bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing an ontology and database of Japanese lexical properties
Authors: Joyce Terry , Hodošček Bor , Masuda Hisashi 
Published: October 2017

Abstract
As a significant milestone within ongoing efforts to construct a comprehensive database in the form of a lexical resource (LR) of Japanese Lexical Properties (JLP-LR), this paper outlines the initial construction of an Ontology of Japanese Lexical Properties (JLP-O) (Joyce & Hodošček 2014), and, in particular, describes some of its key aspects specifically incorporated in order to satisfactorily handle the orthographic complexity of the Japanese writing system (Joyce 2013, 2016; Joyce, Hodošček & Nishina 2012). While motivated primarily by issues of orthographic representation for the Japanese lexicon, these key features potentially have wider implications for the effective construction of integrated orthographic databases and lexicons.
The BasisSpellingBank
Authors: Zuidema Johan , Neijt Anneke 
Published: October 2017

Abstract
The BasisSpellingBank is the first lexicon where the spellings and pronunciations of words are documented explicitly and separately for all relevant word parts. Unlike earlier descriptions of Dutch orthography in terms of rules and underlying forms, the BasisSpellingBank departs from the concept of storage and the way spelling is taught in schools. At its core are triplets of phoneme(s), grapheme(s), and the spelling category(s) which describe the correspondences between them. The triplet notation provides a detailed, exhaustive description of Dutch orthography. It is a formal system that could be used to describe other alphabetic writing systems as well. By integrating information about orthographic rules and lexical storage, the triplet notation more adequately describes the knowledge possessed by fluent users. The triplets unlock exact measures of both forward and backward consistency, which opens up detailed analyses of spelling performance. The database provides new insights into spelling education and spelling complexity.
STRESYL
Authors: Sulpizio Simone , Spinelli Giacomo , Burani Cristina 
Published: October 2017

AbstractDuring the last few decades, empirical research on reading has shown increasing interest in syllable units. More recently, stress assignment has become a particular focus of interest. The relation between syllables and stress, however, has yet to be investigated for Italian. In this paper, we describe a new database, STRESYL, that can help researchers to investigate the relation between syllables and stress in Italian. STRESYL offers type and token measures relating stress information to syllable units, both in terms of syllable forms and syllabic structures.
MicroRNA expression and implications for infectious diseases in livestock.
Authors: Taxis T. M. , Casas E. 
Published: October 2017

Abstract
Animal diseases are a significant source of lost revenue in livestock production systems. Reduction and control of diseases has traditionally been done under three management programs: eradication by test and slaughter, vaccination, and use of antibiotics. However, inadequate efficacy of vaccines and restrictions on the use of antibiotics in several countries have prompted the need to develop improved and novel methodologies to identify disease exposure and potentially implement intervention strategies to control various diseases. MicroRNAs (miRNAs) are small non-coding RNA molecules that have been proposed as biomarkers for disease in livestock. MiRNAs function by blocking protein translation, or through direct degradation of messenger RNA. As a result, miRNAs have been widely studied in humans, and their role in animal disease is now being assessed. This review encompasses a summary of miRNAs involved in animal diseases where miRNAs have been explored. This includes miRNAs associated with diseases in cattle, pigs, sheep and poultry. Reliability is necessary to propose a miRNA as a biomarker associated with a specific disease in any given livestock species. Results from the reviewed publications have identified miRNAs associated with the innate immune system; however, further research is necessary to establish miRNAs that are consistently dysregulated for each disease. The regulation of miRNAs appears to be dependent on the livestock species and pathogen evaluated. As research in this area continues, specific miRNA profiles will need to be supported by other assessments to establish their potential use in veterinary medicine in terms of prevention, diagnosis, or treatment of a disease. The possibility and challenges of using these molecules as biomarkers in animal health is discussed in this review.
Rethinking class and culture in Africa: between E. P. Thompson and Pierre Bourdieu
Authors: Werbner Pnina 
Published: October 2017

