bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction
Authors: Alexiadou Artemis , Anagnostopoulou Elena , Schäfer Florian 
Published: March 2015

AbstractThis chapter first presents the key issues of discussion concerning the causative alternation, before proceeding to outline the theory of Voice that is further built on and developed in the rest of the book. The chapter first defines the causative alternation and offer a survey of the issues that have widely been discussed in the literature. It then turns to the introduction of the main hypothesis, according to which the causative alternation is a Voice alternation. It offers the ingredients of the model of Voice that is developed in this book, building on Kratzer (1996) and on work within Distributed Morphology. It develops a theory of Voice, according to which next to active there are three non-active Voice heads involved in transitivity alternations: Passive, Middle, and expletive Voice. The chapter finally provides an outline of the book.
A typology of Voice
Authors: Alexiadou Artemis , Anagnostopoulou Elena , Schäfer Florian 
Published: March 2015

AbstractThis chapter develops a typology of the different Voice heads in anticausatives, reflexives, and passives across languages. The role of Voice in Greek-type anticausatives and in Romance/Germanic-type anticausatives, presented in Chapter 3, is discussed, focusing on the question of how to explain Voice syncretism. It is argued that, cross-linguistically, the presence of Voice morphology in anticausatives does not have any truth-conditional effects. This morphology is associated with a particular type of semantically inert Voice head, which we label expletive Voice. A number of restrictions on the Greek passive suggest that in English and German, the head Passive introducing the passive function is located on top of the Voice projection introducing the external argument, while in Greek, passive formation is built on the basis of the non-active variant of Kratzer’s Voice head (middle, building on Doron 2003 and subsequent work). The properties of Greek Voice are best captured by the underspecification approach to Voice.
Scope and towers
Authors: Barker Chris , Shan Chung-Chieh 
Published: March 2015

AbstractChapter 1 develops the basic formal grammar used in Part I, called the ‘tower’ presentation. This includes a development of the category system used throughout the book. This provides a way to reason about the syntactic category of scope-taking expressions. The type-shifters LIFT and LOWER are discussed, along with the main combination schema. In each case, there is a schematic diagram that illustrates graphically the concept behind the rule. Several derivations are presented in detail. There is a derivation illustrating how the combination schema expresses a bias in favor of linear scope, as well as a derivation of a sentence exhibiting scope ambiguity. There are a number of exercises, along with complete answers, that can help the reader consolidate their grasp of the essential principles.
From generalized quantifiers to dynamic meaning
Authors: Barker Chris , Shan Chung-Chieh 
Published: March 2015

AbstractChapter 3 argues that Montague’s conception of DP meanings as generalized quantifiers is a (limited) form of continuation passing. Likewise, the dynamic semantics conception of sentence meaning as an update function on surrounding context is also seen to be a form of continuation passing. There is a brief comparison of the continuation‐based tower approach to Dynamic Montague Grammar. Montague’s insight follows from making continuations available to expressions in category DP; the dynamic conception of meaning follows from making continuations available to expressions in the category S. Since the continuation‐based approach makes continuations available systematically and uniformly to expressions not only in categories DP and S, but to expressions in any syntactic category, generalized quantifier theory and dynamic semantics turn out to be two special cases of a single general strategy of making continuations available throughout the grammar.
Movement as delayed evaluation: Wh‐fronting
Authors: Barker Chris , Shan Chung-Chieh 
Published: March 2015

AbstractChapter 5 extends the fragment to handle wh‐question formation by introducing the type‐shifter FRONT. This type‐shifter captures the systematic syntactic relationship between in‐situ wh‐questions and fronted wh‐questions. Flexibility in the timing of the application of the type‐shifter accounts for pied piping. Because the type‐shifter adjusts the syntax of a wh‐question without affecting its semantics, the net effect is that the denotation of a fronted wh‐question will be identical to the denotation of the corresponding in‐situ wh‐question. Fronted wh‐phrases combine with question bodies that are clauses missing a DP argument somewhere inside of them. The position of the missing DP is occupied by a gap, where gaps are identity categories, both syntactically and semantically. The account of multiple wh predicts superiority effects through the same evaluation‐order mechanism as the explanation for weak crossover.
Generalized coordination, Flexible Montague Grammar
Authors: Barker Chris , Shan Chung-Chieh 
Published: March 2015

