bluuebunny/crossref_metadata_2025_split huggingface dataset:
Free Indirect Discourse and the syntax of the left periphery
Authors: Giorgi Alessandra 
Published: December 2015

AbstractThis work is concerned with Free Indirect Discourse (FID), a narrative style that gives the reader the impression of listening directly to the thoughts, or to the speech, of the speaker or main character of the narration. The general question to be addressed is the following: to what extent does grammar, particularly of the left periphery, intervene in constraining the expressive possibilities available for a narrator? The thesis developed in this chapter is that language, even when literary, always complies with the rules of grammar. Namely, even if there is a certain degree of freedom in narration, the possible realizations of sentences can only be identified among the options provided by Universal Grammar. In the case of FID, Universal Grammar identifies the general mechanisms determining the reference of indexicals—tenses, adverbs, and pronouns—in the same way as in “normal” sentences, in spite of the apparent differences.
Basic principles: terminology
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo 
Published: December 2015

Abstract
This chapter sets out and defines the terminology that is used in the rest of the volume. This includes the terminology of morphological analysis (morpheme and morph, lexeme and word-form, inflection and derivation, availability and profitability, for example), but also areas on the borders of morphology (suppletion, phonaestheme, word-classes) and matters of verbal diathesis. The notion of ‘word’ is discussed in detail. This is followed by considerations concerning the elements below the level of the word. The next section is devoted to the study of word-classes and their relevance for morphological analysis, followed by treatments of productivity, the distinction between native and non-native vocabulary and other lexical, especially syntactico-semantic, matters.
Basic principles: methods
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo 
Published: December 2015

Abstract
This chapter presents the methods on which this book is based. Large quantities of data were generated from electronic sources. The most important sources used were the Corpus of Contemporary American English, the British National Corpus, various types of dictionary, websites and lexical databases. The chapter discusses the methodological problems with gathering and analyzing the data. Furthermore the conventions for citing data and for deciding which data to include are detailed. Problems of interpretation are also considered.
Adjective and adverb inflection
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo 
Published: December 2015

Abstract
This chapter is concerned with the formation of comparatives and superlatives in English. First the semantic issues involved with comparison are discussed, then the properties of affixal degree-formation. This is followed by a detailed description of the comparison of adverbs and adjectives. In particular, the chapter discusses the different determinants of the choice between synthetic and analytic forms of comparative and superlative with adjectives. A variety of phonological, morphological, syntactic, semantic, and dialectal conditioning factors are considered.
Derived nouns: event, state, result
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo 
Published: December 2015

Abstract
This chapter discusses derived nouns denoting events, states, results, as well as related semantic categories such as products and means. Such nouns are formed with the suffixes -ing, -ation, -ment, -al, -ure, -ance and by conversion. The chapter begins with the formal properties of the processes in question, including the kinds of bases that undergo affixation or conversion, their syntactic category, their status as native or non-native, free or bound, as well as phonological or prosodic restrictions on bases. The chapter then moves on to the range of semantic interpretations available for the different kinds of formation. This includes a discussion of argument referencing and the predictability of meaning.
Derived adjectives
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo 
Published: December 2015

Abstract
This chapter considers the full range of affixes that derive adjectives in contemporary English (‑able, ‑al, ‑an, ‑ant,‑ary, ‑esque, ‑ful, ‑ic, ‑ical, ‑ine, ‑ing, ‑ish, ‑ive,‑ly, ‑oid, ‑ory, ‑ous, ‑some, ‑y, and the past participle). It looks at both their formal characteristics and their semantic range. It takes up the issue of stress placement with this cohort of affixes and the extent to which the various affixes are productive. The chapter also discusses the extent to which some of them are semantically interchangeable. It also deals with the question whether such categories as gradable versus non-gradable, or relational versus qualitative, arise as a function of the specific affix, the base, or the context in which individual items appear.
Compounds: formal considerations
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo 
Published: December 2015

