bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cosmic energy density: particles, fields and the vacuum
Authors: Armendariz-Picon Cristian , Diez-Tejedor Alberto 
Published: November 2023

Abstract
We revisit the cosmic evolution of the energy density of a quantized free scalar field and
assess under what conditions the particle production and classical field approximations reproduce
its correct value. Because the unrenormalized energy-momentum tensor diverges in the ultraviolet,
it is necessary to frame our discussion within an appropriate regularization and renormalization
scheme. Pauli-Villars avoids some of the drawbacks of adiabatic subtraction and dimensional
regularization and is particularly convenient in this context. In some cases, we can predict the
evolution of the energy density irrespectively of the quantum state of the field modes. To
further illustrate our results we focus however on the in vacuum, the preferred quantum
state singled out by inflation, and explore to what extent the latter determines the subsequent
evolution of the energy density regardless of the unknown details of reheating. We contrast this
discussion with examples of transitions to radiation domination that avoid some of the problems of
the one commonly studied in the literature, and point out some instances in which the particle
production or the classical field approximations lead to the incorrect energy density. Along the
way, we also elaborate on the connection of our analysis to dynamical dark energy models and
axion-like dark matter candidates.
On limit fractional Volterra hierarchies
Authors: Zhang Lixiang , Li Chuanzhong 
Published: November 2023

Abstract
For the limit fractional Volterra (LFV) hierarchy, we construct the n-fold Darboux transformation and the soliton solutions. Furthermore, we extend the LFV hierarchy to the noncommutative LFV (NCLFV) hierarchy, and construct the Darboux transformation expressed by quasi determinant of the noncommutative version. Meanwhile, we establish the relationship between new and old solutions of the NCLFV hierarchy. Finally, the quasi determinant solutions of the NCLFV hierarchy are obtained.
Microscopic theory for hyperuniformity in two-dimensional chiral active fluid
Authors: Kuroda Yuta , Miyazaki Kunimasa 
Published: November 2023

Abstract
Some nonequilibrium systems exhibit anomalous suppression of the large-scale density fluctuations, so-called hyperuniformity. Recently, hyperuniformity was found numerically in a simple model of chiral active fluids (Lei et al 2019 Sci. Adv.
5 eaau7423). We revisit this phenomenon and put forward a microscopic theory to explain it. An effective fluctuating hydrodynamic equation is derived for a simple particle model of chiral active matter. We show that the linear analysis of the obtained hydrodynamic equation captures hyperuniformity. Our theory yields hyperuniformity characterized by the same exponents as the numerical observation, but the agreement with the numerical data is qualitative. We also argue that the hydrodynamic equation for the effective particle representation, in which each rotating trajectory is regarded as an effective particle, has the same form as the macroscopic description of the random organization model with the center of mass conservation.
Stray light suppression for Thomson scattering diagnostic on linear magnetized plasma device
Authors: Lin Zhiyi , Xie Jinlin , Zhang Qiaofeng , Xu Mengmeng , Zeng Qingbin 
Published: November 2023

Abstract
In Thomson scattering (TS) diagnostic system, the stray light greatly affects the
signal-to-noise ratio (SNR). The suppression issue is particularly severe for the low density and
low temperature plasma due to very few scattered photons and narrow line broadening. The
traditional methods, such as Brewster window, beam dump and transmission pipe with black-coated
internal surface, have been adopted in the stray light suppression system on our Linear Magnetized
Plasma (LMP) device. Moreover, an assembly of tapered apertures are placed in the optical
path. Via numerical simulation, the optimal configuration of the adjustable aperture tube (size,
location, and orientation) that provide the best suppression has been found. Numerical results
show that the optimal aperture group with 6 mm and 8 mm tapered apertures can maintain over 97%
transmission rate of the main laser energy while reducing stray light by 99.6%.
Trailing-edge fringes enable robust aerodynamic force production and noise suppression in an owl wing model
Authors: Rong Jiaxin , Jiang Yajun , Murayama Yuta , Ishibashi Ryoto , Murakami Masashi , Liu Hao 
Published: November 2023

