bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact study of numerical discretization accuracy on parameter reconstructions and model parameter distributions
Authors: Plock Matthias , Hammerschmidt Martin , Burger Sven , Schneider Philipp-Immanuel , Schütte Christof 
Published: July 2023

Abstract
In optical nano metrology numerical models are used widely for parameter reconstructions. Using the Bayesian target vector optimization method we fit a finite element numerical model to a Grazing Incidence x-ray fluorescence data set in order to obtain the geometrical parameters of a nano structured line grating. Gaussian process, stochastic machine learning surrogate models, were trained during the reconstruction and afterwards sampled with a Markov chain Monte Carlo sampler to determine the distribution of the reconstructed model parameters. The numerical discretization parameters of the used finite element model impact the numerical discretization error of the forward model. We investigated the impact of the polynomial order of the finite element ansatz functions on the reconstructed parameters as well as on the model parameter distributions. We showed that such a convergence study allows to determine numerical parameters which allows for efficient and accurate reconstruction results.
Towards self-consistent modelling of negative ion beam acceleration
Authors: Pimazzoni A. , Sartori E. , Serianni G. , Veltri P. 
Published: July 2023

Abstract
Neutral beams are a valuable option to provide heat and current drive to a magnetically confined plasma. In addition they can be used as a diagnostics for the positive ion temperature and, in case of nuclear fusion reactions, for the amount of helium ash. In the case of ITER, stringent requirements are set on the acceptable beam divergence and aiming in order to propagate such beams up to the tokamak itself. Besides the well-known dependence of the beamlet optics on the beam energy and perveance, other important features affecting the optics are the ion spatial and velocity distribution at the plasma boundary facing the extractor, the so-called plasma meniscus. In a caesiated negative ion source, this distribution is influenced both by the birth energy of the negative ions and by the ion transport in the plasma itself. In this work we use a test particle code to investigate the negative ion transport up to the plasma meniscus and we use a standard ray-tracing code to trace the test particles that reached the meniscus inside the electrostatic accelerator. The coupling of the two codes is iterated up to numerical convergence. By this procedure, the angular distribution of the accelerated particles is found to be much more similar to the experimental ones than the one obtained by simple ray-tracing simulations.
Intrinsic timing properties of ideal 3D-trench silicon sensor with fast front-end electronics
Authors: Cossu Gian Matteo , Brundu Davide , Lai Adriano 
Published: July 2023

Abstract
This paper describes the fundamental timing properties of a
single-pixel sensor for charged particle detection based on the
3D-trench silicon structure. We derive the results both analytically
and numerically by considering a simple ideal sensor and the
corresponding fast front-end electronics in two different case
scenarios: ideal integrator and real fast electronics
(trans-impedance amplifier). The particular shape of the Time of
Arrival (TOA) distribution is examined and the relation between the
time resolution and the spread of intrinsic charge collection time
is discussed, by varying electronics parameters and discrimination
thresholds. The results are obtained with and without simulated
electronics noise. We show that the 3D-trench sensors are
characterized by a synchronous region, i.e. a portion of the
active volume which leads to the same TOA values when charged
particles cross it. The synchronous region size is dependent on the
front-end electronics and discrimination threshold, and the
phenomenon represents an intrinsic physical effect that leads to the
excellent time resolution of these sensors. Moreover, we show that
the TOA distribution is characterized by an intrinsic asymmetry, due
to the 3D geometry only, that becomes negligible in case of
significant electronics jitter.
Non-Hermitian superintegrable systems
Authors: Correa Francisco , Inzunza Luis , Marquette Ian 
Published: July 2023

Abstract
A non-Hermitian generalisation of the Marsden–Weinstein reduction method is introduced to construct families of quantum

-symmetric superintegrable models over an n-dimensional sphere Sn
. The mechanism is illustrated with one- and two-dimensional examples, related to u(2) and u(3) Lie algebras respectively, providing new quantum models with real spectra and spontaneous

