bluuebunny/crossref_metadata_2025_split huggingface dataset:
Point-like vacancies in two-dimensional transition metal dichalcogenides
Authors: Özcan Sibel , Gallardo Aurelio , Biel Blanca 
Published: January 2024

AbstractThis study explores the realm of two-dimensional transition metal dichalcogenides (TMDs), examining some of the most prevalent defects. Employing density functional theory, we scrutinize three common defect types across four extensively studied TMDs: MoS2, MoSe2, WS2, and WSe2. Our investigation spans the energetics of these defects, unveiling the most stable ones, and unraveling the alterations in structural and electronic properties induced by their presence. As a further step towards practical applications, we simulate the images that would be captured by both Atomic and Kelvin Probe Force Microscopes, aiming at a facile identification of these defects when probed at the microscopic level.
ELUQuant: event-level uncertainty quantification in deep inelastic scattering
Authors: Fanelli C , Giroux J 
Published: January 2024

Abstract
We introduce a physics-informed Bayesian neural network with flow-approximated posteriors using multiplicative normalizing flows for detailed uncertainty quantification (UQ) at the physics event-level. Our method is capable of identifying both heteroskedastic aleatoric and epistemic uncertainties, providing granular physical insights. Applied to deep inelastic scattering (DIS) events, our model effectively extracts the kinematic variables x, Q
2, and y, matching the performance of recent deep learning regression techniques but with the critical enhancement of event-level UQ. This detailed description of the underlying uncertainty proves invaluable for decision-making, especially in tasks like event filtering. It also allows for the reduction of true inaccuracies without directly accessing the ground truth. A thorough DIS simulation using the H1 detector at HERA indicates possible applications for the future electron–ion collider. Additionally, this paves the way for related tasks such as data quality monitoring and anomaly detection. Remarkably, our approach effectively processes large samples at high rates.
Pyroelectric influence on lithium niobate during the thermal transition for cryogenic integrated photonics
Authors: Thiele Frederik , Hummel Thomas , Lange Nina Amelie , Dreher Felix , Protte Maximilian , Bruch Felix vom , Lengeling Sebastian , Herrmann Harald , Eigner Christof , Silberhorn Christine , Bartley Tim J 
Published: January 2024

Abstract
Lithium niobate has emerged as a promising platform for integrated quantum optics, enabling efficient generation, manipulation, and detection of quantum states of light. However, integrating single-photon detectors requires cryogenic operating temperatures, since the best performing detectors are based on narrow superconducting wires. While previous studies have demonstrated the operation of quantum light sources and electro-optic modulators in LiNbO3 at cryogenic temperatures, the thermal transition between room temperature and cryogenic conditions introduces additional effects that can significantly influence device performance. In this paper, we investigate the generation of pyroelectric charges and their impact on the optical properties of lithium niobate waveguides when changing from room temperature to 25 K, and vice versa. We measure the generated pyroelectric charge flow and correlate this with fast changes in the birefringence acquired through the Sénarmont-method. Both electrical and optical influence of the pyroelectric effect occur predominantly at temperatures above 100 K.
Unveiling the electronic structure of GaSb/AlGaSb quantum dots emitting in the third telecom window
Authors: Leguay Lucie , Chellu Abhiroop , Hilska Joonas , Luna Esperanza , Schliwa Andrei , Guina Mircea , Hakkarainen Teemu 
Published: January 2024

Abstract
Epitaxially-grown semiconductor quantum dots (QDs) provide an attractive platform for the development of deterministic sources of high-quality quantum states of light. Such non-classical light sources are essential for quantum information processing and quantum communication. QDs emitting in the telecom wavelengths are especially important for ensuring compatibility with optical fiber systems required to implement quantum communication networks. To this end, GaSb QDs fabricated by filling local-droplet etched nanoholes are emerging as a viable approach, yet the electronic properties of such nanostructures have not been studied in detail. In this article, an insight into the electronic structure and carrier dynamics in GaSb/AlGaSb QDs is provided through a systematic experimental analysis of their temperature-dependent photoluminescence behavior. A steady-state rate equation model is used to reveal the relevant energy barriers for thermally activated carrier capture and escape processes. Furthermore, results of detailed theoretical simulations of quantum-confined energy states using the multi-band k·p model and the effective mass method are presented. The purpose of the simulations is to reveal the direct and indirect energy states, carrier wavefunctions, and allowed optical transitions for GaSb QDs with different physical dimensions.
Harnessing stochasticity for superconductive multi-layer spike-rate-coded neuromorphic networks
Authors: Edwards Alexander J , Krylov Gleb , Friedman Joseph S , Friedman Eby G 
Published: January 2024

