bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of Ar+16 charge exchange recombination spectroscopy measurements at ASDEX Upgrade
Authors: McDermott R.M. , Dux R. , Guzman F. , Pütterich T. , Fischer R. , Kappatou A. 
Published: October 2020

Abstract
Argon is being considered as a radiator for future fusion devices. To support this, experiments in present day devices are needed to assess its effectiveness as a radiator and to study its compatibility with key aspects of reactor operation. For these purposes, accurate measurement of the Ar density in the confined plasma region are required. Charge exchange recombination spectroscopy is capable of providing this information, but requires validated cross-sections to produce accurate density profiles. For typical ASDEX Upgrade plasma parameters Ar+16 is the charge state of the most interest and the ArXVI n = 15–14 was identified as the best target for these measurements. Due to the fine structure splitting, the Ar charge exchange (CX) emission lines are highly asymmetric and detailed modeling is required to extract accurate ion temperatures or rotations. For the evaluation of Ar+16 densities, there are two main sets of CX cross-sections available: the data calculated by Schultz et al (Whyte et al 2010 J. Phys. B At. Mol. Opt. Phys
43 144002, Schultz et al 2010 J. Phys. B At. Mol. Opt. Phys.
43 144002) (ORNL) and by Errea et al (2006 J. Phys. B At. Mol. Opt. Phys.
39 L91) (UAM). These cross-sections differ by over an order of magnitude and have very different energy dependencies. In this work, the validity of these datasets is tested experimentally. The Ar density profiles calculated using the ORNL cross-sections are 10–50× too large while the UAM densities are a factor of 2.73 too small. The UAM data, however, does a much better job at capturing the observed energy dependence. The authors conclude that the CTMC calculations of Errea, which use a hydrogenic distribution to describe the initial target and donor distributions better reproduce the experimental data. However, to produce accurate Ar density profiles, these cross-sections need to be corrected downward and the best profiles are produced with a small correction to the UAM energy dependence.
The role of collisionless trapped electron mode turbulence on removal of helium ash and transport of deuterium-tritium ions
Authors: Guo Weixin , Zhang Mingzhu , Wang Lu , Zhuang Ge 
Published: October 2020

Abstract
Removal of helium ash and the anomalous transport of deuterium (D) and tritium (T) ions driven by collisionless trapped electron mode (CTEM) turbulence in tokamak plasmas with weak magnetic shear are studied. We derive the eigenvalue of CTEM with helium ash, and calculate the quasi-linear turbulent fluxes of helium ash, D and T ions simultaneously. Based on the analytical results, the parametric dependence of CTEM instability as well as the anomalous transport of helium ash and D-T ions is investigated, in order to explore the parameter region that is favorable for expelling more helium ash than D and T ions. It is found that helium ash with higher temperature and steeper density profile plays a role of destabilizing CTEM instability, and has higher transport level than that of T ions. We also find that increasing electron temperature and flattening electron density profile are favorable for exhausting helium ash. Isotopic effects (i.e. increasing the fraction of T ions) enhance the transport of both helium ash and D-T ions. Moreover, the trend of stronger transport level of helium ash than that of D-T ions is enhanced by raising electron temperature and flattening electron density profile as well as isotopic effects. Besides, the diffusivity is much larger than the convection. This indicates that the CTEM turbulence driven helium ash transport is favorable for removing helium ash under the parameter region used in the present paper. The possible relevance of our theoretical results to experimental observations is also discussed.
Simulations of fusion neutron source based on the axially symmetric mirror trap for the thorium hybrid reactor
Authors: Prikhodko V.V. , Arzhannikov A.V. 
Published: October 2020

Abstract
The axially symmetric open mirror trap is considered as a neutron source for the hybrid thorium reactor. Plasma parameters are optimized in order to achieve the maximum neutron yield in the volume surrounded by the subcritical fuel assembly while meeting the stability criteria. For plasma consisting of equal amounts of deuterium and tritium isotopes, in the fuel assembly region, the neutron yield was found to be 0.6 × 1017 n/s at an input power of 20 MW, and it will increase to 2.6 × 1017 n/s if the input power increases two times. In optimal regimes, the plasma parameters were close to those achieved in experiments at the GDT facility.
Efficiency investigation of a negative hydrogen ion beam production with the use of the gasdynamic ECR plasma source
Authors: Lapin R L , Skalyga V A , Izotov I V , Golubev S V , Razin S V , Bokhanov A F , Kazakov M Yu , Shaposhnikov R A , Kiseleva E M , Tarvainen O 
Published: October 2020

