bluuebunny/crossref_metadata_2025 huggingface dataset:
Pronominal datives
Authors: Ariel Mira , Dattner Elitzur , Du Bois John W. , Linzen Tal
Published: August 2015

Based on a large corpus of dative constructions in Hebrew, we propose that dative-marked pronominals manifest a facilitated path from adjunct to argument. Since datives tend to be pronominal, adding them onto existing argument structures avoids a clash with the Preferred Argument Structure (PAS) Quantity constraint against more than one lexical noun phrase per clause. Supporting a more fluid adjunct/argument distinction, our first claim is that different Hebrew datives are grammaticized as arguments to different degrees. We then demonstrate a correlation between the degree of grammaticization of the dative as an argument and pronoun/lexical ratios. We show that incipient grammaticization phases involve virtually exclusive use of pronominal datives, but deeper grammaticization phases allow increased use of lexical nouns, within the constraints of PAS. Thus, it is pronouns that blaze the path from adjunct to argument status.
Coherence relation and clause linkage
Authors: Jin Dawei
Published: August 2015

Abstract This paper proposes that adjunct island effects (Ross, 1967; Cattell, 1976) receive a discourse-semantic explanation. The exact formulation of this explanation builds upon previous work (e.g. Kehler, 2002) on island effects of conjuncts (Ross, 1967), which explains asymmetrical extraction from coordinate structures in English (that is, violations of the coordinate structure constraint) in terms of certain coherence relations (Hobbs, 1979). I show that asymmetric extraction from adjuncts in Chinese (that is, violations of the adjunct island constraint) is also sensitive to coherence relations. I argue that such similarities exist because coherence relations may be expressed by either a coordinative or a subordinative structure, and the variation in the syntactic realizations of coherence relations can be characterized through an independently motivated interclausal relations hierarchy that governs the mapping between semantics and syntactic linkage (van Valin, 2005).
Limit shapes, real and imagined
Authors: Okounkov Andrei
Published: August 2015

This is an introductory discussion of limit shapes, in particular for random partitions and stepped surfaces, and of their applications to supersymmetric gauge theories.
The Consolation of Boethius as Poetic Liturgy
Authors: Blackwood Stephen
Published: August 2015

This book argues that the metres of Boethius’ Consolation of Philosophy are arranged in patterns that have a therapeutic and liturgical purpose. The argument moves from an examination of the prosodical interplay of metre, meaning, and sound in the Consolation’s first seven poems; to a consideration of the therapeutic use of the same metre in different poems; to the discovery and exploration of an intricate system of metric repetition that comprehends every poem; and finally, to reflection on how this acoustic system shapes the listener’s memory to an intelligible design. It is argued that the metres enable a bodily mediation of the text’s consolation, in which, by repetition and meditation, the hearer comes to discern the eternal in the movement of time.
Modernity, Faith, and the City
Authors: Strhan Anna
Published: August 2015

This chapter examines the growing scholarly interest in urban religion, situating this in relation to the contemporary analytical significance of cities as sites where processes of social change, such as globalization, transnationalism, and the influence of new media technologies, materialize in interrelated ways. The chapter argues that Georg Simmel’s writing on cities offers resources to draw out further the significance of ‘the urban’ in this emerging field. It brings together Simmel’s urban analysis with his approach to religion, focusing on Christianities and individuals’ relations with sacred figures, and suggests that this opens up a new approach to how forms of religious practice respond to experiences of cultural fragmentation in complex urban environments. This provides a lens through which to analyse the extent to which conservative evangelical faith offers a creative response to conditions of cultural and subjective fragmentation in an urban context.
Speaking Subjects
Authors: Strhan Anna
Published: August 2015

This chapter outlines how ideals for evangelistic speaking are promoted at St John’s. It shows how the church leaders aim to encourage a habitus through which the congregants feel compassion for and a sense of distinction from others around them in the city, and develop the desire to speak ‘publicly’ about their faith in the workplace and in other social spaces. The chapter then describes how individuals often struggle with this, revealing how their subjectivities are formed through the complex interaction of behavioural norms associated with different social spaces they inhabit. As they become conscious of tensions in their logics of practice shaped through their simultaneous inhabiting of differentiated social spaces suffused with differing moral norms, they narrate their subjective fragmentation according to biblical narratives of guilt and sin. This enables them to draw these fragments together into an overall pattern of meaning that shapes their sense of self.
Conclusion
Authors: Strhan Anna
Published: August 2015

