bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct Mechanisms of Recognition of Phosphorylated RNAPII C-Terminal Domain by BRCT Repeats of the BRCA1–BARD1 Complex: Insights from Structural and Functional Analyses
Authors: Klapstova V. , Sedova K. , Houser J. , Sebesta M. 
Published: January 2025

AbstractTranscription competes with other DNA-dependent processes, such as DNA repair, for access to its substrate, DNA. However, the principles governing the interplay between these processes remain poorly understood. Evidence suggests that the BRCA1-BARD1 complex, a key player in the DNA damage response, may act as a mediator of this crosstalk. In this study, we investigated the molecular mechanism underpinning the interaction between RNA polymerase II (RNAPII) and the BRCA1-BARD1 complex, as well as its functional implications. Our findings reveal that the BRCT repeat of BRCA1 binds the Ser5-phosphorylated CTD of RNAPII, utilising a mechanism previously established for other BRCT ligands. Furthermore, we demonstrate that this interaction is critical for the organisation of RNAPII into condensates with liquid-like properties. Analysis of disease-associated variants within the BRCT repeats further supports the biological relevance of this condensation. Collectively, our results suggest that the BRCA1-BARD1 complex may coordinate transcription and DNA repair by facilitating the organisation of RNAPII into transcription factories.
The Effects of Acute Trazodone Administration on Sleep in Mice
Authors: Arai Mayuko , Kent Brianne A 
Published: January 2025

AbstractStudy ObjectivesTrazodone is an antidepressant with robust hypnotic effects, frequently prescribed off-label to treat insomnia. Trazodone has gained recent attention in the context of neurodegenerative diseases because sleep has been proposed as a novel target for disease-modifying therapeutics. Preclinical research in rodents examining the effects of trazodone on sleep is limited, so here we aimed to develop a translationally-focused protocol to study the sleep-promoting effects of trazodone in mice.MethodsWe investigated the effects of voluntary oral trazodone administration at doses of 0 mg/kg, 10 mg/kg, 40 mg/kg, and 60 mg/kg on sleep in C57BL/6J mice (n = 15; females = 6; age 10-13 months). Mice were dosed with trazodone for 6 consecutive nights, while being recorded with intracranially implanted 2-channel electroencephalogram (EEG) and electromyography (EMG). EEG/EMG recordings were analyzed for time spent in each vigilance state and power spectra.ResultsA single dose of trazodone, administered prior to the onset of the 12-h rest phase, dose-dependently increased non-rapid eye movement (NREM) sleep and delta power during NREM sleep, at the expense of rapid eye movement (REM) sleep. These effects on sleep persisted after six consecutive days of dosing, albeit to a lesser extent.ConclusionWe have validated a novel voluntary oral administration protocol for trazodone use in mice and have shown that trazodone effectively promotes NREM in mice. Our novel protocol will be useful for future research investigating the effects of trazodone on sleep in mouse models of disease.Statement of significanceTrazodone is an antidepressant known to increase slow wave sleep in humans. Slow wave sleep promotion is being explored as a disease-modifying therapeutic target for neurodegenerative diseases, such as Alzheimer’s disease. We have developed a novel translationally-focused protocol for administering trazodone to mice, which overcomes some of the challenges of using trazodone for preclinical sleep research. Using our protocol we have demonstrated for the first time that trazodone dose-dependently increases the amount of NREM sleep and delta power in mice, recapitulating the enhancement of slow wave sleep in humans treated with trazodone.
Changes in cortical beta power predict motor control flexibility, not vigor
Authors: Pierrieau Emeline , Dussard Claire , Plantey-Veux Axel , Guerrini Cloé , Lau Brian , Pillette Léa , George Nathalie , Jeunet-Kelway Camille 
Published: January 2025

AbstractThe amplitude of beta-band activity (β power; 13-30 Hz) over motor cortical regions is used to assess and decode movement in clinical settings and brain-computer interfaces, as β power is often assumed to predict the strength of the brain’s motor output, or “vigor”. However, recent conflicting evidence challenges this assumption and underscores the need to clarify the relationship between β power and movement. In this study, sixty participants were trained to self-regulate β power using electroencephalography-based neurofeedback before performing different motor tasks. Results showed that β power modulations can impact different motor variables, or the same variables in opposite directions, depending on task constraints. Importantly, downregulation of β power was associated with better task performance regardless of whether performance implied increasing or decreasing motor vigor. These findings demonstrate that β power should be interpreted as a measure of motor flexibility, which underlies adaptation to environmental constraints, rather than vigor.
Resolving inconsistent effects of tDCS on learning using a homeostatic structural plasticity model
Authors: Lu Han , Frase Lukas , Normann Claus , Rotter Stefan 
Published: January 2025

