seek informal rather than formal avenues of support. Barriers to help-seeking behaviors among IPV victims make theoretical evaluations difficult and complicate the development of effective formal resources as a response to those seeking help for IPV.
The Ptolemaic Army
Authors: Fischer-Bovet Christelle
Published: March 2015

This essay discusses the recruitment and payment of soldiers, as well as the ethnic composition, organization, and training of the Ptolemaic army, through the examination of papyri, of inscriptions, and of Polybius’ account of the Ptolemaic victory against the Seleucids at Raphia. It describes the military reforms that took place between the 220s and 160s BCE in response to external and domestic pressures, in particular the integration of large numbers of Egyptian soldiers. It shows how the development of the socio-economic status of diverse groups of soldiers and cultural exchanges occurring among members of the army, although facilitated by these changes, also shaped them. While the Ptolemaic army is best described as multiethnic, it did not lack coordination on the battlefield, due to skilled leadership and to soldiers’ feeling of attachment to the dynasty, which was reinforced by land grants and other privileges.
The Archaeology of Amarna
Authors: Stevens Anna
Published: March 2015

This essay assesses the body of archaeological research connected to the New Kingdom settlement site of Amarna (ancient Akhetaten), the short-lived capital of Egypt founded by king Akhenaten around 1347 BC as the cult centre for the solar god the Aten. Amarna, by far the largest exposure of pharaonic settlement to survive from Egypt, is unsurpassed as a case site for the study of ancient Egyptian urbanism and daily life. This essay provides an overview of the ancient city, evaluates past and ongoing excavations at the site, and summarizes the archaeological discourse on the city as a physical, functioning and experienced space.
Reading Ruth, Reading Desire
Authors: Powell Stephanie Day , Jones Amy Beth , Kim Dong Sung
Published: March 2015

This chapter offers a critical paradigm for reading Ruth through the lens of “narrative desire.” An interdisciplinary method bringing together insights from narratology, psychoanalytic theory, philosophical studies, and queer theory, narrative desire provides a versatile approach to indeterminate texts, highlighting the erotic interplay between a narrative’s form and content and the reader’s response. By playing on readers’ desires for a fulfilling and resolute climax, Ruth often seduces readers into what Peter Brooks terms “the male plot of ambition.” From this perspective, women and other minority characters are rendered utilitarian disruptions in an otherwise male, Israelite story. An alternative strategy of “reading for the middle” encourages readers to reconsider the temporal and spatial dynamics of the narrative in order to resist restrictive forms of emplotment. As one lingers in the “dilatory” spaces of the middle, hidden desires are exposed and emancipatory possibilities are revealed.
(Hi)story Telling in the Books of Samuel
Authors: Gilmour Rachelle
Published: March 2015

This chapter introduces the books of Samuel from three angles. The first angle is an overview of its content and macro-structures. Close attention is paid to the patterns in its narrative: the rise and fall of Israel’s leadership and the comparisons and contrasts between these leaders. Second, the focus shifts from the books themselves to the methods of reading them, tracing the development of narrative studies in Samuel. It advocates the integration of final form readings with investigation into historical and source-critical questions of the book, each informing and developing the other. Finally, an example of this integration is demonstrated in a narrative reading of the story of Shimei, David, and Joab in 2 Samuel 20 through the lens of its characteristics of historiography: causation, meaning, and evaluation. Attention to these categories deepens our literary reading, highlighting its values and conception of significance in the past.
Population Structure of the Late Blight Pathogen Phytophthora infestans in a Potato Germplasm Nursery in Two Consecutive Years
Authors: Tian Yuee , Yin Junliang , Sun Jieping , Ma Hongmei , Ma Yunfang , Quan Junli , Shan Weixing
Published: March 2015

As the causal agent of late blight on potato, Phytophthora infestans is one of the most destructive plant pathogens worldwide and widely known as the Irish potato famine pathogen. Understanding the genetic structure of P. infestans populations is important both for breeding and deployment of resistant varieties and for development of disease control strategies. Here, we investigate the population genetic structure of P. infestans in a potato germplasm nursery in northwestern China. In total, 279 isolates were recovered from 63 potato varieties or lines in 2010 and 2011, and were genotyped by mitochondrial DNA haplotypes and a set of nine simple-sequence repeat markers. Selected isolates were further examined for virulence on a set of differential lines containing each resistance (R) gene (R1 to R11). The overall P. infestans population was characterized as having a low level of genetic diversity and resistance to metalaxyl, and containing a high percentage of individuals that virulent to all 11 R genes. Both A1 and A2 mating types as well as self-fertile P. infestans isolates were present but there was no evidence of sexual reproduction. The low level of genetic differentiation in P. infestans populations is probably due to the action of relatively high levels of migration as supported by analysis of molecular variance (P < 0.01). Migration and asexual reproduction were the predominant mechanisms influencing the P. infestans population structure in the germplasm nursery. Therefore, it is important to ensure the production of pathogen-free potato seed tubers to aid sustainable production of potato in northwestern China.
Early-life reproduction is associated with increased mortality risk but enhanced lifetime fitness in pre-industrial humans
Authors: Hayward Adam D. , Nenko Ilona , Lummaa Virpi
Published: March 2015

