bluuebunny/crossref_metadata_2025 huggingface dataset:
The New Cultural Marketplace
Authors: Patten Robert L.
Published: September 2014

The British Empire ran on print. The manufacture of printed material industrialized, speeded up, expanded, and cheapened through the century. Printers and publishers prospered as financing stabilized and markets expanded. Transportation carried print all over the United Kingdom and to colonies and other countries around the world. Literacy increased; education became more widespread and more extensive. Governing bodies churned out reams of investigative ‘blue books’, laws, reports, charts, maps, and examinations. Science progressed, published its results, and created controversy as well as machines, medicines, and commodities. Authors began to obtain rights in their writings, both at home and by the end of the century abroad. Journalism grew at a compound rate as taxes on knowledge were repealed and markets for inexpensive publications swelled. The reading public enlarged to include the working classes and women. Britain’s material print culture helped create and sustain the empire and its place in world history.
Henry James’s Houses
Authors: Marshall Gail
Published: September 2014

This essay argues that modern theoretical approaches to performativity, and its usefulness as a tool for interpreting the representation of language acts and interpersonal relations, were in large part anticipated by Henry James, in his theatrical criticism, his autobiographical writing, and his fiction. In offering readings of The Portrait of a Lady(1881), The Tragic Muse(1890), and A Small Boy and Others (1913) the essay demonstrates that James’s domestic spaces are his richest performative arenas, framing their occupants, and staging their exchanges. Domesticity and its spaces are indeed for James the root and source of the performative instinct. The essay also seeks to show how Jamesian performances depend on the material things and possessions about which he also writes with such enthralled attention; and concomitantly how an attention to performance adds new dimensions to our understanding of ‘thing theory’.
Conflicts Within the Roman Catholic Church
Authors: Hogan Linda
Published: September 2014

This chapter situates the controversies about sex and gender in the Roman Catholic Church within the context of ongoing debates about the nature of the Church, the dynamism of the tradition, and the authority of the magisterium. It argues that underlying many of the most contentious of these disagreements, including those about reproductive rights, same-sex relationships, and gender-based violence, one can discern fundamentally different theological understandings about the nature of the human body, the relationships between the sexes, and the malleability of sexuality. Having examined these underlying theological controversies, this chapter considers the contours of the contemporary debates about reproductive rights and same-sex relationships. It notes moreover that these controversies are not abating. Rather, the positions are becoming more polarized and the divisions more intractable.
Modeling the Genetics of Social Cognition in the Laboratory
Authors: Ebstein Richard P. , Zhong Songfa , Chark Robin , Lai Poh San , Chew Soo Hong
Published: September 2014

This chapter examines recent advances in the genetics of social cognition, discussing evidence from twin studies that confirm the relevancy of genetic hard wiring in understanding many social phenotypes, with important implications for the social sciences and for genome-wide association studies (GWAS) that may identify specific genes contributing to a wide range of social phenotypes, genoeconomics, and individual and social decision making. Stressing the importance of phenotype definition and precise measurement as key to success in GWAS, the authors argue that laboratory-based behavioral economic paradigms using ethnically homogenous student populations generate the best prospects for successful GWAS. Also discussed are the neurochemical/neurogenetic architecture of behavioral economic games that measure individual and social decision making and the considerable progress made in unraveling the neurogenetics of human parenting and the beginning of a political attitudes neuroscience. The authors’ own GWAS is used to present a set of guidelines for future research directions.
Economists’ Ethics in the Build-Up to the Great Recession
Authors: Wade Robert H.
Published: September 2014

This chapter argues that mainstream economists – mainly American and British contributed to the build-up of the financial fragility which tipped into the Great Recession through their implicit assumption of epistemic asymmetry (hubris) and epistemic sufficiency (close-mindedness, or selective inattention to data and arguments which would upset their way of seeing things). They also contributed, secondarily, through the failure to disclose conflicts of interests, involving collusion between economists and financial organizations. Both these contributions reflect the discipline’s failure to formulate and teach ethical principles for guiding economists as they prescribe policies that may affect the welfare of millions of people and the health of the biosphere. In the absence of ethical restraints economists have too often advocated policies on the assumption that the optimal outcomes will materialize, only to find that their prescriptions bring about unanticipated, harmful effects that catch them off guard.
Understanding and Treating the Psychosocial Consequences of Pregnancy Loss
Authors: Diamond David J. , Diamond Martha O.
Published: September 2014

This chapter reviews research on the psychological impact and treatment of pregnancy loss for women, men, and families. The psychological sequelae of pregnancy loss can include mild to severe grief, complicated grief, depressive disorders, post-traumatic stress disorder (PTSD), and other anxiety disorders. Effects on couples, men, and other family members, including the impact on subsequent pregnancies, parental attachment to subsequent children, and gender differences in how men and women cope and grieve, are discussed. The authors present a conceptual framework for understanding pregnancy loss, positing that reactions largely depend on deeply personal and often unconscious meanings of pregnancy and on how parenthood fits into personal identity and the achievement of adult developmental tasks. The authors discuss unique aspects of pregnancy loss that may explain its broad impact and describe ways in which psychotherapy with pregnancy loss patients differs from psychotherapy with the general population, especially regarding countertransference and attitudes toward self-disclosure.
Public and Elite Perceptions of News Media in Politics
Authors: Tsfati Yariv
Published: September 2014