The concluding chapter situates the book’s argument about experiences of fragmentation, desires for coherence, and the struggles of everyday life in relation to broader debates about how forms of religious practice encourage particular responses to and acknowledgement of disappointment, disjunction, and the tragic conditions of life and culture. It summarizes the argument of the book’s preceding chapters, and suggests future directions for research in relation to questions of ethical subjectivity, everyday urban life, religious intersubjectivity, and techniques of the self. It concludes by addressing the role of transcendental and utopian elements in moral thinking, motivation, and desire, and how these shape both the everyday realities of religious lives and the stories people tell about their engagements with others.
Mechanical Resonators
Authors: Le Bot A.
Published: August 2015

This chapter presents the theory of mechanical resonators randomly excited by white noise forces. The question of the equality of kinetic and elastic energies (locally and globally) is first examined. The notion of weak coupling is next introduced. The power exchanged between resonators is calculated in terms of difference of their vibrational energies.
Modal Densities
Authors: Le Bot A.
Published: August 2015

The sequences of natural frequency are exhibited for various examples in structural vibration and acoustics. The asymptotic relationships of modal densities are then derived in, respectively, dimensions one, two, and three. The effect of boundaries and some correcting terms for the most common boundary conditions are also discussed.
Energy Path
Authors: Le Bot A.
Published: August 2015

This chapter outlines the question of the path of energy propagation from a source to a receiver. The notion of path efficiency is introduced progressively by studying several simple examples. The problem of path classification is examined and the general properties of path decomposition are reviewed.
Introduction
Authors: Progovac Ljiljana
Published: August 2015

This chapter introduces the reader to the basic arguments of this book, as well as to the reconstruction method to be followed, foreshadowing the arguments and achievements of the rest of the book. It also talks briefly about other approaches to the evolution of syntax, including the gradualist approach pursued in Jackendoff (1999, 2002), and the saltationist approach pursued in Berwick and Chomsky (2011). This chapter shows how the proposal in this book builds on the previous gradualist approaches, and how it distinguishes itself from them. The main point of departure from all the other approaches is that this book offers a detailed identification and illustration of each postulated proto-syntactic stage, based on a precise reconstruction method, according to which each stage literally serves as a scaffolding upon which the next stage is constructed.
Made in Africa
Authors: Oqubay Arkebe
Published: August 2015

This book presents the findings of original field research into the design, practice, and varied outcomes of industrial policy in three sectors in Ethiopia, covering export-oriented and import-substitution industries. The three sectors are cement, leather and leather products, and floriculture. Given that there is a single industrial strategy, why do its outcomes vary across sectors? To what extent is this a function of the specific market and political economy features of each sector? The book examines industrial structures and associated global value chains to demonstrate the challenges faced by African firms in international markets. Part of the book’s relevance is the light it throws on the whole question of industrial policy in low-income countries, the subject of renewed discussion among development economists and organizations in recent years. The findings are also discussed in the light of the history of, and the history of thought about, industrialization. Insights for researchers and policymakers emerge from the analysis of failures and successes in the three industrial sectors. The book also challenges prevailing wisdom on how much and what kind of state intervention is required to support transformational industrial policy in Africa. Among other things, the book highlights the significance for policy design of maximizing linkage effects, backward and forward, from particular industries and activities.
Cementing Development? Uneven Development in an Import-Substitution Industry
Authors: Oqubay Arkebe
Published: August 2015

