bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening of lactic acid bacteria that can form mixed-species biofilm with Saccharomyces cerevisiae
Authors: Furukawa Soichi , Isomae Ryosuke , Tsuchiya Noriko , Hirayama Satoru , Yamagishi Asuka , Kobayashi Miho , Suzuki Chise , Ogihara Hirokazu , Morinaga Yasushi 
Published: December 2014

Abstract
The abilities of lactic acid bacteria (LAB) to form mixed-species biofilm with Saccharomyces cerevisiae in a static co-culture were investigated out of 168 LAB stock cultures, and two Lactobacillus plantarum strains (D71 and E31) and one Leuconostoc mesenteroides strain K01 were found to form mixed-species biofilm with S. cerevisiae BY4741. SEM observation showed that there was no significant difference in morphological properties among these three mixed-species biofilms and they resembled that formed by S. cerevisiae with L. plantarum ML11-11 previously isolated from a brewing sample of Fukuyama pot vinegar. The co-aggregation assays showed that L. plantarum D71 and L. plantarum E31 could co-aggregate with S. cerevisiae similarly to L. plantarum ML11-11, while L. mesenteroides K01 had no ability to co-aggregate with yeast. The above results indicate that aggregation followed by direct cell-to-cell contact is required for mixed-species biofilm formation between these L. plantarum strains and S. cerevisiae, though some different mechanism may be involved in biofilm formation between L. mesenteroides strain and S. cerevisiae.
Modeling Linkage Disequilibrium and Performing Association Studies through Probabilistic Graphical Models: a Visiting Tour of Recent Advances
Authors: Sinoquet Christine , Mourad Raphaël 
Published: December 2014

AbstractThis chapter offers an in-depth review of recent developments based on probabilistic graphical models (PGMs) and dedicated to two major concerns: the fundamental task of modeling dependences within genetic data, that is linkage disequilibrium (LD), and the downstream application to genome-wide association studies (GWASs). Throughout the whole chapter, the selected examples illustrate the use of Bayesian networks, as well as that of Markov random fields, including conditional and hidden Markov random fields. First, the chapter surveys PGM-based approaches dedicated to LD modeling. The next section is devoted to PGM-based GWASs and mainly focuses on multilocus approaches, where PGMs allow to fully benefit from LD. This section also provides an illustration for the acknowledgment of confounding factors in GWASs. The next section is dedicated to the detection of epistastic relationships at the genome scale. A recapitulation and a discussion end the chapter. Finally, directions for future works are outlined.
Scoring, Searching and Evaluating Bayesian Network Models of Gene-phenotype Association
Authors: Jiang Xia , Visweswaran Shyam , Neapolitan Richard E. 
Published: December 2014

AbstractThe arrival of genome-wide association studies (GWASs) has opened the exciting possibility of identifying genetic variations (single nucleotide polymorphisms (SNPs)) that underlie common diseases. However, our knowledge of the genetic architecture of common diseases remains limited. One likely reason for this is the complex interactions between genes, the environment, and the studied disease. This chapter addresses three aspects which are expected to help make progress to reveal some of these complex interactions using GWAS data sets. First, results are shown that compare the performances of various Bayesian network scoring criteria. Second, developing heuristic search algorithms for learning complex interactions from high-dimensional data is a hot topic. Third, the hypothesis testing involved in genome-wide epistasis detection is substantially different from that involved in a standard GWAS analysis, where only a null hypothesis and an alternative are considered.
Prediction of Clinical Outcomes from Genome-wide Data
Authors: Visweswaran Shyam 
Published: December 2014

AbstractPrognosis is an essential tool in medicine for estimating the likely outcomes of a disease and for preventing it. The traditional approach relies on measuring physiological and environmental parameters. With the recent availability of genome-wide data, it is now possible to incorporate the genetic information for predicting complex diseases. Probabilistic graphical models are well-known for their efficiency in predictive issue and thus represent good candidate models in this context. The probabilistic graphical model framework provides many assets: data uncertainty modeling, fast probabilistic inference algorithms, easy incorporation of expert knowledge and good predictive performance.
On the age and origins of spoken Arabic vernaculars
Authors: Wilmsen David 
Published: December 2014

Abstract
The labels ‘Old Arabic’, ‘Middle Arabic’, and ‘Neo-Arabic’ used in Arabic linguistics give the impression of a chronological sequence, implying that the oldest form of Arabic is something like the language that was codified as the Arabic of writing in the 8th–10th centuries ad. Not based in any linguistic principles, these labels have tended to channel inquiries into the history of Arabic into narrow, predetermined conclusions, one being that negation in the relatively young dialects of Arabic follows a Jespersen’s Cycle. Yet the Arabic dialects retain many archaic Arabic features, now rare in modern Arabic writing. Furthermore, they exhibit features shared with other Semitic languages that written Arabic lacks, indicating that the dialects, too, are old.
fīš wa biddīš
Authors: Wilmsen David 
Published: December 2014

