bluuebunny/crossref_metadata_2025_split huggingface dataset:
A short history of English epistemic indefinites
Authors: Slade Benjamin 
Published: August 2015

AbstractIn modern English there are two primary epistemic indefinites, some NP and some NP or other which bear distinct pragmatic properties, differing from one another both with respect to signalling how the speaker is (un)able to identify the individual in question and with respect to their relation to specificity. This chapter provides a preliminary examination of the synchronic and diachronic properties of these two English epistemic indefinites, along with other constructions associated with epistemicity, such as Old English postnominal nathw-. Texts from the Old English, Middle English, Early Modern English, and Modern English periods are examined in order to determine the development of the epistemic and specific uses of various constructions.
The Statistical Mechanics of Interacting Walks, Polygons, Animals and Vesicles
Authors: Janse van Rensburg E.J. 
Published: August 2015

AbstractThis book is an account of the theory and mathematical approaches in polymer entropy, with particular emphasis on mathematical approaches to directed and undirected lattice models. Results in the scaling and critical behaviour of models of directed and undirected models of self-avoiding walks, paths, polygons, animals and networks are presented. The general theory of tricritical scaling is reviewed in the context of models of lattice clusters, and the existence of a thermodynamic limit in these models is discussed in general and for particular models. Mathematical approaches based on subadditive and convex functions, generating function methods and percolation theory are used to analyse models of adsorbing, collapsing and pulled walks and polygons in the hypercubic and in the hexagonal lattice. These methods show the existence of thermodynamic limits, pattern theorems, phase diagrams and critical points and give results on topological properties such as knotting and writhing in models of lattice polygons. The use of generating function methods and scaling in directed models is comprehensively reviewed in relation to scaling and phase behaviour in models of directed paths and polygons, including Dyck paths and models of convex polygons. Monte Carlo methods for the self-avoiding walk are discussed, with particular emphasis on dynamic algorithms such as the pivot and BFACF algorithms, and on kinetic growth algorithms such as the Rosenbluth algorithms and its variants, including the PERM, GARM and GAS algorithms.
Scaling, criticality and tricriticality
Authors: Van Rensburg E.J. Janse 
Published: August 2015

AbstractChapter 4 is an overview of tricritical scaling in models of interacting lattice clusters. Tricritical exponents, the tricritical phase diagram, and crossover scaling are discussed. Finite size scaling of the free energy and of the partition function is examined, as are tricritical scaling relations. In addition, the homogeneity of the generating function, uniform asymptotics of the generating function and tricritical scaling are covered.
Directed lattice paths
Authors: Van Rensburg E.J. Janse 
Published: August 2015

AbstractChapter 5 is an overview of Dyck, Motzkin and partially directed path models of polymer entropy. Adsorbing paths, the Temperley method and factorisation methods are discussed, including the Bethe ansatz and models of random walks in the square lattice. The chapter also discusses solution of directed path models by the kernel method. In addition, staircase polygons and directed path models in layered environments and in wedges are reviewed.
Interacting Models of Vesicles and Surfaces
Authors: Van Rensburg E.J. Janse 
Published: August 2015

AbstractChapter 12 provides an overview of the square lattice vesicle and its phase diagram. Tricritical scaling of square lattice vesicles and the inflation transition are detailed. Surfaces in the cubic lattice and a model of crumpling lattice surfaces are reviewed. Finally, the free energy of crumpling lattice surfaces is explored.
Transcription of Romanian intonation
Authors: Jitcă Doina , Apopei Vasile , Păduraru Otilia , Maruşca Samuil 
Published: August 2015

AbstractThis chapter analyses the main standard and non-standard Romanian melodic contours of two Romanian linguistic areas corresponding to distinct intonational varieties: Moldova and Transylvania. For this purpose, we used a compatible ToBI annotation system (Ro_ToBI) and a speech corpus based on a questionnaire designed to elicit various types of utterances. Each type of intonational contour was analyzed starting from a description based on a sequence of Ro_ToBI pitch events. Special attention was paid to the pitch events that generated the focus in each prosodic phrase. Our descriptions of the Romanian intonational contours agree with those presented by other authors. All labels of the Ro_ToBI set are also found in the annotation systems defined for other languages. The cross-linguistic differences in contour annotation result from different interpretations of the pitch events whose F0 patterns do not match the standard definitions of the labels.
Sardinian intonational phonology: Logudorese and Campidanese varieties
Authors: Mar Vanrell Maria del , Ballone Francesc , Schirru Carlo , Prieto Pilar 
Published: August 2015