Abstract
This chapter deals with the formal properties of compounds. First it considers which kinds of constructs should be classified as compounds and which ones should not. This is followed by a discussion of the internal structure of compounds (including issues of headedness, stress, and orthography), and of the formal properties of nominal, verbal, adjectival, and prepositional compounds, as well as neoclassical, phrasal, and reduplicative compounds. It is argued that blends are also best analyzed as compounds. The chapter ends with a consideration of the formal characteristics of blends.
Inflection versus derivation
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo 
Published: December 2015

Abstract
This chapter reviews the notion of conversion and its correlates, concentrating on two points. First, it is concerned with which of the various types of systematic homonymy or polysemy that can be found in English are instances of conversion. This discussion includes canonical cases like noun-to-verb conversion and less canonical cases such as type coercion or adverb formation. This is approached by considering the extent to which they match the canonical pattern of English conversion. Second, the chapter also considers and evaluates the various theoretical approaches to conversion (zero-derivation, relisting, underspecification, etc.) which can be found in the literature.
The nature of stratification
Authors: Bauer Laurie , Lieber Rochelle , Plag Ingo 
Published: December 2015

Abstract
The chapter is concerned with the question of where English stands with respect to the types of morphology displayed in the languages of the world. It begins with a consideration of the traditional way of characterizing morphology as isolating, agglutinating, fusional, or polysynthetic that goes back to the work of Humboldt and Sapir. It also looks at more modern attempts at large-scale classification, concluding that such schemas do not tell us much that is interesting or useful. It is argued, however, that typological comparisons on a more local level have the potential to be more illuminating. This is illustrated with a comparison of English with Germanic and Romance morphology.
WKB approximation
Authors: Manousakis Efstratios 
Published: December 2015

Abstract
This chapter presents a simple way to derive the semiclassical approximation of Wenzel, Kramers, and Brillouin (WKB). This approximation is valid in the limit where the external potential varies smoothly over a length scale much larger than the particle local de Broglie wavelength. The chapter discusses the concept of asymptotic matching the WKB solution with the exact solution very close to the classical turning points.
Identical particles
Authors: Manousakis Efstratios 
Published: December 2015

Abstract
This chapter discusses the case of a many-body system of identical particles. It considers the consequencies of the symmetry of the Hamiltonian under particle permutations in this case. It discusses how to build many-body Boson and Fermion states. It then introduces the formalism of so-called second quantization, which is usefu, in the case of identical particles. It also expresses the many-body Hamiltonian in terms of creation and annihilation operators.
Basic grammatical concepts
Authors: Pinkster Harm 
Published: December 2015

Abstract
One part of the chapter is devoted to the various components that together constitute a sentence. The terms involved, like sentence and clause, are not used in a uniform way in the older literature and vary also from one (national or theoretical) linguistic community to the other. The items discussed are ‘sentence’, ‘clause’, ‘phrase’, ‘word’, ‘clitic’, and ‘constituent’. A second part is devoted to the structure of the clause and the importance of the concept of valency in describing the structure of clauses. Some constituents of a clause are determined by the valency of the verb (so-called arguments), other are not (so-called satellites). A third part is devoted to the notions of syntactic, semantic, and pragmatic functions. A final part deals with linguistic entities of a higher level than the sentence: discourse and text type.
Agreement
Authors: Pinkster Harm 
Published: December 2015

Abstract
A distinction is made between grammatical and notional agreement. Agreement exists at the clause level and at the noun phrase level. At the clause level grammatical agreement concerns the relationship between the subject and the finite verb form and between the subject and various nominal forms, both the nominal components of finite and infinite verb forms, and subject and object complements. The formal properties of the subject are copied onto the constituents showing agreement. There are a number of well-defined deviations from the general rule, which itself is more complicated if the subject is compound, i.e. if it exists of more than one noun or comparable expression. Notional agreement ignores formal properties of subjects but takes semantic properties into account. At the noun phrase level the head may determine the form of its attribute(s) notably of determiners, adjectives, and quantifiers. Here, too, the rules are more complicated with compound heads.
Oblation, Non-conception, and Body
Authors: Sugiki Tsunehiko 
Published: December 2015