Abstract
Explanations of the grammatical reflexes of the Arabic particle šī, especially in interrogation and negation, are generally mistaken on two counts: they begin their developmental sequences (clines) with the Arabic of writing, and they propose structures that, while appearing to be well-formed, are nevertheless not idiomatic. Assuming an origin in the Arabic of writing is especially perilous because, without supporting evidence, it assumes that that variety is the original, when the gatekeepers of Arabic writing proscribe the types of change proposed for the spoken language that are supposed to have originated with it. Consideration of the many grammatical functions of šī provides contrary evidence that the phenomena were always elements of the dialects, arising independently of and probably before writing.
Morphologically conditioned phonology
Authors: Inkelas Sharon 
Published: December 2014

AbstractMorphologically conditioned phonology is the phenomenon in which a particular phonological pattern is imposed on a proper subset of morphological constructions (affixation, reduplication, compounding) and thus is not fully general in the word‑internal phonological patterning of the language. This chapter focuses on the types of morphological information that can condition phonological patterns and the types of phonological patterns that can be conditioned by morphology. The chapter addresses conditioning by lexical classes, part of speech, and individual morphological constructions. Also covered are several of the most influential theories of morphologically conditioned phonology, which aim to capture language‑specific as well as cross‑linguistic generalizations about the phenomenon. The range of variation that a given language can exhibit in its phonological patterns is discussed.
Interleaving
Authors: Inkelas Sharon 
Published: December 2014

AbstractThis chapter discusses the phonological properties of morphologically complex words, i.e. those formed by more than one word-formation process. This chapter discusses both “cyclicity”, in the strict sense of the same phonological alternation or constraint applying at each step of word formation, and “layering”, in which phonology is imposed at each step of word formation, but the phonological mappings associated with the individual morphological constructions in question are not identical. Both types of interleaving share the same essential property that phonology applies to nested subconstituents in a word from the inside out: the output of applying phonology to a daughter is the input to the application of phonology to its mother. The best treatment of interleaving effects is the subject of hot theoretical debate; approaches covered include Lexical Morphology and Phonology, Stratal Optimality Theory, cophonology theory, indexed constraint Theory, and Output-Output correspondence theory.
When phonology interferes with morphology
Authors: Inkelas Sharon 
Published: December 2014

AbstractThis chapter discusses cases in which morphological constructions are prevented from combining with certain bases, or from combining with each other in the expected manner, because of phonological conditions that the combinations would violate. These situations are described in Optimality Theoretic terms as instantiating the P » M ranking, in which a phonological consideration outranks a morphological consideration. Suppletive allomorphy, ineffability (blocking), haplology (e.g. the Repeated Morph Constraint), and phonologically conditioned affix ordering are explored, along with theoretical treatments of each. The chapter concludes that phonological interference with morphology, especially in the area of affix ordering, is not nearly as common as many theories predict that it should be.
Nonparallelism between phonological and morphological structure
Authors: Inkelas Sharon 
Published: December 2014

AbstractThis chapter explores cases in which it appears necessary to posit a prosodic parse of a word (into constituents like “Prosodic Root”, “Prosodic Stem”, “Prosodic Word” which do not line up perfectly with the morphological constituent structure of that word. This occurs most commonly in compounding constructions, with “noncohering” (vs. “cohering”) affixes, and in reduplication and infixation (exfixation). Mismatches are often phonologically driven by the need for subconstituents of a word to be phonologically well-formed. This chapter addresses the question of whether apparent cases of morphologically conditioned phonology might be subsumed under reference to prosodic structure, and concludes that the two phenomena are distinct.
Paradigmatic effects
Authors: Inkelas Sharon 
Published: December 2014

AbstractWord formation and the phonological interpretation of words are sometimes influenced not only by properties of the word in question, but also by other words. This chapter explores the topic of paradigmatic cross-word correspondences and paradigmatic well-formedness, focusing on “leveling” or “Base-Identity” effects and on anti-homophony, or paradigmatic distinctiveness, effects. A number of cases suggest that the need to keep stem shape constant throughout a paradigm, or the need to keep cells of a paradigm distinct, can interfere with the otherwise normal operations of phonology and affixation. Questions addressed include the nature of the morphological relationship that is required for one word to influence another and whether leveling and anti-homophony are pervasive or whether they are sporadic, perhaps even epiphenomenal. The chapter also addresses the question of whether word-based paradigmatic constraints can do the work of cyclicity or interleaving, concluding that the two approaches are both needed.
The Silencing of God’s Dear Ministers
Authors: Davies Michael 
Published: December 2014

