bluuebunny/crossref_metadata_2025_split huggingface dataset:
Auditory Brainstem Implantation: An Overview
Authors: Deep Nicholas , Choudhury Baishakhi , Roland J. 
Published: February 2019

AbstractAn auditory brainstem implant (ABI) is a surgically implanted central neural auditory prosthesis for the treatment of profound sensorineural hearing loss in children and adults who are not cochlear implant candidates due to a lack of anatomically intact cochlear nerves or implantable cochleae. The device consists of a multielectrode surface array which is placed within the lateral recess of the fourth ventricle along the brainstem and directly stimulates the cochlear nucleus, thereby bypassing the peripheral auditory system. In the United States, candidacy criteria for ABI include deaf patients with neurofibromatosis type 2 (NF2) who are 12 years or older undergoing first- or second-side vestibular schwannoma resection. In recent years, several non-NF2 indications for ABI have been explored, including bilateral cochlear nerve avulsion from trauma, complete ossification of the cochlea due to meningitis, or a severe cochlear malformation not amenable to cochlear implantation. In addition, growing experience with ABI in infants and children has been documented with encouraging outcomes. While cochlear implantation generally remains the first-line option for hearing rehabilitation in NF2 patients with stable tumors or post hearing preservation surgery where hearing is lost but a cochlear nerve remains accessible for stimulation, an ABI is the next alternative in cases where the cochlear nerve is absent and/or if the cochlea cannot be implanted. Herein, we review ABI device design, clinical evaluation, indications, operative technique, and outcomes as it relates to lateral skull base pathology.
Social threat learning transfers to decision making in humans
Authors: Lindström Björn , Golkar Armita , Jangard Simon , Tobler Philippe N. , Olsson Andreas 
Published: February 2019

Significance
In today’s world, indirect exposure to threatening situations is more common than ever, as illustrated by footage of terror and disaster in social media. How do such social threat learning experiences shape our decisions? We found that learning about threats from both observation and verbal information strongly influenced decision making. As with learning from our own experience, this influence could be either adaptive or maladaptive depending on whether the social information provided accurate expectations about the environment. Our findings can help explain both adaptive and pathological behaviors resulting from the indirect exposure to threatening events.
The status of punctuation marks in Cognitive Grammar
Authors: Hamawand Zeki 
Published: February 2019

Abstract
This paper seeks to provide a new analysis of punctuation marks in English. To do so, it substantiates two claims of Cognitive
Grammar. One claim is that the meaning of a linguistic expression is best understood in terms of the domain to which it belongs.
In light of this claim, the paper argues that punctuation marks form sets in which they highlight similarities in general but
differences in specifics. The other claim is that the use of a linguistic expression is governed by the particular construal
imposed on its content. In view of this claim, the paper argues that the use of a punctuation mark stems from the particular
construal the speaker chooses to describe a situation. The occurrence of two or more punctuation marks gives rise to semantic
contrast, in which each mark represents a different construal, and so a different meaning. The aim of the analysis is to emphasise
the roles which punctuation marks play in the interpretation of sentences, namely in conveying meaning.
Foodsemic metaphors of love in Gĩkũyũ: Insights from cognitive semantics
Authors: Gathigia Moses Gatambuki , Orwenjo Daniel Ochieng , Ndungu Ruth Wangeci 
Published: February 2019

AbstractUsing the Conceptual Metaphor Theory, this study discusses the transfer of semantic aspects of foodsemic metaphors upon the abstraction of love. An interview schedule was administered to 48 respondents of different gender by the researchers assisted by two research assistants. The data collected were subjected to the Metaphor Identification ProcedureVrije Universiteit(MIPVU). 12 foodsemic metaphors which play an indispensable role in the understanding of love in Gĩkũyũ were identified. In addition, the study noted that gender is a dominant variable that provides people with lens through which they view love in Gĩkũyũ. This study concludes that metaphor is an integral component of the way people conceptualize and embody love in Gĩkũyũ. Further, foodsemic metaphors provide a way of understanding the nexus between gender and love in Gĩkũyũ.
A cross-linguistic study of metaphors of death
Authors: Gathigia Moses Gatambuki , Wang Ruiming , Shen Manqiong , Tirado Carlos , Tsaregorodtseva Oksana , Khatin-Zadeh Omid , Minervino Ricardo , Marmolejo-Ramos Fernando 
Published: February 2019