This chapter provides an overview of the research on individual’s perceptions about and attitudes toward the news media. It discusses research on trust in media, hostile media perceptions, and perceptions of media influence, also known as third person perceptions. All three perceptions are shaped by both cognitive and self-enhancement mechanisms and all have important political consequences. The chapter argues that perceptions about the news media among the elite have largely been ignored by scholars but are consequential in shaping the political world. When politicians perceive that media are powerful, they react by initiating coverage and cooperating with the requests of journalists. When a certain issue is expected to receive substantial media attention, politicians react by initiating legislation or discussion about that topic. Thus, politicians’ perceptions of media the may be at the heart of a decades-long process of mediatization of politics.
Affect and Political Choice
Authors: Crigler Ann N. , Hevron Parker R.
Published: September 2014

Whether political observers and participants applaud or decry the presence of emotions in political decision-making, scholars have begun to view the relationship between affect and reason as a key component of decision-making. This chapter provides an overview of the research on affect and political choice. The authors argue that emotions undergird acts of political choice, not simply as additional variables to explain preferences or actions but also as integral to the processing of information and decision-making. They briefly define affect, emotion and mood and outline some of the methodologies commonly used to measure each of the four emotion functions that are central to political communication and choice. These four functions of emotion – expressive, perceptual/attentional, appraisal, and behavioral – are discussed in relation to political decision-making.
Positive Development and Resilience in Emerging Adulthood
Authors: O'Connor Meredith , Sanson Ann V. , Toumbourou John W , Hawkins Mary T. , Letcher Primrose , Williams Paige , Olsson Craig
Published: September 2014

Recently, calls have been made for an increased focus on successful development in young people and how optimal developmental pathways can be promoted. The concept of healthy functioning or positive development is particularly relevant to the emerging-adulthood period because of the significant potential for positive change and redirection of life pathways observed during this time. This chapter focuses on one empirically tested model of positive development in emerging adulthood developed with data from the Australian Temperament Project. Positive development is conceptualized as comprising the dimensions of civic action and engagement, trust and tolerance of others, trust in authorities and organizations, social competence, and life satisfaction. A growing body of research suggests that positive development in emerging adulthood is an important asset for young people, with distinct developmental antecedents and consequences for later functioning. The findings provide possible targets for interventions to promote healthy developmental pathways into adulthood.
Moral Development During Emerging Adulthood
Authors: Padilla-Walker Laura M.
Published: September 2014

Morality is an extremely broad and yet nuanced topic and field of development, with a multitude of factors that are thought to contribute to moral behavior. Although an exhaustive review is outside the scope of this chapter, the author examines the broad areas of moral cognition, moral emotion, moral identity, and prosocial behavior with a particular emphasis on how these aspects of morality are characterized during emerging adulthood. The chapter asserts that moral development is alive, well, and developing during the third decade of life. Perhaps because of the salient focus on negative aspects of development, our understanding of moral development during emerging adulthood is relatively underdeveloped, especially from a developmental framework and outside of a college student population. Thus, multiple suggestions for future directions in the area of moral development during emerging adulthood are discussed throughout.
Selves in a World of Stories During Emerging Adulthood
Authors: McLean Kate C. , Breen Andrea
Published: September 2014

In this chapter, the authors review research on self-esteem and self-concept in emerging adulthood. Drawing from traditional cognitive-developmental theories of self-development, as well as dialogical theories, they take a narrative approach to argue that emerging adults story their selves by engaging with cultural processes that emerge via media (e.g., television, movies, books, Facebook). The authors offer some suggestions for bridging cognitive-developmental and dialogical theories in the context of narrative construction of personal selves as they intersect with larger cultural stories.
Omar ibn Said’s Rhetorical Discourse Against Slavery
Authors: Kahera Akel Ismail
Published: September 2014

Ibn Said’s description of the servile spaces he encountered, his Africa captivity and his attempt to escape, provoke several dichotomies such as manumission, freedom and bondage, power and knowledge, and life and death. In fact both parts of the Memoir—the prologue and the epilogue—coexist and work together to extend the meaning of these dichotomies, and they go a long way toward explaining Ibn Said’s intellectual poise. The rhetorical gesture of using the Qur’an is a further indication of his knowledge of exegesis of al-Mulk (chapter 67), which may attest to his protest against slavery, adding yet another piece of damming evidence against the servile estate in antebellum America.
African American and Immigrant Muslim Interaction
Authors: Kahn Saeed
Published: September 2014