Abstract
This chapter addresses how ‘the silencing of God's dear Ministers’ in 1662 affected John Bunyan and the Independent congregation at Bedford. It examines the history of this congregation, from its establishment in the 1650s under Oliver Cromwell's regime, in order to reassess the impact of the ejections of 1660–2 upon the life of Bunyan's church and upon some of his later writings, including The Pilgrim's Progress. Focusing particularly on I Will Pray with the Spirit, this essay shows how the Act of Uniformity unsettled not just those ministers forced to leave their parishes on Black Bartholomew's Day but also Restoration nonconformists like Bunyan: typically considered ‘separatist’, and therefore as largely untouched by the events of 1662, and who would be left without a place in Edmund Calamy's famous account of the Great Ejection.
Crisis and Opportunity
Authors: Stanwood Owen 
Published: December 2014

Abstract
This chapter is an interpretation of New England's Restoration which argues that the return of Charles II, and more especially the Act of Uniformity and Great Ejection of 1662, started a process that led to the closer integration of New England into the nascent British empire. The result was a transformation of the region in ways that combined the dissenting and imperial visions. New England retained its peculiar religious culture—but the influx of new migrants led to a marked pluralism. And the imperial movement for reform did eventually lead to tighter control, but with safeguards for the practice of religion. In essence, imperial officials and the old Puritans learned to tolerate each other, and exist within the same empire—an interesting outgrowth of the events of 1660–2.
John Walker’s Sufferings of the Clergy and Church of England Responses to the Ejections of 1660–2
Authors: Burden Mark 
Published: December 2014

Abstract
John Walker, a Tory and High Churchman, published a book‐length rejoiner to Calamy's Abridgment (1702) of Baxter's life, titled An Attempt to Towards Recovering an Account of the Numbers and Sufferings of the Clergy. The full extent of the debate about 1662 is revealed by studying the 25 surviving volumes of Walker's Bodleian manuscripts for the first time in 70 years. These manuscripts include notes, drafts, indices and rejected passages in relation to the Attempt, alongside 1,000 letters between Walker and other clergymen, some sympathetic to his project, others hostile. Above all, Walker's correspondence reveals the inherited bitterness of many High Churchmen towards the ejected puritans, engendered by a combination of familial loyalty and a deep sense of former injustices.
Interrogation and Treatment of Detainees in the Global War on Terror
Authors: Jackson Dick 
Published: December 2014

Abstract
The U.S. practice on interrogation and treatment of detainees has been consistent and extensive since the adoption of the Geneva Conventions, through the war in Vietnam, the foreign internal defense missions in Central America, the first Gulf War, and the peacekeeping operations of the 1990s. U.S. service members were trained to apply the minimum humane treatment standards outlined in common article 3 of the Conventions and usually applied the more extensive provisions applicable to prisoners of war or civilian internees, as a matter of policy, even when the full Conventions did not apply as a matter of law. But U.S. policymakers changed that practice after 9/11, in an effort to free interrogators to apply “harsh interrogation techniques,” tantamount to torture. This chapter describes the arc of change in those policies from elimination of the standards to the congressional and public pressure that ultimately led to their return.
Fitness costs in spatially structured environments
Authors: Débarre F. 
Published: December 2014

AbstractThe clustering of individuals that results from limited dispersal is a double-edged sword: while it allows for local interactions to be mostly among related individuals, it also results in increased local competition. Here I show that, because they mitigate local competition, fitness costs such as reduced fecundity or reduced survival are less costly in spatially structured environments than in non spatial settings. I first present a simple demographic example to illustrate how spatial structure weakens selection against fitness costs. Then, I illustrate the importance of disentangling the evolution of a trait from the evolution of potential associated costs, using an example taken from a recent study investigating the effect of spatial structure on the evolution of host defense. In this example indeed, the differences between spatial and non-spatial selection gradients are due to differences in the fitness costs, thereby undermining interpretations of the results made in terms of the trait only. This illustrates the need to consider fitness costs as proper traits in both theoretical and empirical studies.
Presenting the History ofAfricans in ProvincialBritain:Norfolk as a Case Study
Authors: Maguire Richard C. 
Published: December 2014

AbstractThis article addresses the important topic of how we discuss the history of theAfrican population inBritain in our public historical spaces. In recent decades historians have established that theAfrican presence inBritain is long‐standing and we have also accepted the importance of discussing the impact of the system ofAtlantic slavery in our national history. In consequence, information aboutBritish involvement in the transatlantic slaving economy has entered school curricula, public historical spaces and public debate. This article suggests that we might want to revisit the presentation of this history as we gain more information about theAfrican presence away fromLondon and the major ports. It suggests that the story ofAfricans in the provinces is, perhaps, not best explained using the histories of large metropolitan centres and ports deeply entangled with slavery. It argues that the information fromNorfolk indicates that we should explore an idea that different regions might have responded to the arrival ofAfricans in different ways and we might be best served by assuming that there was no such thing as a ‘model’ ofBritish responses to this process. It suggests that we consider a presentation of the history ofNorfolk'sAfrican population that emphasizes integration, personal agency and the lack of antipathy towardsAfricans, and does not start from a default assumption of enslavement.
Black knights and elections in authoritarian regimes: Why and how Russia supports authoritarian incumbents in post‐Soviet states
Authors: Tolstrup Jakob 
Published: December 2014