Abstract
As one of the unique owl-wing morphologies, trailing-edge (TE) fringes are believed to play a critical role in the silent flight of owls and have been widely investigated using idealized single/tandem airfoils. However, the effect of TE fringes and associated mechanisms on the aeroacoustics of owl wings, which feature curved leading edges, wavy TEs, and several feather slots at the wingtips, have not yet been addressed. In this study, we constructed two 3D owl wing models, one with and one without TE fringes, based on the geometric characteristics of a real owl wing. Large-eddy simulations and the Ffowcs Williams‒Hawkings analogy were combined to resolve the aeroacoustic characteristics of the wing models. Comparisons of the computed aerodynamic forces and far-field acoustic pressure levels demonstrate that the fringes on owl wings can robustly suppress aerodynamic noise while sustaining aerodynamic performance comparable to that of a clean wing. By visualizing the near-field flow dynamics in terms of flow and vortex structures as well as flow fluctuations, the mechanisms of TE fringes in owl wing models are revealed. First, the TE fringes on owl wings are reconfirmed to robustly suppress flow fluctuations near the TE by breaking up large TE vortices. Second, the fringes are observed to effectively suppress the shedding of wingtip vortices by mitigating the flow interaction between feathers (feather-slot interaction). These complementary mechanisms synergize to enhance the robustness and effectiveness of the TE fringe effects in owl wing models, in terms of aerodynamic force production and noise suppression. This study thus deepens our understanding of the role of TE fringes in real owl flight gliding and points to the validity and feasibility of employing owl-inspired TE fringes in practical applications of low-noise fluid machinery.
The classification of rebit quantum channels
Authors: Aldé Michele , Berthier Michel , Provenzi Edoardo 
Published: November 2023

Abstract
The classification of qubit channels is known since 2002. However, that of rebit channels has never been studied so far, maybe because of the scarcity of concrete rebit examples. In this paper we point out that the strategy used to classify qubit channels cannot be pursued in the rebit case and we propose an alternative which allows us to complete the rebit channel classification. This mathematical result has not only a purely abstract interest: as we shall briefly mention, it may have applications in the analysis of local properties and temporal evolution of real quantum systems and also in a recent color vision model based on quantum information.
Looking at the posterior: accuracy and uncertainty of neural-network predictions
Authors: Linander Hampus , Balabanov Oleksandr , Yang Henry , Mehlig Bernhard 
Published: November 2023

Abstract
Bayesian inference can quantify uncertainty in the predictions of neural networks using posterior distributions for model parameters and network output. By looking at these posterior distributions, one can separate the origin of uncertainty into aleatoric and epistemic contributions. One goal of uncertainty quantification is to inform on prediction accuracy. Here we show that prediction accuracy depends on both epistemic and aleatoric uncertainty in an intricate fashion that cannot be understood in terms of marginalized uncertainty distributions alone. How the accuracy relates to epistemic and aleatoric uncertainties depends not only on the model architecture, but also on the properties of the dataset. We discuss the significance of these results for active learning and introduce a novel acquisition function that outperforms common uncertainty-based methods. To arrive at our results, we approximated the posteriors using deep ensembles, for fully-connected, convolutional and attention-based neural networks.
The American Society for Clinical Pathology 2022 Vacancy Survey of medical laboratories in the United States
Authors: Garcia Edna , Kundu Iman , Kelly Melissa , Soles Ryan 
Published: November 2023

Abstract

Objectives
To determine the extent and distribution of laboratory workforce shortages within the nation’s medical laboratories.

Methods
The Vacancy Survey was conducted through collaboration between the American Society for Clinical Pathology (ASCP) Institute for Science, Technology and Public Policy in Washington, DC, and the Evaluation, Measurement, and Assessment Department and ASCP Board of Certification in Chicago, IL. Data were collected through an internet survey distributed to individuals who were able to report on staffing and certifications for their laboratories.

