bluuebunny/crossref_metadata_2025_split huggingface dataset:
Twisting waves increase the visibility of nonlinear behaviour
Authors: Richard Grace , Lay Holly S , Giovannini Daniel , Cochran Sandy , Spalding Gabriel C , Lavery Martin P J 
Published: April 2020

Abstract
Nonlinear behaviour for acoustic systems is readily measured at high acoustic pressures in gasses or bulk materials. However, at low acoustic pressures nonlinear effects are not commonly observed. We find that by phase structuring acoustic beams, one observes evidence of nonlinear behaviour at an acoustic pressure of 66.78 dB lower than non-structured beams in room temperature air. A bespoke 28-element ultrasonic phased array antenna was developed to generate short pulses that carry orbital angular momentum and are propagated over a short air channel. When sampling small areas of the wavefront, we observed a distinctive change in the frequency components near phase singularities. At these phase singularities the local propagation path is screwed, resulting in the collection signals from pulses travelling along different paths across the aperture of a microphone. The usually negligible frequency chirping that arises from nonlinear behaviour in air interfere at these singularity points and produce a distinctive distortion of the acoustic pulse. Simple physical movement in the system or super-sonic wave speeds do not yield similar results. Such distortions in measured frequency response near phase singularities could lead to errors for SONAR or acoustic communication systems, where received signals are integrated over a finite-area detector. With further development this behaviour could potentially lead to accurate measurement techniques for determining a material’s nonlinear properties at lower acoustic pressure.
Broadband nonreciprocal linear acoustics through a non-local active metamaterial
Authors: Sasmal Aritra , Geib Nathan , Popa Bogdan-Ioan , Grosh Karl 
Published: April 2020

Abstract
The ability to create linear systems that manifest broadband nonreciprocal wave propagation would provide for exquisite control over acoustic signals for electronic filtering in communication and noise control. Acoustic nonreciprocity has predominately been achieved by approaches that introduce nonlinear interaction, mean-flow biasing, smart skins, and spatio-temporal parametric modulation into the system. Each approach suffers from at least one of the following drawbacks: the introduction of modulation tones, narrow band filtering, and the interruption of mean flow in fluid acoustics. We now show that an acoustic media that is non-local and active provides a new means to break reciprocity in a linear fashion without these deleterious effects. We realize this media using a distributed network of interlaced subwavelength sensor–actuator pairs with unidirectional signal transport. We exploit this new design space to create a stable metamaterial with non-even dispersion relations and electronically tunable nonreciprocal behavior over a broad range of frequencies.
Supervised learning of time-independent Hamiltonians for gate design
Authors: Innocenti Luca , Banchi Leonardo , Ferraro Alessandro , Bose Sougato , Paternostro Mauro 
Published: April 2020

Abstract
We present a general framework to tackle the problem of finding time-independent dynamics generating target unitary evolutions. We show that this problem is equivalently stated as a set of conditions over the spectrum of the time-independent gate generator, thus translating the task into an inverse eigenvalue problem. We illustrate our methodology by identifying suitable time-independent generators implementing Toffoli and Fredkin gates without the need for ancillae or effective evolutions. We show how the same conditions can be used to solve the problem numerically, via supervised learning techniques. In turn, this allows us to solve problems that are not amenable, in general, to direct analytical solution, providing at the same time a high degree of flexibility over the types of gate-design problems that can be approached. As a significant example, we find generators for the Toffoli gate using only diagonal pairwise interactions, which are easier to implement in some experimental architectures. To showcase the flexibility of the supervised learning approach, we give an example of a non-trivial four-qubit gate that is implementable using only diagonal, pairwise interactions.
A general formulation of time-optimal quantum control and optimality of singular protocols
Authors: Wakamura Hiroaki , Koike Tatsuhiko 
Published: April 2020