Abstract
The chapter examines several important early Buddhist tantric texts in this study. The chapter focuses on what it calls the “psychosomatic fire-oblation,” which is an internalized means of performing the ritual within the practitioner’s body. This employs the system of esoteric physiology (cakras, winds, and channels) that provided a basis for much of tantric and yogic practice. As a consequence of this close study of several early medieval Buddhist tantras, the chapter is able to establish a chronological sequence of the texts. This sequence corresponds to a trajectory from the actual performance of sexual rites to symbolized forms. The latter, internalized practices involve a psychophysiological symbolism of fire burning up the obscurations (kleśas).
Fire Rituals by the Queen of Siddhas
Authors: Halkias Georgios T. 
Published: December 2015

AbstractThis chapter discusses how Buddhist practitioners adapted the Brahmanic homa for their own use. As adopted by the Tibetans, homa rites were employed both for the accomplishment of worldly goals, such as safety, prosperity, and power, but also for the accomplishment of the highest goals of liberation from the rounds of saṃsara. Focusing on a little known buddha, Aparimitāyus, the chapter shows that this buddha is also part of the broader Pure Land tradition. Like the much better known Pure Land buddha, Amitāyus, Aparimitāyus has the attribute of granting longevity. The manual, attributed to the Queen of Siddhas, a dākini, includes discussions of the four different kinds of rites. Like most tantric rituals it includes ritual identification, in this case at the beginning of the ritual. The chapter closes with a discussion of the rationales employed in the adoption of Brahmanic rites into the context of Buddhist practice.
TheNavarātra Homa
Authors: Chaulagain Nawaraj 
Published: December 2015

AbstractThe navarātra is a nine-day festival held in the autumn. At the start of this festival, a yantra is consecrated in the same way that images are for the installation of a deity in them. This involves the first of the three kinds of homa included in the festival. This first wakes up the goddess residing within the yantra. The second involves the offering of a goat’s liver into the fire, and the last is used to empower weapons and other royal insignia. While the first opens the festival, the second takes place during the nights of the eighth and ninth days of the festival. This involves the sacrifice of a goat and feeding the goddess by offering the liver into the fire. The third homa is performed daily up to the eighth day of the festival.
Computational identification of piRNA targets on mouse mRNAs
Authors: Yuan Jiao , Zhang Peng , Cui Ya , Wang Jiajia , Skogerbø Geir , Huang Da-Wei , Chen Runsheng , He Shunmin 
Published: December 2015

Abstract
Motivation: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly abundant in the germline. One important role of piRNAs is to defend genome integrity by guiding PIWI proteins to silence transposable elements (TEs), which have a high potential to cause deleterious effects on their host. The mechanism of piRNA-mediated post-transcriptional silencing was also observed to affect mRNAs, suggesting that piRNAs might play a broad role in gene expression regulation. However, there has been no systematic report with regard to how many protein-coding genes might be targeted and regulated by piRNAs.
Results: We trained a support vector machine classifier based on a combination of Miwi CLIP-Seq-derived features and position-derived features to predict the potential targets of piRNAs on mRNAs in the mouse. Reanalysis of a published microarray dataset suggested that the expression level of the 2587 protein-coding genes predicted as piRNA targets showed significant upregulation as a whole after abolishing the slicer activity of Miwi, supporting the conclusion that they are subject to piRNA-mediated regulation.
Availability and implementation: A web version of the method called pirnaPre as well as our results for browse is available at http://www.regulatoryrna.org/software/piRNA/piRNA_target_mRNA/index.php.
Contact: crs@sun5.ibp.ac.cn or heshunmin@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
DeNovo: virus-host sequence-based protein–protein interaction prediction
Authors: Eid Fatma-Elzahraa , ElHefnawi Mahmoud , Heath Lenwood S. 
Published: December 2015