The physiology of reproductive senescence in women is well understood, but the drivers of variation in senescence rates are less so. Evolutionary theory predicts that early-life investment in reproduction should be favoured by selection at the cost of reduced survival and faster reproductive senescence. We tested this hypothesis using data collected from preindustrial Finnish church records. Reproductive success increased up to age 25 and was relatively stable until a decline from age 41. Women with higher early-life fecundity (ELF; producing more children before age 25) subsequently had higher mortality risk, but high ELF was not associated with accelerated senescence in annual breeding success. However, women with higher ELF experienced faster senescence in offspring survival. Despite these apparent costs, ELF was under positive selection: individuals with higher ELF had higher lifetime reproductive success. These results are consistent with previous observations in both humans and wild vertebrates that more births and earlier onset of reproduction are associated with reduced survival, and with evolutionary theory predicting trade-offs between early reproduction and later-life survival. The results are particularly significant given recent increases in maternal ages in many societies and the potential consequences for offspring health and fitness.
Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence
Authors: Tilston-Lunel Natasha L. , Hughes Joseph , Acrani Gustavo Olszanski , da Silva Daisy E. A. , Azevedo Raimunda S. S. , Rodrigues Sueli G. , Vasconcelos Pedro F. C. , Nunes Marcio R. T. , Elliott Richard M.
Published: March 2015

Oropouche virus (OROV) is a public health threat in South America, and in particular in northern Brazil, causing frequent outbreaks of febrile illness. Using a combination of deep sequencing and Sanger sequencing approaches, we determined the complete genome sequences of eight clinical isolates that were obtained from patient sera during an Oropouche fever outbreak in Amapa state, northern Brazil, in 2009. We also report the complete genome sequences of two OROV reassortants isolatd from two marmosets in Minas Gerais state, south-east Brazil, in 2012 that contained a novel M genome segment. Interestingly, all 10 isolates possessed a 947 nt S segment that lacked 11 residues in the S-segment 3′ UTR compared with the recently redetermined Brazilian prototype OROV strain BeAn19991. OROV maybe circulating more widely in Brazil and in the non-human primate population than previously appreciated, and the identification of yet another reassortant highlights the importance of bunyavirus surveillance in South America.
BamHash: a checksum program for verifying the integrity of sequence data
Authors: Óskarsdóttir Arna , Másson Gísli , Melsted Páll
Published: March 2015

Large resequencing projects require a significant amount of storage for raw sequences, as well as alignment files. Since the raw sequences are redundant once the alignment has been generated, it is possible to keep only the alignment files. We present BamHash, a checksum based method to ensure that the read pairs in FASTQ files match exactly the read pairs stored in BAM files, regardless of the ordering of reads. BamHash can be used to verify the integrity of the files stored and discover any discrepancies. Thus, BamHash can be used to determine if it is safe to delete the FASTQ files storing raw sequencing reads after alignment, without the loss of data.

Availability and Implementation

The software is implemented in C++, GPL licensed and available athttps://github.com/DecodeGenetics/BamHash

Contact

pmelsted@hi.is
Distinctive Features of a Saudi Genome
Authors: Alabdulkareem Ibrahim , Robertson Anthony J. , Garawi Sami Al , Aljumah Mohammed , Al-Turki Saeed , AlBalwi Mohammed A.
Published: March 2015