Abstract
Negative hydrogen ion sources are of great demand in modern physics as injectors into accelerators and drivers for neutral beam injectors for fusion devices. It has been shown earlier that the use of the gasdynamic ECR discharge provides the opportunity to extract up to 80 mA/cm2 of negative ion current density. We studied experimentally the volumetric negative hydrogen ion production and vacuum ultraviolet emission in a gasdynamic ECR discharge. The high-density plasma was sustained by the pulsed 37 GHz / 100 kW gyrotron radiation in a magnetic configuration consisting of two consecutive simple mirror traps. The future prospects of the volumetric H− source based on the gasdynamic ECR discharge related to the transition from pulsed to continuous operating mode with the use of an improved magnetic confinement system are discussed. Numerical simulation of the negative hydrogen ion beam extraction at the continuous operating mode facility was performed. Optimal configuration of the extraction electrodes and the electron damping magnets was found.
Numerical simulations of nanosecond discharge in gas-dynamic flows
Authors: Ermakov E A , Ivanov I E , Kryukov I A , Mursenkova I V , Znamenskaya I A 
Published: October 2020

Abstract
Numerical simulations were performed of the nanosecond high-voltage breakdown in nitrogen at a voltage of 25–35 kV in the sub-centimeter discharge gaps. The streamer configurations were studied at two constant pressures, as well as at the radially varying pressure, simulating the pressure distribution in the axial region of the vortex “columnar” gas-dynamic flow. In each case, the characteristic parameters and propagation velocities of the primary and secondary streamers were calculated. It was ascertained that the law of pressure change in the radial direction strongly affects the spatial structure of the negative streamer.
Combined thermomechanical and optical simulations of planar-optical polymer waveguides
Authors: Suar Monali , Baran Murat , Günther Axel , Roth Bernhard 
Published: October 2020

Abstract
In this work, we describe a theoretical approach for combined thermal, mechanical and optical simulation and analysis of planar polymer waveguides. We consider a finite element approach for thermal and stress/deformation simulation. Also, a Crank-Nicholson finite difference beam propagation method (CN-BPM) is implemented to perform the optical simulation. The results of the finite element (thermo-mechanical) analysis are coupled with the CN-BPM results to carry out the optical simulation of poly(methyl methacrylate) (PMMA) waveguides as function of temperature. For thermal simulation, a model was designed where a polysilicon microheater was added to the upper cladding of the PMMA waveguides to vary the temperature between 20 °C and 200 °C. Thus, the impact of the induced temperature gradients on the refractive index modulation of the PMMA waveguides and the corresponding change in numerical aperture are obtained. In addition, the temperature gradients influence the beam intensity profiles and the movement of the primary eyes within the optical waveguides, thus, impacting the optical properties. Furthermore, the thermally induced mechanical stress and deformation were calculated for transverse and axial directions. In the next step, validation of the model by systematic experimental studies will be performed. In general, our approach provides a toolbox for more comprehensive multi-physics theoretical analysis of polymer-optical waveguides which, in future, can be extended to more complex and functional structures as required for flexible sensor networks, as example.
Solvent screening for efficient chemical exfoliation of graphite
Authors: Nu Thanh Ton Nhan , Ha Minh-Quyet , Ikenaga Takuma , Thakur Ashutosh , Dam Hieu-Chi , Taniike Toshiaki 
Published: October 2020

