bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seeing what is not shown
Authors: Hengesbach Nicole , McInerny Greg J. , Albuquerque João Porto de 
Published: November 2022

Abstract
Critical studies of data visualization often highlight how the reductive nature of visualization methods excludes
data limitations and qualities that are crucial to understanding those data. This case study explores how a data visualization
could express contingent, situated, and contextual facets of data. We examine how such data limitations might be surfaced and
represented within visualizations through an interplay between the critique of an existing data visualization and the development
of alternative designs. Based on a case study of urban tree data, we interrogate data limitations in relation to four different
types of missingness: Incompleteness, Emptiness, Absence, and Nothingness. Our study enables reflections on how data limitations
can be investigated using visualizations and considers the development of a critical visualization practice.
Tunable phase transitions in half-Heusler TbPtBi compound
Authors: Patel Pratik D , Sharma Akariti , Devanarayanan Bharathiganesh , Dutta Paramita , Singh Navinder 
Published: November 2022

Abstract
We report various phase transitions in half-Heusler TbPtBi compound using density functional theory. Specifically, the inclusion of spin–orbit coupling (SOC) leads to the band inversion resulting in the transition from the metallic to the topological semimetallic phase. However, in the presence of SOC, there is a phase transition from the topological semimetal to the trivial semimetal when the material is subjected to compressive strain

−
7

%

. Subsequently, under the further increase of compressive strain

(

⩾
−
7
%

)

, we find an opening of a direct band gap at the point, driving the system from the trivial semimetallic to a semiconducting state with changes in the sequence of the bands. In the absence of SOC, only the transition from the metallic to the semiconducting phase is noticed. Under tensile strain, the TbPtBi compound maintains its phase as in the unstrained condition but with an increase in the hole pocket at the Fermi level, both in the absence and presence of SOC. These tunable phase transitions (especially as a fraction of strain) make this compound very promising for application in various quantum devices, such as highly sensitive strain gauges.
On the effect of forcing on fold bifurcations and early-warning signals in population dynamics
Authors: Remo F , Fuhrmann G , Jäger T 
Published: November 2022

Abstract
The classical fold bifurcation is a paradigmatic example of a critical transition. It has been used in a variety of contexts, including in particular ecology and climate science, to motivate the role of slow recovery rates and increased autocorrelations as early-warning signals of such transitions. We study the influence of external forcing on fold bifurcations and the respective early-warning signals. Thereby, our prime examples are single-species population dynamical models with Allee effect under the influence of either quasiperiodic forcing or bounded random noise. We show that the presence of these external factors may lead to so-called non-smooth fold bifurcations, and thereby has a significant impact on the behaviour of the Lyapunov exponents (and hence the recovery rates). In particular, it may lead to the absence of critical slowing down prior to population collapse. More precisely, unlike in the unforced case, the question whether slow recovery rates can be observed or detected prior to the transition crucially depends on the chosen time-scales and the size of the considered data set.
Measuring the kinematic parameters of a rotating object in circular motion using the magnetometer of a smartphone
Authors: Puttharugsa Chokchai , Khemmani Supitch , Pimanpang Samuk 
Published: November 2022

Abstract
This paper describes a method to measure the kinematic parameters of a rotating object in circular motion using the magnetometer of a smartphone. A wheel with four legs had magnetic buttons attached to the ends of the legs. The smartphone was placed on the ground to measure the magnetic field when the wheel rotated. The experimental data can be calculated to obtain an angular position, an angular velocity, and an angular acceleration. The results show that the smartphone can be a useful tool to determine kinematic parameters in circular motion. The experiment is easy to set up using simple available objects, and students can conduct this experiment at home.
Comparing the performance of 850 GHz integrated bias-tee superconductor-insulator-superconductor (SIS) mixers with single- and parallel-junction tuner
Authors: Tan B-K , Rudakov K , Koshelets V P , Khudchenko A , Baryshev A M , Yassin G 
Published: November 2022

