bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of metonymy and metaphor in the conceptualization of the nation
Authors: Perak Benedikt 
Published: April 2019

Abstract
This corpus-based study presents an emergent ontological analysis of syntactic-semantic constructions of the concept nation. Using large Croatian corpora, I analysed the ontological congruence of the collocations of the lexeme nacija ‘nation’ in five types of syntactic-semantic constructions. This approach enabled a formal hierarchical description of the metaphorical conceptualization of the nation and the cognitive mechanism of eliciting reification, personification and social appraisal of the nation. Metaphorical mappings are seen as a powerful instrument for conceptualizing the institutional status of the nation, reinforcing the interaction between members, and the creation of collective identity that influences a person’s self-appraisal, and vice versa.
Metaphorical and non-metaphorical dimensions of the term nacija in Croatian online discourse
Authors: Stanojević Mateusz-Milan 
Published: April 2019

Abstract
In this chapter I argue that the Croatian term nacija ‘nation’ exhibits local rather than global metaphoricity. The study is based on 990 concordances of nacija from the hrWaC corpus of online Croatian, combined with several threads focusing on the notion of the nation from an online forum. Metaphors account for one quarter of the corpus examples. They are related to the non-metaphorical aspects of meaning through motivational links, depend on the conceptual characteristics of the grammatical constructions in which they appear, and on conventional extensions of source-domain terms. Forum participants use metaphors to serve current communicative purposes. It is shown that global organizational conceptual metaphors are a sum of local conceptualizations.
Two-particle quantum correlations in stochastically-coupled networks
Authors: de J León-Montiel Roberto , Méndez Vicenç , Quiroz-Juárez Mario A , Ortega Adrian , Benet Luis , Perez-Leija Armando , Busch Kurt 
Published: April 2019

Abstract
Quantum walks in dynamically-disordered networks have become an invaluable tool for understanding the physics of open quantum systems. Although much work has been carried out considering networks affected by diagonal disorder, it is of fundamental importance to study the effects of fluctuating couplings. This is particularly relevant in materials science models, where the interaction forces may change depending on the species of the atoms being linked. In this work, we make use of stochastic calculus to derive a master equation for the dynamics of one and two non-interacting correlated particles in tight-binding networks affected by off-diagonal dynamical disorder. We show that the presence of noise in the couplings of a quantum network creates a pure-dephasing-like process that destroys all coherences in the single-particle Hilbert subspace. Moreover, we show that when two or more correlated particles propagate in the network, coherences accounting for particle indistinguishability are robust against the impact of off-diagonal noise, thus showing that it is possible, in principle, to find specific conditions for which many indistinguishable particles can traverse stochastically-coupled networks without losing their ability to interfere.
Calculation of the wide-angle neutron spectra from the 9Be(d, xn) reaction in a thick beryllium target *
Authors: Wei Zheng , Wang Jun-Run , Zhang Ya-Ling , Huang Zhi-Wu , Ma Zhan-Wen , Zhang Jie , Ding Yan-Yan , Xia Li , Li Jian-Yi , Lu Xiao-Long , Zhang Yu , Xu Da-Peng , Yang Lei , Yao Ze-En 
Published: April 2019

Abstract
The multi-layer computing model is developed to calculate wide-angle neutron spectra, in the range from 0° to 180° with a 5° step, produced by bombarding a thick beryllium target with deuterons. The double-differential cross-sections (DDCSs) for the 9Be(d, xn) reaction are calculated using the TALYS-1.8 code. They are in agreement with the experimental data, and are much better than the PHITS-JQMD/GEM results at 15° , 30° , 45° and 60° neutron emission angles for deuteron energy of 10.0 MeV. In the TALYS-1.8 code, neutron contributions from direct reactions (break-up, stripping and knock-out reactions) are controlled by adjustable parameters, which describe the basic characteristics of typical direct reactions and control the relative intensity and the position of the ridgy hillock at the tail of DDCSs. It is found that the typical calculated wide-angle neutron spectra for different neutron emission angles and neutron angular distributions agree quite well with the experimental data for 13.5 MeV deuterons. The multi-layer computing model can reproduce the experimental data reasonably well by optimizing the adjustable parameters in the TALYS-1.8 code. Given the good agreement with the experimental data, the multi-layer computing model could provide better predictions of wide-angle neutron energy spectra, neutron angular distributions and neutron yields for the 9Be(d, xn) reaction neutron source.
Geometric anisotropy on biomaterials surface for vascular scaffold design: engineering and biological advances
Authors: Wang Zuyong , Zhang Wanqi , Xie Chao , Wen Feng , Ma Chao , Lin Nan , Thian Eng San , Wang Xianwei 
Published: April 2019

