bluuebunny/crossref_metadata_2025_split huggingface dataset:
Models for the self-heating evaluation of a gallium nitride-based high electron mobility transistor
Authors: Florovič M , Kováč J , Kováč J , Chvála A , Weis M , Jacquet J-C , Delage S L 
Published: December 2020

Abstract
We propose a novel model approach for temperature evaluation in the channel region of a InAlN/AlN/gallium nitride high electron mobility transistor (HEMT) due to self-heating effects. The heat transfer in a HEMT device has been investigated experimentally by the nearby temperature sensor and compared by theoretical models solved by both numerical and analytical methods. The average temperature of the channel area of almost 160 °C for dissipated power of 2 W was determined using the drain-source current variation analysis. The electrical and thermal behavioral numerical model under quasi-static conditions have been used to describe the HEMT device. In contrast, the one-dimensional thermal model for analytical evaluation has been proposed as an alternative approach. Surprisingly, the experimental results verified not only the validity of precise numerical simulation but also the simplified analytical model that makes it a reliable tool even for complex electronic devices.
Study of contact resistivity of a no-insulation superconducting coil
Authors: Liu Yingzhen , Ou Jing , Gyuraki Roland , Schreiner Fabian , de Sousa Wescley T B , Noe Mathias , Grilli Francesco 
Published: December 2020

Abstract
Previous studies of test coils have demonstrated the high thermal and electrical stability of no-insulation (NI) high temperature superconducting (HTS) coils thanks to the presence of turn-to-turn current paths. These turn-to-turn current paths in a NI coil are significantly influenced by the contact resistivity. In practice, it is very challenging to measure the contact resistivity of a NI coil by direct experiments of short samples, since the contact resistivity of superconducting tapes is influenced by surface roughness and tolerance, stress, temperature etc. A proper simulation model is needed to investigate the contact resistivity of the NI coils with dedicated experiments. Hence, in this paper a distributed circuit model is employed. This model, implemented in Matlab 2018a, considers the local contact resistivity, self and mutual inductance, and HTS resistance, which depends on the supplied current, magnetic field and temperature. To validate the model, experimental results from literature, including sudden discharge, and charge–discharge processes, are employed and the results from simulations are consistent with experimental results. Then the model is used to investigate the equivalent contact resistivity of a 157-turn NI coil. Through the comparison of simulated and experimental results, it is found that the contact resistivity of the NI coil has an inhomogeneous distribution. When the current changes with different speeds, ramping rates or frequency, a different number of turn-to-turn contacts carries radial current. Since the turn-to-turn contacts have different contact resistivity, the equivalent contact resistivity calculated from sudden discharge cannot be used in simulations to reproduce all the experimental data.
A scalable superconducting nanowire memory cell and preliminary array test
Authors: Butters Brenden A , Baghdadi Reza , Onen Murat , Toomey Emily A , Medeiros Owen , Berggren Karl K 
Published: December 2020

Abstract
There has been a demand for a scalable superconducting memory technology for cryogenic computing for some time. This demand has proven difficult to satisfy due to the simultaneous need for high speed operation, low power consumption, and high density, all while maintaining cryogenic and SFQ compatibility. In an effort to satisfy this demand, we have developed a simple memory cell based on our prior work with nanowire-based memories. Due to the memory cell’s reliance on kinetic inductance, the cell can be scaled to almost any size. The cell has been designed specifically such that it can easily form into an array simply by arranging in a 2D pattern. This design eliminated the need for external addressing circuitry. This new cell, when operated in isolation and without the heater, performs very well with predicted bit error rates around 10−17. However, preliminary array tests show that while the memory operates, the predicted error rates rise to 1.5 × 10−3. We believe that this issue is predominantly due to the hTron-channel kinetic inductance dramatically changing upon the application of the row-select heaters. This issue might be addressed by designing the cell to compensate for the change in kinetic inductance when the heater is activated. If this remedy proves to be effective, then this memory would enable the development of compact and scalable memory arrays.
Waveform analysis of a large-area superconducting nanowire single photon detector
Authors: Marvinney Claire E , Lerner Brian E , Puretzky Alexander A , Miller Aaron J , Lawrie Benjamin J 
Published: December 2020