Abstract
Motivation Can we predict protein–protein interactions (PPIs) of a novel virus with its host? Three major problems arise: the lack of known PPIs for that virus to learn from, the cost of learning about its proteins and the sequence dissimilarity among viral families that makes most methods inapplicable or inefficient. We develop DeNovo, a sequence-based negative sampling and machine learning framework that learns from PPIs of different viruses to predict for a novel one, exploiting the shared host proteins. We tested DeNovo on PPIs from different domains to assess generalization.
Results: By solving the challenge of generating less noisy negative interactions, DeNovo achieved accuracy up to 81 and 86% when predicting PPIs of viral proteins that have no and distant sequence similarity to the ones used for training, receptively. This result is comparable to the best achieved in single virus-host and intra-species PPI prediction cases. Thus, we can now predict PPIs for virtually any virus infecting human. DeNovo generalizes well; it achieved near optimal accuracy when tested on bacteria–human interactions.
Availability and implementation: Code, data and additional supplementary materials needed to reproduce this study are available at: https://bioinformatics.cs.vt.edu/~alzahraa/denovo.
Contact: alzahraa@vt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Uncertainties in projecting climate-change impacts in marine ecosystems
Authors: Payne Mark R. , Barange Manuel , Cheung William W. L. , MacKenzie Brian R. , Batchelder Harold P. , Cormon Xochitl , Eddy Tyler D. , Fernandes Jose A. , Hollowed Anne B. , Jones Miranda C. , Link Jason S. , Neubauer Philipp , Ortiz Ivonne , Queirós Ana M. , Paula José Ricardo 
Published: December 2015

AbstractProjections of the impacts of climate change on marine ecosystems are a key prerequisite for the planning of adaptation strategies, yet they are inevitably associated with uncertainty. Identifying, quantifying, and communicating this uncertainty is key to both evaluating the risk associated with a projection and building confidence in its robustness. We review how uncertainties in such projections are handled in marine science. We employ an approach developed in climate modelling by breaking uncertainty down into (i) structural (model) uncertainty, (ii) initialization and internal variability uncertainty, (iii) parametric uncertainty, and (iv) scenario uncertainty. For each uncertainty type, we then examine the current state-of-the-art in assessing and quantifying its relative importance. We consider whether the marine scientific community has addressed these types of uncertainty sufficiently and highlight the opportunities and challenges associated with doing a better job. We find that even within a relatively small field such as marine science, there are substantial differences between subdisciplines in the degree of attention given to each type of uncertainty. We find that initialization uncertainty is rarely treated explicitly and reducing this type of uncertainty may deliver gains on the seasonal-to-decadal time-scale. We conclude that all parts of marine science could benefit from a greater exchange of ideas, particularly concerning such a universal problem such as the treatment of uncertainty. Finally, marine science should strive to reach the point where scenario uncertainty is the dominant uncertainty in our projections.
How big can a black hole grow?
Authors: King Andrew 
Published: December 2015

Abstract
I show that there is a physical limit to the mass of a black hole, above which it cannot grow through luminous accretion of gas, and so cannot appear as a quasar or active galactic nucleus (AGN). The limit is Mmax ≃ 5 × 1010 M⊙ for typical parameters, but can reach Mmax ≃ 2.7 × 1011 M⊙ in extreme cases (e.g. maximal prograde spin). The largest black hole masses so far found are close to but below the limit. The Eddington luminosity ≃6.5 × 1048 erg s−1 corresponding to Mmax is remarkably close to the largest AGN bolometric luminosity so far observed. The mass and luminosity limits both rely on a reasonable but currently untestable hypothesis about AGN disc formation, so future observations of extreme supermassive black hole masses can therefore probe fundamental disc physics. Black holes can in principle grow their masses above Mmax by non-luminous means such as mergers with other holes, but cannot become luminous accretors again. They might nevertheless be detectable in other ways, for example through gravitational lensing. I show further that black holes with masses ∼Mmax can probably grow above the values specified by the black-hole–host-galaxy scaling relations, in agreement with observation.
Mycobacterium marinum Infection After Exposure to Coal Mine Water
Authors: Huaman Moises A. , Ribes Julie A. , Lohr Kristine M. , Evans Martin E. 
Published: December 2015

