bluuebunny/crossref_metadata_2025_split huggingface dataset:
ON THE COMPLEXITY OF FINDING A NECESSARY AND SUFFICIENT CONDITION FOR BLASCHKE-OSCILLATORY EQUATIONS
Authors: HEITTOKANGAS JANNE , REIJONEN ATTE 
Published: December 2014

AbstractIf A(z) belongs to the Bergman space , then the differential equation f″+A(z)f=0 is Blaschke-oscillatory, meaning that the zero sequence of every nontrivial solution satisfies the Blaschke condition. Conversely, if A(z) is analytic in the unit disc such that the differential equation is Blaschke-oscillatory, then A(z) almost belongs to . It is demonstrated that certain “nice” Blaschke sequences can be zero sequences of solutions in both cases when A ∈ or A ∉ . In addition, no condition regarding only the number of zeros of solutions is sufficient to guarantee that A ∈ .
Collecting “Tribal Art”—Sacred or Secular?
Authors: Paterson Robert K. 
Published: December 2014

Abstract:This article explores the history of collecting and dealing in non-Western cultural objects—primarily from the Pacific Islands—from the earliest explorers to the modern auction houses. It considers international and domestic laws relating to indigenous cultural material that might be seen as religious or sacred in character and concludes that while these rules clearly influence both private and institutional practices they fall short of legally impacting the functioning of otherwise lawful markets.
Remarks in Honor of the Legal and Public Policy Legacies of John
Henry Merryman: Cultural Property and Human Cells
Authors: Feldman Robin 
Published: December 2014

Abstract:It is an honor to be invited to speak at this symposium, both for the kind
invitation to address this society, and for the opportunity to honor an esteemed
scholar from my alma mater, Stanford.I come to this symposium, not as an expert in cultural property, but as an
inhabitant of the field of biotechnology and intellectual property law. Although
the view from a distance can provide different perspectives, it lacks the layers
of understanding and meaning that are accumulated by those who are steeped in
the field. I cannot possibly hope to offer solutions to issues with which many
brilliant minds have spent a lifetime grappling. Thus, I temper my comments with
the caution appropriate for the exercise. What I can do is offer comparisons
from the treatment of human cells, as well as observations I have suggested in
that context.
Immovable Cultural Heritage at Risk: Past – Present – Future
Authors: Siehr Kurt G. 
Published: December 2014

Abstract:Immovable cultural heritage is still at risk of being neglected by the state responsible for heritage sites, by urban planning of big cities, and by armed conflicts around the world. Normally, because it is immovable, the international community cannot do very much. It can ban the trade of items that became movable property when detached from buildings or illegally excavated in certain protected sites. In other cases, it is the responsibility of the national state to care for cultural heritage and cultural objects. International conventions may furnish help and advice and provide for monitoring any risk to the cultural heritage of state parties.
Versatile physiological functions of the Nudix hydrolase family in Arabidopsis
Authors: Yoshimura Kazuya , Shigeoka Shigeru 
Published: December 2014

Abstract
Nudix hydrolases are widely distributed in all kingdoms of life and have the potential to hydrolyze a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, nucleotide coenzymes, nucleotide sugars, and RNA caps. However, except for E. coli MutT and its orthologs in other organisms that sanitize oxidized nucleotides to prevent DNA and RNA mutations, the functions of Nudix hydrolases had largely remained unclear until recently, because many members of this enzyme family exhibited broad substrate specificities. There is now increasing evidence to show that their functions extend into many aspects of the regulation of cellular responses. This review summarizes current knowledge on the molecular and enzymatic properties as well as physiological functions of Arabidopsis Nudix hydrolases. The information presented here may provide novel insights into the physiological roles of these enzymes in not only plant species, but also other organisms.
Probabilistic Graphical Models for Next-generation Genomics and Genetics
Authors: Sinoquet Christine 
Published: December 2014