Abstract
Superconducting nanowire single photon detectors (SNSPDs) are typically used as single-mode-fiber-coupled single-pixel detectors, but large area detectors are increasingly critical for applications ranging from microscopy to free-space quantum communications. However, the long meander-line length of such large-area SNSPDs results in a proportionately large kinetic inductance that affects the waveform generated by the device. Here, we explore changes in the rising edge of the readout pulse for a single-pixel large-area SNSPD as a function of the optical spot size on the detector and compare to the rising edge of the dark-count waveform. We observe a bimodal distribution of bright-count rise times and show that the probability of a slow rise time increases in the limit of large spot sizes, indicative of a position sensitive response. Additionally, in the limit of low bias currents, the dark-count readout pulse is most similar to the large spot-size bright-count readout pulse, which suggests that dark counts arise from locations spanning the device. These results are consistent with a simple model of traveling microwave modes excited by single photons incident at varying positions along the length of the nanowire.
Protein subcellular localization based on deep image features and criterion learning strategy
Authors: Su Ran , He Linlin , Liu Tianling , Liu Xiaofeng , Wei Leyi 
Published: December 2020

AbstractThe spatial distribution of proteome at subcellular levels provides clues for protein functions, thus is important to human biology and medicine. Imaging-based methods are one of the most important approaches for predicting protein subcellular location. Although deep neural networks have shown impressive performance in a number of imaging tasks, its application to protein subcellular localization has not been sufficiently explored. In this study, we developed a deep imaging-based approach to localize the proteins at subcellular levels. Based on deep image features extracted from convolutional neural networks (CNNs), both single-label and multi-label locations can be accurately predicted. Particularly, the multi-label prediction is quite a challenging task. Here we developed a criterion learning strategy to exploit the label–attribute relevancy and label–label relevancy. A criterion that was used to determine the final label set was automatically obtained during the learning procedure. We concluded an optimal CNN architecture that could give the best results. Besides, experiments show that compared with the hand-crafted features, the deep features present more accurate prediction with less features. The implementation for the proposed method is available at https://github.com/RanSuLab/ProteinSubcellularLocation.
Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
Authors: Stiehler Felix , Steinborn Marvin , Scholz Stephan , Dey Daniela , Weber Andreas P M , Denton Alisandra K 
Published: December 2020

Abstract

Motivation
Current state-of-the-art tools for the de novo annotation of genes in eukaryotic genomes have to be specifically fitted for each species and still often produce annotations that can be improved much further. The fundamental algorithmic architecture for these tools has remained largely unchanged for about two decades, limiting learning capabilities. Here, we set out to improve the cross-species annotation of genes from DNA sequence alone with the help of deep learning. The goal is to eliminate the dependency on a closely related gene model while also improving the predictive quality in general with a fundamentally new architecture.

Results
We present Helixer, a framework for the development and usage of a cross-species deep learning model that improves significantly on performance and generalizability when compared to more traditional methods. We evaluate our approach by building a single vertebrate model for the base-wise annotation of 186 animal genomes and a separate land plant model for 51 plant genomes. Our predictions are shown to be much less sensitive to the length of the genome than those of a current state-of-the-art tool. We also present two novel post-processing techniques that each worked to further strengthen our annotations and show in-depth results of an RNA-Seq based comparison of our predictions. Our method does not yet produce comprehensive gene models but rather outputs base pair wise probabilities.