AbstractThe avoidance of directly addressing human mortality indicates fear of death. This fear elicits psychological, social and religious interdictions in language such that people resort to the use of metaphors to avoid confronting death. Under the premise that metaphor is a conceptual mapping from a concrete source to an abstract target domain, this study aims to identify and categorize euphemistic metaphors of death in six languages: Chinese, Farsi, Gĩkũyũ, Russian, Spanish, and Swedish. Those metaphors are interpreted via the Conceptual Metaphor Theory (CMT). In doing so, 40 speakers in each of the languages were asked to complete a short questionnaire. Various metaphors of death were identified in each language and categorized into four conceptual metaphors:death is a journey; death is the end; death is a rest; anddeath is a summons. The key finding is that the most common metaphor of death isdeath is a journey. This holds across linguistic groups regardless of gender and age factors. This study also discusses the role of embodied cognition theories in accounting for how metaphors of death are created and their role within cognition in general.
Mental models, (de)compressions, and the actor’s process in body-swap movies
Authors: Abdel-Raheem Ahmed 
Published: February 2019

AbstractThe body-swap comedy, where someone finds themselves inhabiting an entirely different body, is a well-established Hollywood tradition. Crucially, American filmmakers have tried every twist and contortion of this genre premise at a point or another over the past few decades. And yet, other countries, such as Egypt, Japan, and South Africa, seem to have just now put different spins on the theme. Nevertheless, this genre is under-theorized and under-explored. Drawing on insights from blending theory (Fauconnier and Turner 2002), mental models (van Dijk 2014), and the actor’s process as described by, among others, Stanislavsky (1995,2008) and Brecht (1964,1970), this article provides cognitively plausible answers to the perennial questions: What is so funny in body-swap films? How do spectators make sense of this genre? How do blending processes operate in body-swap movies? Do spectators “live in the blend?” What patterns of compression or decompression are at work in body-swap templates? Can humor be a strong determiner of moral-political cognition? And what connections can be drawn between acting and cognitive neuroscience? A discussion of English and Arabic examples (i) points to some of the cultural concepts involved in body-swap films, (ii) shows how conceptual blending in humorous films serves to both perpetuate and modify culturally relevant concepts, and (iii) highlights the necessity to expand the current scope in compression, embodiment and identity research. More generally, then, this article presents a new cognitive theory of how cinema, television, or theatre communicates meaning. The most important aim of this study is thus to contribute to the small but growing number of publications that use the cognitive sciences to inform scholarly and practical explorations in theatre and performance studies, as well as to the study of Arab theatre and cinema, which are among the most neglected subjects in the field.
Laughter and identity construction in political interviews
Authors: Kantara Argyro 
Published: February 2019

AbstractPrevious conversation analytic work on the use and function of laughter in broadcast talk has mostly focused on itsaffiliativeuse as response to something the participants had constructed as humorous (Eriksson 2009,2010;Ekström 2009,2011;Baym 2013). Fewer studies have focused on itsdisaffiliativeuse as a response to something that hasnotbeen constructed as humorous (Clayman 1992;Romaniuk 2009,2013a,2013b). This paper contributes to this second line of research by investigating the use of laughter by a specific politician, namely Alexis Tsipras, in interview openings in three out of four one-on-one election campaign interviews he gave during the 2012 double Greek general elections campaigns. I will argue that Alexis Tsipras’ laughter is not only disaffiliative, undermining the journalists’ questions and projecting either an evasive answer or a counterchallenge, but that it also establishes a “cool but assertive” persona for the ears of the overhearing electorate.
Childcare deserts and distributional disadvantages: the legacies of split childcare policies and programmes in Canada
Authors: Prentice Susan , White Linda A. 
Published: February 2019