We have fully sequenced the genome of an individual from the region of Saudi Arabia. In order to facilitate comparative analysis, an initial characterization of the new genome was undertaken based on single nucleotide polymorphism (SNP). The SNP data having associated population statistics, essentially the HapMap, served to identify features that were rare by comparison. Methods were developed and applied to tag observed SNPs as different and were extended to identify strings or clusters of difference in the individual relative to comparison populations to effectively increase the significance over single SNP comparison. Difference strings identified in the individual relative to each comparison population showed a genome location pattern with various levels of overlap between the comparison populations. The SNP frequencies from the HapMap population samples Ceu and Yri showed a difference inversion relative to the sample genome. The total SNP difference count was greatest between the individual and the Yri population sample while the number and total span of SNP difference clusters was greatest in comparison with the Ceu population sample. The final pattern of difference clusters has served to define distinctive features in the individual genome toward preliminary characterization.
Phaseitrials in melanoma: A framework to translate preclinical findings to the clinic
Authors: Kim Eunjung , Rebecca Vito W. , Smalley Keiran S.M. , Anderson Alexander R.A.
Published: March 2015

We present a, mathematical model driven, framework to implement virtual or imaginary clinical trials (phaseitrials) that can be used to bridge the gap between preclinical studies and the clinic. The trial implementation process includes the development of an experimentally validated mathematical model, generation of a cohort of heterogeneous virtual patients, an assessment of stratification factors, and optimization of treatment strategy. We show the detailed process through application to melanoma treatment, using a combination therapy of chemotherapy and an AKT inhibitor, which was recently tested in a phase 1 clinical trial. We developed a mathematical model, composed of ordinary differential equations, based on experimental data showing that such therapies differentially induce autophagy in melanoma cells. Model parameters were estimated using an optimization algorithm that minimizes differences between predicted cell populations and experimentally measured cell numbers. The calibrated model was validated by comparing predicted cell populations with experimentally measured melanoma cell populations in twelve different treatment scheduling conditions. By using this validated model as the foundation for a genetic algorithm, we generated a cohort of virtual patients that mimics the heterogeneous combination therapy responses observed in a companion clinical trial. Sensitivity analysis of this cohort defined parameters that discriminated virtual patients having more favorable versus less favorable outcomes. Finally, the model predicts optimal therapeutic approaches across all virtual patients.

One Sentence Summary

We propose a computational framework to implement phaseitrials (virtual/imaginary yet informed clinical trials) in cancer, using an experimentally calibrated mathematical model of melanoma combination therapy, that can readily capture observed heterogeneous clinical outcomes and be used to optimize future clinical trial design.
Tudor Staphylococcal Nuclease Links Formation of Stress Granules and Processing Bodies with mRNA Catabolism in Arabidopsis
Authors: Gutierrez-Beltran Emilio , Moschou Panagiotis N. , Smertenko Andrei P. , Bozhkov Peter V.
Published: March 2015

Tudor Staphylococcal Nuclease (TSN or Tudor-SN; also known as SND1) is an evolutionarily conserved protein involved in the transcriptional and posttranscriptional regulation of gene expression in animals. Although TSN was found to be indispensable for normal plant development and stress tolerance, the molecular mechanisms underlying these functions remain elusive. Here, we show that Arabidopsis thaliana TSN is essential for the integrity and function of cytoplasmic messenger ribonucleoprotein (mRNP) complexes called stress granules (SGs) and processing bodies (PBs), sites of posttranscriptional gene regulation during stress. TSN associates with SGs following their microtubule-dependent assembly and plays a scaffolding role in both SGs and PBs. The enzymatically active tandem repeat of four SN domains is crucial for targeting TSN to the cytoplasmic mRNA complexes and is sufficient for the cytoprotective function of TSN during stress. Furthermore, our work connects the cytoprotective function of TSN with its positive role in stress-induced mRNA decapping. While stress led to a pronounced increase in the accumulation of uncapped mRNAs in wild-type plants, this increase was abrogated in TSN knockout plants. Taken together, our results establish TSN as a key enzymatic component of the catabolic machinery responsible for the processing of mRNAs in the cytoplasmic mRNP complexes during stress.
Greenhouse gas reporting quality in the oil and gas industry
Authors: Comyns Breeda , Figge Frank
Published: March 2015

Purpose

– The purpose of this paper is to explore the evolution of greenhouse gas (GHG) reporting quality and to determine whether the evolution of reporting quality is linked with the type of information reported based on the “search”, “experience”, and “credence” typology.

Design/methodology/approach

– The method is based on the content analysis of GHG reporting in 245 sustainability reports by 45 oil and gas companies between 1998 and 2010. The content analysis disclosure index developed links GHG reporting requirements with seven quality dimensions. The information associated with each item on the content analysis index is classified as “search”, “experience” or “credence”. Statistical analysis is used to determine whether any significant change occurred in either overall GHG reporting quality or in the quality of reporting in any of the individual dimensions of quality over the period of the study.

Findings

– GHG reporting quality has not improved significantly between 1998 and 2010. The quality of reporting is not the same in each of the seven dimensions of quality and this can be explained by information typology.

