bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cold-hot coupled waves in a flowing magnetized plasma
Authors: Uk Lee Min , Ji Jeong-Young , Yun Gunsu S. 
Published: September 2020

Abstract
Nonlinear coupling of cold and hot waves in a flowing magnetized plasma is analyzed with the Vlasov equation. An analytical solution is obtained for cold waves of a small amplitude (weak flow) and a long wavelength. The distribution function is obtained by integrating the kinetic equation along a perturbed phase-space trajectory for a time-varying plasma flow. The kinetic description presents a generalized dispersion relation that involves resonances depending on cold and hot wave dispersions. Coherent fluid motion leads to radiation peaks in addition to the cyclotron harmonics, where the wavenumber of the cold wave determines the peak frequencies. The peaks appear narrow when the wave propagates perpendicular to the time-averaged flow while they become broad due to the Doppler effect when the wave propagates parallel to the flow. Fully kinetic particle-in-cell simulations corroborate the theoretical predictions. The dispersion relation and resulting wave spectra provide information about plasma parameters and flow properties.
Quantitative analysis of the Schottky interface of reduced graphene oxide Schottky diodes
Authors: Aodah Souad , Bano N , Hussain I , AlSalhi Mohamad S 
Published: September 2020

Abstract
A Schottky contact is greatly vital for electronic devices; therefore, a quantitative analysis of the Schottky interface is important in realizing a high-performance Schottky diode. In this study, we fabricate an r-GO-based Schottky diode and elucidate the charge traps in r-GO by analyzing the current–voltage characteristics. The conduction becomes space charge limited (at high voltage) because of these traps. The trap energy and concentration were calculated as ∼0.20 ± 0.02 eV and 2.11 × 1015 cm−3, respectively. Quantitative information about charge traps will help in the fabrication of high-quality r-GO-based electronic devices. The trap density is the core challenge for the material community; therefore, controlling the traps is essential in improving the performance of r-GO-based electronic devices. We believe that the quantitative analysis of the Schottky interface could be beneficial for the improvement of the charge transport in r-GO-based electronic devices.
The Dark Money Subsidy? Tax Policy and Donations to Section 501(c)(4) Organizations
Authors: Galle Brian 
Published: September 2020

AbstractThis article presents the first empirical examination of giving to §501(c)(4) organizations, which have recently become important players in U.S. politics. Unlike gifts to charity, donations to a 501(c)(4) are not legally deductible. Yet, gifts to c(4) organizations are highly elastic to the after-tax price of charitable giving. At the lower end of the observed tax price range, c(4) giving falls with tax price, consistent with the hypothesis that giving to c(3) and c(4) organizations are substitutes. Over the top quarter of the distribution of tax price, however, gifts to c(4) organizations are negatively correlated with the after-tax price of giving to charity. That is, donors appear to respond as though the deduction subsidized their gift to a c(4). Donor responses to benefits for which they are not eligible may reflect the low salience of legal limitations or deliberate overclaiming. These results imply subsidies for charity can crowd out or in donations to c(4) organizations, with potential implications for U.S. politics. I cannot observe whether donors claim tax deductions for ineligible gifts, so the net results for the Treasury are unclear.
GRaSP: a graph-based residue neighborhood strategy to predict binding sites
Authors: Santana Charles A , Silveira Sabrina de A , Moraes João P A , Izidoro Sandro C , de Melo-Minardi Raquel C , Ribeiro António J M , Tyzack Jonathan D , Borkakoti Neera , Thornton Janet M 
Published: September 2020

Abstract

Motivation
The discovery of protein–ligand-binding sites is a major step for elucidating protein function and for investigating new functional roles. Detecting protein–ligand-binding sites experimentally is time-consuming and expensive. Thus, a variety of in silico methods to detect and predict binding sites was proposed as they can be scalable, fast and present low cost.