ABSTRACT
The article considers the historiography of labour and class studies in sub-Saharan Africa in relation to the contemporary ‘cultural turn’ in sociological studies of class. It identifies three phases: from the 1960s, a highly empiricist Marxist approach which drew on Fanon’s notion of an aristocracy of labour; from the 1980s, a shift to a stress on culture, agency and identity, following E. P. Thompson; the final move has focused on the African middle classes, drawing on Pierre Bourdieu’s theory of consumption. Research on a public sector manual workers’ union in Botswana exemplifies, the author argues, the Thompsonian approach.
ThreaDNA: predicting DNA mechanics’ contribution to sequence selectivity of proteins along whole genomes
Authors: Cevost Jasmin , Vaillant Cédric , Meyer Sam 
Published: October 2017

Abstract

Motivation
Many DNA-binding proteins recognize their target sequences indirectly, by sensing DNA’s response to mechanical distortion. ThreaDNA estimates this response based on high-resolution structures of the protein–DNA complex of interest. Implementing an efficient nanoscale modeling of DNA deformations involving essentially no adjustable parameters, it returns the profile of deformation energy along whole genomes, at base-pair resolution, within minutes on usual laptop/desktop computers. Our predictions can also be easily combined with estimations of direct selectivity through a generalized form of position-weight-matrices. The formalism of ThreaDNA is accessible to a wide audience.

Results
We demonstrate the importance of indirect readout for the nucleosome as well as the bacterial regulators Fis and CRP. Combined with the direct contribution provided by usual sequence motifs, it significantly improves the prediction of sequence selectivity, and allows quantifying the two distinct physical mechanisms underlying it.

Availability and implementation
Python software available at bioinfo.insa-lyon.fr, natively executable on Linux/MacOS systems with a user-friendly graphical interface. Galaxy webserver version available.

Supplementary information
Supplementary data are available at Bioinformatics online.
Squeakr: an exact and approximate k-mer counting system
Authors: Pandey Prashant , Bender Michael A , Johnson Rob , Patro Rob 
Published: October 2017

Abstract

Motivation
k-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing data. These algorithms span the gamut of the analysis pipeline from k-mer counting (e.g. for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very different k-mer representations and data structures. In this article, we show how to build a k-mer-counting and multiset-representation system using the counting quotient filter, a feature-rich approximate membership query data structure. We introduce the k-mer-counting/querying system Squeakr (Simple Quotient filter-based Exact and Approximate Kmer Representation), which is based on the counting quotient filter. This off-the-shelf data structure turns out to be an efficient (approximate or exact) representation for sets or multisets of k-mers.

Results
Squeakr takes 2×–4.3× less time than the state-of-the-art to count and perform a random-point-query workload. Squeakr is memory-efficient, consuming 1.5×–4.3× less memory than the state-of-the-art. It offers competitive counting performance. In fact, it is faster for larger k-mers, and answers point queries (i.e. queries for the abundance of a particular k-mer) over an order-of-magnitude faster than other systems. The Squeakr representation of the k-mer multiset turns out to be immediately useful for downstream processing (e.g. de Bruijn graph traversal) because it supports fast queries and dynamic k-mer insertion, deletion, and modification.

Availability and implementation
https://github.com/splatlab/squeakr available under BSD 3-Clause License.

Supplementary information
Supplementary data are available at Bioinformatics online.
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins
Authors: Schad Eva , Fichó Erzsébet , Pancsa Rita , Simon István , Dosztányi Zsuzsanna , Mészáros Bálint 
Published: October 2017

Abstract

Motivation
Intrinsically Disordered Proteins (IDPs) mediate crucial protein–protein interactions, most notably in signaling and regulation. As their importance is increasingly recognized, the detailed analyses of specific IDP interactions opened up new opportunities for therapeutic targeting. Yet, large scale information about IDP-mediated interactions in structural and functional details are lacking, hindering the understanding of the mechanisms underlying this distinct binding mode.

Results
Here, we present DIBS, the first comprehensive, curated collection of complexes between IDPs and ordered proteins. DIBS not only describes by far the highest number of cases, it also provides the dissociation constants of their interactions, as well as the description of potential post-translational modifications modulating the binding strength and linear motifs involved in the binding. Together with the wide range of structural and functional annotations, DIBS will provide the cornerstone for structural and functional studies of IDP complexes.