AbstractIn the last decade, studies have documented how autocrats use elections as a way of legitimising and stabilising their regimes. Simultaneously, a literature on negative external actors (also known as ‘black knights’) has developed, emphasising how various international actors use anti‐democracy promotion strategies to undergird authoritarian regimes. In this article, these two literatures are fused in an attempt to shed light on the external dimension of authoritarian elections and what is termed ‘black knight election bolstering’. First, five mechanisms are elucidated, through which external assistance increases the chances of ‘winning’ elections in authoritarian settings (signaling invincibility, deterring elite defection, undermining opposition activities, dealing with popular protests, and countervailing pressure from foreign democracy promoters). Second, it is argued that external actors are most likely to offer election bolstering when they face a particularly acquiescent partner or when electoral defeat is perceived to lead to radical and undesired regime change. The relevance of both factors is augmented when uncertainty of the electoral outcome is high. Finally, four cases of Russian intervention during elections in three authoritarian neighbour countries (Ukraine in 2004, Belarus in 2006, and Moldova in 2005 and 2009) are analysed. The case studies corroborate the theoretical arguments: not only does Russia engage in all five types of black knight election bolstering, but it does so only when one or more of the three explanatory factors are present.
Reading abilities in school‐aged preterm children: a review and meta‐analysis
Authors: Kovachy Vanessa N , Adams Jenna N , Tamaresis John S , Feldman Heidi M 
Published: December 2014

AimChildren born preterm (at ≤32wks) are at risk of developing deficits in reading ability. This meta‐analysis aims to determine whether or not school‐aged preterm children perform worse than those born at term in single‐word reading (decoding) and reading comprehension.MethodElectronic databases were searched for studies published between 2000 and 2013, which assessed decoding or reading comprehension performance in English‐speaking preterm and term‐born children aged between 6 years and 13 years, and born after 1990. Standardized mean differences in decoding and reading comprehension scores were calculated.ResultsNine studies were suitable for analysis of decoding, and five for analysis of reading comprehension. Random‐effects meta‐analyses showed that children born preterm had significantly lower scores (reported as Cohen's d values [d] with 95% confidence intervals [CIs]) than those born at term for decoding (d=−0.42, 95% CI −0.57 to −0.27, p<0.001) and reading comprehension (d=−0.57, 95% CI −0.68 to −0.46, p<0.001). Meta‐regressions showed that lower gestational age was associated with larger differences in decoding (Q[1]=5.92, p=0.02) and reading comprehension (Q[1]=4.69, p=0.03) between preterm and term groups. Differences between groups increased with age for reading comprehension (Q[1]=5.10, p=0.02) and, although not significant, there was also a trend for increased group differences for decoding (Q[1]=3.44, p=0.06).InterpretationPreterm children perform worse than peers born at term on decoding and reading comprehension. These findings suggest that preterm children should receive more ongoing monitoring for reading difficulties throughout their education.
Larval traits of the Caribbean amphidromous goby Sicydium punctatum (Gobioidei: Sicydiinae) in Guadeloupe
Authors: Lejeune Léa , Tabouret Hélène , Taillebois Laura , Monti Dominique , Keith Philippe 
Published: December 2014

AbstractAmphidromous fish are the biggest contributor to the diversity of fish communities in river systems of Caribbean islands. Among them, Sicydium punctatum Perugia, 1896, which is endemic to the West Indies, represents the vast majority of fish in these rivers. The otolith microstructure and the biometry of S. punctatum postlarvae from Guadeloupe were investigated to explore the dispersal modalities of this species through an appreciation of the growth pattern, the pelagic larval duration (PLD) and the size‐at‐recruitment. The study was made on one cohort of 83 recruited postlarvae, fished at the Capesterre River's mouth on 2 November 2011. The mean (±SD) size‐at‐recruitment of the postlarvae was 24.6 ± 1.3 mm (range of 20.5–28.1 mm, n = 83). We found a mean (±SD) PLD of 72.2 ± 10.5 days (range of 54–101.5 days, n = 67). The growth rate estimated from the otolith increments showed a globally decreasing pattern during the marine larval phase. Growth rates at the beginning of the larval stage were significantly different between hatching periods, suggesting a relation between the hatching period and the growth rate in S. punctatum. This study adds on to the general understanding of the life cycle of S. punctatum in Guadeloupe that will help implement strategies to manage amphidromous fish populations in the Caribbean region.