Results
We proposed Graph-based Residue neighborhood Strategy to Predict binding sites (GRaSP), a novel residue centric and scalable method to predict ligand-binding site residues. It is based on a supervised learning strategy that models the residue environment as a graph at the atomic level. Results show that GRaSP made compatible or superior predictions when compared with methods described in the literature. GRaSP outperformed six other residue-centric methods, including the one considered as state-of-the-art. Also, our method achieved better results than the method from CAMEO independent assessment. GRaSP ranked second when compared with five state-of-the-art pocket-centric methods, which we consider a significant result, as it was not devised to predict pockets. Finally, our method proved scalable as it took 10–20 s on average to predict the binding site for a protein complex whereas the state-of-the-art residue-centric method takes 2–5 h on average.

Availability and implementation
The source code and datasets are available at https://github.com/charles-abreu/GRaSP.

Supplementary information
Supplementary data are available at Bioinformatics online.
methylclock: a Bioconductor package to estimate DNA methylation age
Authors: Pelegí-Sisó Dolors , de Prado Paula , Ronkainen Justiina , Bustamante Mariona , González Juan R 
Published: September 2020

Abstract

Motivation
Ageing is a biological and psychosocial process related to diseases and mortality. It correlates with changes in DNA methylation (DNAm) in all human tissues. Therefore, epigenetic markers can be used to estimate biological age using DNAm profiling across tissues.

Results
We developed a Bioconductor package that allows computation of several existing DNAm adult/childhood and gestational age clocks. Functions to visualize the DNAm age prediction versus chronological age and the correlation between DNAm clocks are also available as well as other features, such as missing data imputation of cell types’ estimates, that are required for DNAm age clocks.

Availability and implementation
https://github.com/isglobal-brge/methylclock.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bayesian analysis of longitudinal and multidimensional functional data
Authors: Shamshoian John , Şentürk Damla , Jeste Shafali , Telesca Donatello 
Published: September 2020

Summary
Multi-dimensional functional data arises in numerous modern scientific experimental and observational studies. In this article, we focus on longitudinal functional data, a structured form of multidimensional functional data. Operating within a longitudinal functional framework we aim to capture low dimensional interpretable features. We propose a computationally efficient nonparametric Bayesian method to simultaneously smooth observed data, estimate conditional functional means and functional covariance surfaces. Statistical inference is based on Monte Carlo samples from the posterior measure through adaptive blocked Gibbs sampling. Several operative characteristics associated with the proposed modeling framework are assessed comparatively in a simulated environment. We illustrate the application of our work in two case studies. The first case study involves age-specific fertility collected over time for various countries. The second case study is an implicit learning experiment in children with autism spectrum disorder.
Top–Down Attentional Modulation in Human Frontal Cortex: Differential Engagement during External and Internal Attention
Authors: Kam Julia W Y , Helfrich Randolph F , Solbakk Anne-Kristin , Endestad Tor , Larsson Pål G , Lin Jack J , Knight Robert T 
Published: September 2020

AbstractDecades of electrophysiological research on top–down control converge on the role of the lateral frontal cortex in facilitating attention to behaviorally relevant external inputs. However, the involvement of frontal cortex in the top–down control of attention directed to the external versus internal environment remains poorly understood. To address this, we recorded intracranial electrocorticography while subjects directed their attention externally to tones and responded to infrequent target tones, or internally to their own thoughts while ignoring the tones. Our analyses focused on frontal and temporal cortices. We first computed the target effect, as indexed by the difference in high frequency activity (70–150 Hz) between target and standard tones. Importantly, we then compared the target effect between external and internal attention, reflecting a top–down attentional effect elicited by task demands, in each region of interest. Both frontal and temporal cortices showed target effects during external and internal attention, suggesting this effect is present irrespective of attention states. However, only the frontal cortex showed an enhanced target effect during external relative to internal attention. These findings provide electrophysiological evidence for top–down attentional modulation in the lateral frontal cortex, revealing preferential engagement with external attention.
DNA Methylation and Immune Cell Markers Demonstrate Evidence of Accelerated Aging in Patients with Chronic Hepatitis B Virus or Hepatitis C Virus, with or without Human Immunodeficienct Virus Co-infection
Authors: Gindin Yevgeniy , Gaggar Anuj , Lok Anna S , Janssen Harry L A , Ferrari Carlo , Subramanian G Mani , Jiang Zhaoshi , Masur Henry , Emmanuel Benjamin , Poonia Bhawna , Kottilil Shyam 
Published: September 2020