AbstractChapter 7 argues that Partee and Rooth’s theory of generalized coordination implicitly involves a limited form of continuation‐capture. On a continuation account, coordination can be analyzed as reuse of a continuation: first, the continuation of the coordinated expression is combined with one coordinand, then with the other one. Continuations are implicit also in Hendriks’ Flexible Montague Grammar, a conceptually related type‐shifting system. Like the continuation‐based tower fragment, Flexible Montague Grammar is a simple type‐shifting system that provides a robust account of scope relations. However, it is not well‐suited to reasoning about order, and therefore is not able to explain crossover contrasts. This claim is explored by extending Flexible Montague Grammar with a binding type‐shifter, and noting that the type‐shifter generates crossover violations.
Order effects in negative polarity licensing
Authors: Barker Chris , Shan Chung-Chieh 
Published: March 2015

AbstractChapter 8 extends the explanation for crossover to a phenomenon that involves scope, but not binding, namely, the licensing of negative polarity items. It has long been a mystery why negative polarity licensing appears to be sensitive not only to scope relations, but also to linear order. We argue that the pattern of configurations in which a quantificational DP is able to bind a pronoun is similar to the pattern of configurations in which an NPI‐licensing quantifier is able to license a negative polarity item. An account is developed in the tower fragment on which the link between a negative polarity item and its licensor is mediated by the same syntactic mechanism that establishes the link between a quantifier and a pronoun that it binds. As a result, NPI licensing shows a sensitivity to evaluation order in the same class of structures that trigger a weak crossover violation.
Parasitic scope forsame
Authors: Barker Chris , Shan Chung-Chieh 
Published: March 2015

AbstractChapter 14 uses the type‐logical grammar developed in the previous chapter to provide an analysis of the notoriously challenging compositional semantics of adjectives such as ‘‘same’’ and ‘‘different’’. The behavior of ‘‘same’’ when it occurs in a nominal motivates an analysis on which it takes scope over the nominal. In order to extend that basic analysis to the general case, NL‐lambda allows an account in terms of parasitic scope, on which ‘‘same’’ takes scope in a way that depends on the scope of some other scope‐taking element in the sentence. We present Solomon’s argument that ‘‘same’’ in the presence of partitives motivates recursive (parasitic) scope, in which ‘‘same’’ takes scope over a containing DP, turning that larger DP into an expression that is itself a scope‐taker. We briefly compare the parasitic scope approach to other accounts of the semantics of ‘‘same’’ and ‘‘different’’.
The null morpheme POS
Authors: Rett Jessica 
Published: March 2015

AbstractThis chapter is the first installment of a history of the treatment of evaluativity in degree semantics. It begins with a brief tutorial in degree semantics and a short discussion of the ontological status of degrees. It details the origins of degree semantics (Bartsch and Vennemann 1972; Cresswell 1976), which was also the origin of POS, a null degree modifier proposed to treat evaluativity in positive constructions. The second half of the chapter includes a review of semantic and philosophical discussions about the nature of the standard invoked by evaluativity, as well as a review of recent applications of POS outside of evaluative adjectival constructions, particularly in event semantics.
Evaluativity as implicature
Authors: Rett Jessica 
Published: March 2015

AbstractThis chapter presents the main theoretical proposal of the book: the claim that evaluativity and its distribution can be accounted for using a Gricean notion of conversational implicature. In cases like equatives in which evaluativity is sensitive to the polarity of the adjective, evaluativity is a strengthening of meaning resulting from a Manner implicature. In cases like the positive construction in which evaluativity is not sensitive to polarity, evaluativity is a strengthening of meaning resulting from a Quantity implicature, similar to those associated with tautologies like War is war. This chapter includes a discussion of why evaluativity is the resulting strengthened meaning in degree constructions, based largely on work by Bolinger (1972). The analysis draws on independent observations of the sensitivity of implicature to topic and questions under discussion to explain the asymmetrical status of evaluativity in equatives. The account is extended to absolute adjectives as well as relative ones.
Extensions of the evaluativity implicature
Authors: Rett Jessica 
Published: March 2015

AbstractThis chapter explores extensions of the claim that evaluativity is an implicature outside of the canonical data set. The first section parallels claims in Rett (2008) that a cross-linguistic difference in evaluativity between analytic (e.g. more tall) and synthetic (e.g. taller) comparatives is easily predicted by a manner implicature treatment of evaluativity. The second section speculates about contrasts in evaluativity across adjectival classes, with a particular focus on relative, absolute, and extreme adjectives (and the work in Kennedy and McNally 2005). The third section explores the notion of evaluativity in gradable nouns (Morzycki 2009) like a looker and a number. The final section discusses the notion of evaluativity generally, and the apparent asymmetry in natural language between positive (e.g. so big) and negative (e.g. so little) speaker evaluativity (Bolinger 1972).
Multiscale reaction-diffusion simulations with Smoldyn
Authors: Robinson Martin , Andrews Steven S. , Erban Radek 
Published: March 2015

