bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphosyntactic coding of proper names and its implications for
the Animacy Hierarchy
Authors: Helmbrecht Johannes , Denk Lukas , Thanner Sarah , Tonetti Ilenia 
Published: July 2018

Abstract
The Animacy Hierarchy (AH) is an important construct employed for the
description and explanation of variation and splits in case marking
and agreement in various grammatical domains. The AH is a scale that
combines person, definiteness and semantic animacy and is used to
state clear preferences of certain morphosyntactic coding types over
others. One assumption of the AH is that proper names (PNs) occupy
an intermediate place between personal pronouns and common nouns.
Despite the large body of research since its first extensive
formulation in Silverstein
(1976), it is astonishing that there has been almost no
empirical evidence published for this claim. Since the AH has been
formulated mostly on the basis of case marking and agreement
phenomena in languages with split ergativity or hierarchical
alignment, we compiled a sample of more than 30 such languages in
order to find data on the morphosyntactic coding of PNs. While there
are only a very few instances that confirm the claim, there are more
instances that contradict it. We concluded that PNs should be
removed from the AH, since their assumed position has no predictive
value for typological generalizations.
Generic person marking in Japhug and other Gyalrong
languages
Authors: Jacques Guillaume 
Published: July 2018

Abstract
This paper discusses the history of generic person marking systems in
several Gyalrong languages. While closely related, Japhug and
Tshobdun differ considerably: the inverse prefix marks generic A in
Japhug, while it appears in the generic P form in Tshobdun. We
propose a historical scenario to explain how such radically
different systems came into being, proposing in particular that one
of the generic human markers was grammaticalized from a nominalizer,
and show that our reconstruction can also explain the origin of the
local scenario portmanteau 1→2 and 2→1 prefixes. These
reconstructions allow us to establish the existence of several
previously unattested grammaticalization pathways.
Characterization and abolishment of the cyclopiazonic acids produced by Aspergillus oryzae HMP-F28
Authors: Cao Ting , Ling Junhong , Liu Yi , Chen Xiaoqi , Tian Xiaoyue , Meng Dali , Pan Huaqi , Hu Jiangchun , Wang Nan 
Published: July 2018

ABSTRACT
Extracellular alkalinization and H2O2 production are important early events during induced resistance establishment in plants. In a screen for metabolites as plant resistance activators from 98 fungal isolates associated with marine sponge Hymeniacidon perleve, the cyclopiazonic acids (CPAs) produced by Aspergillus oryzae HMP-F28 induced significant extracellular alkalinization coupled with augmented H2O2 production in tobacco cell suspensions. Bioassay-guided fractionation led to the isolation and structural elucidation of a new CPA congener (4, 3-hydroxysperadine A) and three known ones (1–3). To construct a mutasynthetic strain to generate unnatural CPA analogues, a hybrid pks-nrps gene (cpaS) was disrupted to abolish the production of the critical precursor of cyclo-acetoacetyl-l-tryptophan (cAATrp) and all the downstream CPA products. Elimination of cAATrp will allow cAATrp mimics being processed by the CPA biosynthetic machinery to produce CPA derivatives with designed structural features.
Forty years of wicked problems literature: forging closer links to policy studies
Authors: Head Brian W 
Published: July 2018

AbstractRittel and Webber boldly challenged the conventional assumption that ‘scientific’ approaches to social policy and planning provide the most reliable guidance for practitioners and researchers who are addressing complex, and contested, social problems. This provocative claim, that scientific-technical approaches would not ‘work’ for complex social issues, has engaged policy analysts, academic researchers and planning practitioners since the 1970s. Grappling with the implications of complexity and uncertainty in policy debates, the first generation of ‘wicked problem’ scholars generally agreed that wicked issues require correspondingly complex and iterative approaches. This tended to quarantine complex ‘wicked’ problems as a special category that required special collaborative processes. Most often they recommended the inclusion of multiple stakeholders in exploring the relevant issues, interests, value differences and policy responses. More than four decades later, however, there are strong arguments for developing a second-generation approach which would ‘mainstream’ the analysis of wicked problems in public policy. While continuing to recognize the centrality of complexity and uncertainty, and the need for creative thinking, a broader approach would make better use of recent public policy literatures on such topics as problem framing, policy design, policy capacity and the contexts of policy implementation.
Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts
Authors: Togninalli Matteo , Roqueiro Damian ,   COPDGene Investigators, Borgwardt Karsten M 
Published: July 2018