The narrative of Islam in America took a significant turn with the influx of a critical mass of Muslims migrating from the Middle East and South Asia in the twentieth century. The interaction between these immigrant Muslims and African American Muslims has shaped the current landscape for American Islam through the development of new institutions and modes of engagement. At the same time, however, the history of this interaction reveals the complexities that exist between multiethnic, multiracial and multi-ideological groups on an intrafaith level. This chapter explores the relationship between African American and immigrant Muslims over the past century. It will chart the engagement of individual immigrant Muslims, like Inayat Khan and Mohammad Sadiq, as well as groups and organizations, including the Ahmadiyya, Federation of Islamic Association, the Hanafi Madhab Center and the Muslim Students Association, with the African American Muslim community.
Exercise for Mood and Anxiety Disorders
Authors: Szuhany Kristin L. , Smits Jasper A.J. , Asmundson Gordon J. G. , Otto Michael W.
Published: September 2014

Mood and anxiety disorders represent the most common psychiatric conditions in the United States. Psychological and pharmacological treatments are the most commonly utilized interventions for these disorders; however, many individuals do not fully respond to these treatments. Exercise interventions represent a novel and efficacious form of alternative treatment for individuals suffering from mood and anxiety disorders. This review discusses the evidence for efficacy of exercise interventions for decreasing mood and anxiety symptoms as well as potential psychological (e.g., distress intolerance, behavioral activation) and physiological (e.g., neurotransmitters, brain-derived neurotrophic factor) mechanisms of action. In addition, we discuss measures to promote exercise adherence and to reduce barriers to exercise. We conclude with a discussion of dissemination of exercise interventions to a broader population.
God, Creation, and Providence in Early Modern Lutheranism
Authors: Kolb Robert
Published: September 2014

Seventeenth-century Lutheran theologians, preachers, and devotional writers reproduced the traditional Trinitarian theology which Luther and Melanchthon had espoused, reflecting though not emphasizing elements of Luther’s distinction of God Hidden and God Revealed. Their creative treatment of the doctrine of creation accentuated the creatio ex nihilo and the nature of God’s Word as creative, applying this insight to the recreation of sinners through the forgiveness of sins. They affirmed the fundamental goodness of creation and extended the doctrine of creation into a strong emphasis on God’s creatio continua, his providing care in the midst of tribulations that serve to call believers to repentance. Although the Lutheran dogmaticians tried to avoid detailed theodical argument they did attempt explanations that defended God from the charge that he causes evil.
Arminian, Remonstrant, and Early Methodist Theologies
Authors: Stanglin Keith D.
Published: September 2014

This essay describes the principal and distinctive theological elements of various forms of early modern Arminianism. Beginning with Jacob Arminius, it sketches the historical development and background of Arminianism in the Netherlands, its continuation in Dutch Remonstrant theology, and its manifestation in the Methodism of John and Charles Wesley in England. These contexts were quite different from one another. Arminius forged his theology in the context of the Dutch Reformed Church. Remonstrant theology developed outside the state church and in conjunction with Enlightenment philosophy. Wesleyan Methodism was nurtured by an Anglican Arminianism that found new life in evangelical revival. Despite the differences, the essay also traces elements of the common legacy that unites these divergent forms of Arminianism, such as the abiding concern over antinomianism, the plea for religious toleration, and the doctrine of a God who wants to be in eternal communion with all people.
Forensic Justification and Mysticism in Early Modern Lutheranism
Authors: Saarinen Risto
Published: September 2014

This article discusses forensic justification and mysticism, from the Lutheran Book of Concord (1580) to Pietism and the Enlightenment. The views of Matthias Flacius Illyricus, Martin Chemnitz, Johann Arndt, Johann Gerhard, Johann Friedrich König, August Hermann Francke, and Nikolaus Ludwig von Zinzendorf are highlighted. Special attention is paid to König’s analytical treatment of forensic justification and unio mystica; König’s view is regarded as the summary of Lutheran orthodoxy and a bridge to Pietism. The article argues that the Pietist emphasis on subjective involvement has its roots in the elaboration of forensic justification in Lutheran orthodoxy. This elaboration aims at replying to the Roman Catholic criticism that Protestants neglect the inner life or “hearts” of believers when they assume that justification is only by the goodwill of God. While faith is not a human work, justification by faith ascribes an “organic causality” to faith, enabling the believer’s personal involvement.
Kant’s Philosophical and Theological Commitments
Authors: Yong Peter , Watkins Eric
Published: September 2014

This essay attempts to lay out some of the most central aspects of Kant’s relationship to Christianity, which is as influential as it is complex. The first section explains several core claims in Kant’s philosophical theology by elucidating both Kant’s criticisms of the traditional arguments for the existence of God (i.e., the cosmological, teleological and ontological arguments) and his own positive theistic arguments, which he believes to be more compelling. The second section examines some important elements of Kant’s constructive Christian theology by looking at his interpretations of the doctrines of (i) creation in the image of God, (ii) original sin, (iii) redemption, and (iv) grace.
The History of Catholic Exegesis, 1600–1800
Authors: Reiser Marius
Published: September 2014