This chapter provides a sector-specific analysis of the uneven development of cement production—a strategic import-substitution industry driven by and contributing to the growth of the domestic market. The industry has acted as a binding agent of economic development and transformation. It has undergone major changes in the period under consideration, growing faster than in most developing countries. The chapter also examines the industrial structure, linkage effects, policy instruments, and institutions of the sector. In sharp contrast to the overall domination by multinationals of the African cement industry, domestically owned firms continue to dominate the industry in Ethiopia. The analysis explores the role that government policy has played through direct and indirect interventions. It probes the successes and failures in policymaking and asks what learning experiences there have been in the cement sector, given the high-risk trade-offs involved in a context of very scarce resources.
The Last Project
Authors: Francis Kimberly A.
Published: August 2015

This chapter marks the beginning of the end for Stravinsky and Boulanger’s creative dialogue. It addresses Boulanger’s complicated connection to the events surrounding Stravinsky’s opera The Rake’s Progress—her joy at its premiere at the Venice Biennale and her frustration at being so distant from its creator. In an effort to aid in its European reception, Boulanger worked to secure performances and send reviews of French productions to Stravinsky. She became involved in the translation of the work into French, and was also the recipient of three volumes of Stravinsky’s summary sketches for the opera. The chapter then places Stravinsky’s reactions to Boulanger’s work alongside a discussion of the influence of Robert Craft, Stravinsky’s amanuensis and advisor post 1946. It also considers changing perceptions of Boulanger’s power as a cultural agent, particularly from the vantage point of postwar America.
An Introduction
Authors: Rajendran Aneeta
Published: August 2015

Narratives of homosexual experience that escape the ‘alternormativity’ of ‘out-ness’ that is often the unspoken basis of much mainstream LGBT political work today can be found in a number of South Asian subcontinental spaces and discourses. These queer, (un)familiar subjectivities, as this chapter calls them, are liable to be missed altogether if one privileges visibility over all else. This project looks for the lesbian un/familiar within the ‘realms’ of familiar space, of home, family, nation and diaspora, in postcolonial India, finding her not only in the ‘lesbian’ coming-out story, but in a multitude of narratives where being female and homosexual is one aspect of subjecthood. Adopting an intersectional analysis, it locates (un)familiar feminine engagements with the normative within a penumbra of intersections of caste, gender, space, race and sexuality. This chapter lays out the potentials this (un)familiar feminine has for exploding normative narrativizations of family, nation, diaspora, citizenship and sexual selving.
Conclusions
Authors: Rajendran Aneeta
Published: August 2015

This book has analysed through the rubric of the (un)familiar different constructions of queerness available to female protagonists in texts generated in South Asia and its diaspora. Imagining queerness not as absolute ‘other’ to heterosexuality, this book in conclusion re-states how the (un)familiar is both a space and an identity wherein productive but quotidian quarrels with heteronormativity may be had and are had in non-Western and/or hybridized worlds. These quarrels, however, will not be visible to an analytic that privileges ‘outness’ or stable ‘modern’ lesbian identity. Rather, this book suggests that queerness seen as unfamiliarity penetrates the familiar so thoroughly, destabilizing heteronormativity not through meta-moments of visibilized conflict, but through everyday small practices of resistance capable of performing the political work that transforms heteronormative/homophobic violence and discrimination when read thus through a prism of (un)familiarity.
A short history of English epistemic indefinites
Authors: Slade Benjamin
Published: August 2015

In 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

This 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

Chapter 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

Chapter 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

Chapter 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

This 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

This 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

This 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

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

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>r∗ to r<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

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

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

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

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

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

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  < .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  < .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

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

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 <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.
The Use of an “Internal Fixator Technique” to Stabilize Pathologic Fractures Developing Secondary to Osteomyelitis
Authors: Yildirim Azad , Kapukaya Ahmet , Atiç Ramazan , Mertsoy Yilmaz , Yiğit Şehmus , Çaçan Mehmet A. , Alemdar Celil
Published: August 2015

Background:

There is no consensus on the materials and the techniques to use in fixing pathologic fractures secondary to osteomyelitis. This study reports the results of the fixation of pathologic fractures secondary to osteomyelitis using the “internal fixator technique.”

Methods:

The internal fixator technique was performed on 11 children and adolescents with fractures secondary to osteomyelitis between 2003 and 2010. A retrospective chart review was conducted to record the following: age, sex, the anatomic region of infection, the time delay from symptom onset to fracture, the classification of chronic osteomyelitis, the Cierny-Mader classification, the causative organism, surgeries, the length of hospitalization, the location and the pattern of fracture, the duration of infection, the length of follow-up, and complications.