Availability and implementation
DIBS is freely accessible at http://dibs.enzim.ttk.mta.hu/. The DIBS application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created.

Supplementary information
Supplementary data are available at Bioinformatics online.
Tropical Chow Hypersurfaces
Authors: Tripoli Paolo 
Published: October 2017

Abstract
Given a projective variety $X\subset\mathbb{P}^n$ of codimension $k+1$, the Chow hypersurface $Z_X$ is the hypersurface of the Grassmannian $\operatorname{Gr}(k, n)$ parametrizing projective linear spaces that intersect $X$. We introduce the tropical Chow hypersurface $\operatorname{Trop}(Z_X)$. This object only depends on the tropical variety $\operatorname{Trop}(X)$ and we provide an explicit way to obtain $\operatorname{Trop}(Z_X)$ from $\operatorname{Trop}(X)$. We also give a geometric description of $\operatorname{Trop}(Z_X)$. We conjecture that, as in the classical case, $\operatorname{Trop}(X)$ can be reconstructed from $\operatorname{Trop}(Z_X)$ and prove it for the case when $X$ is a curve in $\mathbb{P}^3$. This suggests that tropical Chow hypersurfaces could be the key to construct a tropical Chow variety.
Consumer and Object Experience in the Internet of Things: An Assemblage Theory Approach
Authors: Hoffman Donna L , Novak Thomas P 
Published: October 2017

AbstractThe consumer Internet of Things (IoT) has the potential to revolutionize consumer experience. Because consumers can actively interact with smart objects, the traditional, human-centric conceptualization of consumer experience as consumers’ internal subjective responses to branded objects may not be sufficient to conceptualize consumer experience in the IoT. Smart objects possess their own unique capacities and their own kinds of experiences in interaction with the consumer and each other. A conceptual framework based on assemblage theory and object-oriented ontology details how consumer experience and object experience emerge in the IoT. This conceptualization is anchored in the context of consumer-object assemblages, and defines consumer experience by its emergent properties, capacities, and agentic and communal roles expressed in interaction. Four specific consumer experience assemblages emerge: enabling experiences, comprising agentic self-extension and communal self-expansion, and constraining experiences, comprising agentic self-restriction and communal self-reduction. A parallel conceptualization of the construct of object experience argues that it can be accessed by consumers through object-oriented anthropomorphism, a nonhuman-centric approach to evaluating the expressive roles objects play in interaction. Directions for future research are derived, and consumer researchers are invited to join a dialogue about the important themes underlying our framework.
Immune Activation and Benefit From Avelumab in EBV-Positive Gastric Cancer
Authors: Panda Anshuman , Mehnert Janice M , Hirshfield Kim M , Riedlinger Greg , Damare Sherri , Saunders Tracie , Kane Michael , Sokol Levi , Stein Mark N , Poplin Elizabeth , Rodriguez-Rodriguez Lorna , Silk Ann W , Aisner Joseph , Chan Nancy , Malhotra Jyoti , Frankel Melissa , Kaufman Howard L , Ali Siraj , Ross Jeffrey S , White Eileen P , Bhanot Gyan , Ganesan Shridar 
Published: October 2017

Abstract
Response to immune checkpoint therapy can be associated with a high mutation burden, but other mechanisms are also likely to be important. We identified a patient with metastatic gastric cancer with meaningful clinical benefit from treatment with the anti–programmed death–ligand 1 (PD-L1) antibody avelumab. This tumor showed no evidence of high mutation burden or mismatch repair defect but was strongly positive for presence of Epstein-Barr virus (EBV) encoded RNA. Analysis of The Cancer Genome Atlas gastric cancer data (25 EBV+, 80 microsatellite-instable [MSI], 310 microsatellite-stable [MSS]) showed that EBV-positive tumors were MSS. Two-sided Wilcoxon rank-sum tests showed that: 1) EBV-positive tumors had low mutation burden (median = 2.07 vs 3.13 in log10 scale, P < 10-12) but stronger evidence of immune infiltration (median ImmuneScore 2212 vs 1295, P < 10-4; log2 fold-change of CD8A = 1.85, P < 10-6) compared with MSI tumors, and 2) EBV-positive tumors had higher expression of immune checkpoint pathway (PD-1, CTLA-4 pathway) genes in RNA-seq data (log2 fold-changes: PD-1 = 1.85, PD-L1 = 1.93, PD-L2 = 1.50, CTLA-4 = 1.31, CD80 = 0.89, CD86 = 1.31, P < 10-4 each), and higher lymphocytic infiltration by histology (median tumor-infiltrating lymphocyte score = 3 vs 2, P < .001) compared with MSS tumors. These data suggest that EBV-positive low–mutation burden gastric cancers are a subset of MSS gastric cancers that may respond to immune checkpoint therapy.
A progenitor model of SN 1987A based on the slow-merger scenario
Authors: Urushibata Takaki , Takahashi Koh , Umeda Hideyuki , Yoshida Takashi 
Published: October 2017