Abstract

Background
Several chronic diseases accelerate biological aging. We investigated age acceleration and the association between peripheral blood DNA methylation (DNAm) and immune cell markers in patients chronically infected with the hepatitis B virus (HBV) or the hepatitis C virus (HCV) with and without human immunodeficiency virus (HIV) co-infection.

Methods
Age acceleration was measured as the difference between epigenetic age (Horvath clock) and chronological age. The immune marker model of age acceleration was developed using Elastic Net regression to select both the immune markers and their associated weights in the final linear model.

Results
Patients with chronic HBV (n = 51) had a significantly higher median epigenetic age compared to chronological age (age accelerated) (P &lt; .001). In patients with chronic HCV infection (n = 63), age acceleration was associated with liver fibrosis as assessed by histology (P &lt; .05), or presence of HIV co-infection (P &lt; .05), but not HCV mono-infection. Age acceleration defined by immune markers was concordant with age acceleration by DNA methylation (correlation coefficient = .59 in HBV; P = .0025). One-year treatment of HBV patients with nucleoside therapy was associated with a modest reduction in age acceleration, as measured using the immune marker model (−.65 years, P = .018).

Conclusion
Our findings suggest that patients with chronic viral hepatitis have accelerated epigenetic aging, that immune markers define biological age, and have the potential to assess the effects of therapeutic intervention on age acceleration.
Private Set Operations Over Encrypted Cloud Dataset and Applications
Authors: Rafiee Mojtaba , Khazaei Shahram 
Published: September 2020

Abstract
We introduce the notion of private set operations (PSO) as a symmetric-key primitive in the cloud scenario, where a client securely outsources his dataset to a cloud service provider and later privately issues queries in the form of common set operations. We define a syntax and security notion for PSO and propose a general construction that satisfies it. There are two main ingredients to our PSO scheme: an adjustable join (Adjoin) scheme (MIT-CSAIL-TR-2012-006 (2012) Cryptographic treatment of CryptDB’s adjustable join. http://people.csail.mit.edu/nickolai/papers/popa-join-tr.pdf) and a tuple set (TSet) scheme (Cash, D., Jarecki, S., Jutla, C. S., Krawczyk, H., Rosu, M.-C., and Steiner, M. (2013) Highly-Scalable Searchable Symmetric Encryption With Support for Boolean Queries. 33rd Annual Cryptology Conf., Santa Barbara, CA, August 18–22, pp. 353–373. Springer, Berlin, Heidelberg). We also propose an Adjoin construction that is substantially more efficient (in computation and storage) than the previous ones (Mironov, I., Segev, G., and Shahaf, I. (2017) Strengthening the Security of Encrypted Databases: Non-Transitive Joins. 15th Int. Conf., TCC 2017, Baltimore, MD, USA, November 12–15, pp. 631–661. Springer, Cham) due to the hardness assumption that we rely on, while retaining the same security notion. The proposed PSO scheme can be used to perform join queries on encrypted databases without revealing the duplicate patterns in the unqueried columns, which is inherent to an Adjoin scheme. In addition, we also show that the PSO scheme can be used to perform Boolean search queries on a collection of encrypted documents. We also provide standard security proofs for our constructions and present detailed efficiency evaluation and compare them with well-known previous ones.
A checklist recipe: making species data open and FAIR
Authors: Reyserhove Lien , Desmet Peter , Oldoni Damiano , Adriaens Tim , Strubbe Diederik , Davis Amy J S , Vanderhoeven Sonia , Verloove Filip , Groom Quentin 
Published: September 2020