Abstract
Scaffold designs in combination with drug, growth factor and other bioactive chemicals account for lasting progress of vascular tissue engineering in the past decades. It is a great achievement to adjust tissue matrix composition and cell behaviour effectively. However, regenerating the innate physiologies of a blood vessel still needs its precise architecture to supply the vessel with structural basis for vascular functionality. Recent developments in biomaterial engineering have been explored in designing anisotropic surface geometries, and in turn to direct biological effects for recapitulating vascular tissue architecture. Here, we present current efforts, and propose future perspectives for the guidance on the architectural reconstruction and scaffold design of blood vessel.
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data
Authors: Lima Leandro , Marchet Camille , Caboche Ségolène , Da Silva Corinne , Istace Benjamin , Aury Jean-Marc , Touzet Hélène , Chikhi Rayan 
Published: April 2019

Abstract

Motivation
Nanopore long-read sequencing technology offers promising alternatives to high-throughput short read sequencing, especially in the context of RNA-sequencing. However this technology is currently hindered by high error rates in the output data that affect analyses such as the identification of isoforms, exon boundaries, open reading frames and creation of gene catalogues. Due to the novelty of such data, computational methods are still actively being developed and options for the error correction of Nanopore RNA-sequencing long reads remain limited.

Results
In this article, we evaluate the extent to which existing long-read DNA error correction methods are capable of correcting cDNA Nanopore reads. We provide an automatic and extensive benchmark tool that not only reports classical error correction metrics but also the effect of correction on gene families, isoform diversity, bias toward the major isoform and splice site detection. We find that long read error correction tools that were originally developed for DNA are also suitable for the correction of Nanopore RNA-sequencing data, especially in terms of increasing base pair accuracy. Yet investigators should be warned that the correction process perturbs gene family sizes and isoform diversity. This work provides guidelines on which (or whether) error correction tools should be used, depending on the application type.

Benchmarking software
https://gitlab.com/leoisl/LR_EC_analyser
Multiple paternity and precocial breeding in wild Tasmanian devils, Sarcophilus harrisii (Marsupialia: Dasyuridae)
Authors: Russell Tracey , Lane Amanda , Clarke Judy , Hogg Carolyn , Morris Katrina , Keeley Tamara , Madsen Thomas , Ujvari Beata 
Published: April 2019

Abstract
Polyandry, a common reproductive strategy in various animal species, has potential female benefits, which include enhanced offspring fitness. Benefits can be direct, such as reduced risk of male infanticide of offspring, or indirect, such as increased genetic diversity of offspring and the acquisition of ‘good genes’. Multiple paternity of litters has been recorded in numerous marsupial species but has not been reported in Tasmanian devils, Sarcophilus harrisii (Boitard). We investigated whether multiple paternity occurred in litters within a wild population of Tasmanian devils. Using major histocompatibility complex-linked and neutral microsatellite markers, the paternity of nine litters was analysed. We found multiple paternity in four out of nine litters and that yearling (> 1, < 2 years old) male devils were siring offspring. This is the first record of multiple paternity and of male precocial breeding in wild Tasmanian devils. To date, there are no data relating to the subsequent survival of devils from single- vs. multiple-sired litters; therefore, we do not know whether multiple paternity increases offspring survival in the wild. These results have implications for the Tasmanian devil captive insurance programme, because group housing can lead to multiple-sired litters, making the maintenance of genetic diversity over time difficult to manage.
Use of Routine Complete Blood Count Results to Rule Out Anaplasmosis Without the Need for Specific Diagnostic Testing
Authors: Turbett Sarah E , Anahtar Melis N , Pattanayak Vikram , Azar Marwan M , Coffey K C , Eng George , Rudolf Joseph W , Lewandrowski Kent B , Baron Jason , Rosenberg Eric S , Branda John A 
Published: April 2019

Abstract

Background
Anaplasmosis presents with fever, headache, and laboratory abnormalities including leukopenia and thrombocytopenia. Polymerase chain reaction (PCR) is the preferred diagnostic but is overutilized. We determined if routine laboratory tests could exclude anaplasmosis, improving PCR utilization.