AbstractThe explosion in omics and other types of biological data has increased the demand for solid, large-scale statistical methods. These data can be discrete or continuous, dependent or independent, from many individuals or tissue types. There might be millions of correlated observations from a single individual, observations at different scales and levels, in addition to covariates. The study of living systems encompasses a wide range of concerns, from prospective to predictive and causal questions, reflecting the multiple interests in understanding biological mechanisms, disease etiology, predicting outcome, and deciphering causal relationships in data. Precisely, probabilistic graphical models provide a flexible statistical framework that is suitable to analyze such data. Notably, graphical models are able to handle dependences within data, which is an almost defining feature of cellular and other biological data.
Graphical Models and Multivariate Analysis of Microarray Data
Authors: Kiiveri Harri 
Published: December 2014

Abstract
The usual analysis of gene expression data ignores the correlation between gene expression values. Biologically, this assumption is unreasonable. The approach presented in this chapter allows for correlation between genes through a sparse Gaussian graphical model: sparse inverse covariance matrices and their associated graphical representations are used to capture the notion of gene networks. Existing methods find their limitations in the issue posed by the identification of the pattern of zeroes in such inverse covariance matrices. A workable solution for determining the zero pattern is provided in this chapter. Two other important contributions of this chapter are a method for very high-dimensional model fitting and a distribution-free approach to hypothesis testing. Such tests address assessment of differential expression and of differential connection, a novel notion introduced in this chapter. An example dealing with real data is presented.
Network Inference in Breast Cancer with Gaussian Graphical Models and Extensions
Authors: Jeanmougin Marine , Charbonnier Camille , Guedj Mickaël , Chiquet Julien 
Published: December 2014

Abstract
Clustering genes with high correlations will group genes with close expression profiles, defining clusters of co-expressed genes. However, such correlations do not provide any clue on the chain of information going from gene to gene. Partial correlation consists in quantifying the correlation between two genes after excluding the effects of the other genes. Partial correlation thus makes it possible to distinguish between the correlation of two genes due to direct causal relationships from the correlation that originates via intermediate genes. In this chapter, Gaussian graphical model (GGM) learning is set up as a covariate selection problem. Two least absolute shrinkage and selection operator (LASSO)-type techniques are described, the graphical LASSO approach and the neighborhood selection. Then two extensions to the classical GGM are presented. GGMs are extended in structured GGMs, to account for modularity, and more generally heterogeneity in the gene connection features. The extension using a biological prior on the network structure is illustrated on real data.
Utilizing Genotypic Information as a Prior for Learning Gene Networks
Authors: Chipman Kyle , Singh Ambuj 
Published: December 2014

Abstract
The combination of genotypic and genome-wide expression data arising from segregating populations offers an unprecedented opportunity to model and dissect complex phenotypes. Leading studies have augmented Bayesian networks with genotypic data, providing a powerful framework for learning and modeling causal relationships. However, one major drawback of these methods is that they are generally limited to resolving causal orderings for transcripts most proximal to the genomic loci. This chapter reviews two methods where all interactions between genotype and gene transcripts are considered collectively in order to better resolve causal relationships between gene transcripts. The likelihood-based causality model selection (LCMS) of Schadt and collaborators is first described. Then, the stochastic causal tree (SCT) method is depicted. The information provided by such methods is intended to be used as a prior for Bayesian network structure learning, resulting in enhanced performance for gene network reconstruction.
Bayesian, Systems-based, Multilevel Analysis of Associations for Complex Phenotypes: from Interpretation to Decision
Authors: Antal Péter , Millinghoffer András , Hullám Gábor , Hajós Gergely , Sárközy Péter , Gézsi András , Szalai Csaba , Falus András 
Published: December 2014

AbstractThe relative scarcity of the results reported by genetic association studies (GAS) prompted many research directions. Despite the centrality of the concept of association in GASs, refined concepts of association are missing; meanwhile, various feature subset selection methods became de facto standards for defining multivariate relevance. On the other hand, probabilistic graphical models, including Bayesian networks (BNs) are more and more popular, as they can learn nontransitive, multivariate, nonlinear relations between complex phenotypic descriptors and heterogeneous explanatory variables. To integrate the advantages of Bayesian statistics and BNs, the Bayesian network based Bayesian multilevel analysis of relevance (BN-BMLA) was proposed. This approach allows the processing of multiple target variables, while ensuring scalability and providing a multilevel view of the results of multivariate analysis. This chapter discusses the use of Bayesian BN-based analysis of relevance in exploratory data analysis, optimal decision and study design, and knowledge fusion, in the context of GASs.
Andalusi Arabic negators and interrogatives
Authors: Wilmsen David 
Published: December 2014