-symmetric breaking. In certain limits, the models reduce to known non-Hermitian systems and complex extensions of previously studied real superintegrable systems.
Comparative coherence between layered and traditional semiconductors: unique opportunities for heterogeneous integration
Authors: Chen Zhuofan , Deng Xiaonan , Zhang Simian , Wang Yuqi , Wu Yifei , Ke Shengxian , Zhang Junshang , Liu Fucheng , Liu Jianing , Liu Yingjie , Lin Yuchun , Hanna Andrew , Li Zhengcao , Wang Chen 
Published: July 2023

Abstract
As Moore’s law deteriorates, the research and development of new materials system are crucial for transitioning into the post Moore era. Traditional semiconductor materials, such as silicon, have served as the cornerstone of modern technologies for over half a century. This has been due to extensive research and engineering on new techniques to continuously enrich silicon-based materials system and, subsequently, to develop better performed silicon-based devices. Meanwhile, in the emerging post Moore era, layered semiconductor materials, such as transition metal dichalcogenides (TMDs), have garnered considerable research interest due to their unique electronic and optoelectronic properties, which hold great promise for powering the new era of next generation electronics. As a result, techniques for engineering the properties of layered semiconductors have expanded the possibilities of layered semiconductor-based devices. However, there remain significant limitations in the synthesis and engineering of layered semiconductors, impeding the utilization of layered semiconductor-based devices for mass applications. As a practical alternative, heterogeneous integration between layered and traditional semiconductors provides valuable opportunities to combine the distinctive properties of layered semiconductors with well-developed traditional semiconductors materials system. Here, we provide an overview of the comparative coherence between layered and traditional semiconductors, starting with TMDs as the representation of layered semiconductors. We highlight the meaningful opportunities presented by the heterogeneous integration of layered semiconductors with traditional semiconductors, representing an optimal strategy poised to propel the emerging semiconductor research community and chip industry towards unprecedented advancements in the coming decades.
Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis
Authors: Kubovčiak Jan , Kolář Michal , Novotný Jiří 
Published: July 2023

Abstract

Motivation
While the workflow for primary analysis of single-cell RNA-seq (scRNA-seq) data is well established, the secondary analysis of the feature-barcode matrix is usually done by custom scripts. There is no fully automated pipeline in the R statistical environment, which would follow the current best programming practices and requirements for reproducibility.

Results
We have developed scdrake, a fully automated workflow for secondary analysis of scRNA-seq data, which is fully implemented in the R language and built within the drake framework. The pipeline includes quality control, cell and gene filtering, normalization, detection of highly variable genes, dimensionality reduction, clustering, cell type annotation, detection of marker genes, differential expression analysis and integration of multiple samples. The pipeline is reproducible and scalable, has an efficient execution, provides easy extendability and access to intermediate results and outputs rich HTML reports. Scdrake is distributed as a Docker image, which provides a straightforward setup and enhances reproducibility.

Availability and implementation
The source code and documentation are available under the MIT license at https://github.com/bioinfocz/scdrake and https://bioinfocz.github.io/scdrake, respectively.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Ubiquitous lognormal distribution of neuron densities in mammalian cerebral cortex
Authors: Morales-Gregorio Aitor , van Meegen Alexander , van Albada Sacha J 
Published: July 2023

Abstract
Numbers of neurons and their spatial variation are fundamental organizational features of the brain. Despite the large corpus of cytoarchitectonic data available in the literature, the statistical distributions of neuron densities within and across brain areas remain largely uncharacterized. Here, we show that neuron densities are compatible with a lognormal distribution across cortical areas in several mammalian species, and find that this also holds true within cortical areas. A minimal model of noisy cell division, in combination with distributed proliferation times, can account for the coexistence of lognormal distributions within and across cortical areas. Our findings uncover a new organizational principle of cortical cytoarchitecture: the ubiquitous lognormal distribution of neuron densities, which adds to a long list of lognormal variables in the brain.
Rediscovering Arnold Dolmetsch: going back to the sources of the early music revival
Authors: Irving David R M 
Published: July 2023