Abstract
We present a general theoretical framework for finding the time-optimal unitary evolution of the quantum systems when the Hamiltonian is subject to arbitrary constraints. Quantum brachistochrone (QB) is such a framework based on the variational principle, whose drawback is that it only deals with equality constraints. While inequality constraints can be reduced to equality ones in some situations, they usually cannot, especially when a drift field, an uncontrollable part, is present in the Hamiltonian. We first develop a framework based on Pontryagin’s maximum principle (MP) in order to deal with inequality constraints as well. The new framework contains QB as a special case, and their detailed correspondence is given. Second, we address the problem of singular controls, which satisfy MP trivially so as to cause a trouble in determining the optimal protocol. To overcome this difficulty, we derive an additional necessary condition for a singular protocol to be optimal by applying the generalized Legendre–Clebsch condition. Third, we discuss general relations among the drift, the singular controls, and the inequality constraints. Finally, we demonstrate how our framework and results work in some examples. We also discuss the physical meaning of singular controls.
Past long-term summer warming over western Europe in new generation climate models: role of large-scale atmospheric circulation
Authors: Boé Julien , Terray Laurent , Moine Marie-Pierre , Valcke Sophie , Bellucci Alessio , Drijfhout Sybren , Haarsma Rein , Lohmann Katja , Putrasahan Dian A. , Roberts Chris , Roberts Malcom , Scoccimarro Enrico , Seddon Jon , Senan Retish , Wyser Klaus 
Published: April 2020

AbstractPast studies have concluded that climate models of previous generations tended to underestimate the large warming trend that has been observed in summer over western Europe in the last few decades. The causes of this systematic error are still not clear. Here, we investigate this issue with a new generation of climate models and systematically explore the role of large-scale circulation in that context.As an ensemble, climate models in this study warm less over western Europe and warm more over eastern Europe than observed on the 1951–2014 period, but it is difficult to conclude this is directly due to systematic errors given the large potential impact of internal variability. These differences in temperature trends are explained to an important extent by an anti-correlation of sea level pressure trends over the North Atlantic / Europe domain between models and observations. The observed trend tends to warm (cool) western (eastern) Europe but the simulated trends generally have the opposite effect, both in new generation and past generation climate models. The differences between observed and simulated sea level pressure trends are likely the result of systematic model errors, which might also impact future climate projections. Neither a higher resolution nor the realistic representation of the evolution of sea surface temperature and sea ice leads to a better simulation of sea level pressure trends.
Antibacterial and anticancer activity of hydrothermally-synthesized zinc oxide nanomaterials using natural extracts of neem, pepper and turmeric as solvent media
Authors: Abinaya C , Manjula Devi R , Suresh P , Balasubramanian N , Muthaiya N , Kannan N D , Annaraj J , Shanmugaiah V , Pearce J M , Shanmugapriya P , Mayandi J 
Published: April 2020

Abstract
A novel and simple wet chemical hydrothermal synthesis method was employed in the preparation of zinc oxide (ZnO) nanoparticles using neem (N), pepper (P) and turmeric (T) extracts as solvent media. The structural and optical properties as well as the antibacterial and anticancer properties of all the samples (ZnO, N/ZnO, P/ZnO, T/ZnO and NPT/ZnO) were characterized and analyzed. Solvent media was found to have an effect on both the size and the morphology of the nanoparticles, which in turn effected their optical and cytotoxic properties. The colony forming unit (CFU) assays were done for E. coli, S. aureus and S. typhi in which T/ZnO (∼2) and P/ZnO (∼3) showed a remarkable effect on S. aureus for 100 μg ml−1 and nearly zero for 150 μg/ml. The zone of inhibition (ZoI) was measured for S. agalactiae, S. dysgalactiae and S. pyogenes.The results showed that S. dysgalactiae is more sensitive to N/ZnO.Finally, the anticancer properties of these compounds towardsprostate cancer cells was investigated. Among the active compounds T ZnO showed the highest activity with low IC50 value (37.751 μg/ml) followed by P ZnO (45.68 μg ml−1).
Relativism and the Metaphysics of Value: A Comment on Daan Evers
Authors: Wright Crispin 
Published: April 2020