AbstractTranscranial direct current stimulation (tDCS) is increasingly used to modulate motor learning. Current polarity and intensity, electrode montage, and application before or during learning had mixed effects. Both Hebbian and homeostatic plasticity were proposed to account for the observed effects, but the explanatory power of these models is limited. In a previous modeling study, we showed that homeostatic structural plasticity (HSP) can explain long-lasting after-effects of tDCS and transcranial magnetic stimulation (TMS). The interference between motor learning and tDCS, which are both based on HSP in our model, is a candidate mechanism to resolve complex and seemingly contradictory experimental observations. We implemented motor learning and tDCS in a spiking neural network subject to HSP. The anatomical connectivity of the engram induced by motor learning was used to quantify the impact of tDCS on motor learning. Our modeling results demonstrated that transcranial direct current stimulation applied before learning had weak modulatory effects. It led to a small reduction in connectivity if it was applied uniformly. When applied during learning, targeted anodal stimulation significantly strengthened the engram, while targeted cathodal or uniform stimulation weakened it. Applied after learning, targeted cathodal, but not anodal, tDCS boosted engram connectivity. Strong tDCS would distort the engram structure if not applied in a targeted manner. Our model explained both Hebbian and homeostatic phenomena observed in human tDCS experiments by assuming memory strength positively correlates with engram connectivity. This includes applications with different polarity, intensity, electrode montage, and timing relative to motor learning. The HSP model provides a promising framework for unraveling the dynamic interaction between learning and transcranial DC stimulation.
Chronic chemogenetic slow-wave-sleep enhancement in mice
Authors: Gompf Heinrich S. , Ferrari Loris L. , Anaclet Christelle 
Published: January 2025

AbstractWhile epidemiological associations and brief studies of sleep effects in human disease have been conducted, rigorous long-term studies of sleep manipulations and in animal models are needed to establish causation and to understand mechanisms. We have previously developed a mouse model of acute slow-wave-sleep (SWS) enhancement using chemogenetic activation of parafacial zone GABAergic neurons (PZGABA) in the parvicellular reticular formation of the pontine brainstem. However, it was unknown if SWS could be enhanced chronically in this model.In the present study, mice expressing the chemogenetic receptor hM3Dq in PZGABAwere administered daily with one of three chemogenetic ligands, clozapine N-oxide (CNO), deschloroclozapine (DCZ) and compound 21 (C21), and sleep-wake phenotypes were analyzed using electroencephalogram (EEG) and electromyogram (EMG).We found that SWS time is increased for three hours, and at the same magnitude for at least six months. This phenotype is associated with an increase of slow wave activity (SWA) of similar magnitude throughout the 6-month dosing period. Interestingly, at the end of the 6-month dosing period, SWA remains increased for at least a week.This study validates a mouse model of chronic SWS enhancement that will allow mechanistic investigations into how SWS promotes physiological function and prevents diseases. The approach of a rotating schedule of three chemogenetic ligands may be broadly applicable in chemogenetic studies that require chronic administration.
Effect of frequency-dependent shear and volume viscosities on molecular friction in liquids
Authors: Kiefer Henrik , Vitali Domenico , Dalton Benjamin A. , Scalfi Laura , Netz Roland R. 
Published: January 2025

The relation between the frequency-dependent friction of a molecule in a liquid and the hydrodynamic properties of the liquid is fundamental for molecular dynamics. We investigate this connection for a water molecule moving in liquid water using all-atomistic molecular dynamics (MD) simulations and linear hydrodynamic theory. We analytically calculate the frequency-dependent friction of a sphere with finite surface slip moving in a viscoelastic compressible fluid by solving the linear transient Stokes equation, including frequency-dependent shear and volume viscosities, both determined from MD simulations of bulk liquid water. From MD simulation trajectories, we also determine the frequency-dependent friction of a single water molecule moving in liquid water, as defined by the generalized Langevin equation. The frequency dependence of the shear viscosity of liquid water requires careful consideration of hydrodynamic finite-size effects to observe the asymptotic hydrodynamic power-law tail. By fitting the effective sphere radius and the slip length, the frequency-dependent friction and velocity autocorrelation function from the transient Stokes equation and simulations quantitatively agree. This shows that the transient Stokes equation accurately describes the important features of the frequency-dependent friction of a single water molecule in liquid water and thus applies down to molecular length and time scales, provided accurate frequency-dependent viscosities are used. In contrast, for a methane molecule moving in water, the frequency-dependent friction cannot be predicted based on a homogeneous model, which, supported by the extraction of the frequency-dependent surface slip, suggests that a methane molecule is surrounded by a finite-thickness hydration layer with viscoelastic properties that differ significantly from those of bulk water.