Abstract
This article provides a retrospective overview of the discussion of Arnold Dolmetsch, his family, students and friends in Early Music since its first issue in 1973. It connects these cases with a broad range of other literature, suggests the need to rethink and recontextualize the lifetime of Arnold Dolmetsch and considers the significance of archival materials in the Jeanne-Marie Dolmetsch Collection newly available at Cambridge University Library (Ms. Add. 10371). In particular, it demonstrates the largely overlooked intercultural dimension of the Dolmetsch family’s contribution to the early music revival, highlighting their interactions with people and music cultures from beyond western Europe. Finally, it suggests a programme for possible future research on the Dolmetsch phenomenon.
Evaluation of a new treadmill exercise protocol to unmask type 1 Brugada electrocardiographic pattern: can we improve diagnostic yield?
Authors: Pichara Nemer L , Sacilotto Luciana , Scanavacca Maurício I , Cardoso Acácio Fernandes , Soares Beatriz Moreira Ayub Ferreira , Falcochio Paola P PN F , Falcão Andrea M G , Olivetti Natalia , da Costa Darrieux Francisco Carlos , Chalela William A 
Published: July 2023

Abstract

Aims
High precordial leads (HPL) on the resting electrocardiogram (ECG) are widely used to improve diagnostic detection of type 1 Brugada ECG pattern (Br1ECGp). A parasympathetic activation marks the initial recovery phase of treadmill stress testing (TET), and this can be useful for detecting the typical ECG pattern. Our study aimed to evaluate the role of a new HPL-treadmill exercise testing (TET) protocol in detecting Br1ECGp fluctuation compared to resting HPL-ECG.

Methods and results
74 out of 163 patients of a Brugada syndrome (BrS) Brazilian cohort (GenBra Registry) underwent exercise testing with HPL-TET protocol. Precordial leads were displayed in strategic positions in the right and left parasternal spaces. The step-by-step analysis included ECG classification (as presence or absence of Br1ECGp) in standard vs. HPL leads placement in the following sequences: resting phase, maximal exercise, and the passive recovery phase (including ‘quick lay down’). For heart rate recovery (HRR) measurements and comparisons, a Student’s t-test was applied. McNemar tests compared the detection of Br1ECGp. The significance level was defined as P &lt; 0.05. Fifty-seven patients (57/74; 77%) were male, the mean age was 49.0 ± 14, 78.4% had spontaneous BrS, and the mean Shanghai score was 4.5. The HPL-TET protocol increased Br1ECGp detection by 32.4% against resting HPL-ECG (52.7% vs. 20.3%, P = 0.001) alone.

Conclusion
Stress testing using HPL with the passive recovery phase in the supine position offers an opportunity to unmask the type 1 Br1ECGp, which could increase the diagnostic yield in this population.
Comparison of towed electromagnetic with airborne electromagnetic and electrical resistivity tomography in a hydrogeophysical context
Authors: Maurya Pradip Kumar , Foged Nikolaj , Madsen Line Meldgaard , Christiansen Anders Vest 
Published: July 2023