Abstract
We present and compare the design and performance of two 850 GHz radial probe fed superconductor-insulator-superconductor mixers, where the antenna is aligned perpendicular to the E-Plane of the input full-height rectangular waveguide connected to a multiple flare-angles smooth-walled horn. Both designs are comprised of 0.5 µm2 hybrid niobium/aluminium-nitride/niobium-nitride tunnel junction, fabricated on top of a niobium titanium nitride ground plane with an Al wiring layer. The entire superconducting circuit is supported with a 40 µm thick quartz substrate. The major difference between the two designs is the method used to cancel out the parasitic junction capacitance for broadband performance. The first design utilises two identical junctions connected in parallel with a short transmission line to convert the capacitance of one junction into the equivalent inductance of the other junction, commonly known as the twin-junction tuning scheme; whilst the second design employs an end-loaded scheme with only one tunnel junction. We found that both methods offer similar radio frequency performances, with close to 2× the double sideband quantum noise temperature, but the twin-junction design is more resilient to fabrication tolerances. However, the end-loaded design offers a much better intermediate frequency (IF) bandwidth performance, made possible by the sub-micron and high current density tunnel junction technology. The improved IF performance is important for many millimetre (mm) and sub-mm observatories, such as future upgrades of Atacama Large Millimetre/sub-mm Array receivers, as well as forthcoming space-borne far-infrared missions. Therefore, we conclude that the single-junction mixer design is the preferred option for THz applications, as long as the fabrication error can be minimised within a certain limit.
Black hole production, eternal inflation, and information in quasi-de Sitter space
Authors: Seo Min-Seok 
Published: November 2022

AbstractWhen the slow-roll parameter ϵHis smaller thanH2/MPl2, the quantum fluctuations of the inflaton after the horizon crossing are large enough to realize eternal inflation. Whereas they do not generate a sufficient amount of density fluctuation of the inflaton to produce the black hole in quasi-de Sitter space, they can also generate the sizeable density fluctuation of the radiation when the number of degrees of freedom increases rapidly in time, as predicted by the distance conjecture. We argue that the condition that the density fluctuation of the radiation is not large enough to produce the black hole until the end of inflation is equivalent to the no eternal inflation condition. When the radiation emitted by the horizon does not produce the black hole, even if the number of degrees of freedom increases in time, the information paradox does not arise for ϵHlarger than 10-7(H2/MPl2) and time scale shorter than 104(MPl/H2). Regardless of the presence of the information paradox, a static observer cannot retrieve a sufficient amount of information, which is consistent with the complementarity.
Singularities of regular black holes and the monodromy method for asymptotic quasinormal modes*
Authors: Lan Chen , Wang Yi-Fan 
Published: November 2022

Abstract
We use the monodromy method to investigate the asymptotic quasinormal modes of regular black holes based on the explicit Stokes portraits. We find that, for regular black holes with spherical symmetry and a single shape function, the analytical forms of the asymptotic frequency spectrum are not universal and do not depend on the multipole number but on the presence of complex singularities and the trajectory of asymptotic solutions along the Stokes lines.
Numerical error analysis of SOLPS-ITER simulations of EAST
Authors: Boeyaert Dieter , Carli Stefano , Ghoos Kristel , Dekeyser Wouter , Wiesen Sven , Baelmans Martine 
Published: November 2022

Abstract
Plasma edge simulations with codes like SOLPS-ITER are widely employed to interpret fusion experiments. However, numerical errors appearing in such simulations are rarely investigated, despite their potential large impact on simulation results. These errors consist of the statistical error and the bias, both resulting from the finite number of employed EIRENE Monte Carlo particles and incomplete convergence, and the discretization error due to the finite resolution of the computational grids. In this contribution, the resulting numerical errors on simulations of pure deuterium and neon seeded H-mode EAST discharges are examined. The statistical error can be kept small compared to other numerical error contributions by averaging the plasma profiles. This allows investigating the bias and discretization errors using Richardson extrapolation. It is shown that grid refinement and the number of employed Monte Carlo particles have the largest influence on the result, in agreement with similar studies of an ITER deuterium case. For the first time, numerical error bars on the entire simulated target profiles are determined showing that the largest numerical error is 17.9%, mainly due to the plasma grid discretization. On top, also numerical errors on simulated neutral pressures are investigated in detail, for which the statistical error is dominant. The analysis demonstrates which setup is needed to keep numerical errors limited: the SOLPS-ITER averaging procedure should be employed including enough EIRENE particles, and the involved grids should be sufficiently refined to reduce discretization errors.
Stability of solitary waves in nonlinear Klein–Gordon equations
Authors: Rabán Pablo , Alvarez-Nodarse Renato , Quintero Niurka R 
Published: November 2022