Originality/value

– This paper provides the first longitudinal analysis of the quality of GHG reporting. The methodology developed advances current measures of reporting quality by linking reporting requirements with particular quality dimensions. The results show that the type of information is important in terms of quality evolution and that this can dictate the measures required to improve quality.
How do climate and topography influence the greening of the forest‐tundra ecotone in northern Québec? A dendrochronological analysis ofBetula glandulosa
Authors: Ropars Pascale , Lévesque Esther , Boudreau Stéphane
Published: March 2015

NDVIanalysis and repeated aerial photographs have revealed significant shrub expansion in many subarctic regions. While the recent increase in temperature is usually considered to be the main driver of this phenomenon at regional scales, very little is known about the local heterogeneity of shrub responses across the landscape.

In this study, we aim to identify the climatic factors controlling the growth of the largely distributed shrub speciesBetula glandulosain three types of environments (terrace, hilltop and snowbed). We also aim to evaluate the relationship betweenB. glandulosagrowth and theNDVIdata for the Boniface River region, in north‐western Québec, where the study took place.

In the field, we harvested 180B. glandulosaindividuals (20 per site, 3 sites per type of environment). We constructed specific growth‐ring width chronologies and mean axial growth rate chronologies for each site and used them for dendroclimatic analysis (response functions). We also used linear regressions to evaluate the relative influence of dwarf birch growth on theNDVItrend.

We found a sharp increase inB. glandulosaradial growth in the 1990s followed by a sharp decreasing trend from 2002 on terraces and hilltops, while growth remained high in snowbeds.Betula glandulosagrowth was positively correlated with summer temperatures on terraces and hilltops, whereas winter precipitation promoted growth on snowbeds. TheNDVItrend was largely correlated toB. glandulosagrowth on terraces and hilltops for the period between 1986 and 2002 (71–80% explained variance).

Synthesis. Our results suggest that topography plays a major role inB. glandulosagrowth and therefore in shrub community dynamics. Because terraces and hilltops represent 70% of the land surface, the sharpB. glandulosagrowth increase at these sites promoted an important overall expansion of the shrub community in the region. However, the decline inB. glandulosagrowth observed after 2002 suggests that the expansion could be slowed down in the near future, therefore limiting shrub growth contribution to the regionalNDVIsignal.
Novel vascular endothelial growth factor blocker improves cellular viability and reduces hypobaric hypoxia‐induced vascular leakage and oedema in rat brain
Authors: Saraswat Deepika , Nehra Sarita , Chaudhary Kamal , CVS Siva Prasad
Published: March 2015

Vascular endothelial growth factor (VEGF) is an important cerebral angiogenic and permeability factor under hypoxia. There is a need to find effective molecules that may ameliorate hypoxia‐induced cerebral oedema. In silico identification of novel candidate molecules that block VEGF‐A site were identified and validated with a Ramachandran plot. The active site residues of VEGF‐A were detected by Pocketfinder, CASTp, and DogSiteScorer. Based on in silico data, three VEGF‐A blocker (VAB) candidate molecules (VAB1, VAB2, and VAB3) were checked for improvement in cellular viability and regulation of VEGF levels in N2a cells under hypoxia (0.5% O2). Additionally, the best candidate molecule's efficacy was assessed in male Sprague‐Dawley rats for its ameliorative effect on cerebral oedema and vascular leakage under hypobaric hypoxia 7260 m. All experimental results were compared with the commercially available VEGF blocker sunitinib. Vascular endothelial growth factor‐A blocker 1 was found most effective in increasing cellular viability and maintaining normal VEGF levels under hypoxia (0.5% oxygen) in N2a cells. Vascular endothelial growth factor‐A blocker 1 effectively restored VEGF levels, decreased cerebral oedema, and reduced vascular leakage under hypobaric hypoxia when compared to sunitinib‐treated rats. Vascular endothelial growth factor‐A blocker 1 may be a promising candidate molecule for ameliorating hypobaric hypoxia‐induced vasogenic oedema by regulating VEGF levels.
Making Sense of Ambiguity through Dialogue and Collaborative Action
Authors: Carroll John S.
Published: March 2015