AbstractEarly childhood education and care (ECEC) policies and services in Canada exhibit marked gaps in access, creating ‘childcare deserts’ and distributional disadvantages. Cognate family policies that support children and families, such as parental leave and child benefits, are also underdeveloped. This article examines the current state of ECEC services in Canada and the reasons behind the uncoordinated array of services and policy, namely, a liberal welfare state tradition that historically has encouraged private and market-based care, a comparatively decentralised federal system that militates against coordinated policy-making, and a welfare state built on gendered assumptions about care work. The article assesses recent government initiatives, including the federal 2017 Multilateral Framework on Early Learning and Child Care, concluding that existing federal and provincial initiatives have limited potential to bring about paradigmatic third-order change.
Compositional data network analysis via lasso penalized D-trace loss
Authors: Yuan Huili , He Shun , Deng Minghua 
Published: February 2019

AbstractMotivationWith the development of high-throughput sequencing techniques for 16S-rRNA gene profiling, the analysis of microbial communities is becoming more and more attractive and reliable. Inferring the direct interaction network among microbial communities helps in the identification of mechanisms underlying community structure. However, the analysis of compositional data remains challenging by the relative information conveyed by such data, as well as its high dimensionality.ResultsIn this article, we first propose a novel loss function for compositional data called CD-trace based on D-trace loss. A sparse matrix estimator for the direct interaction network is defined as the minimizer of lasso penalized CD-trace loss under positive-definite constraint. An efficient alternating direction algorithm is developed for numerical computation. Simulation results show that CD-trace compares favorably to gCoda and that it is better than sparse inverse covariance estimation for ecological association inference (SPIEC-EASI) (hereinafter S-E) in network recovery with compositional data. Finally, we test CD-trace and compare it to the other methods noted above using mouse skin microbiome data.Availability and implementationThe CD-trace is open source and freely available from https://github.com/coamo2/CD-trace under GNU LGPL v3.Supplementary informationSupplementary data are available at Bioinformatics online.
Bacterial Feature Finder (BaFF)—a system for extracting features overrepresented in sets of prokaryotic organisms
Authors: López-Ibáñez Javier , Martín Laura T , Chagoyen Mónica , Pazos Florencio 
Published: February 2019

Abstract

Motivation
The results of some experimental and computational techniques are given in terms of large sets of organisms, especially prokaryotic. While their distinctive features can provide useful data regarding specific phenomenon, there are no automated tools for extracting them.

Results
We present here the Bacterial Feature Finder web server, a tool to automatically interrogate sets of prokaryotic organisms provided by the user to evaluate their specific biological features. At the core of the system is a searchable database of qualitative and quantitative features compiled for more than 23 000 prokaryotic organisms. Both the input set of organisms and the background set used to calculate the enriched features can be directly provided by the user, or they can be obtained by searching the database. The results are presented via an interactive graphical interface, with links to external resources.

Availability and implementation
The web server is freely available at http://csbg.cnb.csic.es/BaFF. It has been tested in the main web browsers and does not require any especial plug-ins or additional software.

Supplementary information
Supplementary data are available at Bioinformatics online.
Higher Trough Vedolizumab Concentrations During Maintenance Therapy are Associated With Corticosteroid-Free Remission in Inflammatory Bowel Disease
Authors: Ungaro Ryan C , Yarur Andres , Jossen Jacqueline , Phan Becky L , Chefitz Ezra , Sehgal Priya , Kamal Kanika , Bruss Alexandra , Beniwal-Patel Poonam , Fox Caroline , Patel Amir , Bahur Bayda , Jain Anjali , Stein Daniel , Naik Snehal , Dubinsky Marla C 
Published: February 2019

Abstract

Background and Aims
Vedolizumab is an anti-α4β7 biologic approved for ulcerative colitis [UC] and Crohn’s disease [CD]. We aimed to examine the association of maintenance vedolizumab concentrations with remission.

Methods
We performed a cross-sectional multi-centre study of inflammatory bowel disease [IBD] patients on maintenance vedolizumab. A homogeneous mobility shift assay [HMSA] was used to determine trough serum concentrations of vedolizumab and anti-drug antibodies [ATVs]. The primary outcome was corticosteroid-free clinical and biochemical remission defined as a composite of clinical remission, normalized C-reactive protein [CRP] and no corticosteroid use in 4 weeks. Secondary outcomes included corticosteroid-free endoscopic and deep remission. Vedolizumab concentrations were compared between patients in remission and with active disease. Logistic regression, adjusting for confounders, assessed the association between concentrations and remission.