Abstract
Species checklists are a crucial source of information for research and policy. Unfortunately, many traditional species checklists vary wildly in their content, format, availability and maintenance. The fact that these are not open, findable, accessible, interoperable and reusable (FAIR) severely hampers fast and efficient information flow to policy and decision-making that are required to tackle the current biodiversity crisis. Here, we propose a reproducible, semi-automated workflow to transform traditional checklist data into a FAIR and open species registry. We showcase our workflow by applying it to the publication of the Manual of Alien Plants, a species checklist specifically developed for the Tracking Invasive Alien Species (TrIAS) project. Our approach combines source data management, reproducible data transformation to Darwin Core using R, version control, data documentation and publication to the Global Biodiversity Information Facility (GBIF). This checklist publication workflow is openly available for data holders and applicable to species registries varying in thematic, taxonomic or geographical scope and could serve as an important tool to open up research and strengthen environmental decision-making.
Multimodality imaging in valvular heart disease: how to use state-of-the-art technology in daily practice
Authors: Reid Anna , Blanke Philipp , Bax Jeroen J , Leipsic Jonathon 
Published: September 2020

Abstract
Our understanding of the complexities of valvular heart disease (VHD) has evolved in recent years, primarily because of the increased use of multimodality imaging (MMI). Whilst echocardiography remains the primary imaging technique, the contemporary evaluation of patients with VHD requires comprehensive analysis of the mechanism of valvular dysfunction, accurate quantification of severity, and active exclusion extravalvular consequences. Furthermore, advances in surgical and percutaneous therapies have driven the need for meticulous multimodality imaging to aid in patient and procedural selection. Fundamental decision-making regarding whom, when, and how to treat patients with VHD has become more complex. There has been rapid technological advancement in MMI; many techniques are now available in routine clinical practice, and their integration into has the potential to truly individualize management strategies. This review provides an overview of the current evidence for the use of MMI in VHD, and how various techniques within each modality can be used practically to answer clinical conundrums.
The contribution of employment and working conditions to occupational inequalities in non-communicable diseases in Europe
Authors: McNamara Courtney L , Toch-Marquardt Marlen , Albani Viviana , Eikemo Terje A , Bambra Clare 
Published: September 2020

Abstract

Background
Social inequalities in non-communicable diseases (NCDs) are evident across all European regions. Employment and working conditions are important determinants of NCDs, however, few comparative studies have examined how these conditions contribute to health inequalities. This study therefore examines the association of non-standard employment and poor working conditions with occupational inequalities in multiple NCDs and whether there are differences by gender and across European regions.

Methods
We used cross-sectional data from 20 European countries for women and men aged 25–75 (n = 19 876), from round 7 of the European Social Survey. Data were analyzed for self-rated health (SRH) and 9 NCDs: heart/circulatory problems, high blood pressure, arm/hand pain, breathing problems, diabetes, severe headaches, cancer, obesity and depression. We used logistic regression models, stratified by gender, and adjusted rate ratios to examine whether occupational inequalities in NCDs were reduced after adjusting for non-standard employment and poor working conditions, across European regions.

Results
After adjustment, occupational inequalities were significantly reduced across all regions of Europe. Reductions were particularly large among the lowest occupational group and for poor-SRH, depression and obesity. For these conditions, reductions were in the range of 60–99%.

Conclusions
Employment and working conditions are important determinants of occupational inequalities in NCDs. Labour market regulations should therefore be considered in the formulation of NCD prevention strategies.
Regional 3-D lithosphere structure of the northern half of Iran by local earthquake tomography
Authors: Rezaeifar M , Kissling E 
Published: September 2020