Abstract
Conventional semiconductor-based integrated circuits are gradually approaching fundamental scaling limits. Many prospective solutions have recently emerged to supplement or replace both the technology on which basic devices are built and the architecture of data processing. Neuromorphic circuits are a promising approach to computing where techniques used by the brain to achieve high efficiency are exploited. Many existing neuromorphic circuits rely on unconventional and useful properties of novel technologies to better mimic the operation of the brain. One such technology is single flux quantum (SFQ) logic—a cryogenic superconductive technology in which the data are represented by quanta of magnetic flux (fluxons) produced and processed by Josephson junctions embedded within inductive loops. The movement of a fluxon within a circuit produces a quantized voltage pulse (SFQ pulse), resembling a neuronal spiking event. These circuits routinely operate at clock frequencies of tens to hundreds of gigahertz, making SFQ a natural technology for processing high frequency pulse trains. This work harnesses thermal stochasticity in superconducting synapses to emulate stochasticity in biological synapses in which the synapse probabilistically propagates or blocks incoming spikes. The authors also present neuronal, fan-in, and fan-out circuitry inspired by the literature that seamlessly cascade with the synapses for deep neural network construction. Synapse weights and neuron biases are set with bias current, and the authors propose multiple mechanisms for training the network and storing weights. The network primitives are successfully demonstrated in simulation in the context of a rate-coded multi-layer XOR neural network which achieves a wide classification margin. The proposed methodology is based solely on existing SFQ technology and does not employ unconventional superconductive devices or semiconductor transistors, making this proposed system an effective approach for scalable cryogenic neuromorphic computing.
Eurosceptic Vote Deviation and the Impact of News Media
Authors: Kritzinger Sylvia , Johann David 
Published: January 2024

Abstract
The chapter examines first how many voters deviate from the party they are closest to in left‐right terms, but rather vote for a Eurosceptic party. In addition, the contestation of the European issue is regarded. As voters require information about the political agenda to make a decision, the chapter explores contestation effects by analysing the impact of news media reporting. Using public opinion and media data of the 1999, 2004, and 2009 European Election Studies, it finds that only a few voters deviate from their left‐right preferences and choose a Eurosceptic party. Moreover, the news media hardly exert an influence on changes in ideological vote deviations even when taking individuals’ pre‐held EU attitudes into account.
Talking It Up or Talking It Down?
Authors: Boomgaarden Hajo G. 
Published: January 2024

Abstract
The chapter explains public opinion about the state of European democracy by focusing on the role of communication. It is argued that political talk, described as a core component of democratic life, is likely to be consequential for public assessments of EU democracy, but that the direction of relationship depends on context characteristics. Following prior literature the chapter focuses on the democratic quality of national political institutions. The findings indeed show that, in particular, in countries in which national institutions perform rather poorly, talking about the EP election is related to better assessments of EU democracy. The reverse pattern, however, is less evident. Overall people to some degree do rely on their national political institutions as a benchmark against which to talk about EU democracy.
SimService: a lightweight library for building simulation services in Python
Authors: Sego T J 
Published: January 2024

Abstract

Summary
Integrative biological modeling requires software infrastructure to launch, interconnect, and execute simulation software components without loss of functionality. SimService is a software library that enables deploying simulations in integrated applications as memory-isolated services with interactive proxy objects in the Python programming language. SimService supports customizing the interface of proxies so that simulation developers and users alike can tailor generated simulation instances according to model, method, and integrated application.

Availability and implementation
SimService is written in Python, is freely available on GitHub under the MIT license at https://github.com/tjsego/simservice, and is available for download via the Python Package Index (package name “simservice”) and conda (package name “simservice” on the conda-forge channel).
MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data
Authors: Barth Jackson , Yang Yuqiu , Xiao Guanghua , Wang Xinlei 
Published: January 2024

Abstract

Motivation
Non-informative or diffuse prior distributions are widely employed in Bayesian data analysis to maintain objectivity. However, when meaningful prior information exists and can be identified, using an informative prior distribution to accurately reflect current knowledge may lead to superior outcomes and great efficiency.

Results
We propose MetaNorm, a Bayesian algorithm for normalizing NanoString nCounter gene expression data. MetaNorm is based on RCRnorm, a powerful method designed under an integrated series of hierarchical models that allow various sources of error to be explained by different types of probes in the nCounter system. However, a lack of accurate prior information, weak computational efficiency, and instability of estimates that sometimes occur weakens the approach despite its impressive performance. MetaNorm employs priors carefully constructed from a rigorous meta-analysis to leverage information from large public data. Combined with additional algorithmic enhancements, MetaNorm improves RCRnorm by yielding more stable estimation of normalized values, better convergence diagnostics and superior computational efficiency.