Results
Results of the ASCP 2022 Vacancy Survey show increased overall vacancy rates for laboratory positions in all departments compared with 2020. Overall retirement rates for laboratory professionals increased across most departments.

Conclusions
Current Vacancy Survey data show continued increases in the numbers of laboratory vacancies and retirements as well as changes in certification requirements, with trends amplified during the pandemic continuing into the present. Qualitative analysis results showed that there is an urgent need to focus not only on recruitment but—equally important—on retention of laboratory professionals.
Evolution of secondary growth: have pattern, got process? A commentary on ‘Molecular phylogeny of Urvillea (Paullinieae, Sapindaceae) and its implications in stem vascular diversity’
Authors: Tomescu Alexandru M F 
Published: November 2023

This article comments on:
Israel L. Cunha Neto, Yanã C. Rizzieri, Pablo A. Cabanillas, Fabiano M. Martins, Natália F. Marques, Genise V. Somner, Pedro Acevedo-Rodríguez and Joyce G. Onyenedum. Molecular phylogeny of Urvillea (Paullinieae, Sapindaceae) and its implications in stem vascular diversity, Annals of Botany, Volume 132, Issue 5, 10 October 2023, Pages 929–948, https://doi.org/10.1093/aob/mcad093
FG-BERT: a generalized and self-supervised functional group-based molecular representation learning framework for properties prediction
Authors: Li Biaoshun , Lin Mujie , Chen Tiegen , Wang Ling 
Published: November 2023

Abstract
Artificial intelligence-based molecular property prediction plays a key role in molecular design such as bioactive molecules and functional materials. In this study, we propose a self-supervised pretraining deep learning (DL) framework, called functional group bidirectional encoder representations from transformers (FG-BERT), pertained based on ~1.45 million unlabeled drug-like molecules, to learn meaningful representation of molecules from function groups. The pretrained FG-BERT framework can be fine-tuned to predict molecular properties. Compared to state-of-the-art (SOTA) machine learning and DL methods, we demonstrate the high performance of FG-BERT in evaluating molecular properties in tasks involving physical chemistry, biophysics and physiology across 44 benchmark datasets. In addition, FG-BERT utilizes attention mechanisms to focus on FG features that are critical to the target properties, thereby providing excellent interpretability for downstream training tasks. Collectively, FG-BERT does not require any artificially crafted features as input and has excellent interpretability, providing an out-of-the-box framework for developing SOTA models for a variety of molecule (especially for drug) discovery tasks.
aPEAR: an R package for autonomous visualization of pathway enrichment networks
Authors: Kerseviciute Ieva , Gordevicius Juozas 
Published: November 2023

Abstract

Summary
The interpretation of pathway enrichment analysis results is frequently complicated by an overwhelming and redundant list of significantly affected pathways. Here, we present an R package aPEAR (Advanced Pathway Enrichment Analysis Representation) which leverages similarities between the pathway gene sets and represents them as a network of interconnected clusters. Each cluster is assigned a meaningful name that highlights the main biological themes in the experiment. Our approach enables an automated and objective overview of the data without manual and time-consuming parameter tweaking.

Availability and implementation
The package aPEAR is implemented in R, published under the MIT open-source licence. The source code, documentation, and usage instructions are available on https://gitlab.com/vugene/aPEAR as well as on CRAN (https://CRAN.R-project.org/package=aPEAR).
Cartography of Afro-Asian relations in America: co-racialization and nanohealing
Authors: Cheng Hsin-I 
Published: November 2023