Abstract
Chemical exfoliation of graphite is an effective method to produce graphene of relative high quality, where the choice of solvents plays an important role in the product yield and quality. Here, we performed screening of different solvents and their mixtures for the liquid-phase exfoliation of graphite under ultrasonication. A synergistic effect among aromatic, amine, and halogen groups was identified. The synergy was more effectively exploited when these functional groups were combined through solvent mixtures compared to when they were introduced in the molecular structure of single solvents. The screening results were utilized for a novel machine learning technique based on the Dempster–Shafer theory of evidence to systematically investigate synergistic effects and recommend new solvent combinations. The proposed combination of the experiment and the data-driven approach was demonstrated to be powerful for exploring synergistic solvent combinations.
Metastability triggered reactivity in clusters at realistic conditions: a case study of N-doped (TiO2)
n
for photocatalysis
Authors: Saini Shikha , Basera Pooja , Kumar Manish , Bhumla Preeti , Bhattacharya Saswata 
Published: October 2020

Abstract
We present a strategy, by taking a prototypical model system for photocatalysis (viz. N-doped (TiO2)
n
clusters), to accurately design photocatalyst with enhanced reactivity at a given environmental conditions (i.e. temperature (T), pressure (

p

O

2

) and doping (µ

e
)). Since free energy potential energy surface consists of many competing isomers even in a small energy window, computational design of specific metastable photocatalysts with enhanced activity is extremely challenging. This requires fixing various parameters as follows; (i) favorable formation energy, (ii) low fundamental gap, (iii) low excitation energy, (iv) high vertical electron affinity (VEA) and (v) low vertical ionization potential (VIP) to drive the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) for water splitting. Here, we show that by integrating several first principles based methodologies that consideration of the global minimum structure alone can severely underestimate the activity. First, we have used a suite of genetic algorithms (namely, searching clusters with conventional minimum total energy ((GA)

E

); searching clusters with specific property i.e. high VEA ((GA)

P

EA

), and low VIP ((GA)

P

IP

)) to model the N-doped (TiO2)
n
( n = 4–10, 15, 20) (meta)stable clusters. Next, we have identified its free energy using ab initio atomistic thermodynamics to confirm that the metastable structures are not too far from the free energy global minima. We find that N-substitution ((N)

O

) prefers to reside at highly coordinated oxygen site, whereas N-interstitial ((NO)

O

) and split-interstitial ((N

2

)

O

) favor the dangling oxygen site. (NO)

O

and (N

2

)

O

doped states are thermodynamically stable at finite temperature (T) and pressure (

p

O

2

). Interestingly, each types of defect (viz. substitution, interstitials) reduce the fundamental gap and excitation energy substantially. However, (N

2

)

O

doped clusters are found to be less probable in the Pourbaix phase diagram, whereas (N)

O

and (NO)

O

doped metastable clusters show significant occupance probability near the phase boundaries. The latter ensures much higher electrocatalytic activity for water splitting than the most stable configurations.
Independent component analysis for pulse compressed frequency modulated thermal wave imaging for inspection of mild steel
Authors: Kaur Kirandeep , Mulaveesala Ravibabu , Rani Anju , Kher Vansha 
Published: October 2020

Abstract
Non-destructive testing & evaluation plays a crucial role in various sectors for testing the reliability of materials. Of the different available non-destructive examination techniques, thermal non-destructive testing provides fast and remote inspection of the materials. Among various widely used thermal non-destructive testing techniques, frequency modulated thermal wave imaging gained its importance due to its higher test sensitivity and resolution. The adopted matched filter approach on the obtained temporal temperature distribution further concentrates supplied excitation energy into a narrow duration high peak power pulse. In this paper, the merits of the reconstructed high peak power pulsed data have been considered and emphasized in the context of independent component analysis. The obtained results clearly indicate that pulse compressed data improves defect detectability, reliability, memory usage, and computational complexity.
A summons to the magistrates’ courts in South Africa and Uganda
Authors: Cooper-Knock S J , Macdonald Anna 
Published: October 2020