Availability and implementation
R Code for replicating the meta-analysis and the normalization function can be found at github.com/jbarth216/MetaNorm.
Exposome in ischaemic heart disease: beyond traditional risk factors
Authors: Montone Rocco A , Camilli Massimiliano , Calvieri Camilla , Magnani Giulia , Bonanni Alice , Bhatt Deepak L , Rajagopalan Sanjay , Crea Filippo , Niccoli Giampaolo 
Published: January 2024

Abstract
Ischaemic heart disease represents the leading cause of morbidity and mortality, typically induced by the detrimental effects of risk factors on the cardiovascular system. Although preventive interventions tackling conventional risk factors have helped to reduce the incidence of ischaemic heart disease, it remains a major cause of death worldwide. Thus, attention is now shifting to non-traditional risk factors in the built, natural, and social environments that collectively contribute substantially to the disease burden and perpetuate residual risk. Of importance, these complex factors interact non-linearly and in unpredictable ways to often enhance the detrimental effects attributable to a single or collection of these factors. For this reason, a new paradigm called the ‘exposome’ has recently been introduced by epidemiologists in order to define the totality of exposure to these new risk factors. The purpose of this review is to outline how these emerging risk factors may interact and contribute to the occurrence of ischaemic heart disease, with a particular attention on the impact of long-term exposure to different environmental pollutants, socioeconomic and psychological factors, along with infectious diseases such as influenza and COVID-19. Moreover, potential mitigation strategies for both individuals and communities will be discussed.
Michener’s group-size paradox in cooperatively breeding birds
Authors: Downing Philip A 
Published: January 2024

Abstract
According to Michener’s paradox, most altruistic groups in nature should be small and large groups should not exist. This is because per capita productivity is thought to decrease as groups get larger, meaning that the share of indirect fitness available to each group member declines, which favours dispersal. The empirical evidence for a decrease in per capita productivity is contradictory, however, and limited to the social Hymenoptera. I report that per capita reproductive success decreased with increasing group size across 26 cooperatively breeding bird species. Small groups comprising two or three individuals were the most common (79% of 16,101 groups), and these had the highest per capita reproductive success. This close fit between per capita reproductive success and the distribution of group sizes in nature suggests that it may indeed be difficult for large groups to evolve through indirect fitness benefits alone.
Ling-Gui-Zhu-Gan decoction protects against doxorubicin-induced myocardial injury by downregulating ferroptosis
Authors: Yang Ya-li , Zhao Chuan-zhi , Zhao Chun-chun , Wen Zhong-yu , Ma Yao-yao , Zhao Xiao-ni , Wang Liang , Huang Jin-ling , Zhou Peng 
Published: January 2024

Abstract

Objective
To investigate the mechanism of Ling-Gui-Zhu-Gan decoction (LGZGD) protects against doxorubicin (DOX)-induced myocardial injury.

Methods
In vivo experiment, rats were divided into six groups: normal group, model group (15 mg/kg, DOX), Dex group(150 mg/kg, Dex), LGZGD-L group (2.1 g/kg), LGZGD-M group (4.2 g/kg), and LGZGD-H group (8.4 g/kg). We used HE and Masson staining to observe the histopathological changes, echocardiography to assess the cardiac function, and western blot and RT-qPCR to detect the expressions of Nrf2, GPX4, Fpn1, and Ptgs2. In vitro experiment, we used immunofluorescence to detect ROS production, and RT-qPCR to detect gene expression of GPX4, Fpn1, and Ptgs2.

Key findings
In vivo, LGZGD improved cardiac systolic function. LGZGD significantly reduced MDA, LDH, and CK levels, increased SOD activity, enhanced the protein expression of Nrf2, GPX4, and Fpn1, and decreased Ptgs2 levels. In vitro, LGZGD-containing serum significantly reduced ROS, increased the gene expression of GPX4 and Fpn1, and decreased the gene expression of Ptgs2. Furthermore, compared with the LGZGD (si-NC) group, the LGZGD (si-Nrf2) group had decreased gene expression of Nrf2, GPX4, and Fpn1 and increased gene expression of Ptgs2.

Conclusions
LGZGD can ameliorate DOX-cardiotoxicity by activating the Nrf2 signaling pathway and inhibiting ferroptosis in cardiomyocytes.
Temporal Dynamics, Discovery, and Emergence of Human-Transmissible RNA Viruses
Authors: Lu Lu , Zhang Feifei , Brierley Liam , Robertson Gail , Chase-Topping Margo , Lycett Samantha , Woolhouse Mark 
Published: January 2024