Abstract
Mycobacterium marinum infection has been historically associated with exposure to aquariums, swimming pools, fish, or other marine fauna. We present a case of M marinum left wrist tenosynovitis and elbow bursitis associated with a puncture injury and exposure to coal mine water in Illinois.
Acute respiratory failure after drowning: a retrospective multicenter survey
Authors: Michelet Pierre , Bouzana Fouad , Charmensat Olivia , Tiger Fabrice , Durand-Gasselin Jacques , Hraiech Sami , Jaber Samir , Dellamonica Jean , Ichai Carole 
Published: December 2015

Objectives
Despite the extensive literature on drowning, clinical data are still lacking on the best medical strategy to use. Acute respiratory failure (ARF) is the main component of drowning pathophysiology. The objectives of this multicenter study were to analyze the clinical course of drowning-related ARF patients and to describe the efficacy of the ventilatory strategies used.

Methods
Medical records of drowned adult patients admitted in seven ICUs after prehospital emergency medical care during three consecutive summer periods were retrospectively analyzed.

Results
Among the 126 patients (58±21 years) admitted, 38 patients with cardiac arrest at the scene were not analyzed, 26 received mechanical ventilation (MV), and 48 patients received noninvasive ventilation (NIV). Compared with patients placed under MV, the NIV patients presented a better initial neurological (Glasgow Coma Scale of 7±4 vs. 12±3, P<0.05) and hemodynamic status from the prehospital stage (mean arterial pressure of 77±18 vs. 96±18, P<0.001). With comparable ARF-related hypoxemia to MV, the NIV was maintained with success in 92% (44/48). Both MV and NIV were associated with rapid improvement of oxygenation and short ICU length of stay [3 (1–14) and 2 (1–7), respectively].

Conclusion
Despite the absence of recommendation for NIV use in case of drowning-related ARF, this technique was often used with safety and efficacy. The decision for NIV use was mainly based on the preserved or improved neurological status.
Cognitive Endophenotypes of Modern and Extinct Hominins Associated withNTNGGene Paralogs
Authors: Prosselkov Pavel , Hashimoto Ryota , Polygalov Denis , Ohi Kazutaka , Zhang Qi , McHugh Thomas J. , Takeda Masatoshi , Itohara Shigeyoshi 
Published: December 2015

ABSTRACTA pair of vertebrate-specific and brain-expressed pre-synaptic genes,NTNG1andNTNG2,contributes to the Intellectual Quotient (IQ) test scores in a complementary manner. Single nucleotide polymorphisms (SNPs) ofNTNG1are associated with attenuated verbal comprehension (VC) or processing speed (PS) whileNTNG2SNPs affect working memory (WM) and perceptual organization (PO), forming cognitive endophenotypes in healthy and schizophrenia (SCZ)-affected human subjects. Regions of interest (ROIs), defined as 21 nucleotide (nu) longNTNGgene loci symmetrically embedding the IQ-affecting mutation alleles (VC/PS and WM/PO), underwent dramatic evolutionary changes from mice through primates to hominins, at the accelerated rates. Mutation alleles associated with the higher VC and WM IQ scores are found in the genomes of extinct hominins of Neolithic times, however, lower WM scores associated allele is also detectable in Mesolithic hunters genomes. Protein sequence ofNTNG1is 100% conserved among the primates, archaic and modern extinct hominins whileNTNG2underwent a recent selection sweep encoding a primate-specific S371A/V (~50,000 yrs BC), and a modern human (5,300 yrs BC) T346A substitutions. We show that a 500 mln yrs old genomic duplication of a synapse primordial gene provided a substrate for further synapse elaborations and its ultimate capacitive expansion of what evolved into a vertebrate cognitive superior complexity – intelligence.