AbstractThis chapter describes the intonation and phrasing patterns that characterize the Logudorese and Campidanese varieties of Sardinian, and examines how intonation interacts with the lexicosyntactic structure to convey specific pragmatic meanings. Using the Discourse Completion Task methodology, data were collected in the Sardinian locales of Ìttiri, Òschiri, Lodè, Biddecrèsia, and Sìnnia. The analysis revealed the existence of a mid tone (!H-) to mark non-finality or continuation, the absence of rising patterns in yes-no questions, and the abundance of initial prominences. On the basis of the results presented in the chapter, it is claimed that although intonation seems not to be a strong cue to distinguish between the two macro-varieties of Sardinian, dialectal differences are found in the use of lexicosyntactic markers that introduce yes-no questions and in the application of truncation in vocatives.
Intonational variation in Spanish
Authors: Hualde José Ignacio , Prieto Pilar 
Published: August 2015

AbstractThis chapter offers an overview of intonational patterns in Spanish within the Autosegmental Metrical model. In all sections, both cross-dialectal patterns and differences among dialects are pointed out. In broad-focus statements, usually there is a fall throughout the syllable with nuclear accent. A rise and fall within this syllable conveys greater emphasis. In prenuclear accents, the general tendency is to have very late peaks, but this tendency is less prevalent in some varieties. Spanish dialects differ in their unmarked yes-no questions. One contour, found for instance in Madrid and Mexico City, has a low tone on the syllable with nuclear accent, followed by a final rise. The other main contour, typical of Caribbean and Canarian varieties, has a high plateau up to the last stressed syllable, where it falls. In wh-questions, there are less clear dialectal distinctions. Finally, there appears to be no unambiguous imperative intonation, even though imperatives are often segmentally identical to declaratives.
Special Relativity: Flat Spacetime
Authors: Cheng Ta-Pei 
Published: August 2015

Abstract
The relativistic invariant interval is presented geometrically as a length in a four-dimensional manifold, called Minkowski spacetime, having a flat-space metric diag(−1, 1, 1, 1). The physics of special relativity follows directly from the Lorentz transformation, which is a rotation in Minkowski spacetime. In this chapter, 4-tensors in Minkowski space are introduced in order to deduce relativistic equations. Besides the 4-position vector, the 4-velocity and 4-momentum are introduced, as well as the rank-2 electromagnetic field tensor and energy–momentum–stress tensor. Lorentz transformation can change different components of the same tensor into each other. This shows the equivalence of space and time, energy and momentum, electric and magnetic fields, as well as density and pressure of a field system. The principal features of a spacetime diagram and its representation of Lorentz transformations are presented. In particular, the causal structure of relativity is clarified in terms of lightcones.
Black Holes
Authors: Cheng Ta-Pei 
Published: August 2015

Abstract
A black hole is an object that is inside its event horizon at r=r*: a one-way surface that particles and light can only traverse inward. This chapter studies the spherically symmetric nonrotating Schwarzschild black hole. The metric elements change their respective signs when crossing from r&gt;r∗ to r&lt;r*, leading to a role change between space and time. A sufficiently large collection of matter can collapse gravitationally into a (Kerr) black hole. The physical reality of, and observational evidence for, black holes are discussed. There is a correspondence between the laws of black hole physics and those of thermodynamics. In particular, surface gravity at the event horizon behaves like temperature, and horizon area like entropy. This connection is strengthened with the discovery of Hawking radiation, resulting from quantum fluctuations around the event horizon, as particles falling into a black hole can have negative energy.
Impact of Antihypertensive Agents on Central Systolic Blood Pressure and Augmentation Index: A Meta-Analysis
Authors: McGaughey Tracey J. , Fletcher Emily A. , Shah Sachin A. 
Published: August 2015

Abstract

BACKGROUND
New evidence suggests that central systolic blood pressure (cSBP) and augmentation index (AI) are superior predictors of adverse cardiovascular outcomes compared to peripheral systolic BP (pSBP). We performed a meta-analysis assessing the impact of antihypertensives on cSBP and AI.