Abstract

Motivation
Methods based on summary statistics obtained from genome-wide association studies have gained considerable interest in genetics due to the computational cost and privacy advantages they present. Imputing missing summary statistics has therefore become a key procedure in many bioinformatics pipelines, but available solutions may rely on additional knowledge about the populations used in the original study and, as a result, may not always ensure feasibility or high accuracy of the imputation procedure.

Results
We present ARDISS, a method to impute missing summary statistics in mixed-ethnicity cohorts through Gaussian Process Regression and automatic relevance determination. ARDISS is trained on an external reference panel and does not require information about allele frequencies of genotypes from the original study. Our method approximates the original GWAS population by a combination of samples from a reference panel relying exclusively on the summary statistics and without any external information. ARDISS successfully reconstructs the original composition of mixed-ethnicity cohorts and outperforms alternative solutions in terms of speed and imputation accuracy both for heterogeneous and homogeneous datasets.

Availability and implementation
The proposed method is available at https://github.com/BorgwardtLab/ARDISS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Crumble: reference free lossy compression of sequence quality values
Authors: Bonfield James K , McCarthy Shane A , Durbin Richard 
Published: July 2018

AbstractMotivationThe bulk of space taken up by NGS sequencing CRAM files consists of per-base quality values. Most of these are unnecessary for variant calling, offering an opportunity for space saving.ResultsOn the Syndip test set, a 17 fold reduction in the quality storage portion of a CRAM file can be achieved while maintaining variant calling accuracy. The size reduction of an entire CRAM file varied from 2.2 to 7.4 fold, depending on the non-quality content of the original file (see Supplementary Material S6 for details).Availability and implementationCrumble is OpenSource and can be obtained from https://github.com/jkbonfield/crumble.Supplementary informationSupplementary data are available at Bioinformatics online.
Goblet cell-produced retinoic acid suppresses CD86 expression and IL-12 production in bone marrow-derived cells
Authors: Xiao Yangyan , de Paiva Cintia S , Yu Zhiyuan , de Souza Rodrigo G , Li De-Quan , Pflugfelder Stephen C 
Published: July 2018

Abstract
Conjunctival goblet cell loss in ocular surface diseases is accompanied by increased number of interleukin-12 (IL-12)-producing antigen-presenting cells (APCs) and increased interferon-γ (IFN-γ) expression. This study tested the hypothesis that mouse conjunctival goblet cells produce biologically active retinoic acid (RA) that suppresses CD86 expression and IL-12 production by myeloid cells. We found that conditioned media from cultured conjunctival goblet cells (CjCM) suppressed stimulated CD86 expression, NF-κB p65 activation and IL-12 and IFN-γ production in unstimulated and lipopolysaccharide-stimulated cultured bone marrow-derived cells (BMDCs) containing a mixed population of APCs. Goblet cell-conditioned, ovalbumin-loaded APCs suppressed IFN-γ production and increased IL-13 production in co-cultured OTII cells. The goblet cell suppressive activity is due in part to their ability to synthesize RA from retinol. Conjunctival goblet cells had greater expression of aldehyde dehydrogenases Aldh1a1 and a3 and ALDEFLUOR activity than cornea epithelium lacking goblet cells. The conditioning activity was lost in goblet cells treated with an ALDH inhibitor, and a retinoid receptor alpha antagonist blocked the suppressive effects of CjCM on IL-12 production. Similar to RA, CjCM increased expression of suppressor of cytokine signaling 3 (SOCS3) in BMDCs. SOCS3 silencing reversed the IL-12-suppressive effects of CjCM. Our findings indicate that conjunctival goblet cells are capable of synthesizing RA from retinol secreted by the lacrimal gland into tears that can condition APCs. Evidence suggests goblet cell RA may function in maintaining conjunctival immune tolerance and loss of conjunctival goblet cells may contribute to increased Th1 priming in dry eye.
Electrocochleographic Responses Before and After Short-Term Suprathreshold Electrical Stimulation in Human Cochlear Implant Recipients
Authors: Hoesli Marco , Huber Alexander , Pfiffner Flurin , Veraguth Dorothe , Roosli Christof , Dalbert Adrian 
Published: July 2018

Objective:
To assess changes in electrocochleographic (ECoG) responses following short-term suprathreshold electrical stimulation during cochlear implant (CI) telemetry in CI recipients.