Modern critical exegesis began with Erasmus of Rotterdam. During the sixteenth and seventeenth centuries, it was predominantly Jesuits who emphasized a literal exegesis. The most prominent commentators included Benito Perera (Pererius) (1535–1610) on Genesis, Juan Maldonado (1533–83) on the four Gospels, and Luis de Alcázar (1554–1613) on Revelation. The founder of biblical hermeneutics and the discipline of exegetical introduction, Richard Simon (1638–1712), drew a sharp distinction between textual criticism and theology. The scandal surrounding exegete Johann L. Isenbiehls demonstrated how hard it was to maintain such a separation. During the eighteenth century, Dom Augustin Calmet (1672–1757) was undoubtedly the most distinguished Catholic exegete, although despite his erudition, he falls short of Simon’s achievements. The Catholic hierarchy was very cautious and anxious about exegetes who worked with the philosophical premises of the Enlightenment, and often persecuted even orthodox exegetes or impeded their work.
Sources, Methods, and Forms of Early Modern Theology
Authors: Leinsle Ulrich G.
Published: September 2014

For all denominations, the sources of early modern theology were the Bible and the Church Fathers, but with a varying emphasis. Furthermore, medieval theologians and philosophers must be taken into consideration. In Catholic theology, a flexible system of Loci theologici was developed; in Protestant theology, the teaching of verbal inspiration was replaced by the theory of accommodation and historical biblical criticism. While the humanistic position still demanded an introductory manual (Methodus) for the Bible, at the Council of Trent the catechism took its place. The Christian denominations agreed on the primacy of the literal sense of scripture, but differed in their evaluation of it as the only source of revelation. Scriptural comments were supplemented with systematic works: commentaries on Peter Lombard, Aquinas’s Summa theologica, Cursus theologici, and manuals of Protestant theology. They were often developed as disputations, rather than a basic explanation of the doctrine of positive and controversial theology.
Eighteenth-Century Neology
Authors: Carlsson Eric
Published: September 2014

This chapter summarizes key aspects of neology, the main expression of the German Protestant theological Enlightenment in the second half of the eighteenth century. Neology construed Christianity as a practical, ethically oriented religion, consonant with modern knowledge and grounded in the self-reflective experience of the pious, reasonable subject. Steering a course between Protestant Orthodoxy, Pietism, and freethinking, proponents deployed history as a useful tool for their apologetic and reconstructive efforts. Historical scholarship offered a means of rethinking the nature and authority of scripture, of distancing the claims of the dogmatic tradition, and of recasting theology as a progressive academic enterprise. In historicizing scripture and creeds, neology shifted focus from dogma to the religious experience of the believing subject. While many of its concepts were developed in a more secular direction in later German intellectual history, neology’s central concerns were taken up by the liberal Protestant tradition of the following century.
Scripture and Exegesis in Early Modern Lutheranism
Authors: Mayes Benjamin T. G.
Published: September 2014

Lutheran exegesis in the seventeenth and eighteenth centuries took place in a wide variety of contexts. Lutherans viewed the canonical Scriptures as God’s Word in human form, although they also paid attention to the uniqueness of Scripture’s human authors and cultivated intensive biblical studies. The dogmatic exegesis of the period was motivated not just by polemics, but also especially by the desire to make salutary application of the biblical text to Christian faith and life in teaching, consolation, admonition, and warning. Lutherans made rich use also of the mystical sense of Scripture, finding Jesus Christ prophesied in Old Testament mysteries. Lutherans responded—with limited success—to many criticisms of Scripture’s authority, coming from within their own ranks, from Socinians, from Roman Catholics, and from new discoveries in science and philosophy. By the end of the eighteenth century, the orthodox Lutheran view of Scripture no longer prevailed in Europe.
A Comparison of Propofol- and Dexmedetomidine-induced Electroencephalogram Dynamics Using Spectral and Coherence Analysis
Authors: Akeju Oluwaseun , Pavone Kara J. , Westover M. Brandon , Vazquez Rafael , Prerau Michael J. , Harrell Priscilla G. , Hartnack Katharine E. , Rhee James , Sampson Aaron L. , Habeeb Kathleen , Gao Lei , Pierce Eric T. , Walsh John L. , Brown Emery N. , Purdon Patrick L.
Published: September 2014

Background

Electroencephalogram patterns observed during sedation with dexmedetomidine appear similar to those observed during general anesthesia with propofol. This is evident with the occurrence of slow (0.1 to 1 Hz), delta (1 to 4 Hz), propofol-induced alpha (8 to 12 Hz), and dexmedetomidine-induced spindle (12 to 16 Hz) oscillations. However, these drugs have different molecular mechanisms and behavioral properties and are likely accompanied by distinguishing neural circuit dynamics.