Abstract
Summary: Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains. Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have.
Availability and Implementation: Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.
Contact: martin.robinson@maths.ox.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online and include additional details on model specification and modelling of surfaces, as well as the Smoldyn configuration file used to generate Figure 1.
Efficient visualization of high-throughput targeted proteomics experiments: TAPIR
Authors: Röst Hannes L. , Rosenberger George , Aebersold Ruedi , Malmström Lars 
Published: March 2015

Abstract
Motivation: Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required.
Results: We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses.
Availability and implementation: TAPIR is available for all computing platforms under the 3-clause BSD license at https://github.com/msproteomicstools/msproteomicstools.
Contact: lars@imsb.biol.ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
4DGenome: a comprehensive database of chromatin interactions
Authors: Teng Li , He Bing , Wang Jiahui , Tan Kai 
Published: March 2015

Abstract
Motivation: The 3D structure of the genome plays a critical role in regulating gene expression. Recent progress in mapping technologies for chromatin interactions has led to a rapid increase in this kind of interaction data. This trend will continue as research in this burgeoning field intensifies.
Results: We describe the 4DGenome database that stores chromatin interaction data compiled through comprehensive literature curation. The database currently covers both low- and high-throughput assays, including 3C, 4C-Seq, 5C, Hi-C, ChIA-PET and Capture-C. To complement the set of interactions detected by experimental assays, we also include interactions predicted by a recently developed computational method with demonstrated high accuracy. The database currently contains ∼8 million records, covering 102 cell/tissue types in five organisms. Records in the database are described using a standardized file format, facilitating data exchange. The vast major of the interactions were assigned a confidence score. Using the web interface, users can query and download database records via a number of annotation dimensions. Query results can be visualized along with other genomics datasets via links to the UCSC genome browser. We anticipate that 4DGenome will be a valuable resource for investigating the spatial structure-and-function relationship of genomes.
Availability and Implementation: 4Dgenome is freely accessible at http://4dgenome.int-med.uiowa.edu. The database and web interface are implemented in MySQL, Apache and JavaScript with all major browsers supported.
Contact: kai-tan@uiowa.edu
Supplementary Information: Supplementary Materials are available at Bioinformatics online.
A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human
Authors: Liang Cheng , Li Yue , Luo Jiawei , Zhang Zhaolei 
Published: March 2015

Abstract
Motivation: Interplays between transcription factors (TFs) and microRNAs (miRNAs) in gene regulation are implicated in various physiological processes. It is thus important to identify biologically meaningful network motifs involving both types of regulators to understand the key co-regulatory mechanisms underlying the cellular identity and function. However, existing motif finders do not scale well for large networks and are not designed specifically for co-regulatory networks.
Results: In this study, we propose a novel algorithm CoMoFinder to accurately and efficiently identify composite network motifs in genome-scale co-regulatory networks. We define composite network motifs as network patterns involving at least one TF, one miRNA and one target gene that are statistically significant than expected. Using two published disease-related co-regulatory networks, we show that CoMoFinder outperforms existing methods in both accuracy and robustness. We then applied CoMoFinder to human TF-miRNA co-regulatory network derived from The Encyclopedia of DNA Elements project and identified 44 recurring composite network motifs of size 4. The functional analysis revealed that genes involved in the 44 motifs are enriched for significantly higher number of biological processes or pathways comparing with non-motifs. We further analyzed the identified composite bi-fan motif and showed that gene pairs involved in this motif structure tend to physically interact and are functionally more similar to each other than expected.
Availability and implementation: CoMoFinder is implemented in Java and available for download at http://www.cs.utoronto.ca/∼yueli/como.html.
Contact: luojiawei@hnu.edu.cn or zhaolei.zhang@utoronto.ca
Supplementary information: supplementary data are available at Bioinformatics online.
Lopinavir/Ritonavir Monotherapy as Second-line Antiretroviral Treatment in Resource-Limited Settings: Week 104 Analysis of AIDS Clinical Trials Group (ACTG) A5230
Authors: Kumarasamy Nagalingeswaran , Aga Evgenia , Ribaudo Heather J. , Wallis Carole L. , Katzenstein David A. , Stevens Wendy S. , Norton Michael R. , Klingman Karin L. , Hosseinipour Mina C. , Crump John A. , Supparatpinyo Khuanchai , Badal-Faesen Sharlaa , Bartlett John A. 
Published: March 2015