Published by the American Physical Society
2025
Primary quantum thermometry of mm-wave blackbody radiation via induced state transfer in Rydberg states of cold atoms
Authors: Schlossberger Noah , Rotunno Andrew P. , Eckel Stephen P. , Norrgard Eric B. , Manchaiah Dixith , Prajapati Nikunjkumar , Artusio-Glimpse Alexandra B. , Berweger Samuel , Simons Matthew T. , Shylla Dangka , Watterson William J. , Patrick Charles , Meraki Adil , Talashila Rajavardhan , Younes Amanda , La Mantia David S. , Holloway Christopher L. 
Published: January 2025

Rydberg states of alkali-metal atoms are highly sensitive to electromagnetic radiation in the GHz-to-THz regime because their transitions have large electric dipole moments. Consequently, environmental blackbody radiation (BBR) can couple Rydberg states together at µs timescales. Here, we track the BBR-induced transfer of a prepared Rydberg state to its neighbors and use the evolution of these state populations to characterize the BBR field at the relevant wavelengths, primarily at 130 GHz. We use selective field ionization readout of Rydberg states with principal quantum number n∼30 in Rb85 and substantiate our ionization signal with a theoretical model. With this detection method, we measure the associated blackbody-radiation-induced time dynamics of these states, reproduce the results with a simple semiclassical population transfer model, and demonstrate that this measurement is temperature sensitive with a statistical sensitivity to the fractional temperature uncertainty of 0.09 Hz−1/2, corresponding to 26 K Hz−1/2 at room temperature. This represents a calibration-free SI-traceable temperature measurement, for which we calculate a systematic fractional temperature uncertainty of 0.006, corresponding to 2 K at room temperature when used as a primary temperature standard.

Published by the American Physical Society
2025
Risk communication in risk-based planning: a practice in coastal area of Subang regency, Indonesia
Authors: Soejarwo Permana Ari , Fahmi Fikri Zul , Suroso Djoko Santoso Abi 
Published: January 2025

PurposeThis paper aims to explore the extent to which risk communication has been implemented into spatial planning practice in Indonesia by using the coastal area of Subang Regency as a case study. Risk communication in risk-based planning (RBP) is the process of exchanging information about risk and hazards between all actors which emphasizes determining the level of risk acceptance of communities to support appropriate decision making in spatial planning. It has been proven effective in developed countries, but it remains unclear in Indonesia.Design/methodology/approachThe study uses qualitative methods by analyzing documents and interviews with local stakeholders to explain how risk communication is implemented in RBP at the regency level.FindingsThis study reveals that risk communication is not explicitly incorporated into RBP regulations and impacts its practices. The absence of a clear definition and guidelines in regulations is leading to limited understanding at all government levels. The emphasis on community risk acceptance levels as the core of risk communication in RBP has not been conducted, where the existing focus is still majorly on disaster events. This has led to improper spatial planning decisions.Practical implicationsIncorporating risk communication in RBP is important in spatial planning practice in Indonesia. Without effective community engagement, clear definition and guidelines on community’s acceptable risk levels, spatial planning efforts may not align with local needs, leading to social conflicts and hindering appropriate spatial planning. For instance, land use policy for community that is willing to tolerate the risk should be permitted with specified consideration instead of offering relocation options that potentially lead to social unrest by conflicting with their social, economic and cultural. Integrating risk communication into RBP can result in a more adaptive and appropriate spatial planning decisions.Originality/valueThis study offers a novel exploration of risk communication which is important to be integrated into the RBP in a locality in Indonesia, focusing on both regulatory factors and practices to support appropriate decision making in spatial planning. This paper is important because study on risk communication in RBP in Indonesia is still scarce.
Towards inclusive gender diversity training – a critical framework
Authors: Mahajan Rasika , Bleijenbergh Inge , Benschop Yvonne 
Published: January 2025

PurposeThe purpose of this paper is to design and apply a critical framework for assessing the inclusivity of gender diversity training. The framework combines insights from intersectional feminist and postcolonial feminist theory. It is applied to assess whether and how influential gender diversity training manuals question the (re)production of systems of inequality and promote the recognition of varied lived experiences of women particularly in global workplaces.Design/methodology/approachThis qualitative research was done in two stages. First, we designed a critical framework consisting of five elements taking inspiration from intersectional and postcolonial feminist theories. Second, we analysed four gender diversity training manuals from prominent international organizations to assess their inclusivity.FindingsWe found that gender diversity training manuals construct a binary understanding of gender, implying that being a woman is a universal experience. Second, the documents take a systemic approach to intersectionality, acknowledging societal systems, but the focus is on oppression as opposed to privilege, obscuring possible complexities of intersecting social categories. Third, the narratives of gender diversity trainings reflect western hegemony in referring to “global norms” and women from the global south.Originality/valueThe paper brings together complex theoretical strands of intersectional and postcolonial feminist theory in the form of a critical framework that can not only be used to assess gender diversity training but also be applied to other gender diversity interventions. Practical suggestions for trainers to develop more inclusive gender diversity trainings are discussed.
DSEN-EK: Dual-layer Semantic Information Extraction Network with External Knowledge for Fake News Detection
Authors: Qiu Yanfang , Ma Kun , Zhang Weijuan , Pan Run , Chen Zhenxiang 
Published: January 2025