Methods

The authors measured 64-channel electroencephalogram under dexmedetomidine (n = 9) and propofol (n = 8) in healthy volunteers, 18 to 36 yr of age. The authors administered dexmedetomidine with a 1-µg/kg loading bolus over 10 min, followed by a 0.7 µg kg−1 h−1 infusion. For propofol, the authors used a computer-controlled infusion to target the effect-site concentration gradually from 0 to 5 μg/ml. Volunteers listened to auditory stimuli and responded by button press to determine unconsciousness. The authors analyzed the electroencephalogram using multitaper spectral and coherence analysis.

Results

Dexmedetomidine was characterized by spindles with maximum power and coherence at approximately 13 Hz (mean ± SD; power, −10.8 ± 3.6 dB; coherence, 0.8 ± 0.08), whereas propofol was characterized with frontal alpha oscillations with peak frequency at approximately 11 Hz (power, 1.1 ± 4.5 dB; coherence, 0.9 ± 0.05). Notably, slow oscillation power during a general anesthetic state under propofol (power, 13.2 ± 2.4 dB) was much larger than during sedative states under both propofol (power, −2.5 ± 3.5 dB) and dexmedetomidine (power, −0.4 ± 3.1 dB).

Conclusion

The results indicate that dexmedetomidine and propofol place patients into different brain states and suggest that propofol enables a deeper state of unconsciousness by inducing large-amplitude slow oscillations that produce prolonged states of neuronal silence.
Neuropathic Pain in Multiple Sclerosis Improved With Oral Famciclovir: A Case Report
Authors: Emeriewen Krisztina , Macgregor Cheryl , Athanasiadis Yannis , Tsatsos Michael
Published: September 2014

Multiple sclerosis can be a debilitating disease that is often associated with neuropathic pain and discomfort in the trigeminal region. This can pose a therapeutic challenge as the benefits of the treatment options have to be outweighed against significant side effects. The authors present the case of a 67-year-old man, whose control of trigeminal neuralgia with botulinum toxin A injections was lost after an episode of herpes labialis and herpes zoster infection. The pain management of the patient during the episodes of herpes simplex and varicella zoster infections was greatly improved with famciclovir treatment, and subsequently control of trigeminal neuralgia was regained with botulinum toxin A injections. This case serves to highlight the potential association of multiple sclerosis with herpetic infections as well as the treatment challenges, especially management of pain, which they can possess.
Novel Risk Factors for Recurrent Clostridium difficile Infection in Children
Authors: Nicholson Maribeth R. , Thomsen Isaac P. , Slaughter James C. , Creech C. Buddy , Edwards Kathryn M.
Published: September 2014

Objectives:

Clostridium difficile, a common cause of antibiotic‐associated diarrhea, has been reported to recur in high rates in adults. The rates and risk factors for recurrent C difficile infection (rCDI) in children have not been well established.

Methods:

We conducted a retrospective cohort study of 186 pediatric patients seen at a tertiary care referral center for a 5‐year period diagnosed as having a primary C difficile infection. Children with recurrent disease, defined as return of symptoms of C difficile infection and positive testing ≤60 days after the completion of therapy, were compared with children who did not experience an episode of recurrence.

Results:

Of the 186 pediatric patients included in this study, 41 (22%) experienced rCDI. On univariable analysis, factors significantly associated with rCDI included malignancy, recent hospitalization, recent surgery, antibiotic use, number of antibiotic exposures by class, acid blocker use, immunosuppressant use, and hospital‐acquired disease. On multivariable analysis, malignancy (odds ratio [OR] 3.39, 95% confidence interval [CI] 1.52–7.85), recent surgery (OR 2.40, 95% CI 1.05–5.52), and the number of antibiotic exposures by class (OR 1.33, 95% CI 1.01–1.75) were significantly associated with recurrent disease in children.

Conclusions:

The rate of rCDI in children was 22%. Recurrence was significantly associated with the risk factors of malignancy, recent surgery, and the number of antibiotic exposures by class.
Mixed Model with Correction for Case-Control Ascertainment Increases Association Power
Authors: Hayeck Tristan , Zaitlen Noah A. , Loh Po-Ru , Vilhjalmsson Bjarni , Pollack Samuela , Gusev Alexander , Yang Jian , Chen Guo-Bo , Goddard Michael E. , Visscher Peter M. , Patterson Nick , Price Alkes L.
Published: September 2014