Availability and implementation
The source code of this work is available at https://github.com/weberlab-hhu/Helixer under the GNU General Public License v3.0. The trained models are available at https://doi.org/10.5281/zenodo.3974409

Supplementary information
Supplementary data are available at Bioinformatics online.
Development of an HPLC-UV Method to Assay Empagliflozin Tablets and Identification of the Major Photoproduct by Quadrupole Time-of-Flight Mass Spectrometry
Authors: Burin Suelen Leticia , Lourenço Rebeca Lino , Doneda Morgana , Müller Edson Irineu , Paula Fávero Reisdorfer , Adams Andréa Inês Horn 
Published: December 2020

Abstract
Diabetes is a set of metabolic disorders that affect &gt;400 million individuals worldwide. Empagliflozin belongs to the gliflozin class and is used orally to treat type 2 diabetes. In this study, a simple stability-indicating HPLC-UV method was developed to assay empagliflozin tablets and its main photoproduct was identified by high-resolution mass spectrometry. The mobile phase, which was optimized by Central Composite Design, was composed of methanol, acetonitrile and purified water (60:5:35 v/v), at a flow rate of 1 mL min−1. The calibration curve was linear in the range of 5–150 μg mL−1. All the validation parameters were met and the method was specific, even in the presence of degradation products. In the forced degradation study, empagliflozin standard and empagliflozin tablets were submitted to several conditions (acidic, alkaline, neutral and oxidant media, thermal, photolytic and humidity), and empagliflozin showed instability under all these conditions. A degradation product generated after drug exposure to ultraviolet C radiation was isolated and analyzed by quadrupole time-of-flight mass spectrometry, and the results suggested that empagliflozin undergoes decomposition by a dechlorination pathway. In silico toxicity was predicted for the degradation product, which showed a high risk of genotoxicity and hepatotoxicity.
Influence of sea ice dynamics on population energetics of Western Hudson Bay polar bears
Authors: Johnson Amy C , Reimer Jody R , Lunn Nicholas J , Stirling Ian , McGeachy David , Derocher Andrew E 
Published: December 2020

Abstract
The Arctic marine ecosystem has experienced extensive changes in sea ice dynamics, with significant effects on ice-dependent species such as polar bears (Ursus maritimus). We used annual estimates of the numbers of bears onshore in the core summering area, age/sex structure and body condition data to estimate population energy density and storage energy in Western Hudson Bay polar bears from 1985 to 2018. We examined intra-population variation in energetic patterns, temporal energetic trends and the relationship between population energetics and sea ice conditions. Energy metrics for most demographic classes declined over time in relation to earlier sea ice breakup, most significantly for solitary adult females and subadult males, suggesting their greater vulnerability to nutritional stress than other age/sex classes. Temporal declines in population energy metrics were related to earlier breakup and longer lagged open-water periods, suggesting multi-year effects of sea ice decline. The length of the open-water period ranged from 102 to 166 days and increased significantly by 9.9 days/decade over the study period. Total population energy density and storage energy were significantly lower when sea ice breakup occurred earlier and the lagged open-water period was longer. At the earliest breakup and a lagged open-water period of 180 days, population energy density was predicted to be 33% lower than our minimum estimated energy density and population storage energy was predicted to be 40% lower than the minimum estimated storage energy. Consequently, over the study, the total population energy density declined by 53% (mean: 3668 ± 386 MJ kg-1/decade) and total population storage energy declined by 56% (mean: 435900 ± 46770 MJ/decade). This study provides insights into ecological mechanisms linking population responses to sea ice decline and highlights the significance of maintaining long-term research programs.
Fully coupled dynamic simulations of bioprosthetic aortic valves based on an embedded strategy for fluid–structure interaction with contact
Authors: Nestola Maria G C , Zulian Patrick , Gaedke-Merzhäuser Lisa , Krause Rolf 
Published: December 2020

Abstract

Aims
This work aims at presenting a fully coupled approach for the numerical solution of contact problems between multiple elastic structures immersed in a fluid flow. The key features of the computational model are (i) a fully coupled fluid–structure interaction with contact, (ii) the use of a fibre-reinforced material for the leaflets, (iii) a stent, and (iv) a compliant aortic root.