Results
In total, 258 IBD patients were included [55% CD and 45% UC]. Patients in clinical and biochemical remission had significantly higher vedolizumab concentrations [12.7 µg/mL vs 10.1 µg/mL, p = 0.002]. Concentrations were also higher among patients in endoscopic and deep remission [14.2 µg/mL vs 8.5 µg/mL, p = 0.003 and 14.8 µg/mL vs 10.1 µg/mL, p = 0.01, respectively]. After controlling for potential confounders, IBD patients with vedolizumab concentrations &gt;11.5 µg/mL were nearly 2.4 times more likely to be in corticosteroid-free clinical and biochemical remission. Only 1.6% of patients had ATVs.

Conclusions
In a large real-world cohort of vedolizumab maintenance concentrations, IBD patients with remission defined by objective measures [CRP and endoscopy] had significantly higher trough vedolizumab concentrations and immunogenicity was uncommon.
A Third Strike Against Perfect Phylogeny
Authors: Iersel Leo Van , Jones Mark , Kelk Steven 
Published: February 2019

AbstractPerfect phylogenies are fundamental in the study of evolutionary trees because they capture the situation when each evolutionary trait emerges only once in history; if such events are believed to be rare, then by Occam’s Razor such parsimonious trees are preferable as a hypothesis of evolution. A classical result states that 2-state characters permit a perfect phylogeny precisely if each subset of 2 characters permits one. More recently, it was shown that for 3-state characters the same property holds but for size-3 subsets. A long-standing open problem asked whether such a constant exists for each number of states. More precisely, it has been conjectured that for any fixed number of states $r$ there exists a constant $f(r)$ such that a set of $r$-state characters $C$ has a perfect phylogeny if and only if every subset of at most $f(r)$ characters has a perfect phylogeny. Informally, the conjecture states that checking fixed-size subsets of characters is enough to correctly determine whether input data permits a perfect phylogeny, irrespective of the number of characters in the input. In this article, we show that this conjecture is false. In particular, we show that for any constant $t$, there exists a set $C$ of $8$-state characters such that $C$ has no perfect phylogeny, but there exists a perfect phylogeny for every subset of at most $t$ characters. Moreover, there already exists a perfect phylogeny when ignoring just one of the characters, independent of which character you ignore. This negative result complements the two negative results (“strikes”) of Bodlaender et al. (1992,2000). We reflect on the consequences of this third strike, pointing out that while it does close off some routes for efficient algorithm development, many others remain open.
Genome-Wide CRISPR Screening Identifies the Tumor Suppressor Candidate OVCA2 As a Determinant of Tolerance to Acetaldehyde
Authors: Sobh Amin , Loguinov Alex , Stornetta Alessia , Balbo Silvia , Tagmount Abderrahmane , Zhang Luoping , Vulpe Chris D 
Published: February 2019

Abstract
Acetaldehyde, a metabolite of ethanol, is a cellular toxicant and a human carcinogen. A genome-wide CRISPR-based loss-of-function screen in erythroleukemic K562 cells revealed candidate genetic contributors affecting acetaldehyde cytotoxicity. Secondary screening exposing cells to a lower acetaldehyde dose simultaneously validated multiple candidate genes whose loss results in increased sensitivity to acetaldehyde. Disruption of genes encoding components of various DNA repair pathways increased cellular sensitivity to acetaldehyde. Unexpectedly, the tumor suppressor gene OVCA2, whose function is unknown, was identified in our screen as a determinant of acetaldehyde tolerance. Disruption of the OVCA2 gene resulted in increased acetaldehyde sensitivity and higher accumulation of the acetaldehyde-derived DNA adduct N2-ethylidene-dG. Together these results are consistent with a role for OVCA2 in adduct removal and/or DNA repair.
Evaluating the Concurrent Validity of PROMIS Physical Function in Anterior Cervical Discectomy and Fusion
Authors: Khechen Benjamin , Patel Dil V. , Haws Brittany E. , Cardinal Kaitlyn L. , Guntin Jordan A. , Ahn Junyoung , Singh Kern 
Published: February 2019

Study Design:
This study was a retrospective cohort analysis.

Objectives:
This study aims to evaluate the concurrent validity of Patient-Reported Outcomes Measurement Information System (PROMIS) Physical Function (PF) domain as compared with legacy measures of patient-reported outcomes (PROs) among patients undergoing anterior cervical discectomy and fusion (ACDF).