Abstract
Transmissibility, the ability to spread within host populations, is a prerequisite for a pathogen to have epidemic or pandemic potential. Here, we estimate the phylogenies of human infectivity and transmissibility using 1,408 genome sequences from 743 distinct RNA virus species/types in 59 genera. By repeating this analysis using data sets censored by virus discovery date, we explore how temporal changes in the known diversity of RNA viruses—especially recent increases in recognized nonhuman viruses—have altered these phylogenies. Over time, we find significant increases in the proportion of RNA virus genera estimated to have a nonhuman-infective ancestral state, in the fraction of distinct human virus lineages that are purely human-transmissible or strictly zoonotic (compared to mixed lineages), and in the number of human viruses with nearest relatives known not to infect humans. Our results are consistent with viruses that are capable of spreading in human populations commonly emerging from a nonhuman reservoir. This is more likely in lineages that already contain human-transmissible viruses but is rare in lineages that contain only strictly zoonotic viruses.
BIL9 Promotes Both Plant Growth via BR Signaling and Drought Stress Resistance by Binding with the Transcription Factor HDG11
Authors: Surina Surina , Yamagami Ayumi , Miyaji Tomoko , Chagan Zhana , Chung KwiMi , Mitsuda Nobutaka , Nishida Kaisei , Tachibana Ryo , Zhu Zhangliang , Miyakawa Takuya , Shinozaki Kazuo , Sakuta Masaaki , Asami Tadao , Nakano Takeshi 
Published: January 2024

Abstract
Drought stress is a major threat leading to global plant and crop losses in the context of the climate change crisis. Brassinosteroids (BRs) are plant steroid hormones, and the BR signaling mechanism in plant development has been well elucidated. Nevertheless, the specific mechanisms of BR signaling in drought stress are still unclear. Here, we identify a novel Arabidopsis gene, BRZ INSENSITIVE LONG HYPOCOTYL 9 (BIL9), which promotes plant growth via BR signaling. Overexpression of BIL9 enhances drought and mannitol stress resistance and increases the expression of drought-responsive genes. BIL9 protein is induced by dehydration and interacts with the HD-Zip IV transcription factor HOMEODOMAIN GLABROUS 11 (HDG11), which is known to promote plant resistance to drought stress, in vitro and in vivo. BIL9 enhanced the transcriptional activity of HDG11 for drought-stress-resistant genes. BIL9 is a novel BR signaling factor that enhances both plant growth and plant drought resistance.
Epistemic Arguments for a Democratic Right to Silence
Authors: Degerman Dan , Bellazzi Francesca 
Published: January 2024

Abstract
While much ink has been spilt over the political importance of speech, much less has been dedicated to the political importance of silence. This article seeks to fill that gap. We propose the need for a robust, democratic right to silence in public life and argue that there are politically salient epistemic reasons for recognising that right. We begin by defining what silence is and what a robust right to silence entails. We then argue that the right to silence offers two politically salient epistemic benefits. The first is that, if the right to silence is maintained, we can avoid the epistemic harm that may be caused when an individual is compelled to lie in public. The second is that the right to silence can protect marginalised individuals against the epistemic injustices that may arise when others are likely to misconstrue their speech.
Developmental exposure to pesticides that disrupt retinoic acid signaling causes persistent retinoid and behavioral dysfunction in zebrafish
Authors: Hawkey Andrew B , Shekey Nathan , Dean Cassandra , Asrat Helina , Koburov Reese , Holloway Zade R , Kullman Seth W , Levin Edward D 
Published: January 2024

Abstract
Early developmental exposure to environmental toxicants may play a role in the risk for developing autism. A variety of pesticides have direct effects on retinoic acid (RA) signaling and as RA signaling has important roles in neurodevelopment, such compounds may cause developmental neurotoxicity through an overlapping adverse outcome pathway. It is hypothesized that a pesticide’s embryonic effects on retinoid function may correspond with neurobehavioral disruption later in development. In the current studies, we determined the effects of RA-acting pesticides on neurobehavioral development in zebrafish. Buprofezin and imazalil caused generalized hypoactivity in the larval motility test, whereas chlorothalonil and endosulfan I led to selective hypoactivity and hyperactivity, respectively. With buprofezin, chlorothalonil, and imazalil, hypoactivity and/or novel anxiety-like behaviors persisted in adulthood and buprofezin additionally decreased social attraction responses in adulthood. Endosulfan I did not produce significant adult behavioral effects. Using qPCR analyses of adult brain tissue, we observed treatment-induced alterations in RA synthesis or catabolic genes, indicating persistent changes in RA homeostasis. These changes were compound-specific, with respect to expression directionality, and potential patterns of homeostatic disruption. Results suggest the likely persistence of disruptions in RA signaling well into adulthood and may represent compensatory mechanisms following early life stage exposures. This study demonstrates that early developmental exposure to environmental toxicants that interfere with RA signaling causes short as well as long-term behavioral disruption in a well-established zebrafish behavioral model and expand upon the meaning of the RA adverse outcome pathway, indicating that observed effects likely correspond with the nature of underlying homeostatic effects.