Methods
Anaplasma PCR results from a 3-year period, with associated complete blood count (CBC) and liver function test results, were retrospectively reviewed. PCR rejection criteria, based on white blood cell (WBC) and platelet (PLT) counts, were developed and prospectively applied in a mock stewardship program. If rejection criteria were met, a committee mock-refused PCR unless the patient was clinically unstable or immunocompromised.

Results
WBC and PLT counts were the most actionable routine tests for excluding anaplasmosis. Retrospective review demonstrated that rejection criteria of WBC ≥11 000 cells/µL or PLT ≥300 000 cells/µL would have led to PCR refusal in 428 of 1685 true-negative cases (25%) and 3 of 66 true-positive cases (5%) involving clinically unstable or immunocompromised patients. In the prospective phase, 155 of 663 PCR requests (23%) met rejection criteria and were reviewed by committee, which endorsed refusal in 110 of 155 cases (71%) and approval in 45 (29%), based on clinical criteria. PCR was negative in all 45 committee-approved cases. Only 1 of 110 mock-refused requests yielded a positive PCR result; this patient was already receiving doxycycline at the time of testing.

Conclusions
A CBC-based stewardship algorithm would reduce unnecessary Anaplasma PCR testing, without missing active cases. Although the prospectively evaluated screening approach involved medical record review, this was unnecessary to prevent errors and could be replaced by a rejection comment specifying clinical situations that might warrant overriding the algorithm.
Heartburn and dyspepsia symptom severity improves after treatment and correlates with histology in adults with eosinophilic esophagitis
Authors: Eluri Swathi , Perjar Irina , Betancourt Renee , Randall Cara , Raja Soha , Woosley John T , Shaheen Nicholas J , Dellon Evan S 
Published: April 2019

SUMMARY
Non-dysphagia symptoms, such as heartburn and dyspepsia, are poorly characterized in adults with eosinophilic esophagitis (EoE). It is unclear if treatment improves these symptoms. The aim of this paper was to assess (i) heartburn and dyspepsia symptom severity in adult EoE patients using validated symptom measures; (ii) change in symptoms after treatment; and (iii) symptom association with endoscopic and histologic features. In a prospective cohort of adult EoE patients who were not responsive to proton pump inhibitor therapy, non-dysphagia symptoms were assessed with heartburn items from the validated GERD-HRQL (gastroesophageal reflux disease health-related quality of life) and SODA (severity of dyspepsia assessment) instruments. Subjects completed the questionnaires at baseline and after treatment. Association of baseline symptoms with endoscopic and histologic features, and before and after treatment with diet or topical steroids, was assessed. Eighty-six EoE patients (mean age 39 years, 57% male, 95% white) completed a baseline questionnaire and 62 completed the follow-up questionnaire. The mean baseline GERD-HRQL score was 4.5 ± 6.5 and the mean total SODA score was 41.0 ± 12.6. At baseline, there was a weak but significant correlation between peak eosinophils and the SODA score (r = 0.28; p = 0.03) and no association between heartburn and SODA scores and endoscopic or other histologic findings. After treatment, there was a decrease in GERD-HRQL heartburn (4.3 vs. 2.6; p = 0.04) and SODA (49.5 vs. 35.5; p = 0.04) scores in histologic responders, but not in nonresponders. In a prospective cohort of EoE patients, baseline eosinophils positively correlated with dyspepsia severity. Heartburn and dyspepsia symptoms improved after treatment in histologic responders.
The other explanation for dyspnea: giant paraesophageal hiatal hernia repair routinely improves pulmonary function
Authors: Wirsching Andrea , Klevebro Fredrik , Boshier Piers R , Hubka Michal , Kuppusamy Madhan K , Kirtland Steve H , Low Donald E 
Published: April 2019