Results:

The patients included 7 male and 4 female patients with a mean age of 8.7 (range, 6 to 13) years. Pathologic fractures were as follows: 7 femur and 4 tibia. Nine of them were in the metaphysis and 2 others were located in the diaphysis. The time delay from symptom onset to fracture was 3.36 (1 to 9) months. The anatomic region of infection was the diaphysis in 2 cases and the metaphysis in 9 cases. Fractures patterns were short oblique and transverse. The length of hospitalization was a mean of 7 days. The duration of infection ranged from 1 to 12 (mean, 4.38) months. The mean duration of follow-up was 57.09 (range, 36 to 73) months from the initial presentation. Only 2 patients developed shortening, for which no additional intervention was performed.

Conclusions:

This case series demonstrates that the “internal fixator technique” is an acceptable alternative to the management of pathologic fractures of the femur or the tibia in children and adolescents with unresolved acute and chronic osteomyelitis. Infections were resolved in all cases and fractures were sufficiently stabilized to allow union with a low complication rate.

Level of Evidence:

Level IV—therapeutic.
The Fate of DDH Hips Showing Cartilaginous or Fibrous Tissue-filled Joint Spaces Following Primary Reduction
Authors: Kim Hui Taek , Lee Tae Hoon , Ahn Tae Young , Jang Jae Hoon
Published: August 2015

Background:

Because the use of magnetic resonance imaging is still not universal for the patients with developmental dysplasia of the hip patients, orthopaedists do not generally distinguish widened joint spaces which are “empty” after primary treatment (and therefore still reducible), from those which are filled and much more difficult to treat. To date no studies have focused on the latter hips. We treated and observed the outcomes for 19 hips which showed filled joint spaces after primary treatment.

Methods:

We retrospectively reviewed 19 cases of developmental dysplasia of the hip: (1) who showed a widened joint space on radiographs after primary treatment; and (2) whose magnetic resonance imaging showed that the widened joint space was accompanied by acetabular cartilage hypertrophy and/or was filled with fibrous tissues. All patients were over 1 year old at the time of primary reduction (reduction was closed in 4 patients, open in 6, and open with pelvic osteotomy in 9). Thirteen patients received at least 1 secondary treatment. Final results were classified using a modified Severin classification.

Results:

Final outcomes were satisfactory in 10 (52.6%) and unsatisfactory in 9 (47.4%). The widened joint spaces gradually filled with bone, resulting in a shallow acetabulum in the patients with unsatisfactory results. Of 9 patients who underwent combined pelvic osteotomy at the time of primary reduction, results were satisfactory in 6 (66.7%), whereas all patients who had only closed or open primary reduction had unsatisfactory results.

Conclusions:

Combined pelvic osteotomy at the time of primary reduction is advisable in hips with widened joint spaces. However, hips with filled joint spaces after primary treatment often have unsatisfactory results even after additional pelvic and/or femoral osteotomy.

Level of Evidence:

Level IV—prognostic study.
Reliable Change Estimates for Assessing Recovery From Concussion Using the ANAM4 TBI-MIL
Authors: Haran F. J. , Alphonso Aimee L. , Creason Alia , Campbell Justin S. , Johnson Dagny , Young Emily , Tsao Jack W.
Published: August 2015

Objective:

To establish the reliable change parameters for the Automated Neuropsychological Assessment Metrics (ANAM) using a healthy normative sample of active duty service members (SMs) and apply the parameters to sample of recently deployed SMs.

Methods:

Postdeployment neurocognitive performance was compared in 1893 US Marines with high rates of combat exposure during deployment. Of the sample, 289 SMs had data for 2 predeployment assessments and were used as a normative subsample and 502 SMs had data for predeployment and postdeployment assessments and were used as a deployed subsample. On the basis of self-report, the deployed subsample were further classified as concussed (n = 238) or as nonconcussed controls (n = 264). Reliable change parameters were estimated from the normative sample and applied data for both deployed groups. Postdeployment performance was quantified using a general linear model (2 group × 2 time) multivariate analysis of variance with repeated measures.