METHODS
PubMed, Cochrane Library, and CINAHL were searched until September 2014 to identify eligible articles. A DerSimonian and Laird random-effects model was used to calculate the weighted mean difference (WMD) and its 95% confidence interval (CI). Fifty-two and 58 studies incorporating 4,381 and 3,716 unique subjects were included for cSBP and AI analysis, respectively.

RESULTS
Overall, antihypertensives reduced pSBP more than cSBP (WMD 2.52mm Hg, 95% CI 1.35 to 3.69; I2 = 21.9%). β-Blockers (BBs) posed a significantly greater reduction in pSBP as compared to cSBP (WMD 5.19mm Hg, 95% CI 3.21 to 7.18). α-Blockers, angiotensin converting enzyme inhibitors, angiotensin II receptor blockers, calcium channel blockers, diuretics, renin-angiotensin aldosterone system inhibitors and nicorandil reduced cSBP and pSBP in a similar manner. The overall reduction in AI from baseline was 3.09% (95% CI 2.28 to 3.90; I2 = 84.5%). A significant reduction in AI was seen with angiotensin converting enzyme inhibitors, angiotensin II receptor blockers, calcium channel blockers, diuretics, renin-angiotensin aldosterone system inhibitors, BBs, α-blockers (ABs), nicorandil, and moxonidine reduced AI nonsignificantly.

CONCLUSIONS
BBs are not as beneficial as the other antihypertensives in reducing cSBP and AI.
Pairwise RNA secondary structure alignment with conserved stem pattern
Authors: Chiu Jimmy Ka Ho , Chen Yi-Ping Phoebe 
Published: August 2015

Abstract
Motivation: The regulatory functions performed by non-coding RNAs are related to their 3D structures, which are, in turn, determined by their secondary structures. Pairwise secondary structure alignment gives insight into the functional similarity between a pair of RNA sequences. Numerous exact or heuristic approaches have been proposed for computational alignment. However, the alignment becomes intractable when arbitrary pseudoknots are allowed. Also, since non-coding RNAs are, in general, more conserved in structures than sequences, it is more effective to perform alignment based on the common structural motifs discovered.
Results: We devised a method to approximate the true conserved stem pattern for a secondary structure pair, and constructed the alignment from it. Experimental results suggest that our method identified similar RNA secondary structures better than the existing tools, especially for large structures. It also successfully indicated the conservation of some pseudoknot features with biological significance. More importantly, even for large structures with arbitrary pseudoknots, the alignment can usually be obtained efficiently.
Availability and implementation: Our algorithm has been implemented in a tool called PSMAlign. The source code of PSMAlign is freely available at http://homepage.cs.latrobe.edu.au/ypchen/psmalign/.
Contact: phoebe.chen@latrobe.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning
Authors: Ma Jianzhu , Wang Sheng , Wang Zhiyong , Xu Jinbo 
Published: August 2015

Abstract
Motivation: Protein contact prediction is important for protein structure and functional study. Both evolutionary coupling (EC) analysis and supervised machine learning methods have been developed, making use of different information sources. However, contact prediction is still challenging especially for proteins without a large number of sequence homologs.
Results: This article presents a group graphical lasso (GGL) method for contact prediction that integrates joint multi-family EC analysis and supervised learning to improve accuracy on proteins without many sequence homologs. Different from existing single-family EC analysis that uses residue coevolution information in only the target protein family, our joint EC analysis uses residue coevolution in both the target family and its related families, which may have divergent sequences but similar folds. To implement this, we model a set of related protein families using Gaussian graphical models and then coestimate their parameters by maximum-likelihood, subject to the constraint that these parameters shall be similar to some degree. Our GGL method can also integrate supervised learning methods to further improve accuracy. Experiments show that our method outperforms existing methods on proteins without thousands of sequence homologs, and that our method performs better on both conserved and family-specific contacts.
Availability and implementation: See http://raptorx.uchicago.edu/ContactMap/ for a web server implementing the method.
Contact: j3xu@ttic.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism
Authors: Yang Jing , Wu Su-Juan , Li Yi-Xue , Li Yuan-Yuan 
Published: August 2015