SUMMARY
Paraesophageal hiatal hernias (PEHs) are most commonly associated with gastrointestinal symptoms; less widely appreciated is their potentially important influence on respiratory function. We hypothesize that surgical repair of PEH will significantly improve not only gastrointestinal symptoms, but also preoperative dyspnea and spirometry scores. A prospective Institutional Review Board-approved database was used to review all patients undergoing PEH repair from 2000 to 2016. Patients with pre- and postoperative pulmonary function tests assessed by spirometry were included. Postoperative changes in spirometry measurements were compared to PEH size as reflected by the percentage of intrathoracic stomach observed on preoperative contrast studies. Patients were stratified according to improvement in forced expiratory volume in 1 second (FEV1). Patients with >12% (‘significant’) improvement in FEV1 after surgery were compared to the remaining patient population. In total, 299 patients met the inclusion criteria. Symptomatic improvement in respiratory function was noted in all patients after PEH repair. Age, gender, BMI, presenting symptoms, Charlson comorbidity index as well as preoperative comorbidities did not significantly impact the functional outcome. Spirometry results improved in 80% of the patients, 21% of whom showed an improvement of >20% compared to the preoperative level. ‘Significant’ improvement in respiratory function was seen in 122 of 299 (41%) patients. Patients presenting with moderate and severe preoperative pulmonary obstruction demonstrated ‘significant’ improvement in FEV1 in 48% and 40% of cases, respectively. Large PEHs, characterized by a percentage of intrathoracic stomach >75%, was strongly associated with ‘significant’ improvement in FEV1 (P = 0.001). PEHs can impact subjective and objective respiratory status and surgical repair can result in a significant improvement in dyspnea and pulmonary function score that is independent of preoperative pulmonary disease. Gastric herniation of more than 75% was associated with higher possibility for improvement of pulmonary function tests. Patients with persistent and unexplained dyspnea and coexistent PEH should be assessed by an experienced surgeon for consideration of elective repair.
WGS more accurately predicts susceptibility of Mycobacterium tuberculosis to first-line drugs than phenotypic testing
Authors: Jajou Rana , van der Laan Tridia , de Zwaan Rina , Kamst Miranda , Mulder Arnout , de Neeling Albert , Anthony Richard , van Soolingen Dick 
Published: April 2019

AbstractBackgroundDrug-susceptibility testing (DST) of Mycobacterium tuberculosis complex (MTBC) isolates by the Mycobacteria Growth Indicator Tube (MGIT) approach is the most widely applied reference standard. However, the use of WGS is increasing in many developed countries to detect resistance and predict susceptibility. We investigated the reliability of WGS in predicting drug susceptibility, and analysed the discrepancies between WGS and MGIT against the first-line drugs rifampicin, isoniazid, ethambutol and pyrazinamide.MethodsDST by MGIT and WGS was performed on MTBC isolates received in 2016/2017. Nine genes and/or their promotor regions were investigated for resistance-associated mutations: rpoB, katG, fabG1, ahpC, inhA, embA, embB, pncA and rpsA. Isolates that were discrepant in their MGIT/WGS results and a control group with concordant results were retested in the MGIT, at the critical concentration and a lower concentration, and incubated for up to 45 days after the control tube became positive in the MGIT.ResultsIn total, 1136 isolates were included, of which 1121 were routine MTBC isolates from the Netherlands. The negative predictive value of WGS was ≥99.3% for all four first-line antibiotics. The majority of discrepancies for isoniazid and ethambutol were explained by growth at the lower concentrations, and for rifampicin by prolonged incubation in the MGIT, both indicating low-level resistance.ConclusionsApplying WGS in a country like the Netherlands, with a low TB incidence and low prevalence of resistance, can reduce the need for phenotypic DST for ∼90% of isolates and accurately detect mutations associated with low-level resistance, often missed in conventional DST.
The Importance of the Arms Trade Treaty for the Implementation of the Sustainable Development Goals
Authors: Nave Eva 
Published: April 2019

Abstract
The availability, propagation and excessive accumulation of arms are a serious impediment to countries’ achievement of Sustainable Development Goals (SDGs). Irresponsible arms trade leads to permanent insecurity, which forces people to leave their homes and impacts on the diversion of funds from inter alia health, education, social–economic stability and peace-building processes to defence and the military. Goal 16 of the SDGs sets out, noting its indicator 16.4, that the significant reduction of illicit arms flows is a way to promote just, peaceful and inclusive societies. This is a target to be met by 2030. The Arms Trade Treaty (ATT), aiming at preventing and eradicating the unregulated arms flows by laying down criteria to be assessed before authorising arms transfers, is a crucial international legally binding instrument in that quest. This study advocates that, applying an integrative approach to the ATT, the potentially negative impact in the recipient country’s achievement of the SDGs is to be considered when pondering upon arms transfers.
Information of valence charge of 3d transition metal elements observed in L-emission spectra
Authors: Terauchi Masami 
Published: April 2019