Methods:
Extracochlear ECoG recordings were conducted before and after intraoperative short-term suprathreshold electrical stimulation. Tone bursts at 500, 750, and 1000 Hz as well as clicks were used as acoustic stimuli. Changes of ECoG responses were correlated to calculated maximum electrical charge levels.

Results:
Fourteen subjects were included. On average, no significant changes of ECoG responses occurred in the earliest postoperative phase; therefore, also following short-term suprathreshold electrical stimulation. However, one subject (S7) showed a decrease of ECoG responses. Neural as well as hair cell components of the ECoG signal were affected. On average, the maximum electrical charge level was 22 nC (range, 15–37 nC). In S7, the maximum electrical charge level was 17 nC. No correlations were found between maximum electrical charge levels and changes of ECoG signals.

Conclusion:
In a majority of cases, electrophysiological responses to acoustic stimuli remain unchanged in the earliest postoperative phase. However, deterioration of cochlear function occurs in this phase. Neural as well as hair cell components of the ECoG signal are affected. Such deterioration is not associated with unusually high electrical charge levels during CI telemetry. Overall, our results support the notion that an electrical charge applied at levels used in the clinical routine does not have an acute deleterious effect on cochlear function.
The Hand-eye Coordination of Professional Baseball Players: The Relationship to Batting
Authors: Laby Daniel M. , Kirschen David G. , Govindarajulu Usha , DeLand Paul 
Published: July 2018

SIGNIFICANCE
A visuomotor skill (eye-hand visual-motor reaction time [EH-VMRT]) important for baseball performance is described. Eye-hand visual-motor reaction time represents the integration of visual information, perceptually based decisions, and motor movements to accomplish a specific task. The speed at which this occurs depends on many factors, some visual, some perceptual, and some motor related.

PURPOSE
The purpose of this study was to describe the EH-VMRT ability and evaluate its relationship to the baseball batting performance of professional baseball players.

METHODS
A commercially available EH-VMRT system was used on 450 professional baseball players. Results were retrospectively compared with standard, career, plate discipline metrics.

RESULTS
Statistically significant correlations were found between the EH-VMRT metrics and plate discipline batting metrics. Better EH-VMRT ability also correlated with longer service in, and likelihood to achieve, the major-league level. The better (top 20%) EH-VMRT group had three fewer at bats before gaining a walk (22% decrease), as well as swinging 10 to 12% less often at pitches outside the strike zone and 6 to 7% less often at pitches in the strike zone as compared with the bottom 20% group. In addition, EH-VMRT displays a threshold-like relationship with the ability to gain a walk.

CONCLUSIONS
These results describe the EH-VMRT ability of professional baseball players and show a significant relationship between the EH-VMRT ability and batting performance. These results may suggest a possible role in player selection, indicating that batters with better EH-VMRT may be more likely to reach the major-league level and be more productive for their team. Further studies will be needed to demonstrate whether training better EH-VMRT results in improved batting performance.
Branch/mode competition in the flow-induced vibration of a square cylinder
Authors: Zhao Jisheng , Nemes András , Lo Jacono David , Sheridan John 
Published: July 2018

The flow-induced vibration response of a square cross-sectional cylinder with low mass and damping ratio is analysed using continuous wavelet transforms (CWT) for three representative angles of attack of the cylinder to the incoming flow. The amplitude and frequency responses over a range of flow velocities map out multiple regimes (branches) of oscillation. Analysis of the time–frequency domain for boundary regions between branches using CWT reveals intermittency at the synchronization region boundaries as well as mode competition at branch boundaries. Complementary recurrence analysis shows that periodic dynamical states are interrupted by chaotic bursts in the transition regions around the higher branch at an angle of attack of
α
= 20° (a new branch first observed by Nemes
et al.
(2012
J. Fluid Mech.
710
, 102–130 (
doi:10.1017/jfm.2012.353
))), supporting the CWT-based frequency–time analysis.