Abstract
The stability of topological solitary waves and pulses in one-dimensional nonlinear Klein–Gordon systems is revisited. The linearized equation describing small deviations around the static solution leads to a Sturm–Liouville problem, which is solved in a systematic way for the

−
l
(
l
+
1
)

s
e
c
h

2

(
x
)

-potential, showing the orthogonality and completeness relations fulfilled by the set of its solutions for all values

l
∈

N

. This approach enables the linear stability of kinks and pulses of certain nonlinear Klein–Gordon equations to be determined. The inverse problem, which starts from Sturm–Liouville problem and obtains nonlinear Klein–Gordon potentials, is also revisited and solved in a direct way. The exact solutions (kinks and pulses) for these potentials are calculated, even when the nonlinear potential is not explicitly known. The kinks are found to be stable, whereas the pulses are unstable. The stability of the pulses is achieved by introducing certain spatial inhomogeneities.
Realization of divertor configuration discharge in J-TEXT tokamak
Authors: CHEN Zhipeng , ZHU Lizhi , XU Xin , ZHENG Wei , ZHANG Ming , GAO Li , XIA Minghui , YANG Jie , ZHU Mingchong , HAO Zhigang , JIAO Shaodong , CHENG Zhifeng , YANG Zhoujun , ZHANG Xiaoqing , CHEN Zhongyong , WANG Nengchao , DING Yonghua , ZHUANG Ge , GENTLE Kenneth W , LIANG Yunfeng , PAN Yuan 
Published: November 2022

Abstract
To extend the operation region of the Joint-Texas Experimental tokamak (J-TEXT) to the divertor configuration and even the H-mode, the divertor configuration discharge has been realized for the first time in the J-TEXT tokamak. Along with the establishment of a power supply for the divertor configuration, the construction of relevant diagnostics, and the installation of the divertor target on the high-field side, divertor discharge has been tested. Through the equilibrium calculation and position stability analysis, the control strategy has evolved to be more stable. High-density experiments and auxiliary heating experiments have been carried out on the divertor configuration. The special midplane single-null (MSN) divertor configuration is shown to be more stable than the limiter configuration in the density limit condition and can reach a higher density in the experiment. In the ECRH experiment, the power injection enhances the electron temperature and density, while more heat outflux is loaded on the divertor target tiles and causes more intensive recycling and impurity release. The future plan for the divertor configuration operation in the J-TEXT tokamak is also included.
Open Access Academic Lectures as Sources for Incidental Vocabulary Learning: Examining the Role of Input Mode, Frequency, Type of Vocabulary, and Elaboration
Authors: Dang Thi Ngoc Yen , Lu Cailing , Webb Stuart 
Published: November 2022

Abstract
Open access academic lectures are potential sources for incidental vocabulary learning. These lectures are available in various formats (transcripts, audios, videos, and video with captions), but no studies have compared the learning of vocabulary in these lectures through different input modes. This study adopted a pretest–posttest design to compare learning at the meaning recall level of 50 words in the same academic lecture through five input modes: reading, listening, reading while listening, viewing, and viewing with captions. One hundred sixty-five English for Academic Purposes learners in China were assigned to five experimental groups and a control group. The experimental groups received the treatment with the assigned input mode while the control group received no treatment. Results show that although learning occurred through all input modes, only viewing significantly contributed to the learning gains. Frequency of occurrence and type of vocabulary significantly predicted the learning gains, but the type of verbal elaboration and nonverbal elaboration did not. This study provides further insights into the value of academic lectures for incidental vocabulary learning and supports the multimedia learning theory and its principles.
Factors Influencing Trust and Trustworthiness: Cosmetic Injectable Patient Experience Exploratory Study (CIPEES)—Part 3
Authors: McDonald Cara B , Heydenrych Izolda 
Published: November 2022

Abstract

Background
Despite the widely recognized importance of trust in professional relationships, it remains elusive, complex, multidimensional, and difficult to quantify due to the lack of validated tools.