Abstract
Background.  The AIDS Clinical Trials Group (ACTG) A5230 study evaluated lopinavir/ritonavir (LPV/r) monotherapy following virologic failure (VF) on first-line human immunodeficiency virus (HIV) regimens in Africa and Asia.
Methods.  Eligible subjects had received first-line regimens for at least 6 months and had plasma HIV-1 RNA levels 1000–200 000 copies/mL. All subjects received LPV/r 400/100 mg twice daily. VF was defined as failure to suppress to &lt;400 copies/mL by week 24, or confirmed rebound to &gt;400 copies/mL at or after week 16 following confirmed suppression. Subjects with VF added emtricitabine 200 mg/tenofovir 300 mg (FTC/TDF) once daily. The probability of continued HIV-1 RNA &lt;400 copies/mL on LPV/r monotherapy through week 104 was estimated with a 95% confidence interval (CI); predictors of treatment success were evaluated with Cox proportional hazards models.
Results.  One hundred twenty-three subjects were enrolled. Four subjects died and 2 discontinued prematurely; 117 of 123 (95%) completed 104 weeks. Through week 104, 49 subjects met the primary endpoint; 47 had VF, and 2 intensified treatment without VF. Of the 47 subjects with VF, 41 (33%) intensified treatment, and 39 of 41 subsequently achieved levels &lt;400 copies/mL. The probability of continued suppression &lt;400 copies/mL over 104 weeks on LPV/r monotherapy was 60% (95% CI, 50%–68%); 80%–85% maintained levels &lt;400 copies/mL with FTC/TDF intensification as needed. Ultrasensitive assays on specimens with HIV-1 RNA level &lt;400 copies/mL at weeks 24, 48, and 104 revealed that 61%, 62%, and 65% were suppressed to &lt;40 copies/mL, respectively.
Conclusions.  LPV/r monotherapy after first-line VF with FTC/TDF intensification when needed provides durable suppression of HIV-1 RNA over 104 weeks.
Clinical Trials Registration.  NCT00357552.
Lymph formation, composition and circulation: a proteomics perspective
Authors: Hansen Kirk C. , D’Alessandro Angelo , Clement Cristina C. , Santambrogio Laura 
Published: March 2015

AbstractDuring the last 20 years a deeper understanding of the lymphatic circulatory system, lymph formation and composition has emerged. This review will examine the current knowledge on the organization of the lymphatic vascular tree, the formation of lymph from the extracellular fluid, lymph circulation and the lymph proteomic composition during physiological and pathological conditions. Formation of the lymph fluid is dependent on pressure gradients in the capillary beds and the composition of the endothelial cell glycocalyx, which acts as a molecular sieve. Fluid propulsion toward the draining node is dependent on the intrinsic pumping mechanism of the lymphangions and their unidirectional valves. The lymph ‘omics’ composition is dependent on the ultrafiltration of plasma proteins as well as proteins and molecules derived from the metabolic and catabolic activities of each parenchymal organ from which the lymph drains. Altogether, these new insights have brought about a new awareness of the importance of the lymphatic system in human physiology and pathology.
New RR Lyrae variables in binary systems
Authors: Hajdu G. , Catelan M. , Jurcsik J. , Dékány I. , Drake A. J. , Marquette J.-B. 
Published: March 2015

Abstract
Despite their importance, very few RR Lyrae (RRL) stars have been known to reside in binary systems. We report on a search for binary RRL in the OGLE-III Galactic bulge data. Our approach consists in the search for evidence of the light-travel time effect in so-called observed minus calculated (O−C) diagrams. Analysis of 1952 well-observed fundamental-mode RRL in the OGLE-III data revealed an initial sample of 29 candidates. We used the recently released OGLE-IV data to extend the baselines up to 17 yr, leading to a final sample of 12 firm binary candidates. We provide O−C diagrams and binary parameters for this final sample, and also discuss the properties of eight additional candidate binaries whose parameters cannot be firmly determined at present. We also estimate that ≳ 4 per cent of the RRL reside in binary systems.
Elastic properties of polycrystalline dense matter
Authors: Kobyakov D. , Pethick C. J. 
Published: March 2015

Abstract
Elastic properties of the solid regions of neutron star crusts and white dwarfs play an important role in theories of stellar oscillations. Matter in compact stars is presumably polycrystalline and, since the elastic properties of single crystals of such matter are very anisotropic, it is necessary to relate elastic properties of the polycrystal to those of a single crystal. We calculate the effective shear modulus of polycrystalline matter with randomly oriented crystallites using a self-consistent theory that has been very successful in applications to terrestrial materials and show that previous calculations overestimate the shear modulus by approximately 28 per cent.