Results:

Both deployed groups demonstrated a pattern of meaningful decreases in performance over time.

Conclusions:

Information from this effort, specifically the reliable change parameters and the base rates of reliable decline, can be used to assist with the identification of postdeployment cognitive issues.
Self-Reported Traumatic Brain Injury, Health and Rate of Chronic Multisymptom Illness in Veterans From the 1990-1991 Gulf War
Authors: Yee Megan K. , Seichepine Daniel R. , Janulewicz Patricia A. , Sullivan Kimberly A. , Proctor Susan P. , Krengel Maxine H.
Published: August 2015

Background:

Traumatic brain injury (TBI) was not considered to be common in the 1990-1991 Gulf War (GW). Therefore, the relationship between TBI and chronic health symptoms experienced by GW veterans is unknown. Health symptoms reported by veterans deployed more recently to this region (Operations Enduring and Iraqi Freedom) are similar to those of GW veterans and have been primarily attributed to TBI.

Objective:

To examine the relationships among self-reported TBI, health symptoms, chronic multisymptom illness (CMI), and health-related quality of life among GW veterans.

Participants:

Participants included 1 274 GW veterans from the Devens Cohort Study, 156 of whom self-reported a history of TBI (12.2% of the sample).

Design:

Cross-sectional retrospective analysis of existing survey data.

Main Measures:

A 52-item health symptom checklist and the RAND 36-Item Health short Form Survey.

Results:

Self-reported TBI in GW Veterans is related to increased rates of health symptoms, CMI, and poorer health-related quality of life.

Conclusions:

Gulf War veterans' self-reported exposure to TBI is related to increased rates of chronic health symptoms and CMI, which interfere with everyday activities of daily living.
Evidence-Based Practice for the Use of Internal Strategies as a Memory Compensation Technique After Brain Injury: A Systematic Review
Authors: O'Neil-Pirozzi Therese M. , Kennedy Mary R.T. , Sohlberg McKay M.
Published: August 2015

Objective:

To complete a systematic review of internal memory strategy use with people who have brain injury and provide practitioners with information that will impact their clinical work.

Methods:

A systematic literature search to identify published intervention studies that evaluated an internal memory strategy or technique to improve memory function of individuals with brain injury. Relevant data from reviewed articles were coded using 4 clinical questions targeting participants, interventions, research methods, and outcomes.

Results:

A comprehensive search identified 130 study citations and abstracts. Forty-six met inclusion/exclusion criteria and were systematically reviewed. Visual imagery was most frequently studied, in isolation or in combination with other internal strategies. Despite significant variability in research methods and outcomes across studies, the evidence provides impetus for use of internal memory strategies with individuals following brain injury.

Conclusions:

Individuals with traumatic brain injury may benefit from internal memory strategy use, and clinicians should consider internal memory strategy instruction as part of intervention plans. Further research needs to better delineate influences on intervention candidacy and outcomes.
Impact of Gender-Specific Human Papillomavirus Vaccine Recommendations on Uptake of Other Adolescent Vaccines: Analysis of the NIS-Teen (2008-2012)
Authors: Bednarczyk Robert A. , Orenstein Walter A. , Omer Saad B.
Published: August 2015

In the United States, human papillomavirus vaccination was routinely recommended for adolescent females in 2006 and provisionally recommended for adolescent males in 2009. We evaluated the hypothesis that gender-specific human papillomavirus vaccination recommendations would impact gender-specific uptake of other vaccines using National Immunization Survey-Teen public use data sets (2008-2012). Female adolescents had higher coverage than males of at least 1 other adolescent vaccine in 2008 (3.0% higher) and 2009 (4.3% higher). Gender differences abated in 2010, 2011, and 2012 (0.2%, 0.9%, and 0.4%, respectively). To evaluate unintended consequences of gender-based recommendations, countries with female-only human papillomavirus vaccination recommendations should evaluate gender-specific uptake of other adolescent vaccines.