Abstract
L-emission spectra of 3d transition metal elements from Sc to Zn and some oxides were measured to examine the relation between L-emission intensities of Lα, Lβ, Lℓ, and Lη and valences of those elements by using a soft X-ray emission spectrometer attached to a scanning electron microscope. Lα,β emission intensity due to transitions from valence bands to core 2p levels compared with Lℓ,η emission intensity due to transitions from core 3 s to deeper 2p levels, Lα,β/Lℓ,η was found to be a key parameter. A linear relation was found between the number of 3d electrons and the intensity ratio of Lα,β/(Lα,β+ Lℓ,η) from Sc to Ni, except for Cr. It takes into account not only a change in N3d but also a change of transition probability due to a change in N3d In the case of 3d metal oxides, the evaluation based on the equation showed an overestimation of the calculated number of 3d electrons, which could be due to a charge transfer from ligand oxygen atoms to the transition metal element, resulting from a core-hole effect in the intermediate state.
Integration or Isolation? Refugees’ Social Connections and Wellbeing
Authors: Strang Alison B. , Quinn Neil 
Published: April 2019

Abstract
The Indicators of Integration framework—a conceptual framework defining core domains of refugee integration—has had a significant impact on the discourse surrounding refugee integration and a major role in shaping policy, practice and academic debate. Drawing on an innovative participatory mapping approach, this study examined the social connections of isolated single refugee men from Iran and Afghanistan (highlighted as particularly marginalized) and the implications for their mental health and wellbeing. Findings indicated very low levels of contact with family, local friends or local services, difficulties establishing trust and few opportunities for reciprocal relationships. The article makes an important contribution to the field of refugee integration in a number of ways. It suggests that the role of trust should be made explicit within the Indicators of Integration framework and be included as a ‘Facilitator’ of integration. It challenges Putnam’s simple binary distinction between bonding and bridging relationships and suggests a new conceptualization based on a continuum between bonds and bridges. It offers theoretical innovation by bringing together the concept of reciprocity with Hobfoll’s resource-conservation model to offer new insights into the way domains of the Framework interact. Its important contribution is in critiquing Putnam’s reliance on the idealization of community solidarity and suggesting conceptualizations of integration must be informed by the impact of intersecting but differentiated communities. Two key priorities emerge for policy and practice: enabling asylum seekers and refugees to develop sufficient close bonding relationships and finding more effective ways of building knowledge and trust of relevant resources and services.
OsMADS18, a membrane-bound MADS-box transcription factor, modulates plant architecture and the abscisic acid response in rice
Authors: Yin Xiaoming , Liu Xiong , Xu Buxian , Lu Piaoyin , Dong Tian , Yang Di , Ye Tiantian , Feng Yu-Qi , Wu Yan 
Published: April 2019

AbstractThe APETALA1 (AP1)/FRUITFULL (FUL)-like transcription factor OsMADS18 plays diverse functions in rice development, but the underlying molecular mechanisms are far from fully understood. Here, we report that down-regulation of OsMADS18 expression in RNAi lines caused a delay in seed germination and young seedling growth, whereas the overexpression of OsMADS18 produced plants with fewer tillers. In targeted OsMADS18 genome-edited mutants (osmads18-cas9), an increased number of tillers, altered panicle size, and reduced seed setting were observed. The EYFP-OsMADS18 (full-length) protein was localized to the nucleus and plasma membrane but the EYFP-OsMADS18-N (N-terminus) protein mainly localized to the nucleus. The expression of OsMADS18 could be stimulated by abscisic acid (ABA), and ABA stimulation triggered the cleavage of HA-OsMADS18 and the translocation of OsMADS18 from the plasma membrane to the nucleus. The inhibitory effect of ABA on seedling growth was less effective in the OsMADS18-overexpressing plants. The expression of a set of ABA-responsive genes was significantly reduced in the overexpressing plants. The phenotypes of transgenic plants expressing EYFP-OsMADS18-N resembled those observed in the osmads18-cas9 mutants. Analysis of the interaction of OsMADS18 with OsMADS14, OsMADS15, and OsMADS57 strongly suggests an essential role for OsMADS18 in rice development.