Abstract
Daan Evers argues that relativists about aesthetic and other types of evaluative language face some distinctive and largely overlooked metaphysical difficulties concerning the nature of the states of affairs that such statements are intended to be about. These difficulties, as Evers notes, all rest on the assumption that evaluative language is representational. Evers takes it that it is only on this assumption that evaluative relativism is distinguished from expressivism. I argue that this is incorrect and that, without falling into some form of expressivism, relativists can and must drop the representational assumption, but that the resulting position is one in which relativism no longer offers any distinctive dialectical or theoretical advantage.
GlyGen data model and processing workflow
Authors: Kahsay Robel , Vora Jeet , Navelkar Rahi , Mousavi Reza , Fochtman Brian C , Holmes Xavier , Pattabiraman Nagarajan , Ranzinger Rene , Mahadik Rupali , Williamson Tatiana , Kulkarni Sujeet , Agarwal Gaurav , Martin Maria , Vasudev Preethi , Garcia Leyla , Edwards Nathan , Zhang Wenjin , Natale Darren A , Ross Karen , Aoki-Kinoshita Kiyoko F , Campbell Matthew P , York William S , Mazumder Raja 
Published: April 2020

Abstract

Summary
Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions. The GlyGen project is a data integration, harmonization and dissemination project for carbohydrate and glycoconjugate-related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources.

Availability and implementation
GlyGen web portal is freely available to access at https://glygen.org. The data portal, web services, SPARQL endpoint and GitHub repository are also freely available at https://data.glygen.org, https://api.glygen.org, https://sparql.glygen.org and https://github.com/glygener, respectively. All code is released under license GNU General Public License version 3 (GNU GPLv3) and is available on GitHub https://github.com/glygener. The datasets are made available under Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Supplementary information
Supplementary data are available at Bioinformatics online.
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants
Authors: Kuksa Pavel P , Lee Chien-Yueh , Amlie-Wolf Alexandre , Gangadharan Prabhakaran , Mlynarski Elizabeth E , Chou Yi-Fan , Lin Han-Jen , Issen Heather , Greenfest-Allen Emily , Valladares Otto , Leung Yuk Yee , Wang Li-San 
Published: April 2020

Abstract

Summary
We report Spark-based INFERence of the molecular mechanisms of NOn-coding genetic variants (SparkINFERNO), a scalable bioinformatics pipeline characterizing non-coding genome-wide association study (GWAS) association findings. SparkINFERNO prioritizes causal variants underlying GWAS association signals and reports relevant regulatory elements, tissue contexts and plausible target genes they affect. To achieve this, the SparkINFERNO algorithm integrates GWAS summary statistics with large-scale collection of functional genomics datasets spanning enhancer activity, transcription factor binding, expression quantitative trait loci and other functional datasets across more than 400 tissues and cell types. Scalability is achieved by an underlying API implemented using Apache Spark and Giggle-based genomic indexing. We evaluated SparkINFERNO on large GWASs and show that SparkINFERNO is more than 60 times efficient and scales with data size and amount of computational resources.

Availability and implementation
SparkINFERNO runs on clusters or a single server with Apache Spark environment, and is available at https://bitbucket.org/wanglab-upenn/SparkINFERNO or https://hub.docker.com/r/wanglab/spark-inferno.

Contact
lswang@pennmedicine.upenn.edu

Supplementary information
Supplementary data are available at Bioinformatics online
Efficient posterior sampling for high-dimensional imbalanced logistic regression
Authors: Sen Deborshee , Sachs Matthias , Lu Jianfeng , Dunson David B 
Published: April 2020