SUMMARYElectrical and electromagnetic methods are well suited for mapping the top 100 m of the subsurface, particularly electrical resistivity tomography (ERT) and Traseint electromagnetic (TEM). Both methods can provide comparable resolution and depth of investigation for generating continuous 2-D resistivity profiles. TEM measurements taken continuously from moving platforms, whether towed on the ground or airborne, can generate 2-D-like resistivity sections similar to those produced by ERT profiling. However, despite the fact that both ERT and TEM can map the electrical resistivity of the subsurface, their results differ due to fundamental differences in physical principles, sensitivity, system geometry and instrumentation. The main objective of this paper is to provide a one-on-one comparison of the newly developed towed TEM system, tTEM, against ERT and airborne TEM, in our case a SkyTEM system. First, we performed the comparison in terms of model resolution using synthetic data and models. For all methods, synthetic data were generated using a 1-D forward response, and inversions were carried out using smooth layered models in a laterally constrained inversion framework. Overall, the inversion results are comparable across the three methods, and they all capture the key features of the synthetic models. The ERT and tTEM cross-sections from two field cases show very comparable results even in the top 5 m where thin resistive layers (∼60 Ω·m) are clearly mapped by both methods. However, the resistivity of the resistive layer is better resolved using ERT than tTEM because of the high sensitivity close to the surface in the ERT case. In the deeper part of the section, tTEM tends to resolve the boundaries of conductive layers (resistivity &lt; 10 Ω·m) better than the ERT method. Compared to SkyTEM, tTEM has a better vertical and horizontal resolution especially in the top 20 m. The better tTEM resolution compared to SkyTEM is primarily due to a smaller footprint and denser data sampling. Depth of investigation-wise the SkyTEM system is superior compared to tTEM due to its larger magnetic moment.
Individual-based model simulations indicate a non-linear catch equation of drifting Fish Aggregating Device-associated tuna
Authors: Nooteboom Peter D , Scutt Phillips Joe , Senina Inna , van Sebille Erik , Nicol Simon 
Published: July 2023

Abstract
Catch per unit of fishing effort (CPUE) is often used as an indicator of tuna abundance, where it is assumed that the two are proportional to each other. Tuna catch is therefore typically simplified in tuna population dynamics models and depends linearly on their abundance. In this paper, we use an individual-based model of tuna and their interactions with drifting Fish Aggregating Devices (dFADs) to identify which behavioural, ocean flow, and fishing strategy scenarios lead to an emergent, non-linear dependency between catch, and both tuna and dFAD density at the ∼1○ grid scale. We apply a series of catch response equations to evaluate their ability to model associated catch rate, using tuna and dFAD density as terms. Our results indicate that, regardless of ocean flow, behavioural, or fisher strategy scenario, simulated catch is best modelled with a non-linear dependence on both tuna and dFAD abundance. We discuss how estimators of CPUE at the population scale are potentially biased when assuming a linear catch response.
Development and validation of a patient satisfaction survey for pharmaceutical service at primary care settings
Authors: Huang Ruijian , Ding Siyu , Xiao Yue , Jiang Feng , Chen Yanfei , Zhang Jingjing , Zhou Jifang 
Published: July 2023

Abstract
Patient satisfaction is a key quality indicator of pharmacy service. However, there are few studies that develop and validate patient satisfaction surveys applied to pharmaceutical services in primary care settings. It is imperative to establish a well-validated multidimensional instrument for evaluating the viability and sustainability of pharmacy service across geographically diverse regions in low- and middle-income countries.
To develop and validate a patient satisfaction instrument for community pharmaceutical services, we carried out a cross-sectional survey in seven provinces across China. The study was conducted in four phases: (i) literature review–based item generation, (ii) expert panel–endorsed questionnaire refinement, (iii) pilot questionnaire development, and (iv) psychometric validation. Survey respondents were standard patients recruited locally and trained to conduct unannounced visits to preselected primary care centers.
Between December 2020 and November 2021, the pilot survey comprised a total of 166 unannounced standard patient visits from 125 health-care facilities. The final 24-item Likert-type instrument encompassed five domains: relationship, medication counseling, empathy, accessibility, and overall satisfaction. The satisfactory survey revealed excellent internal consistency. Factor analyses resulted in a 4-factor solution that accounted for 70.7% variance.
The results suggest that the questionnaire is a valid and reliable instrument, which has been taken an important step to evaluate patient satisfaction with pharmaceutical services in Chinese primary care settings. Further research on its cross-culture adaptation and applicability in urban retail pharmacy settings is warranted.
Feeling with the Land:Llakichinaand the Emotional Life of Relatedness in Amazonian Kichwa Thinking
Authors: Swanson Tod D , Reddekop Jarrad 
Published: July 2023