This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
Wavelet-based analysis of time-variant adaptive structures
Authors: Dziedziech Kajetan , Nowak Alexander , Hasse Alexander , Uhl Tadeusz , Staszewski Wiesław J. 
Published: July 2018

Wavelet analysis is applied to identify the time-variant dynamics of adaptive structures. The wavelet-based power spectrum of the structural response, wavelet-based frequency response function (FRF) and wavelet-based coherence are used to identify continuously and abruptly varying natural frequencies. A cantilever plate with surface-bonded macro fibre composite—which alters the structural stiffness—is used to demonstrate the application of the methods. The results show that the wavelet-based input–output characteristics—i.e. the FRF and coherence—can identify correctly the dynamics of the analysed time-variant system and reveal the varying natural frequency. The wavelet-based coherence can be used not only for the assessment of the quality of the wavelet-based FRF but also for the identification.
This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
Continuous wavelet transform in the study of the time-scale properties of intracranial pressure in hydrocephalus
Authors: García María , Poza Jesús , Santamarta David , Romero-Oraá Roberto , Hornero Roberto 
Published: July 2018

Normal pressure hydrocephalus (NPH) encompasses a heterogeneous group of disorders generally characterized by clinical symptoms, ventriculomegaly and anomalous cerebrospinal fluid (CSF) dynamics. Lumbar infusion tests (ITs) are frequently performed in the preoperatory evaluation of patients who show NPH features. The analysis of intracranial pressure (ICP) signals recorded during ITs could be useful to better understand the pathophysiology underlying NPH and to assist treatment decisions. In this study, 131 ICP signals recorded during ITs were analysed using two continuous wavelet transform (CWT)-derived parameters: Jensen divergence (JD) and spectral flux (SF). These parameters were studied in two frequency bands, associated with different components of the signal:
B
1
(0.15–0.3 Hz), related to respiratory blood pressure oscillations; and
B
2
(0.67–2.5 Hz), related to ICP pulse waves. Statistically significant differences (
p
< 1.70 × 10
−3
, Bonferroni-corrected Wilcoxon signed-rank tests) in pairwise comparisons between phases of ITs were found using the mean and standard deviation of JD and SF. These differences were mainly found in
B
2
, where a lower irregularity and variability, together with less prominent time-frequency fluctuations, were found in the hypertension phase of ITs. Our results suggest that wavelet analysis could be useful for understanding CSF dynamics in NPH.

This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
California's carbon market and energy prices: a wavelet analysis
Authors: Aguiar-Conraria Luís , Joana Soares Maria , Sousa Rita 
Published: July 2018

Carbon price is a key variable in management and risk decisions in activities related to the burning of fossil fuels. Different major players in this market, such as polluters, regulators and financial actors, have different time horizons. We use innovative multivariate wavelet analysis tools, including partial wavelet coherence and partial wavelet gain, to study the link between carbon prices and final energy prices in the time and frequency dimensions in California's carbon market, officially known as the California cap-and-trade programme. We find that gasoline prices lead an anti-phase relation with carbon prices. This result is very stable at lower frequencies (close to 1-year period cycles), and it is also present before mid-2015 in the 20–34 weeks frequency band. Regarding electricity, we find that at about a 1-year period, a rise in carbon prices is reflected in higher electricity prices. We conclude that the first 5 years of compliance of the California cap-and-trade programme show that emissions trading is a significant measure for climate change mitigation, with visible rising carbon prices. The quantitative financial analytics we present supports the recent decision to extend the current market to 2030 without the need for complementary carbon pricing schemes.This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
A review of Morlet wavelet analysis of radial profiles of Saturn's rings
Authors: Tiscareno Matthew S. , Hedman Matthew M. 
Published: July 2018