SUMMARYThe 3-D P-wave velocity structure of the northern half of Iran crust has been determined from the local earthquake tomography using a high-quality data set of semi-automatically re-picked arrival times. The quality and quantity of these re-picked phase data allow the 3-D imaging of large parts of the northern half of Iran lithosphere between 0 and 60 km depth. Our new P-wave tomography model represents a major improvement over existing models in terms of reliability, resolution and consistency. First-order anomalies such as the crustal roots of the Zagros and Alborz Mountains are clearly resolved. In addition, several shallow smaller-scale features like the Central Iran sedimentary basin and volcanic and igneous rocks are visible in the tomographic image. Our results show deep Moho depressions beneath the Central Alborz and Zagros mountain ranges that are part of the Arabia–Iranian–Eurasia continental collision zone and locally this Moho topography agrees very well with existing models of other studies. The observed P-wave velocity structure suggests that compared to the Sanandaj-Sirjan and Zagros mountain ranges there is a minor crustal thickening beneath the Alborz mountain range and Kopeh Dagh region.
Guiding principles for quality, ethical standards and ongoing learning in implementation research: multicountry learnings from participatory action research to strengthen health systems
Authors: Ozano Kim , Dean Laura , Adekeye Oluwatosin , Bettee Anthony K , Dixon Ruth , Gideon Ntuen Uduak , Gwani Noela , Isiyaku Sunday , Kollie Karsor , Lar Luret , Oluwole Akinola , Piotrowski Helen , Siakeh Alice , Thomson Rachael , Yashiyi James , Zawolo Georgina , Theobald Sally 
Published: September 2020

Abstract
Global health gains can be achieved through strengthening health systems to identify and address implementation challenges in low- and middle-income countries. Participatory research, that promotes joint problem and solution finding between communities and different health systems actors, supports policy implementation analysis at all levels. Within the neglected tropical disease programmes in Liberia and Nigeria, we applied participatory action research (PAR) to address programmatic and health system bottlenecks with health systems strengthening embedded. This paper shares learning from 20 interviews with co-researchers, from national and sub-national levels and academic researchers who worked collaboratively to understand challenges, co-create solutions and advocate for policy change. Through analysis and reflections of existing PAR principles, we inductively identified five additional guiding principles for quality, ethical standards and ongoing learning within PAR projects that aim to strengthen health systems. (1) Recognize communities as units of identity and define stakeholder participation to ensure equitable engagement of all actors; (2) enable flexible action planning that builds on existing structures whilst providing opportunities for embedding change; (3) address health systems and research power differentials that can impede co-production of knowledge and solution development; (4) embed relational practices that lead to new political forms of participation and inquiry within health systems and (5) develop structures for ongoing learning at multiple levels of the health system. PAR can strengthen health systems by connecting and co-creating potentially sustainable solutions to implementation challenges. Additional research to explore how these five additional principles can support the attainment of quality and ethical standards within implementation research using a PAR framework for health systems strengthening is needed.
Framing universal health coverage in Kenya: an interpretive analysis of the 2004 Bill on National Social Health Insurance
Authors: Koon Adam D , Hawkins Benjamin , Mayhew Susannah H 
Published: September 2020

Abstract
In 2004, President Mwai Kibaki of Kenya refused to sign a popular Bill on National Social Health Insurance into law. Drawing on innovations in framing theory, this research provides a social explanation for this decision. In addition to document review, this study involved interpretive analysis of transcripts from 50 semi-structured interviews with leading actors involved in the health financing policy process in Kenya, 2014–15. The frame-critical analysis focused on how actors engaged in (1) sensemaking, (2) naming, which includes selecting and categorizing and (3) storytelling. We demonstrated that actors' abilities to make sense of the Bill were largely influenced by their own understandings of the finer features of the Bill and the array of interest groups privy to the debate. This was reinforced by a process of naming, which selects and categorizes aspects of the Bill, including the public persona of its primary sponsor, its affordability, sustainability, technical dimensions and linkages to notions of economic liberalism. Actors used these understandings and names to tell stories of ideational warfare, which involved narrative accounts of policy resistance and betrayal. This analysis illustrates the difficulty in enacting sweeping reform measures and thus provides a basis for understanding incrementalism in Kenyan health policy.