Abstract
The expansive literature on law and justice across Africa emphasizes why people do not use lower state courts. Consequently, a striking lack of attention is paid to how and why people do engage with lower state courts. Drawing on a systematic literature review and a multi-sited qualitative study, we make three contributions on this topic. First, we explore how this academic gap emerged. Second, we critique the procedural justice model that currently underlies much ‘access to justice’ programming, which seeks to improve citizens’ engagements with the courts. In place of what we describe as its arithmetic assumptions about institutional engagement, value, and legitimacy, we propose a trifactor framework. Citizen engagement, we argue, occurs as people reconcile how they think the courts should act, how they expect them to act, and how they need them to act in any given instance. Third, drawing on our empirical studies, we highlight that this framework is flexible enough to capture people’s actually existing decision-making in a wide variety of settings and to map how those trade-offs shift throughout the process of their case, providing important insights into ideas of justice and statehood.
Identification of Clock Genes Related to Hypertension in Kidney From Spontaneously Hypertensive Rats
Authors: Murata Yusuke , Ueno Takahiro , Tanaka Sho , Kobayashi Hiroki , Okamura Masahiro , Hemmi Seiichiro , Fuke Yoshinobu , Matsumoto Yoshiaki , Abe Masanori , Fukuda Noboru 
Published: October 2020

Abstract

Background
There is a diurnal variation in the blood pressure fluctuation of hypertension, and blood pressure fluctuation abnormality is considered to be an independent risk factor for organ damage including cardiovascular complications. In the current study, we tried to identify molecules responsible for blood pressure circadian rhythm formation under the control of the kidney biological clock in hypertension.

Methods
DNA microarray analysis was performed in kidneys from 5-week-old spontaneously hypertensive rats (SHRs)/Izm, stroke-prone SHR rats (SHRSP)/Izm, and Wistar Kyoto (WKY)/Izm rats. To detect variation, mouse tubular epithelial cells (TCMK-1) were stimulated with dexamethasone. We performed immunostaining and western blot analysis in the renal medulla of kidney from 5-week-old WKY rats and SHRs.

Results
We extracted 1,032 genes with E-box, a binding sequence for BMAL1 and CLOCK using a Gene Set Enrichment Analysis. In a microarray analysis, we identified 12 genes increased as more than 2-fold in the kidneys of SHRs and SHRSP in comparison to WKY rats. In a periodic regression analysis, phosphoribosyl pyrophosphate amidotransferase (Ppat) and fragile X mental retardation, autosomal homolog 1 (Fxr1) showed circadian rhythm. Immunocytochemistry revealed PPAT-positivity in nuclei and cytoplasm in the tubules, and FXR1-positivity in the cytoplasm of TCMK-1. In 5-week-old WKY rat and SHR kidneys, PPAT was localized in the nucleus and cytoplasm of the proximal and distal tubules, and FXR1 was localized to the cytoplasm of the proximal and distal tubules.

Conclusions
PPAT and FXR1 are pivotal molecules in the control of blood pressure circadian rhythm by the kidney in hypertension.
Changes in the brain directly following alcohol consumption—a study of healthy male individuals, with the use of proton magnetic resonance spectroscopy (1HMRS) and diffusion (DWI)
Authors: Urbanik Andrzej , Kozub Justyna , Karcz Paulina , Ostrogórska Monika 
Published: October 2020

Abstract

Aims
To use proton magnetic resonance spectroscopy (1HMRS) and diffusion weighted imaging (DWI) to identify ethanol in the brain directly after consumption, and examine changes in brain metabolite levels and brain microstructure relative to the duration of time following exposure to alcohol.

Methods
The study involved 44 male volunteers (18–55 years). All brain changes were assessed in the frontal lobes, occipital lobes, basal ganglia and cerebellum, however the detailed analyses focused on the frontal lobes. All participants were examined four times, i.e. before and 0.5-hour, 1 hour and 2 hours after consumption of 150 mL pure vodka (60 g of ethanol).

Results
The highest ethanol levels were identified between 0.5 and 1 hour following alcohol intake. There were significant increases in the concentrations of lipids and lactates approximately one hour after alcohol consumption, and the concentration levels were found to normalise during the following two hours. Some statistically insignificant trends of changes were found for tCr, tCho, mI, GABA, Glc, Glx and tNAA. For the DWI and ADC (Apparent Diffusion Coefficient of water) values, the findings showed statistically insignificant decrease and increase, followed by a tendency towards normalisation. Similar associations in changes of metabolite concentrations and DWI and ADC values were found in the other locations investigated in the study.