Purpose
Fake news refers to intentionally fabricated or misleading information designed to deceive the public and manipulate opinions for personal, political or financial gain. Most existing detection methods primarily focus on capturing language features from news content. However, these methods neglect the varying importance of different news entities. Additionally, these methods tend to overlook the auxiliary role of external knowledge, resulting in an incomplete understanding of the entity. To address these issues, this paper aims to propose a Dual-layer Semantic Information Extraction Network with External Knowledge (DSEN-EK) for fake news detection.

Design/methodology/approach
This approach is proposed to comprise three parts: Dual-layer Semantic Information Extraction Network, Entity Integration Network with External Knowledge and Classifier. Specifically, Dual-layer Semantic Information Extraction Network is designed to enhance relationships between entities and the influence of important entity representations. The Entity Integration Network with External Knowledge is proposed to extract entity descriptions from external knowledge bases.

Findings
The DSEN-EK model performs well on the Liar, Constraint, Twitter15 and Twitter16 data sets, achieving accuracy of 98.02%, 94.61%, 90.09% and 93.65%, respectively. These results highlight its effectiveness in detecting fake news across different types of content.

Originality/value
The Dual-layer Semantic Information Extraction Network is proposed to capture the relationships between entities and enhance the continuous semantic information of the news. The Entity Integration Network with External Knowledge is designed to enrich entity descriptions, leading to a more comprehensive capture of semantic details.
Numerical study on contact characteristics and sealing performance of rubber-bellows mechanical seals in ESPs
Authors: Ma Yi , Chen Lei , Xu Yixiao , Meng Xiangkai , Peng Xudong 
Published: January 2025

Purpose
This study aims to evaluate the effects of the downhole environment and auxiliary rubber bellows on the contact mechanical characteristics and sealing performance of rubber-bellows mechanical seals (RBMS) in electric submersible pumps (ESPs), considering the elastic support of the rubber bellows, multi-field coupling effect and actual operating conditions.

Design/methodology/approach
A thermal-fluid-solid multi-field coupling numerical model for RBMS in ESPs is developed using the finite element analysis and influence coefficient method. Based on the contact mechanical characteristics of RBMS, the interactions of multiple physical fields between the sealing rings and lubricating oil are accounted for to assess the liquid lubrication state and sealing performance of RBMS in ESPs.

Findings
The findings indicate the anti-leakage effects of rubber bellows, the transition of lubrication state of the sealing end face and the evolution law of sealing performance with environmental pressure, axial compression amount and contact widths of rubber bellows.

Originality/value
This study innovatively proposes a multi-field numerical research method to reveal the impact of the downhole environment and rubber bellows on RBMS in ESPs. These findings contribute to a more comprehensive understanding of the sealing mechanism of RBMS and optimize the sealing design for ESPs in high-pressure environments.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-10-2024-0369/
Determinants of inflation expectations in Colombia: a VAR-X analysis
Authors: Osorio-Barreto Daniel , Mora Jose , Sierra-Suárez Lya Paola 
Published: January 2025

PurposeThis study aims to investigate the determinants of inflation expectations in Colombia through a vector autoregression model with exogenous variables (VAR-X) and uses quarterly data for survey-based inflation expectations and different supply shocks.Design/methodology/approachWe propose a VAR-X model. Despite data unavailability, we gathered quarterly data for the period 2005–2022 for the following variables: oil price, real exchange rate, headline inflation, output gap, policy interest rate and inflation expectations.FindingsWe identified significant responses to inflation expectations in the first quarter. Although we found a positive response of inflation expectations to the interest rate, the robustness tests show that the interest rate negatively affects inflation expectations in the long run. Additionally, we detected a pass-through effect regarding the positive response of inflation expectations to a real exchange rate shock and the inertia of inflation expectations to their own innovations.Research limitations/implicationsWe must emphasize that reliable data from households would be preferred to follow the trend in international research and thus make feasible comparisons.Practical implicationsInflation expectations play an important role in an inflation targeting scheme. Specifically, this scheme allows monitoring of how those approach the proposed target and how they change in the face of changes in total inflation, demand and supply shocks.Originality/valueThe inclusion of exogenous variables contributed to the stability of the model specification by capturing supply shocks not previously considered in the literature.