Spiral waves propagating in Saturn's rings have wavelengths that vary with radial position within the disc. The best-quality observations of these waves have the form of radial profiles centred on a particular azimuth. In that context, the wavelength of a given spiral wave is seen to change substantially with position along the one-dimensional profile. In this paper, we review the use of Morlet wavelet analysis to understand these waves. When signal to noise is high and the cause of the wave is well understood, wavelet analysis has been used to solve for wave parameters that are diagnostic of local disc properties. Waves that are not readily perceptible in the spatial domain signal can be clearly identified. Furthermore, filtering in wavelet space, followed by the reverse wavelet transform, has been used to isolate the part of the signal that is of interest. When the cause of the wave is not known, comparing the phases of the complex-valued wavelet transforms from many profiles has been used to determine wave parameters that cannot be determined from any single profile. When signal to noise is low, co-adding wavelet transforms while manipulating the phase has been used to boost a wave's signal above detection limits.
This article is part of the theme issue ‘Redundancy rules: the continuous wavelet transform comes of age’.
Aptamer-based biosensor for food allergen determination using graphene oxide/gold nanocomposite on a paper-assisted analytical device
Authors: Tah Amit , Olmos Cordero Jorge M. , Weng Xuan , Neethirajan Suresh 
Published: July 2018

AbstractThe detection of allergens in food are currently conducted by techniques that are time-consuming and complicated which can deter consistent sampling for allergens, which could potentially cause an anaphylactic shock in the consumer by cross-contamination. The need for a technique that is rapid, on-site, cost-effective, disposable, highly sensitive and accurate to identify these molecules urges the development of a point-of-care device. The aim of this work is to develop a microfluidic paper-assisted analytical device (PAD) using hydrophobic channels, set by a wax printer on filter paper, and functionalized gold nanoparticles (AuNP) to help identify the allergens arachin (Ara h 1) for peanuts, β-lactoglobulin (β LG) for milk, and tropomyosin (Pen a 1) for shrimp and other shellfish presence by a colorimetric test. Synthesized AuNP were conjugated with biotinylated aptamers, using the biotin-streptavidin interaction, to make the specific detection of target allergens. Functionalized AuNP are incubated with the sample and are absorbed by graphene oxide (GO), creating GO-AuNP complexes, if the aptamers have not become structured due to conjugation with allergenic proteins. The PAD device is used to filter the resultant mixture which provides superior sensitivity to detect the allergens present down to the nanogram range (allergens were measured from 25 nM - 1000 nM with a LOD of 7.8 nM, 12.4 nM and 6.2 nM for peanut, milk and shrimp allergens respectively), in contrast to the microgram range of commonly used enzymatic immunoassays. The simple color indicator, varying from clear to pink in the presences of allergens allows the readout to be utilized without the need for highly specific equipment or training. Alternatively, the results can be quantified by taking a picture and measuring the color. This presented PAD can provide results in real time and has the potential to become a rapid, low-cost, and accurate portable point-of-care device to avoid cross-reactivity of food-borne allergens.
Genomic inversion drives small colony variant formation and increased virulence inP. aeruginosa
Authors: Irvine Sharon , Bunk Boyke , Bayes Hannah K. , Sprӧer Cathrin , Connolly James P. R. , Six Anne , Evans Thomas J. , Roe Andrew J. , Overmann Jӧrg , Walker Daniel 
Published: July 2018

AbstractPhenotypic change is a hallmark of bacterial adaptation during chronic infection. In the case of chronicPseudomonas aeruginosalung infection in patients with cystic fibrosis, well-characterised phenotypic variants include mucoid and small colony variants (SCVs). It has previously been shown that SCVs can be reproducibly isolated from the murine lung following the establishment of chronic infection with mucoidP. aeruginosastrain NH57388A. Here we show, using a combination of singlemolecule real-time (PacBio) and Illumina sequencing that the genetic switch for conversion to the SCV phenotype is a large genomic inversion through recombination between homologous regions of two rRNA operons. This phenotypic conversion is associated with large-scale transcriptional changes distributed throughout the genome. This global rewiring of the cellular transcriptomic output results in changes to normally differentially regulated genes that modulate resistance to oxidative stress, central metabolism and virulence. These changes are of clinical relevance since the appearance of SCVs during chronic infection is associated with declining lung function.