Summary
Classification with high-dimensional data is of widespread interest and often involves dealing with imbalanced data. Bayesian classification approaches are hampered by the fact that current Markov chain Monte Carlo algorithms for posterior computation become inefficient as the number $p$ of predictors or the number $n$ of subjects to classify gets large, because of the increasing computational time per step and worsening mixing rates. One strategy is to employ a gradient-based sampler to improve mixing while using data subsamples to reduce the per-step computational complexity. However, the usual subsampling breaks down when applied to imbalanced data. Instead, we generalize piecewise-deterministic Markov chain Monte Carlo algorithms to include importance-weighted and mini-batch subsampling. These maintain the correct stationary distribution with arbitrarily small subsamples and substantially outperform current competitors. We provide theoretical support for the proposed approach and demonstrate its performance gains in simulated data examples and an application to cancer data.
Successful Community Resettlement of Men with Learning Disabilities Who Have Completed a Hospital-Based Treatment for Sexual Offending
Authors: Hollomotz Andrea 
Published: April 2020

Abstract
Treatment for sexual offending equips men with learning disabilities with tools required for pro-social community living. In the past, risk aversiveness prevented discharges from hospital, but fieldwork took place at the time of the Transforming Care Agenda, which sought to enable more people to return to their communities. This offered the opportunity to gain unique insights into community resettlement planning in cases that require ongoing risk management. Eleven case studies were examined through qualitative interviews with the men and professionals. A realist evaluation methodology was applied to examine how treatment outcomes manifested longer term. It was evidenced that treatment had equipped men with risk management tools, as well as encouraged them to develop realistic visions for their pro-social futures and that both outcomes come to fruition under conditions that allow positive risk taking. The welfareist and user-led nature of working towards pro-social community living makes this a useful toolkit for social work, whilst input from forensic health services was valued for skilling up the social care workforce. However, discharge practices continued to be influenced by contextual factors, including local availability of resources and personal attributes, such as men’s sexual preferences and levels of compliance and some men remained in hospital.
Sensitivity and Specificity of Treponemal-specific Tests for the Diagnosis of Syphilis
Authors: Park Ina U , Tran Anthony , Pereira Lara , Fakile Yetunde 
Published: April 2020

AbstractWe conducted a systematic review of relevant syphilis diagnostic literature to address the question, “What is the sensitivity and specificity of the treponemal tests currently approved by the Food and Drug Administration (FDA) for the diagnosis of syphilis (by stage)?” There were 16 treponemal assays evaluated: 13 immunoassays and 3 manual assays (fluorescent treponemal antibody absorbed test [FTA-ABS], microhemagglutination assay for Treponema pallidum antibodies [MHA-TP], Treponema pallidum particle agglutination assay [TP-PA]). MHA-TP and FTA-ABS were less sensitive in primary and secondary syphilis than TP-PA; TP-PA is the most specific manual treponemal assay. There is insufficient evidence to recommend one particular treponemal immunoassay (eg, enzyme immunoassays, chemiluminescence immunoassays, microbead immunoassays) over another based on published performance data. For diagnosis of neurosyphilis, cerebrospinal fluid (CSF) TP-PA has similar performance to CSF FTA-ABS in studies with patients with definitive or presumptive neurosyphilis. However, CSF treponemal testing has limitations in its sensitivity and specificity and should be interpreted within the context of the clinical scenario, additional CSF test results and syphilis prevalence.
Testing for SARS-CoV-2: Can We Stop at 2?
Authors: Lee Tau Hong , Junhao Lin Ray , Lin Raymond T P , Barkham Timothy , Rao Pooja , Leo Yee-Sin , Chien Lye David , Young Barnaby ,   for the National Centre for Infectious Diseases COVID-19 Outbreak Research Team
Published: April 2020

Abstract
The COVID-19 epidemic requires accurate identification and isolation of confirmed cases for effective control. This report describes the effectiveness of our testing strategy and highlights the importance of repeat testing in suspected cases in our cohort.
Intra-Tile Parallelization for Two-Level Perfectly Nested Loops With Non-Uniform Dependences
Authors: Abdi Reyhan Zahra , Lotfi Shahriar , Isazadeh Ayaz , Karimpour Jaber 
Published: April 2020