Abstract
In public discourse, there has been hostile communication between Asian and Black communities in the US. This article proposes co-racialization as a lens in examining Asian and Black Americans’ relationality. Co-racialization occurs in and across space and time, in that individuals and groups with various and uneven resources shape their views of themselves and their counterparts. Seventy-two Asian Americans and Black Americans were interviewed. Through the concepts of “racial project” and “hydraulic and nanoracism,” I trace the ways in which these co-racializations are mediated. Themes of their “home and neighborhood as space of mediation;” “segregated learning institutions with hydraulic racism mediated by pop culture;” and “perpetual tensions and nanoracism in the ‘fuzzy zones’” emerged. This article calls for nanohealing—an intentionally sustained relationality-building rooted in on-the-ground spaces of interactions and mediation—as an imperative part of co-racialization to resist the thin relationality between racial minorities.
The role of abiotic and biotic factors in the unequal body shape diversification of a Gondwanan fish radiation (Otophysi: Characiformes)
Authors: Burns Michael D , Knouft Jason H , Dillman Casey B 
Published: November 2023

Abstract
Understanding why some clades diversify greatly while others do not is a major goal of evolutionary biology. Both abiotic and biotic factors are important in driving unequal morphological diversity across the tree of life. However, few studies have quantified how abiotic habitat and community composition differences influence unequal morphological diversification in spatiotemporally diffuse radiations. We use geometric morphometrics, abiotic habitat data generated by Geographic Information Systems (GIS) analyses, evolutionary simulations, and phylogenetic comparative methods to determine whether random evolution, habitat variation, competition for niches, or a combination of factors influenced the unequal body shape diversity of a Gondwanan freshwater fish radiation. We find that Neotropical characiform lineages, which exhibit substantially more body shape diversity than their African counterparts, occupy significantly more slope and elevation habitats than African lineages. Differences in habitat occupation between the continental radiations occur through a combination of likely competition with cypriniform fishes in Africa restricting access to higher slope and elevation habitats and significantly more low-elevation and slope habitats available in the Neotropics. Our findings suggest that spatiotemporally widespread radiations, like Characiformes, do not diversify across homogenized habitats and biotic assemblages, with differences in community structure and physical habitat playing an important role in driving unequal morphological diversification.
The prevalence of killer yeasts and double-stranded RNAs in the budding yeast Saccharomyces cerevisiae
Authors: Crabtree Angela M , Taggart Nathan T , Lee Mark D , Boyer Josie M , Rowley Paul A 
Published: November 2023

Abstract
Killer toxins are antifungal proteins produced by many species of “killer” yeasts, including the brewer's and baker's yeast Saccharomyces cerevisiae. Screening 1270 strains of S. cerevisiae for killer toxin production found that 50% are killer yeasts, with a higher prevalence of yeasts isolated from human clinical samples and winemaking processes. Since many killer toxins are encoded by satellite double-stranded RNAs (dsRNAs) associated with mycoviruses, S. cerevisiae strains were also assayed for the presence of dsRNAs. This screen identified that 51% of strains contained dsRNAs from the mycovirus families Totiviridae and Partitiviridae, as well as satellite dsRNAs. Killer toxin production was correlated with the presence of satellite dsRNAs but not mycoviruses. However, in most killer yeasts, whole genome analysis identified the killer toxin gene KHS1 as significantly associated with killer toxin production. Most killer yeasts had unique spectrums of antifungal activities compared to canonical killer toxins, and sequence analysis identified mutations that altered their antifungal activities. The prevalence of mycoviruses and killer toxins in S. cerevisiae is important because of their known impact on yeast fitness, with implications for academic research and industrial application of this yeast species.
PICKLE RELATED 2 is a Neofunctionalized Gene Duplicate Under Positive Selection With Antagonistic Effects to the Ancestral PICKLE Gene on the Seed Transcriptome
Authors: Dupouy Gilles , Cashell Ronan , Brychkova Galina , Tuteja Reetu , McKeown Peter C , Spillane Charles 
Published: November 2023