Abstract
Even after elaborate investigations spanning 30 years, it is still not understand how the progenitor of SN 1987A has evolved. In order to explain the unusual red-to-blue evolution, previous studies have suggested that in the red giant stage an increase either in the surface helium abundance or in the envelope mass was necessary. It is usually supposed that the helium enhancement is caused by rotational mixing, and that the mass increase is the result of a binary merger. We have thus investigated these scenarios thoroughly. We found that rotating single-star models do not satisfy all the observational constraints and that the enhancement of the envelope mass alone does not explain the observations. Here, we consider a slow-merger scenario in which both the helium abundance and the envelope mass enhancements are expected to occur. We show that most of the observational constraints, such as the red-to-blue evolution, lifetime, total mass and position in the Hertzsprung–Russell diagram at collapse, and the chemical anomalies are well reproduced by a merger model with 14 and 9 M⊙ stars. We also discuss the effects of the added envelope spin in the merger scenarios.
School Resource Officer Perceptions and Correlates of Work Roles
Authors: Rhodes Trisha 
Published: October 2017

Abstract
Officers assigned to schools are highly visible with many opportunities to communicate with citizens, though they are relatively isolated from other officers. School resource officers (SROs) are often expected to perform unconventional police roles, including counselling and teaching. Research is beginning to explore how SROs respond to different work settings and role expectations, which poses practical implications for how officers adapt and how they influence the lives of students, parents, and school staff. The present study first examined the work roles of SROs in a Midwestern region. Secondly, this study explored the relationships between SRO roles, individual characteristics, and school characteristics. SROs assigned to programmes in Nebraska, Kansas, Iowa, and Missouri were surveyed and a subset of 20 officers were interviewed and observed during their shifts. Findings showed SROs performed both conventional and non-conventional roles. Multivariate analyses revealed SROs in urban schools and high schools performed more conventional police tasks involving law enforcement and order maintenance, while SROs who supported community policing engaged in more service, mentoring, and teaching tasks. The results highlight areas to enhance community policing in schools, particularly through selection and training of SROs.
HIV Continuum of Care for Youth in the United States
Authors: Lally Michelle A. , van den Berg Jacob J. , Westfall Andrew O. , Rudy Bret J. , Hosek Sybil G. , Fortenberry J. Dennis , Monte Dina , Tanney Mary R. , McFarland Elizabeth J. , Xu Jiahong , Kapogiannis Bill G. , Wilson Craig M. ,   The Adolescent Medicine Trials Network for HIV/AIDS Interventions (ATN)
Published: October 2017

Background:
Beneficial HIV treatment outcomes require success at multiple steps along the HIV Continuum of Care. Youth living with HIV are a key population, and sites in the Adolescent Medicine Trials Network for HIV/AIDS Interventions (ATN) are known for modeling optimum HIV adolescent care.

Methods:
A longitudinal cohort study conducted at 14 network sites across the United States assessed how the later steps of the Continuum of Care were achieved among the youth: engagement, treatment, and viral load (VL) suppression. Youth aged 13–24 who were behaviorally infected with HIV and linked to care at an ATN-affiliated site were eligible to participate.