Conclusion
A single dose of alcohol as used in this experiment produces increases in lipids and lactates in brain tissues that appear reversible.
The Frequency and Content of Discussions About Alcohol Use in Primary Care and Application of the Chief Medical Officer’s Low-Risk Drinking Guidelines: A Cross-Sectional Survey of General Practitioners and Practice Nurses in the UK
Authors: Birch Jack M , Critchlow Nathan , Calman Lynn , Petty Robert , Rosenberg Gillian , Rumgay Harriet , Vohra Jyotsna 
Published: October 2020

Abstract

Aims
To examine how often general practitioners (GPs) and practice nurses (PNs) working in primary care discuss alcohol with patients, what factors prompt discussions, how they approach patient discussions and whether the Chief Medical Officers’ (CMO) revised low-risk drinking guidelines are appropriately advised.

Methods
Cross-sectional survey with GPs and PNs working in primary care in the UK, conducted January–March 2017 (n = 2020). A vignette exercise examined what factors would prompt a discussion about alcohol, whether they would discuss before or after a patient reported exceeded the revised CMO guidelines (14 units per week) and whether the CMO drinking guidelines were appropriately advised. For all patients, participants were asked how often they discussed alcohol and how they approached the discussion (e.g. used screening tool).

Results
The most common prompts to discuss alcohol in the vignette exercise were physical cues (44.7% of participants) or alcohol-related symptoms (23.8%). Most practitioners (70.1%) said they would wait until a patient was exceeding CMO guidelines before instigating discussion. Two-fifths (38.1%) appropriately advised the CMO guidelines in the vignette exercise, with PNs less likely to do so than GPs (odds ratio [OR] = 0.77, P = 0.03). Less than half (44.7%) reportedly asked about alcohol always/often with all patients, with PNs more likely to ask always/often than GPs (OR = 2.22, P &lt; 0.001). Almost three-quarters said they would enquire by asking about units (70.3%), compared to using screening tools.

Conclusion
Further research is required to identify mechanisms to increase the frequency of discussions about alcohol and appropriate recommendation of the CMO drinking guidelines to patients.
Classification and review of free PCR primer design software
Authors: Guo Jingwen , Starr David , Guo Huazhang 
Published: October 2020

Abstract

Motivation
Polymerase chain reaction (PCR) has been a revolutionary biomedical advancement. However, for PCR to be appropriately used, one must spend a significant amount of effort on PCR primer design. Carefully designed PCR primers not only increase sensitivity and specificity, but also decrease effort spent on experimental optimization. Computer software removes the human element by performing and automating the complex and rigorous calculations required in PCR primer design. Classification and review of the available software options and their capabilities should be a valuable resource for any PCR application.

Results
This article focuses on currently available free PCR primer design software and their major functions (https://pcrprimerdesign.github.io/). The software are classified according to their PCR applications, such as Sanger sequencing, reverse transcription quantitative PCR, single nucleotide polymorphism detection, splicing variant detection, methylation detection, microsatellite detection, multiplex PCR and targeted next generation sequencing, and conserved/degenerate primers to clone orthologous genes from related species, new gene family members in the same species, or to detect a group of related pathogens. Each software is summarized to provide a technical review of their capabilities and utilities.
Sapling: accelerating suffix array queries with learned data models
Authors: Kirsche Melanie , Das Arun , Schatz Michael C 
Published: October 2020

Abstract

Motivation
As genomic data becomes more abundant, efficient algorithms and data structures for sequence alignment become increasingly important. The suffix array is a widely used data structure to accelerate alignment, but the binary search algorithm used to query, it requires widespread memory accesses, causing a large number of cache misses on large datasets.

Results
Here, we present Sapling, an algorithm for sequence alignment, which uses a learned data model to augment the suffix array and enable faster queries. We investigate different types of data models, providing an analysis of different neural network models as well as providing an open-source aligner with a compact, practical piecewise linear model. We show that Sapling outperforms both an optimized binary search approach and multiple widely used read aligners on a diverse collection of genomes, including human, bacteria and plants, speeding up the algorithm by more than a factor of two while adding &lt;1% to the suffix array’s memory footprint.

Availability and implementation
The source code and tutorial are available open-source at https://github.com/mkirsche/sapling.

Supplementary information
Supplementary data are available at Bioinformatics online.