Abstract
The earliest unambiguous evidence for grammatical šī in Arabic comes in a few instances of an indefinite determiner and negator šī in the vernacular poetry and folk proverbs of Arab Spain (al-Andalus), evidence for a copular interrogative formed with a suffixed -š also appearing in two places. Conventionally and mistakenly interpreted as negators, these would show the operation of a Jespersen’s Cycle in Andalusi Arabic. Considering them in the context of exclamatives and rhetorically negative questions in living Arabic dialects and in their indigenous setting allows us to draw a different conclusion: negating with -š began when interrogatives formed with reflexes of šī were negated with mā, thus permitting their reanalysis as negators, even as they retained the post-positive -š of interrogation.
The Debate over Authority
Authors: Rose Jacqueline 
Published: December 2014

Abstract
This chapter explores the triangular relationship between lay government, ecclesiastical authorities, and the individual Christian. Adiaphora constituted non‐doctrinal matters regarded as ‘indifferent’; mainly rites and ceremonies, but perhaps encompassing church government as well. These issues were central to negotiations over comprehension and were rooted in the theology of Christian liberty. However, the royal supremacy of the civil magistrate in the English Church meant that adiaphora unavoidably raised questions about law and authority. Discussions about the casuistry of obedience brought to the fore the psychological dilemmas of conformity. Debating the aesthetics of worship and their relationship to the remnants of Catholic ‘Popery’ rendered problematic the identity of the English Church. This chapter explores what was distinctive about the Restoration phase of an argument as old as the English Reformation, and how this complicates notions of toleration in the seventeenth century.
Circumstantial Temporary Concessions
Authors: Seaward Paul 
Published: December 2014

Abstract
The Acts passed by the Cavalier Parliament in 1661–5 which prevented many ‘Puritans’ and ‘Presbyterians’ from conforming to the Church of England, and punished those who tried to establish alternative forms of religious worship, have often been known as the ‘Clarendon Code’, after Edward Hyde, Earl of Clarendon. Yet Clarendon's writings, and his attitudes to church matters during the early 1640s, suggest someone who was more concerned to promote religious peace than a determined and rigid advocate of uniformity and persecution; moreover, during 1662 he made strenuous efforts to reduce the severity of some aspects of the uniformity bill. This chapter argues that despite his adiaphorist approach, Clarendon, like many others, was firmly and decisively in favour of uniformity, but that he was nevertheless genuinely concerned about the pace of the change that was being driven on—principally by the hierarchy of the Church.
The Bishops of Ireland and the Beasts at Ephesus
Authors: Armstrong Robert 
Published: December 2014

Abstract
This chapter assesses the means whereby Protestant Ireland saw the reimposition of a full‐blown ‘Anglican’ order and the exclusion of large numbers of Presbyterian clergymen, ahead of comparable developments in England, and based explicitly on pre‐war norms. That re‐establishment took on regional and ‘national’ dimensions, with the largest expulsions of ministers occurring among the Scottish communities of north‐east and north‐west Ulster, and it generated disorder and communal tension on the ground closer to the Scottish than the English experience of Restoration. Yet while it was in the interests of later denominational historians and apologists, both Anglican and Presbyterian, to emphasize the sharp and decisive break between them in these years, this chapter will also look at evidence of some ambiguities, and some opportunities, which blur such straightforward conclusions, and it will consider how far these offered the possibility of a different, more comprehensive, settlement.
Going Dutch
Authors: Cotter Cory 
Published: December 2014