Methods and results
The computational model takes inspiration from the immersed boundary techniques and allows the numerical simulation of the blood–tissue interaction of bioprosthetic heart valves (BHVs) as well as the contact among the leaflets. First, we present pure mechanical simulations, where blood is neglected, to assess the performance of different material properties and valve designs. Secondly, fully coupled fluid–structure interaction simulations are employed to analyse the combination of haemodynamic and mechanical characteristics. The isotropic leaflet tissue experiences high-stress values compared to the fibre-reinforced material model. Moreover, elongated leaflets show a stress concentration close to the base of the stent. We observe a fully developed flow at the systolic stage of the heartbeat. On the other hand, flow recirculation appears along the aortic wall during diastole.

Conclusion
The presented FSI approach can be used for analysing the mechanical and haemodynamic performance of a BHV. Our study suggests that stresses concentrate in the regions where leaflets are attached to the stent and in the portion of the aortic root where the BHV is placed. The results from this study may inspire new BHV designs that can provide a better stress distribution.
Optimizing cryoballoon pulmonary vein isolation: lessons from &gt;1000 procedures— the Frankfurt approach
Authors: Bordignon Stefano , Chen Shaojie , Bologna Fabrizio , Thohoku Shota , Urbanek Lukas , Willems Franziska , Zanchi Simone , Bianchini Lorenzo , Trolese Luca , Konstantinou Athanasios , Fuernkranz Alexander , Schmidt Boris , Chun Julian K R 
Published: December 2020

Abstract

Aims
Cryoballoon (CB) pulmonary vein isolation (PVI) is an accepted ablation strategy for rhythm control in atrial fibrillation (AF). We describe efficacy and safety in a high volume centre with a long experience in the use of the second-generation CB (CB2).

Methods and results
Consecutive paroxysmal AF (PAF) or persistent AF (persAF) patients undergoing CB2-PVI were enrolled. Procedural data, efficacy, and safety issues were systematically collected. The 28 mm CB2 was used in combination with an inner lumen spiral catheter, a luminal oesophageal temperature (LET) probe was used with a cut-off of 15°C, the phrenic nerve (PN) monitored during septal PVs ablation. Freeze duration was mainly set at 240 s with a bonus application in case of delayed time-to-isolation (TTI &gt; 75 s). A total of 1017 CB2 procedures were analysed (58% male, 66 ± 12 years old, 70% with PAF). 3964 PVs were identified, 99.8% PVs isolated using solely the 28 mm CB. Mean procedure time was 69 ± 25 min, TTI during the first application was recorded in 77% of PVs after a mean of 48 ± 31 s. We recorded 0.2% cardiac tamponade, 4.8% PN injury (1.6% of PN palsy), and 19% of LET &lt; 15°C. Among 725 patients with follow-up data, 84% with PAF and 75% with persAF were in stable SR at 1 year. Shorter freezing duration and longer TTI were procedural predictors for recurrence.

Conclusion
Cryoballoon procedures are fast and associated with a benign safety profile. Shorter TTI and longer freeze durations are associated with sinus rhythm during follow-up.
A single nucleotide polymorphism in an IgA1 protease gene determines Streptococcus pneumoniae adaptation to the middle ear during otitis media
Authors: Tikhomirova Alexandra , Trappetti Claudia , Paton James C , Watson-Haigh Nathan , Wabnitz David , Jervis-Bardy Jake , Jardeleza Camille , Kidd Stephen P 
Published: December 2020

ABSTRACT
Factors facilitating the chronicity of otitis media (OM) in children are, to date, not fully understood. An understanding of molecular factors aiding bacterial persistence within the middle ear during OM could reveal pathways required for disease. This study performed a detailed analysis of Streptococcus pneumoniae populations isolated from the nasopharynx and middle ear of one OM case. Isolates were assessed for growth in vitro and infection in a mouse intranasal challenge model. Whole genome sequencing was performed to compare the nasopharyngeal and middle ear isolates. The middle ear isolate displayed a reduced rate of growth and enhanced potential to transit to the middle ear in a murine model. The middle ear population possessed a single nucleotide polymorphism (SNP) in the IgA1 protease gene igA, predicted to render its product non-functional. Allelic exchange mutagenesis of the igA alleles from the genetic variant middle ear and nasopharyngeal isolates was able to reverse the niche-adaptation phenotype in the murine model. These results indicate the potential role of a SNP in the gene encoding the IgA1 protease, in determining S. pneumoniae adaptation to the middle ear during chronic OM. In contrast, a functional IgA1 protease was associated with increased colonisation of the nasopharynx.
The parabolic p-Laplacian with fractional differentiability
Authors: Breit Dominic , Diening Lars , Storn Johannes , Wichmann Jörn 
Published: December 2020