We introduce a Liability Threshold Mixed Linear Model (LTMLM) association statistic for ascertained case-control studies that increases power vs. existing mixed model methods, with a well-controlled false-positive rate. Recent work has shown that existing mixed model methods suffer a loss in power under case-control ascertainment, but no solution has been proposed. Here, we solve this problem using a chi-square score statistic computed from posterior mean liabilities (PML) under the liability threshold model. Each individual’s PML is conditional not only on that individual’s case-control status, but also on every individual’s case-control status and on the genetic relationship matrix obtained from the data. The PML are estimated using a multivariate Gibbs sampler, with the liability-scale phenotypic covariance matrix based on the genetic relationship matrix (GRM) and a heritability parameter estimated via Haseman-Elston regression on case-control phenotypes followed by transformation to liability scale. In simulations of unrelated individuals, the LTMLM statistic was correctly calibrated and achieved higher power than existing mixed model methods in all scenarios tested, with the magnitude of the improvement depending on sample size and severity of case-control ascertainment. In a WTCCC2 multiple sclerosis data set with >10,000 samples, LTMLM was correctly calibrated and attained a 4.1% improvement (P = 0.007) in chi-square statistics (vs. existing mixed model methods) at 75 known associated SNPs, consistent with simulations. Larger increases in power are expected at larger sample sizes. In conclusion, an increase in power over existing mixed model methods is available for ascertained case-control studies of diseases with low prevalence.
Leveraging transcript quantification for fast computation of alternative splicing profiles
Authors: Alamancos Gael P , Pagès Amadís , Trincado Juan L , Bellora Nicolás , Eyras Eduardo
Published: September 2014

Alternative splicing plays an essential role in many cellular processes and bears major relevance in the understanding of multiple diseases, including cancer. High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of computation time and storage requirements. We describe SUPPA, a computational tool to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification. SUPPA accuracy is comparable and sometimes superior to standard methods using simulated as well as real RNA sequencing data compared to experimentally validated events. We assess the variability in terms of the choice of annotation and provide evidence that using complete transcripts rather than more transcripts per gene provides better estimates. Moreover, SUPPA coupled with de novo transcript reconstruction methods does not achieve accuracies as high as using quantification of known transcripts, but remains comparable to existing methods. Finally, we show that SUPPA is more than 1000 times faster than standard methods. Coupled with fast transcript quantification, SUPPA provides inclusion values at a much higher speed than existing methods without compromising accuracy, thereby facilitating the systematic splicing analysis of large datasets with limited computational resources. The software is implemented in Python 2.7 and is available under the MIT license at https://bitbucket.org/regulatorygenomicsupf/suppa
A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana
Authors: Lachowiec Jennifer , Shen Xia , Queitsch Christine , Carlborg Örjan
Published: September 2014

Efforts to identify loci underlying complex traits generally assume that most genetic variance is additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the narrow-sense heritability for this trait was statistically zero. This low additive genetic variance likely explains why no associations to root length could be found using standard additive-model-based genome-wide association (GWA) approaches. However, the broad-sense heritability for root length was significantly larger, and we therefore also performed an epistatic GWA analysis to map loci contributing to the epistatic genetic variance. This analysis revealed four interacting pairs involving seven chromosomal loci that passed a standard multiple-testing corrected significance threshold. Explorations of the genotype-phenotype maps for these pairs revealed that the detected epistasis cancelled out the additive genetic variance, explaining why these loci were not detected in the additive GWA analysis. Small population sizes, such as in our experiment, increase the risk of identifying false epistatic interactions due to testing for associations with very large numbers of multi-marker genotypes in few phenotyped individuals. Therefore, we estimated the false-positive risk using a new statistical approach that suggested half of the associated pairs to be true positive associations. Our experimental evaluation of candidate genes within the seven associated loci suggests that this estimate is conservative; we identified functional candidate genes that affected root development in four loci that were part of three of the pairs. In summary, statistical epistatic analyses were found to be indispensable for confirming known, and identifying several new, functional candidate genes for root length using a population of wild-collected A. thaliana accessions. We also illustrated how epistatic cancellation of the additive genetic variance resulted in an insignificant narrow-sense, but significant broad-sense heritability that could be dissected into the contributions of several individual loci using a combination of careful statistical epistatic analyses and functional genetic experiments.
The dark side of theoretical ecology
Authors: Kalmykov Lev V.
Published: September 2014

Good science must be clearly transparent in its theories, models and experiments. Earlier David Tilman drew attention to the fact that ecologists investigate interspecific competition phenomenologically, rather than mechanistically. To create a mechanistic model of a complex dynamic system we need to logically describe interactions of its subsystems which lead to emergence of new properties on the macro-level. There are black-box, grey-box and white-box models of complex systems. Black-box models are completely nonmechanistic. We cannot investigate interactions of subsystems of such non-transparent model. A white-box model of a complex system has “transparent walls” and directly shows underlined mechanistic mechanisms – all events at micro-, meso-and macro-levels of the modeled dynamic system are directly visible at all stages. Grey-box models are intermediate. Basic ecological models are of black-box type, e.g. Malthusian, Verhulst, Lotka-Volterra models. These models are not individual-based and cannot show features of local interactions of individuals of competing species. That is why they principally cannot provide a mechanistic insight into interspecific competition. To create a white-box model we need a physical theory of the object domain and its intrinsic axiomatic system. On the basis of axiomatic system there is a possibility to logically generate a new knowledge by logical deterministic cellular automata. Understanding of biodiversity mechanisms is the global research priority. Only knowledge of mechanisms of interspecific interactions can allow us to efficiently operate in the field of biodiversity conservation. Obviously that such knowledge must be based on mechanistic models of species coexistence. In order to create a serviceable theory of biodiversity it is necessary to renew attempts to create a basic mechanistic model of species coexistence. But the question arises:Why ecological modelers prefer to use the heaviest black-box mathematical methods which cannot produce mechanistic models of complex dynamic systems in principle, and why they do not use simple and long-known pure logical deterministic cellular automata, which easily can produce white-box models and directly generate clear mechanistic insights into dynamics of complex systems?
Visualization of Root Water Uptake: Quantification of Deuterated Water Transport in Roots Using Neutron Radiography and Numerical Modeling
Authors: Zarebanadkouki Mohsen , Kroener Eva , Kaestner Anders , Carminati Andrea
Published: September 2014