Abstract
This chapter explores the cross‐cultural connections of a small but tightly‐knit community of ejected ministers who fled to the Dutch Republic in the wake of the Restoration Settlement (1660–2), focusing on the English‐Scottish community in Holland (c.1660–90), with occasional glances further afield. Mapping out their intellectual networks, both home and abroad, first the statistical significance of Leiden University, especially for Britons (who formed one of its largest contingents of foreign students) is quantified. Second, it is argued that contrary to current historiography, national boundaries proved irrelevant to intellectual and social exchanges between English and Scottish dissenters in Dutch exile. Finally, there is a demonstration of how these general patterns of intellectual exchange and movement specifically applied to a tightly‐knit community of preachers, plotters, and physicians (at Leiden, and beyond) during the post‐Restoration period.
Kablammo: an interactive, web-based BLAST results visualizer
Authors: Wintersinger Jeff A. , Wasmuth James D. 
Published: December 2014

Abstract
Motivation: Kablammo is a web-based application that produces interactive, vector-based visualizations of sequence alignments generated by BLAST. These visualizations can illustrate many features, including shared protein domains, chromosome structural modifications and genome misassembly.
Availability and implementation: Kablammo can be used at http://kablammo.wasmuthlab.org. For a local installation, the source code and instructions are available under the MIT license at http://github.com/jwintersinger/kablammo.
Contact: jeff@wintersinger.org
SMC3 may play an important role in atopic asthma development
Authors: Cheng Qi , Huang Wanjie , Chen Ning , Shang Yunxiao , Zhang Han 
Published: December 2014

AbstractIntroductionAs a common disease with a complex risk, including genetic and environmental factors, atopic asthma is prevalent but treatable. The aim of the study was to predict the underlying mechanism of asthma and identify target genes for the disease.MethodsThe affymetrix chip data, GSE18965, were available from Gene Expression Omnibus and the differentially expressed genes (DEGs) between nine atopic asthmatic specimens and seven healthy nonatopic samples were identified by R. Then Gene Ontology and pathway enrichment analyses were performed to these DEGs. Further, search tool for the retrieval of interacting genes/proteins (STRING) was used to select protein–protein interaction (PPI) for DEGs, and then the network was visualized by Cytoscape. Finally, transcription factor binding site analysis was conducted to the hot gene.ResultsTotal 565 DEGs were identified, including 535 upregulated and 30 downregulated genes. The upregulated genes, such as structural maintenance of chromosome (SMC)3, significantly affected cellular component of extracellular matrix (P = 1.56E‐04). Otherwise, DEGs were remarkably enriched in three pathways, including transforming growth factor‐beta signaling pathway (P = 0.005252649). Further, SMC3 was detected as hot gene in PPI network, and NET (Elk3) was predicted as the significant transcription factor for this gene.ConclusionSMC3 may play an important role in atopic asthma development; therefore, it has the potential to be the target for the disease. Moreover, our findings provide more knowledge about the mechanism of atopic asthma and help the researchers to explore it in future.
The Ethics of Democratic Deceit
Authors: Edyvane Derek 
Published: December 2014

AbstractDeception presents a distinctive ethical problem for democratic politicians. This is because there seem in certain situations to be compelling democratic reasons for politicians both to deceive and not to deceive the public. Some philosophers have sought to negotiate this tension by appeal to moral principle, but such efforts may misrepresent the felt ambivalence surrounding dilemmas of public office. A different approach appeals to the moral character of politicians, and to the variety of forms of manipulative communication at their disposal. The public is usually more indulgent of politicians who ‘spin’ the truth than of those who tell bare‐faced lies, but this could be a mistake. Spin expresses disdain for the democratic value of truthfulness, and so democratic ‘spin‐doctors’ ought to trouble us more than they typically do. The cause of confusion here may reside in the failure to appreciate the distinctiveness of public morality, and in the misguided application of private standards of behaviour to a public context in which they are out of place.
Plant–water relations of intertidal and subtidal seagrasses
Authors: Sandoval‐Gil Jose M. , Barrote Isabel , Silva João , Olivé Irene , Costa Monya M. , Ruiz Juan M. , Marín‐Guirao Lázaro , Sánchez‐Lizaso Jose L. , Santos Rui 
Published: December 2014