Objectives
The authors sought to explore both the important factors for building trust with cosmetic injectable patients and strategies for improving levels of trustworthiness in aesthetic practitioners.

Methods
In order to explore factors in building trust with cosmetic injectable practitioners, a global study was conducted via an online survey. The Cosmetic Injectable Patient Experience Exploratory Study (CIPEES) survey assessed the relative importance of qualifications and training; reviewing of previous work (before and after photos); reputation; connection; time spent; online presence; and personal appearance of the practitioner in developing trust in a cosmetic practitioner.

Results
The CIPEES survey collected 1488 responses across 75 countries, with 66% of participants completing all 15 questions. The respondents were 95.6% female and 4.4% male, with ages ranging from 18 to &gt;65 years old (median 33 years old). The number 1 ranked reason for being able to trust a cosmetic injector was qualifications and training, followed by the reputation of the practitioner, and time spent by the practitioner with the survey respondent. Practitioner online presence was considered the least important factor in helping develop trust.

Conclusions
The CIPEES survey results support patient trust being built through credibility, reliability, and intimacy, with low levels of practitioner self-orientation. The trustworthiness equation provides a framework for identifying practitioner weaknesses in patient relationships and actionable methods of improving trustworthiness.
sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure
Authors: Yan Ke , Lv Hongwu , Guo Yichen , Peng Wei , Liu Bin 
Published: November 2022

AbstractMotivationAntimicrobial peptides (AMPs) are essential components of therapeutic peptides for innate immunity. Researchers have developed several computational methods to predict the potential AMPs from many candidate peptides. With the development of artificial intelligent techniques, the protein structures can be accurately predicted, which are useful for protein sequence and function analysis. Unfortunately, the predicted peptide structure information has not been applied to the field of AMP prediction so as to improve the predictive performance.ResultsIn this study, we proposed a computational predictor called sAMPpred-GAT for AMP identification. To the best of our knowledge, sAMPpred-GAT is the first approach based on the predicted peptide structures for AMP prediction. The sAMPpred-GAT predictor constructs the graphs based on the predicted peptide structures, sequence information and evolutionary information. The Graph Attention Network (GAT) is then performed on the graphs to learn the discriminative features. Finally, the full connection networks are utilized as the output module to predict whether the peptides are AMP or not. Experimental results show that sAMPpred-GAT outperforms the other state-of-the-art methods in terms of AUC, and achieves better or highly comparable performance in terms of the other metrics on the eight independent test datasets, demonstrating that the predicted peptide structure information is important for AMP prediction.Availability and implementationA user-friendly webserver of sAMPpred-GAT can be accessed at http://bliulab.net/sAMPpred-GAT and the source code is available at https://github.com/HongWuL/sAMPpred-GAT/.Supplementary informationSupplementary data are available at Bioinformatics online.
Vaeda computationally annotates doublets in single-cell RNA sequencing data
Authors: Schriever Hannah , Kostka Dennis 
Published: November 2022

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) continues to expand our knowledge by facilitating the study of transcriptional heterogeneity at the level of single cells. Despite this technology’s utility and success in biomedical research, technical artifacts are present in scRNA-seq data. Doublets/multiplets are a type of artifact that occurs when two or more cells are tagged by the same barcode, and therefore they appear as a single cell. Because this introduces non-existent transcriptional profiles, doublets can bias and mislead downstream analysis. To address this limitation, computational methods to annotate and remove doublets form scRNA-seq datasets are needed.