Abstract
We study the parabolic $p$-Laplacian system in a bounded domain. We deduce optimal convergence rates for the space–time discretization based on an implicit Euler scheme in time. Our estimates are expressed in terms of Nikolskiǐ spaces and therefore cover situations when the (gradient of the) solution has only fractional derivatives in space and time. The main novelty is that, different to all previous results, we do not assume any coupling condition between the space and time resolutions $h$ and $\tau $. For this we show that the $L^2$-projection is compatible with the quasi-norm. The theoretical error analysis is complemented by numerical experiments.
A Switchable Solvent-Based Liquid Phase Microextraction Method for the Detection of Cadmium in Water Samples with Flame Atomic Absorption Spectrometry
Authors: Aydin Urucu Oya , Aracier Esra Duygu 
Published: December 2020

Abstract

Background
The natural concentration of trace elements in water and soil depends on the geological, geomorphological, and climate characteristics of the region. The rapid increase of technology in recent years has increased concentrations of trace elements in nature.

Objective
Separation and enrichment methods are needed to detect trace amounts of heavy metals that cannot be detected due to the detection limit of the instruments or the matrix effect in samples. Recently, low hazard solvents compatible with green chemistry have been used in preconcentration/separation studies of Cd(II).

Methods
Switchable solvent-based liquid phase microextraction is an environmentally-friendly, simple, and fast procedure for the determination of Cd(II) ions in environmental samples combined with flame atomic absorption spectrometry (FAAS).

Results
The switchable polarity solvent was prepared with N,N-dimethyl-n-octylamine. 2–(5-Bromo-2-pyridylazo)-5-(diethylamino) phenol was used as the complexing agent. Important parameters such as pH, amount of switchable polarity solvent and NaOH, as well as ligand and sample volume, all of which might affect the microextraction efficiency were optimized. Under optimal experimental conditions, linear range was found to be between 5 and 500 µg/L. The limit of detection, preconcentration factor, and relative standard deviation were 0.89 μg/L, 150, and 3.2%, respectively.

Highlights
The accuracy of our method was confirmed by the analysis of certified reference material SPS-WW1 Batch 106 (Waste Waters). The developed procedure was successfully applied to determine the cadmium contents of environmental water samples. We believe that this environmentally-friendly method will be useful in detecting Cd(II) ions in water samples.
An Overview of the Pepper Weevil (Coleoptera: Curculionidae) as a Pest of Greenhouse Peppers
Authors: Fernández D Catalina , VanLaerhoven Sherah L , McCreary Cara , Labbé Roselyne M 
Published: December 2020

Abstract
The pepper weevil (Anthonomus eugenii Cano) is a destructive insect pest of field and greenhouse pepper crops across North America. Its management remains challenging with significant implications for pepper production, despite a documented presence in Central America, Mexico, the United States, and the Caribbean for approximately a century, and recently in Canada. Currently, the main tools and methods applied to manage pepper weevil populations in greenhouse peppers are the implementation of strict biosecurity protocols, diligent monitoring, physical and cultural management techniques, and chemical insecticides when necessary. However, these tools can be costly, labor-intensive, and insufficient, particularly when new outbreaks go undetected for prolonged periods. Additionally, the use of available insecticides is limited due to significant nontarget effects these have on biological control agents used to manage other important greenhouse pepper pests. Recently, research efforts have focused on developing better tools for pepper weevil management to mitigate a rising incidence of insecticide resistance and the spread of weevils into temperate regions, however, multiple constraints remain. Here, we review the current state of knowledge of the pepper weevil and identify information gaps, which future research should address to improve the targeted management of this pest in greenhouse pepper production systems.