AbstractMost important scientific and engineering applications have complex computations or large data. In all these applications, a huge amount of time is consumed by nested loops. Therefore, loops are the main source of the parallelization of scientific and engineering programs. Many parallelizing compilers focus on parallelization of nested loops with uniform dependences, and parallelization of nested loops with non-uniform dependences has not been extensively investigated. This paper addresses the problem of parallelizing two-level nested loops with non-uniform dependences. The aim is to minimize the execution time by improving the load balancing and minimizing the inter-processor communication. We propose a new tiling algorithm, k-StepIntraTiling, using bin packing problem to minimize the execution time. We demonstrate the effectiveness of the proposed method in several experiments. Simulation and experimental results show that the algorithm effectively reduces the total execution time of several benchmarks compared to the other tiling methods.
The harm of delayed diagnosis of arrhythmogenic cardiac sarcoidosis: a case series
Authors: Hoogendoorn Jarieke C , Ninaber Maarten K , Piers Sebastiaan R D , de Riva Marta , Grauss Robert W , Bogun Frank M , Zeppenfeld Katja 
Published: April 2020

AbstractAimsCardiac sarcoidosis (CS) is a known cause of ventricular tachycardia (VT). However, an arrhythmogenic presentation may not prompt immediate comprehensive evaluation. We aimed to assess the diagnostic and disease course of patients with arrhythmogenic cardiac sarcoidosis (ACS).Methods and resultsFrom the Leiden VT-ablation-registry, consecutive patients with CS as underlying aetiology were retrospectively included. Data on clinical presentation, time-to-diagnosis, cardiac function, and clinical outcomes were collected. Patients were divided in early (&lt;6 months from first cardiac presentation) and late diagnosis. After exclusion of patients with known causes of non-ischaemic cardiomyopathy (NICM), 15 (12%) out of 129 patients with idiopathic NICM were ultimately diagnosed with CS and included. Five patients were diagnosed early; all had early presentation with VTs. Ten patients had a late diagnosis with a median delay of 24 (IQR 15–44) months, despite presentation with VT (n = 5) and atrioventricular block (n = 4). In 6 of 10 patients, reason for suspicion of ACS was the electroanatomical scar pattern. In patients with early diagnosis, immunosuppressive therapy was immediately initiated with stable cardiac function during follow-up. Adversely, in 7 of 10 patients with late diagnosis, cardiac function deteriorated before diagnosis, and in only one cardiac function recovered with immunosuppressive therapy. Six (40%) patients died (five of six with late diagnosis).ConclusionArrhythmogenic cardiac sarcoidosis is an important differential diagnosis in NICM patients referred for VT ablation. Importantly, the diagnosis is frequently delayed, which leads to a severe disease course, including irreversible cardiac dysfunction and death. Early recognition, which can be facilitated by electroanatomical mapping, is crucial.
The Foreclosure Crisis, Community Change, and the Cognitive Health of Older Adults
Authors: Friedman Esther M , Houle Jason N , Cagney Kathleen A , Slaughter Mary E , Shih Regina A 
Published: April 2020

AbstractObjectivesWhile home foreclosures are often thought of as a household-level event, the consequences may be far-reaching, and spill over to the broader community. Older adults, in particular, could be affected by the spiral of community changes that result from foreclosures, but we know very little about how the foreclosure crisis is related to older adult health, in particular cognition.MethodThis article uses growth curve models and data from the Health and Retirement Study matched to Census and county-level foreclosure data to examine whether community foreclosures are related to older adults’ cognitive health and the mechanisms responsible.ResultsWe find that higher rates of county-level foreclosures are associated with a faster decline in individual cognition at older ages. Although we examined an extensive number of individual and community mechanisms, including individual housing wealth and depressive symptoms, community structural factors, social factors, and perceptions of physical disorder and cohesion, none of the mechanisms examined here explained this relationship.DiscussionThis study shows that the adverse consequences of home foreclosures spill over to the local community, with implications for the cognitive health of older adults.