Results:
A total of 467 youth were enrolled and had 1 year of available data. Most were aged 22–24 (57%), male (79%), and black/non-Hispanic (71%). Most used alcohol (81%) and marijuana (61%) in the 3 months before enrollment, and 40% had a history of incarceration. Among this cohort of youth, 86% met criteria for care engagement; among these, 98% were prescribed antiretroviral therapy and 89% achieved VL suppression. Sustained VL suppression at all measured time points was found among 59% with initial suppression. Site characteristics were notable for the prevalence of adherence counseling (100%), case management (100%), clinic-based mental health (93%), and substance use (64%) treatment.

Conclusions:
Youth living with HIV in the United States can be successfully treated at health care sites with experience, excellence, and important resources and services. Sustained VL suppression may be an important step to add to the Continuum of Care for youth.
Discriminability of numerosity-evoked fMRI activity patterns in human intra-parietal cortex reflects behavioral numerical acuity
Authors: Lasne G. , Piazza M. , Dehaene S. , Kleinschmidt A. , Eger E. 
Published: October 2017

AbstractAreas of the primate intraparietal cortex have been identified as an important substrate of numerical cognition. In human fMRI studies, activity patterns in these and other areas have allowed researchers to read out the numerosity a subject is viewing, but the relation of such decodable information with behavioral numerical proficiency remains unknown.Here, we estimated the precision of behavioral numerosity discrimination (internal Weber fraction) in twelve adult subjects based on psychophysical testing in a delayed numerosity comparison task outside the scanner. FMRI data were then recorded during a similar task, to obtain the accuracy with which the same sample numerosities could be read out from evoked brain activity patterns, as a measure of the precision of the neuronal representation. Sample numerosities were decodable in both early visual and intra-parietal cortex with approximately equal accuracy on average. In parietal cortex, smaller numerosities were better discriminated than larger numerosities of the same ratio, paralleling smaller behavioral Weber fractions for smaller numerosities. Furthermore, in parietal but not early visual cortex, fMRI decoding performance was correlated with behavioral number discrimination acuity across subjects (subjects with a more precise behavioral Weber fraction measured prior to scanning showed greater discriminability of fMRI activity patterns in intraparietal cortex, and more specifically, the right LIP region).These results suggest a crucial role for intra-parietal cortex in supporting a numerical representation which is explicitly read out for numerical decisions and behavior.
Modeling neuron–glia interactions with theBrian 2simulator
Authors: Stimberg Marcel , Goodman Dan F. M. , Brette Romain , De Pittà Maurizio 
Published: October 2017

AbstractDespite compelling evidence that glial cells could crucially regulate neural network activity, the vast majority of available neural simulators ignores the possible contribution of glia to neuronal physiology. Here, we show how to model glial physiology and neuron-glia interactions in theBrian 2simulator.Brian 2offers facilities to explicitly describe any model in mathematical terms with limited and simple simulator-specific syntax, automatically generating high-performance code from the user-provided descriptions. The flexibility of this approach allows us to model not only networks of neurons, but also individual glial cells, electrical coupling of glial cells, and the interaction between glial cells and synapses. We therefore conclude thatBrian 2provides an ideal platform to efficiently simulate glial physiology, and specifically, the influence of astrocytes on neural activity.
Correlation structure of grid cells is preserved during sleep
Authors: Gardner Richard J. , Lu Li , Wernle Tanja , Moser May-Britt , Moser Edvard I. 
Published: October 2017

AbstractThe network of grid cells in the medial entorhinal cortex forms a fixed reference frame for mapping physical space. The mechanistic origin of the grid representation is unknown, but continuous attractor network (CAN) models explain multiple fundamental features of grid-cell activity. An untested prediction of CAN grid models is that the grid-cell network should exhibit an activity correlation structure that transcends behavioural or brain states. By recording from MEC cell ensembles during navigation and sleep, we found that spatial phase offsets of grid cells predict arousal-state-independent spike rate correlations. Similarly, state-invariant correlations between conjunctive grid-head-direction and pure head-direction cells were predicted by their head-direction tuning offsets. Spike rates of grid cells were only weakly correlated across modules, and module scale relationships disintegrated during slow-save sleep, suggesting that modules function as independent attractor networks. Collectively, our observations suggest that network states in MEC are expressed universally across brain and behaviour states.