This paper outlines the importance of ambiguity in organizations that manage hazardous operations in a rapidly changing environment. Three kinds of ambiguity are described: fundamental ambiguity in categories and labels for understanding what is happening; causal ambiguity for understanding cause–effect relationships that enable explanation, prediction, and intervention; and role ambiguity of agreeing on responsibilities. Examples of successful and unsuccessful ways that organizations deal with ambiguity are drawn from several industries. Although the most typical response is to avoid ambiguity or to seek a false clarity from confident leaders, more successful strategies engage diverse participants from inside and outside the organization to provide multiple perspectives and innovative suggestions that contribute to learning‐by‐doing.
Managing Safety: Ambiguous Information and Chronic Unease
Authors: Flin Rhona , Fruhen Laura
Published: March 2015

Managers rarely have full and unequivocal data on their external environment or on the state of their internal processes and in this paper we discuss how they deal with ambiguity, in relation to organizational safety. Drawing on our research into managers’ safety intelligence and on the value of chronic unease for safety management, we show how both requisite anxiety and problem solving skills can help managers make the best use of ambiguous safety information.
The surgical management of recurrent stress urinary incontinence: a systematic review
Authors: Nikolopoulos Kostis I. , Betschart Cornelia , Doumouchtsis Stergios K.
Published: March 2015

Background

Despite a wide spectrum of interventions, surgical treatments of recurrent stress urinary incontinence (SUI) are associated with high failure rates.

Objectives

To systematically review current evidence on the effectiveness of surgical interventions for recurrent SUI.

Data sources

An electronic database search was undertaken (1980–2014). Keywords were: “stress urinary incontinence,” “failure,” “recurrence,” “treatment.” References of identified studies and abstracts from conferences were considered.

Study selection

We restricted the search to female patients and currently used surgical procedures, including studies with five or more cases. After the initial yield, studies were selected following title screening, abstract and full text scrutiny.

Results

The pooled objective cure rates of colposuspension for recurrent SUI are 76% (95% CI ±5.04), whereas rates for midurethral sling procedures are 68.5% (95% CI ±3.11). Repeat midurethral sling procedures have pooled success rates of 66.2% (95% CI ±4) but those of the transobturator approach appear lower than retropubic procedures. Pubovaginal slings for recurrent SUI have pooled success of 79.3% (95% CI ±6.54). Success rates for adjustable continence therapy and adjustable slings for recurrent SUI are 53.8% (95% CI ±5.28), whereas for midurethral sling fixation procedures the pooled success is 61% (95% CI ±10.56). Urethral bulking injections have success rates of 38% (95% CI ±10.7). Laparoscopic two‐team sling procedures, salvage spiral slings, and artificial urinary sphincter have shown promising results, but there are limited data on recurrent cases.

Conclusion

There is a wide spectrum of surgical interventions reported for secondary or tertiary treatment of SUI. A common characteristic for all recurrent procedures is a lower success rate compared with those reported following primary procedures.
TRPV4 activates autonomic and behavioural warmth‐defence responses in Wistar rats
Authors: Vizin R. C. L. , Scarpellini C. da S. , Ishikawa D. T. , Correa G. M. , de Souza C. O. , Gargaglioni L. H. , Carrettiero D. C. , Bícego K. C. , Almeida M. C.
Published: March 2015

Aim

In this study, we aimed at investigating the involvement of the warmth‐sensitive channel – TRPV4 (in vitro sensitive to temperatures in the range of approx. 24–34 °C) – on the thermoregulatory mechanisms in rats.

Methods

We treated rats with a chemical selective agonist (RN‐1747) and two antagonists (RN‐1734 and HC‐067047) of the TRPV4 channel and measured core body temperature, metabolism, heat loss index and preferred ambient temperature.

Results

Our data revealed that chemical activation of TRPV4 channels by topical application of RN‐1747 on the skin leads to hypothermia and this effect was blocked by the pre‐treatment with the selective antagonist of this channel. Intracerebroventricular treatment with RN‐1747 did not cause hypothermia, indicating that the observed response was indeed due to activation of TRPV4 channels in the periphery. Intravenous blockade of this channel with HC‐067047 caused an increase in core body temperature at ambient temperature of 26 and 30 °C, but not at 22 and 32 °C. At 26 °C, HC‐067047‐induced hyperthermia was accompanied by increase in oxygen consumption (an index of thermogenesis), while chemical stimulation of TRPV4 increased tail heat loss, indicating that these two autonomic thermoeffectors in the rat are modulated through TRPV4 channels. Furthermore, rats chemically stimulated with TRPV4 agonist choose colder ambient temperatures and cold‐seeking behaviour after thermal stimulation (28–31 °C) was inhibited by TRPV4 antagonist.

Conclusion

Our results suggest, for the first time, that TRPV4 channel is involved in the recruitment of behavioural and autonomic warmth‐defence responses to regulate core body temperature.