AbstractThis article explores how traditional Kichwa people in the Ecuadorian Amazon experience and practice emotional life. In particular, we focus on the centrality accorded to acts intended to elicit compassion in others (llakichina) and on the role these acts play in holding communities together. We argue that the importance given to the eliciting of compassion is tied to the Kichwa construal of the self as inherently relational and, for this reason, precarious. Further, we show how the emotional life of relatedness encompasses relationships with land and other species (particularly birds) in multi-layered ways. Drawing on interviews, songs, and narratives, we show how an understanding of other species as transformed humans informs affective connections with the land and how these in turn mediate emotional relations.
Carrier prevalence of Clostridioides difficile in emergency departments and the association of prior antibiotic consumption: a combined cross-sectional and nested case–control study
Authors: Skjøt-Arkil Helene , Rune Nanthan Kumanan , Chen Ming , Rosenvinge Flemming S 
Published: July 2023

Abstract

Introduction
Clostridioides difficile infection is an urgent public health threat, and the incidence has been increasing over the last decades. Knowledge of the prevalence of C. difficile in acutely admitted patients and risk factors for colonization with C. difficile assists emergency departments (EDs) in prioritizing preventive initiatives. This national study aimed to describe prevalence and risk factors for C. difficile carriers acutely admitted to EDs, focusing on the impact of earlier antibiotic prescription.

Methods
We conducted a nationwide analytic cross-sectional study with prospective data collection combined with a nested case–control study with retrospective data collection. All adults visiting one of eight Danish EDs were interviewed and examined for C. difficile. Using a national register, we collected the antibiotic history within the 2 years prior to enrolment. The primary outcome was the prevalence of C. difficile colonization, and secondary outcomes were related to risk factors and prior antibiotic prescription. Multivariate analyses examined the association between earlier antibiotic prescription and C. difficile colonization.

Results
Of 5019 participants, 89 were colonized with C. difficile (prevalence of 1.8%). A significant and exposure-dependent association was found for penicillins [DDD/person-year(PY) &gt; 20; OR 4.93 (95% CI 2.22–10.97)] and fluoroquinolones [DDD/PY &gt; 20; OR 8.81 (95% CI 2.54–30.55)], but not macrolides. Timing of the prescription did not affect the association.

Conclusions
One out of 55 patients visiting a Danish ED were colonized with C. difficile. Risk factors for colonization included high age, comorbidity and prior prescription of fluoroquinolones and penicillins.
Community-Led Education among Rohingya Refugees and the Politics of Refugee Education in Bangladesh
Authors: Nilsen Marte , Olney Jessica , Maung Khin , Karim Lucky , Ahmad Shabbir , Haque Nurul , Mubarak H Roshid 
Published: July 2023

Abstract
The academic literature on refugee education and education in emergencies is understandably preoccupied with how to improve educational tools and learning platforms for refugees. However, political restrictions on education from host governments are among the main obstacles for quality education in many refugee settings. This article contributes to the refugee education literature by exploring ways in which refugees themselves can mitigate the denial of the right to education through a combination of traditional community mobilization and the use of new technologies. Specifically, the article analyses the educational strategies that Rohingya youths and community-based education networks manoeuvre to secure basic education in the refugee camps in Bangladesh, despite severe political restrictions. Based on qualitative interviews in 2019 and 2021 (in person and phone interviews) with 38 community teachers and 16 refugee students, and digital data collection, including reviews of learning tools of 21 online programmes, the article presents new knowledge on the strategies that Rohingya youths and adolescents pursue to access learning tools and education. It also shows how community-based education networks and teachers tackle political restrictions on education. These networks represent an educated wellspring of untapped resources with close ties to the refugee community, and insights into the grievances and aspirations of Rohingya youths, that humanitarian education providers should engage with to improve their response.