Summary of Background Data:
As PROMIS becomes increasingly utilized, it is important to assess its validity among procedure-specific populations.

Methods:
Patients undergoing a primary, 1–3 level ACDF were retrospectively identified from a prospectively maintained surgical registry. PROMIS PF and legacy PRO scores were obtained at preoperative, 6-week, 12-week, and 6-month postoperative visits. Legacy PROs included Neck Disability Index (NDI), Short Form-12 (SF-12) physical composite, Visual Analog Scale (VAS) neck pain, and VAS arm pain. Postoperative improvements in PROs were assessed using paired t tests. Correlations between PROMIS and legacy PROs were tested using Pearson correlation coefficient.

Results:
A total of 57 ACDF patients were analyzed. The mean preoperative PROMIS PF was 40.0±6.4. PROMIS PF significantly improved at 12-week and 6-month follow-up. NDI, VAS neck pain, and VAS arm pain scores demonstrated significant improvement at all postoperative time points. SF-12 scores only exhibited significant improvement at the 6-month follow-up visit. Significant correlations between PROMIS PF, NDI, and SF-12 were identified at all preoperative and postoperative time points. PROMIS PF exhibited strong correlations with VAS neck pain at postoperative time points, and a moderate correlation preoperatively.

Conclusions:
Patients undergoing a primary 1–3 level ACDF experience significant improvements in PROMIS PF scores at 12-week and 6-month follow-up. Furthermore, PROMIS PF exhibits strong correlations to NDI and SF-12 at all preoperative and postoperative time points. These results suggest that PROMIS PF accurately measures PF and may be used in lieu of legacy PF instruments for patients undergoing ACDF.
Metabolic and Endocrine Disorders in Pseudarthrosis
Authors: Hills Jeffrey M. , Khan Inamullah , Archer Kristin R. , Sivaganesan Ahilan , Daryoush Joshua , Hong Daniel Y. , Dahir Kathryn M. , Devin Clinton J. , Stephens Byron 
Published: February 2019

Study Design:
Retrospective Cohort.

Objective:
Establish 1-year patient-reported outcomes after spine surgery for symptomatic pseudarthrosis compared with other indications. In the subgroup of pseudarthrosis patients, describe preexisting metabolic and endocrine-related disorders, and identify any new diagnoses or treatments initiated by an endocrine specialist.

Summary of Background:
Despite surgical advances in recent decades, pseudarthrosis remains among the most common complications and indications for revision after fusion spine surgery. A better understanding of the outcomes after revision surgery for pseudarthrosis and risk factors for pseudarthrosis are needed.

Methods:
Using data from our institutional spine registry, we retrospectively reviewed patients undergoing elective spine surgery between October 2010 and November 2016. Patients were stratified by surgical indication (pseudarthrosis vs. not pseudarthrosis), and 1-year outcomes for satisfaction, disability, quality of life, and pain were compared. In a descriptive subgroup analysis of pseudarthrosis patients, we identified preexisting endocrine-related disorders, frequency of endocrinology referral, and any new diagnoses and treatments initiated through the referral.

Results:
Of 2721 patients included, 169 patients underwent surgery for pseudarthrosis. No significant difference was found in 1-year satisfaction between pseudarthrosis and nonpseudarthrosis groups (77.5% vs. 83.6%, respectively). A preexisting endocrine-related disorder was identified in 82% of pseudarthrosis patients. Endocrinology referral resulted in a new diagnosis or treatment modification in 58 of 59 patients referred. The most common diagnoses identified included osteoporosis, vitamin D deficiency, diabetes, hyperlipidemia, sex-hormone deficiency, and hypothyroidism. The most common treatments initiated through endocrinology were anabolic agents (teriparatide and abaloparatide), calcium, and vitamin D supplementation.

Conclusions:
Patients undergoing revision spine surgery for pseudarthrosis had similar 1-year satisfaction rates to other surgical indications. In conjunction with a bone metabolic specialist, our descriptive analysis of endocrine-related disorders among patients with a pseudarthrosis can guide protocols for workup, indications for endocrine referral, and guide prospective studies in this field.