AbstractThis work represents the first contribution to (i) examine the changes in plant‐water relations of an inter‐tidal seagrass during air exposure (Zostera noltii), and (ii) compare the water status descriptors between inter‐tidal‐ and subtidal‐adapted species (Cymodocea nodosa,Zostera marina). Two different morphotypes ofZ. noltiithat develop in the highest and lowest inter‐tidal levels in the Portuguese lagoon of Ria Formosa were exposed to natural emersion periods under laboratory conditions, and the evolution of leaf water relations and osmolytes (ions, proline and non‐structural carbohydrates) was measured. Both morphotypes regulated their water potential (Ψw) by reducing the osmotic potential (Ψπ) through osmolyte accumulation, but only high inter‐tidal plants were able to do this by adjusting the turgor pressure through cell wall hardening. This is a conservative mechanism for osmotic acclimation, which occurred only after long emersion periods (7 h). After a rapid increase in ion concentration under air exposure, the high inter‐tidal morphotype replaced them by more physiologically compatible solutes (proline and non‐structural carbohydrates) to maintain the osmotic adjustment. Altered ionic homeostasis was found in low inter‐tidal plants when exposed to such unnatural, long emersion periods. Osmotic unbalances were also observed during the submerged recovery phase. Descriptors of leaf pressure–volume (P–V) curves and Höfler diagrams were derived for seagrasses for the first time. They support the divergences in water relations observed between inter‐tidal and subtidal seagrasses according to their vertical distribution. More negative water and osmotic potentials and higher rigidity of cell walls (higher elastic modulus, ε) were found to be specific osmotic adaptations of seagrasses to the inter‐tidal.
Concurrent psychological stress and infectious colitis is key to sustaining enhanced peripheral sensory signaling
Authors: Spreadbury I. , Ochoa‐Cortes F. , Ibeakanma C. , Martin N. , Hurlbut D. , Vanner S. J. 
Published: December 2014

AbstractBackgroundThe development of postinfectious‐irritable bowel syndrome is associated with psychological stress but this relationship is poorly understood. The mouse Citrobacter rodentium model enhances the postinfectious excitability of colonic nociceptors, which can be further amplified by water‐avoidance stress (WAS). This study tested whether concurrent infectious colitis and chronic stress enhance and sustain nociceptor excitability more than stress after resolution of infection.MethodsMale C57 mice were gavaged with C. rodentium. WAS (1 h/day) was performed at different time‐points relative to the infection. After the final session of WAS, T9–T13 colonic‐projecting DRG neurons were isolated, cultured overnight and patch‐clamped to assess excitability. To investigate potential mechanisms, histological damage scores and colonic cytokine production were assessed.Key ResultsWAS more than 30 days after C. rodentium infection produced no greater DRG excitability than WAS in uninfected mice. However, when overlapped with chronic stress (3 sessions of WAS; 7 days before, 9 days during and 9 days after C. rodentium or sham gavage), C. rodentium significantly enhanced DRG excitability vs saline‐gavaged chronically stressed mice. Bodyweights and colonic damage scores were unchanged. Both WAS and C. rodentium gavage were found to significantly alter colonic cytokines at postinfection day 30.Conclusions & InferencesChronic stress and infectious colitis combine in an additive manner to heighten and prolong the sensitivity of visceral nociceptors. The effect relies on temporal coincidence of stress and infection, does not involve substantial exacerbation of inflammation, and may involve combined direct stress hormone and immune signaling on DRG neurons.
MicroRNAs in melanocyte and melanoma biology
Authors: Mione Marina , Bosserhoff Anja 
Published: December 2014

SummaryThe importance of microRNAs as key molecular components of cellular processes is now being recognized. Recent reports have shown that microRNAs regulate processes as diverse as protein expression and nuclear functions inside cells and are able to signal extracellularly, delivered via exosomes, to influence cell fate at a distance. The versatility of microRNAs as molecular tools inspires the design of novel strategies to control gene expression, protein stability, DNA repair and chromatin accessibility that may prove very useful for therapeutic approaches due to the extensive manageability of these small molecules. However, we still lack a comprehensive understanding of the microRNA network and its interactions with the other layers of regulatory elements in cellular and extracellular functions. This knowledge may be necessary before we exploit microRNA versatility in therapeutic settings. To identify rules of interactions between microRNAs and other regulatory systems, we begin by reviewing microRNA activities in a single cell type: the melanocyte, from development to disease.