Our understanding of soil and plant water relations is limited by the lack of experimental methods to measure water fluxes in soil and plants. Here, we describe a new method to noninvasively quantify water fluxes in roots. To this end, neutron radiography was used to trace the transport of deuterated water (D2O) into roots. The results showed that (1) the radial transport of D2O from soil to the roots depended similarly on diffusive and convective transport and (2) the axial transport of D2O along the root xylem was largely dominated by convection. To quantify the convective fluxes from the radiographs, we introduced a convection-diffusion model to simulate the D2O transport in roots. The model takes into account different pathways of water across the root tissue, the endodermis as a layer with distinct transport properties, and the axial transport of D2O in the xylem. The diffusion coefficients of the root tissues were inversely estimated by simulating the experiments at night under the assumption that the convective fluxes were negligible. Inverse modeling of the experiment at day gave the profile of water fluxes into the roots. For a 24-d-old lupine (Lupinus albus) grown in a soil with uniform water content, root water uptake was higher in the proximal parts of lateral roots and decreased toward the distal parts. The method allows the quantification of the root properties and the regions of root water uptake along the root systems.
Investigating determinants of youth's intentions of seeking microcredit in the post-conflict era
Authors: Jebarajakirthy Charles , C. Lobo Antonio , Hewege Chandana
Published: September 2014

Purpose

– Bottom of pyramid market (BOP) has gained attention of researchers and marketers in recent years. The BOP market comprises many segments, however, little is known about purchase behaviour in BOP market or segments therein. The purpose of this paper is to investigate youth's intentions of seeking microcredit in the post-war era that are an integral part of BOP market.

Design/methodology/approach

– The sample comprised 1,250 youth aged 18 and above from Northern Province of Sri Lanka. Surveys were administered for data collection. After testing measurement model, a structural model was run to test hypotheses.

Findings

– Positive affect, subjective norms and entrepreneurial desire enhanced intentions of seeking microcredit, whereas perceived deterrents negatively influenced those intentions. Perceived benefits, perceived behavioural control and knowledge of microcredit did not have significant effects on these intentions.

Research limitations/implications

– This study was conducted in one war-affected country, Sri Lanka. Also, data were cross-sectional. Hence the model needs replication amongst youth in other post-conflict contexts and with longitudinal data.

Practical implications

– Findings of this study would be of use to market microcredit to youth in post-conflict era and other segments of BOP.

Originality/value

– A unique purchase behavioural model is suggested to enhance youths’ intentions of seeking microcredit in the post-war era, a segment within the BOP market. This study can contribute to purchase behaviour literature in identified contexts.
Plant–herbivore interactions: silicon concentration in tussock sedges and population dynamics of root voles
Authors: Wieczorek Monika , Zub Karol , Szafrańska Paulina A. , Książek Aneta , Konarzewski Marek
Published: September 2014

It has been hypothesized that the induction of silicon (Si)‐based plant defence in response to herbivore damage may engender rodent population cycles. Many studies have also considered accumulation of Si as a process controlled by geo‐hydrological factors.

To test these ideas, we investigated the relationship between concentration of Si in fibrous tussock sedge (Carex appropinquata) and the population density of a major sedge consumer, the root vole (Microtus oeconomus), in field enclosures in natural habitat under a variety of natural water regimes and weather conditions.

We found that a high density of voles at the end of summer resulted in the immediate accumulation of Si by rhizomes, followed by accumulation of Si in leaves with a 1‐year lag time. The level of river flooding in the same year had an additional impact on Si concentration in rhizomes but did not affect silicification of leaves.

Overwinter changes in concentration of Si in sedges were influenced by fluctuations in ambient temperature and the depth of snow cover (multiple freeze–thaw cycles), thus affecting the quality of winter food available for voles.

Smaller voles had lower mortality during early winter than large voles, which seemed to be connected with changes in the quality of the autumn rather than the winter food base. Winter survival of voles was not associated with Si concentration in their faeces, however.