Abstract
The evolution and diversification of proteins capable of remodeling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodeling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologs have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast evolving under positive selection, while PKL is subject to purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein's intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights into how gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.
Alignment-based Protein Mutational Landscape Prediction: Doing More with Less
Authors: Abakarova Marina , Marquet Céline , Rera Michael , Rost Burkhard , Laine Elodie 
Published: November 2023

Abstract
The wealth of genomic data has boosted the development of computational methods predicting the phenotypic outcomes of missense variants. The most accurate ones exploit multiple sequence alignments, which can be costly to generate. Recent efforts for democratizing protein structure prediction have overcome this bottleneck by leveraging the fast homology search of MMseqs2. Here, we show the usefulness of this strategy for mutational outcome prediction through a large-scale assessment of 1.5M missense variants across 72 protein families. Our study demonstrates the feasibility of producing alignment-based mutational landscape predictions that are both high-quality and compute-efficient for entire proteomes. We provide the community with the whole human proteome mutational landscape and simplified access to our predictive pipeline.
‘Thinking in Papua New Guinean Terms’: the Sensitive Files Case of 1972 and Australia’s Migrated Archive
Authors: Piccini Jon 
Published: November 2023

Abstract
Australia’s unsuccessful attempt to remove ‘sensitive’ files from the Territory of Papua and New Guinea (PNG) in 1972 adds new insights into emerging literature on the migrated archive. This paper argues that fears of reputational damage, possessiveness and race-based logics animated Australia’s actions. It illuminates how an unlikely alliance of Australian archivists and academics with PNG nationalist elites saw the removals policy reversed, thus ensuring the nation’s colonial era records remained in place. It also demonstrates the migrated archive’s global nature, as well as locating Australia and PNG within the late twentieth-century narrative of empire’s end.
Ambiguities in the EU's rights-based approach to liberal order
Authors: Saltnes Johanne Døhlie 
Published: November 2023

Abstract
The European Union has been characterized as a vanguard of a rights-based liberal international order. A prime example is making all cooperation agreements with third states conditioned on respect for human rights. But the EU's approach is contested on grounds of inconsistency and power imbalance. This article contributes to a more nuanced understanding of the relationship between authoritative human rights procedures and contestations of the liberal order. In doing so, the article brings to the fore ambiguities that are often glossed over in the literature related to representation in supranational political arrangements. Through a longitudinal case-study of the centrepiece of the EU's external human rights policy, the human rights clause, the article shows that the EU vacillates between supranational and intergovernmental political arrangements. It insists on a human rights clause that allows for sanctioning of non-compliance, but that also maintains core features of intergovernmental decision-making where executives in the EU and partner governments maintain the authority to initiate and settle disputes on human rights. The result is a half-hearted move towards a rights-based liberal order that neither fully respects nation-states' sovereignty nor fully allows for an impartial settlement of human rights disputes.
Rethinking liberal order: the EU and the quest for global justice
Authors: Sjursen Helene 
Published: November 2023

Abstract
The liberal order is facing severe challenges. This article introduces a special section, ‘Liberal order, the EU and global political justice’, which assesses the implications of these challenges for the European Union and for its ability to remain a relevant global actor. To do so, the different contributions inquire into the interconnections between the normative premises of the EU's foreign policy within different issue areas and those of the liberal order. Presenting the core themes, this introductory article suggests that liberal order is not merely a descriptive but also a normative concept. Indicating how a well-ordered international system ought to be organized, the liberal order generates expectations of a contribution to global justice. The article further advances the hypothesis that the troubles of the liberal order are linked to its inability to fulfill these expectations. As the EU's legitimacy is bound up with that of the liberal script, this hypothesis implies a need to reconsider not only core features of liberal order, but also those of the EU's approach to it. Thus highlighting the relevance of normative factors and their capacity for disruption, the article contributes to filling gaps in scholarly literatures both on the challenges to the liberal order and on the changing role of the EU in an increasingly unsettled world.