Abstract
Summary: Elucidation of human disease similarities has provided new insights into etiology, disease classification and drug repositioning. Since dysfunctional regulation would be manifested as the decoupling of expression correlation, disease similarity (DS) in terms of dysfunctional regulation mechanism (DRM) could be estimated by using a differential coexpression based approach, which is described in a companion paper. Due to the lack of tools for estimating DS from the viewpoint of DRM in public domain, we implemented an R package ‘DSviaDRM’ to identify significant DS via DRM based on transcriptomic data. DSviaDRM contains five easy-to-use functions, DCEA, DCpathway, DS, comDCGL and comDCGLplot, for identifying disease relationships and showing common differential regulation information shared by similar diseases.
Availability and implementation: DSviaDRM is available as an R package, with a user’s guide and source code, at http://cran.r-project.org/web/packages/DSviaDRM/index.html.
Contact: yyli@scbit.org or yxli@scbit.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Determining conserved metabolic biomarkers from a million database queries
Authors: Kurczy Michael E. , Ivanisevic Julijana , Johnson Caroline H. , Uritboonthai Winnie , Hoang Linh , Fang Mingliang , Hicks Matthew , Aldebot Anthony , Rinehart Duane , Mellander Lisa J. , Tautenhahn Ralf , Patti Gary J. , Spilker Mary E. , Benton H. Paul , Siuzdak Gary 
Published: August 2015

Abstract
Motivation: Metabolite databases provide a unique window into metabolome research allowing the most commonly searched biomarkers to be catalogued. Omic scale metabolite profiling, or metabolomics, is finding increased utility in biomarker discovery largely driven by improvements in analytical technologies and the concurrent developments in bioinformatics. However, the successful translation of biomarkers into clinical or biologically relevant indicators is limited.
Results: With the aim of improving the discovery of translatable metabolite biomarkers, we present search analytics for over one million METLIN metabolite database queries. The most common metabolites found in METLIN were cross-correlated against XCMS Online, the widely used cloud-based data processing and pathway analysis platform. Analysis of the METLIN and XCMS common metabolite data has two primary implications: these metabolites, might indicate a conserved metabolic response to stressors and, this data may be used to gauge the relative uniqueness of potential biomarkers.
Availability and implementation. METLIN can be accessed by logging on to: https://metlin.scripps.edu
Contact: siuzdak@scripps.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Drivers of information disclosure on health information exchange platforms: insights from an exploratory empirical study
Authors: Yaraghi Niam , Sharman Raj , Gopal Ram , Singh Ranjit , Ramesh R 
Published: August 2015

Abstract
Objective The objective of this research is to empirically explore the drivers of patients’ consent to sharing of their medical records on health information exchange (HIE) platforms.
Materials and Methods The authors analyze a dataset consisting of consent choices of 20 076 patients in Western New York. A logistic regression is applied to empirically investigate the effects of patients’ age, gender, complexity of medical conditions, and the role of primary care physicians on patients’ willingness to disclose medical information on HIE platforms.
Results The likelihood of providing consent increases by age (odds ratio (OR) = 1.055; P  &lt; .0001). Female patients are more likely to provide consent (OR = 1.460; P  = .0003). As the number of different physicians involved in the care of the patient increases, the odds of providing consent slightly increases (OR = 1.024; P  = .0031). The odds of providing consent is significantly higher for the patients whom a primary care physician has been involved in their medical care (OR = 1.323; P  &lt; .0001).
Conclusion Individual-level characteristics are important predictors of patients’ willingness to disclose their medical information on HIE platforms.
Are Staphylococcus intermedius Infections in Humans Cases of Mistaken Identity? A Case Series and Literature Review
Authors: Viau Roberto , Hujer Andrea M. , Hujer Kristine M. , Bonomo Robert A. , Jump Robin L.P. 
Published: August 2015