Our results suggest that changes in Si concentration in fibrous tussock sedge can be induced by changes in vole population density and are also additionally affected by the amount of flooding and weather conditions.
Biocrust morphogroups provide an effective and rapid assessment tool for drylands
Authors: Read Cassia F. , Duncan David H. , Vesk Peter A. , Elith Jane
Published: September 2014

Biological soil crusts (biocrusts) occur across most of the world's drylands and are sensitive indicators of dryland degradation. Accounting for shifts in biocrust composition is important for quantifying integrity of arid and semi‐arid ecosystems, but the best methods for assessing biocrusts are uncertain. We investigate the utility of surveying biocrust morphogroups, a reduced set of biotic classes, compared to species data, for detecting shifts in biocrust composition and making inference about dryland degradation.

We used multivariate regression tree (MRT) analyses to model morphogroup abundance, species abundance and species occurrence data from two independent studies in semi‐arid open woodlands of south‐eastern Australia. We advanced the MRT method with a ‘best subsets’ model selection procedure, which improved model stability and prediction.

Biocrust morphogroup composition responded strongly to surrogate variables of ecological degradation. Further, MRT models of morphogroup data had stronger explanatory power and predictive power than MRT models of species abundance or occurrence data. We also identified morphogroup indicators of degraded and less degraded sites in our study region.

Synthesis and applications. Sustainable management of drylands requires methods to assess shifts in ecological integrity. We suggest that biocrust morphogroups are highly suitable for assessment of dryland integrity because they allow for non‐expert, rapid survey and are informative about ecological function. Furthermore, morphogroups were more robust than biocrust species data, showed a strong response to ecological degradation and were less influenced by environmental variation, and models of morphogroup abundance were more predictive.
Women's Agency in Living Apart Together: Constraint, Strategy and Vulnerability
Authors: Duncan Simon
Published: September 2014

Recent research suggests that women can use living apart together (LAT) for a reflexive and strategic undoing of the gendered norms of cohabitation. In this article we examine this assertion empirically, using a representative survey from Britain in 2011 and follow-up interviews. First, we find little gender differentiation in practices, expectations, or attitudes about LAT, or reasons for LAT. This does not fit in with ideas of undoing gender. Secondly, in examining how women talk about LAT in relation to gender, we distinguish three groups of ‘constrained’, ‘strategic’ and ‘vulnerable’ female interviewees. All valued the extra space and time that LAT could bring, many welcomed some release from traditional divisions of labour, and some were glad to escape unpleasant situations created by partnership with men. However, for the constrained and vulnerable groups LAT was second best, and any relaxation of gendered norms was seen as incidental and inconsequential to their major aim, or ideal, of the ‘proper family’ with cohabitation and marriage. Rather, their agency in achieving this was limited by more powerful agents, or was a reaction to perceived vulnerability. While the strategic group showed more purposeful behaviour in avoiding male authority, agency remained relational and bonded. Overall we find that women, at least in Britain, seldom use LAT to purposefully or reflexively undo gender. Equally, LAT sometimes involves a reaffirmation of gendered norms. LAT is a multi-faceted adaption to circumstances where new autonomies can at the same time incorporate old subordinations, and new arrangements can herald conventional family forms.
Outcomes of Non‐Tunneled Non‐Cuffed Hemodialysis Catheters in Patients on Chronic Hemodialysis in a Resource Limited Sub‐Saharan Africa Setting
Authors: Kaze Francois Folefack , Ashuntantang Gloria , Halle Marie Patrice , Kengne Andre‐Pascal
Published: September 2014

The aim of the present study was to investigate the adverse outcomes of non‐tunneled hemodialysis catheters and determinants in chronic hemodialysis patients receiving care at the Yaoundé General Hospital hemodialysis center, Cameroon. This was a prospective study of 11 months duration (February–December 2008) involving 81 non‐tunneled non‐cuffed catheters (63 femoral, 18 internal jugular) placed in 72 adults (47 men, 65.3%) on chronic hemodialysis. Baseline clinical and laboratory parameters associated with catheter‐related complications during follow‐up were investigated. The difference between variables was assessed using the χ2 test and equivalents. Sixty‐five (80.2%) catheters were inserted for emergency dialysis, 11 (13.6%) for a failed native arteriovenous fistula and five (6.2%) for a failed prior catheter. The mean time‐to‐catheter removal was 35 ± 28 days. Catheter‐related complications accounted for a third of catheter removals. The main catheter‐related complications were infections (17/27, 62.9%) and bleeding (6/27, 22.2%), which were associated with unemployment (P = 0.0002) and longer duration of catheter (P = 0.004). The catheter‐related infections were sepsis (11.8%), exit‐site (29.4%) and both (58.8%); leading to death in 11/17 (64.7%) cases. Fever (94.1%), pain (88.2%) and pus (70.6%) were the main infectious signs with Staphylococcus aureus involved in 70.6%. Unemployment was significantly frequent in patients with infectious complications (76.5% vs. 26.6%, P = 0.0004). Non‐tunneled hemodialysis catheters are mainly used for emergency dialysis through the femoral vein in this setting. Catheter‐related infections due to Staphylococci are the leading complications associated with unemployment and longer utilization. Efforts are needed to improve early transfer of patients to nephrologists for better preparation for renal replacement therapy.