Results
We introduce vaeda (Variational Auto-Encoder for Doublet Annotation), a new approach for computational annotation of doublets in scRNA-seq data. Vaeda integrates a variational auto-encoder and Positive-Unlabeled learning to produce doublet scores and binary doublet calls. We apply vaeda, along with seven existing doublet annotation methods, to 16 benchmark datasets and find that vaeda performs competitively in terms of doublet scores and doublet calls. Notably, vaeda outperforms other python-based methods for doublet annotation. Altogether, vaeda is a robust and competitive method for scRNA-seq doublet annotation and may be of particular interest in the context of python-based workflows.

Availability and implementation
Vaeda is available at https://github.com/kostkalab/vaeda, and the version used for the results we present here is archived at zenodo (https://doi.org/10.5281/zenodo.7199783).

Supplementary information
Supplementary data are available at Bioinformatics online.
Promoting regeneration while blocking cell death preserves motor neuron function in a model of ALS
Authors: Wlaschin Josette J , Donahue Caroline , Gluski Jacob , Osborne Jennifer F , Ramos Leana M , Silberberg Hanna , Le Pichon Claire E 
Published: November 2022

Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating and fatal neurodegenerative disease of motor neurons with very few treatment options. We had previously found that motor neuron degeneration in a mouse model of ALS can be delayed by deleting the axon damage sensor MAP3K12 or dual leucine zipper kinase (DLK). However, DLK is also involved in axon regeneration, prompting us to ask whether combining DLK deletion with a way to promote axon regeneration would result in greater motor neuron protection. To achieve this, we used a mouse line that constitutively expresses ATF3, a master regulator of regeneration in neurons. Although there is precedence for each individual strategy in the SOD1G93A mouse model of ALS, these have not previously been combined. By several lines of evidence including motor neuron electrophysiology, histology and behaviour, we observed a powerful synergy when combining DLK deletion with ATF3 expression. The combinatorial strategy resulted in significant protection of motor neurons with fewer undergoing cell death, reduced axon degeneration and preservation of motor function and connectivity to muscle. This study provides a demonstration of the power of combinatorial therapy to treat neurodegenerative disease.
Cardiac computed tomography following Watchman FLX implantation: device-related thrombus or device healing?
Authors: Kramer Anders Dahl , Korsholm Kasper , Jensen Jesper Møller , Nørgaard Bjarne Linde , Peelukhana Srikara , Herbst Thomas , Horton Rodney , Kar Saibal , Saw Jacqueline , Alkhouli Mohamad , Nielsen-Kudsk Jens Erik 
Published: November 2022

Abstract

Aims
Cardiac computed tomography (CT) is increasingly utilized during follow-up after left atrial appendage closure (LAAC). Hypoattenuated thickening (HAT) is a common finding and might represent either benign device healing or device-related thrombosis (DRT). The appearance and characteristics of HAT associated with the Watchman FLX have not been previously described. Therefore, we sought to investigate cardiac CT findings during follow-up after Watchman FLX implantation with a focus on HAT and DRT.

Methods and results
Retrospective single-centre, observational study including all patients with successful Watchman FLX implantation and follow-up cardiac CT between March 2019 and September 2021 (n = 244). Blinded analysis of CT images was performed describing the localization, extent, and morphology of HAT and correlated to imaging and histology findings in a canine model. Relevant clinical and preclinical ethical approvals were obtained.
Overall, HAT was present in 156 cases (64%) and could be classified as either subfabric hypoattenuation (n = 59), flat sessile HAT (n = 78), protruding sessile HAT (n = 16), or pedunculated HAT (n = 3). All cases of pedunculated HAT and five cases of protruding sessile HAT were considered as high-grade HAT (n = 7). Subfabric hypoattenuation and flat sessile HAT correlated with device healing and endothelialization in histological analysis of explanted devices.

Conclusion
Subfabric hypoattenuation and flat sessile HAT are frequent CT findings for Watchman FLX, likely representing benign device healing and endothelialization. Pedunculated HAT and protruding HAT are infrequent CT findings that might represent DRT.