Abstract
Staphylococcus intermedius and Staphylococcus pseudintermedius are difficult to distinguish using conventional microbiological methods. Molecular diagnostic tools change our understanding of the epidemiology of these 2 organisms. In this study, we present (1) a detailed review of the current literature on molecular diagnostics and (2) a case series in which misidentification was proven in 1 case. We conclude that S pseudintermedius is a more common human pathogen than previously recognized.
Population-Based Surveillance of Neisseria meningitidis Antimicrobial Resistance in the United States
Authors: Harcourt Brian H. , Anderson Raydel D. , Wu Henry M. , Cohn Amanda C. , MacNeil Jessica R. , Taylor Thomas H. , Wang Xin , Clark Thomas A. , Messonnier Nancy E. , Mayer Leonard W. 
Published: August 2015

Abstract
Background.  Antimicrobial treatment and chemoprophylaxis of patients and their close contacts is critical to reduce the morbidity and mortality and prevent secondary cases of meningococcal disease. Through the 1990's, the prevalence of antimicrobial resistance to commonly used antimicrobials among Neisseria meningitidis was low in the United States. Susceptibility testing was performed to ascertain whether the proportions of isolates with reduced susceptibility to antimicrobials commonly used for N meningitidis have increased since 2004 in the United States.
Methods.  Antimicrobial susceptibility testing was performed by broth microdilution on 466 isolates of N meningitidis collected in 2004, 2008, 2010, and 2011 from an active, population-based surveillance system for susceptibility to ceftriaxone, ciprofloxacin, penicillin G, rifampin, and azithromycin. The molecular mechanism of reduced susceptibility was investigated for isolates with intermediate or resistant phenotypes.
Results.  All isolates were susceptible to ceftriaxone and azithromycin, 10.3% were penicillin G intermediate (range, 8% in 2008–16.7% in 2010), and &lt;1% were ciprofloxacin, rifampin, or penicillin G resistant. Of the penicillin G intermediate or resistant isolates, 63% contained mutations in the penA gene associated with reduced susceptibility to penicillin G. All ciprofloxacin-resistant isolates contained mutations in the gyrA gene associated with reduced susceptibility.
Conclusions.  Resistance of N meningitidis to antimicrobials used for empirical treatment of meningitis in the United States has not been detected, and resistance to penicillin G and chemoprophylaxis agents remains uncommon. Therapeutic agent recommendations remain valid. Although periodic surveillance is warranted to monitor trends in susceptibility, routine clinical testing may be of little use.
Operative Intervention of Supracondylar Humerus Fractures More Complicated in July: Analysis of the July Effect
Authors: Bagsby Deren T. , Loder Randall T. , Myung Karen 
Published: August 2015

Background:
The “July Effect” involves the influx of new interns and residents early in the academic year (July and August), which may have greater potential for poorer patient outcomes. Current orthopaedic literature does not demonstrate the validity of this concept in arthroplasty, spine, hand, and arthroscopy. No study has investigated the possibility of this effect on common pediatric orthopaedic procedures, such as closed reduction and percutaneous pin fixation of supracondylar humerus fractures.

Methods:
A retrospective review of all type II or III supracondylar humerus fractures that underwent primary closed reduction and percutaneous pin fixation (CPT code 24538) at a single pediatric level 1 trauma center from July 2009 to June 2013. Patients were grouped according to time in the academic year: early (July and August) and late (May and June). Demographic data included length of follow-up, age at surgery, sex, side of injury, and Wilkin’s modified Gartland classification. Outcomes included length of operation, number of pins used, length of stay, complications, and the need for repeat surgery.

Results:
There were 245 patients, 101 in the early and 144 in the late group. There was no increase in surgical time [33.32±24.74 (early) vs. 28.63±10.06 (late) min, P=0.07) or complication rates [7.0% (early) vs. 2.1% (late), P=0.06) between the early and the late groups. Cases performed with junior residents demonstrated longer operative (31.72±17.07 vs. 28.96±18.71 min, P=0.02) and fluoroscopy (48.63±30.96 vs. 34.12±27.38 s, P=0.01) times.

Conclusions:
The academic orthopaedic surgeon must ensure the education of residents, while providing the highest level of safety to patients. Our study shows that education of young residents early in the academic year results in no increase in operative times, radiation exposure, or complications.

Level of Evidence:
Level III.