bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supporting young people through the COVID-19 pandemic and beyond: A multi-site qualitative longitudinal study
Authors: Whyte Madelyn , Nichol Emily , Hawke Lisa D. , Wuerth Kelli , Quinlan-Davidson Meaghen , O’Reilly Aileen , Duffy Joseph , Mathias Steve , Henderson JL , Barbic Skye 
Published: December 2023

AbstractThroughout the COVID-19 pandemic, youth have experienced substantial stress due to abrupt changes in education, finances, and social life, compounding pre-existing stressors. With youth (ages 15-26) often at critical points in development, they are vulnerable to long-term mental health challenges brought on by pandemic trauma. To identify youth experiences throughout the pandemic and examine changes over time, we conducted semi-structured interviews among n=141 youth in two Canadian provinces (Ontario and British Columbia) and across the country of Ireland at three time points over the course of more than one year (August 2020-October 2021). We conducted a qualitative longitudinal analysis using an inductive content approach. Categories identified were (1) coping with hardship; (2) opportunities for growth; (3) adapting to new ways of accessing services; (4) mixed views on the pandemic: attitudes, behaviour, and perception of policy response; (5) navigating COVID-19 information; (6) transitioning to life after the pandemic; and (7) youth-led recommendations for government and service response. The findings also reveal trends in health and wellness in accordance with prolonged periods of lockdown, changes in weather, and return to normalcy after the availability of COVID-19 vaccines. Key recommendations from youth include incorporating youth voice into decision making, communicating public health information effectively to youth, enhancing service delivery post-pandemic, and planning for future pandemics. These results provide insights into the extensive longitudinal impacts of the COVID-19 pandemic on young people across three geographical locations. Including youth in decision making for future pandemics or public health emergencies is critical.
Linking Structure and Function: Image-Based Virtual Populations of the Retinal Vasculature
Authors: Hernandez Rémi , Madhusudhan Savita , Zheng Yalin , El-Bouri Wahbi K. 
Published: December 2023

AbstractPurposeThis study explores the relationship between microvascular parameters as delineated by optical coherence tomography angiography (OCTA) and retinal perfusion. We introduce a versatile framework to examine the interplay between the retinal vasculature structure and function, generating virtual vasculatures from central retinal vessels to macular capillaries. Alongside this, we develop a haemodynamics model which tests the associations between vascular morphology and retinal perfusion.MethodsThe generation of the vasculature is based on the distribution of four clinical parameters pertaining to the dimension and blood pressure of the central retinal vessels, constructive constrained optimisation and Voronoi diagram. Arterial and venous trees are generated in the temporal retina and connected through three layers of capillaries at different depths in the macula. The correlations between total retinal blood flow and macular flow fraction and vascular morphology are derived as Spearman rank coefficients and uncertainty from input parameters is quantified.ResultsA virtual cohort of 200 healthy vasculatures were generated. Mean and standard deviation for retinal blood flow and macular flow ratio were 19.15±7.34 μL/min and 4.52±1.19 %. Retinal blood flow was correlated with vessel area density, vessel diameter index, fractal dimension and vessel calibre index. The macular flow fraction was not correlated with any morphological metrics.ConclusionsThe proposed framework is able to reproduce vascular networks in the macula that are morphologically and functionally similar to real vasculature. The framework provides quantitative insights into how macular perfusion can be affected by changes in vascular morphology delineated on OCTA.
The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch
Authors: Hertz Laura M , White Elise N , Kuznedelov Konstantin , Cheng Luyi , Yu Angela M , Kakkaramadam Rivaan , Severinov Konstantin , Chen Alan , Lucks Julius B 
Published: December 2023

ABSTRACTA central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination ofE. coliRNA polymerasein vitrotranscription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants. We showed that only variants containing the mesophilic pseudoknot function at 37 °C. We next systematically varied the pseudoknot sequence and found that a single wobble base pair is critical for function. Characterizing thermophilic variants at 65 °C throughThermus aquaticusRNA polymerasein vitrotranscription showed the importance of this wobble pair for function even at elevated temperatures. Finally, we performed all-atom molecular dynamics simulations which supported the experimental findings, visualized the RNA structure switching process, and provided insight into the important role of magnesium ions. Together these studies provide deeper insights into the role of riboswitch sequence in influencing folding and function that will be important for understanding of RNA-based gene regulation and for synthetic biology applications.
Characterization of DNA methylation reader proteins ofArabidopsis thaliana
Authors: Cahn Jonathan , Lloyd James P. B. , Karemaker Ino D. , Jansen Pascal W.T.C. , Pflueger Jahnvi , Duncan Owen , Petereit Jakob , Bogdanovic Ozren , Millar A. Harvey , Vermeulen Michiel , Lister Ryan 
Published: December 2023

AbstractIn plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (GbM). GbM is correlated with ubiquitously expressed genes, however its function, or absence thereof, is highly debated. The different output that mC can have raises questions as to how it is interpreted - or read - differently in these sequence and genomic contexts. To screen for potential mC binding proteins, we performed an unbiased DNA affinity pull-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date were found to preferentially bind to the methylated probes, along with a range of new mC binding protein candidates. Functional characterization of these mC readers, focused on the MBD and SUVH families, was undertaken by ChIP-seq mapping of genome-wide binding sites, their protein interactors, and the impact of high-order mutations on transcriptomic and epigenomic profiles. Together, this highlighted specific context preferences for these proteins, and in particular the ability of MBD2 to bind specifically to GbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodelling processes in plants.
Suppression of theE.coli rnpA49conditionally lethal phenotype via different compensatory mutations
Authors: Babina Arianne M. , Kirsebom Leif A. , Andersson Dan I. 
Published: December 2023

ABSTRACTRNase P is an essential enzyme found across all domains of life that is responsible for the 5’-end maturation of precursor tRNA transcripts. Since its discovery in the 1970s, numerous studies have sought to elucidate the mechanisms and biochemistry governing RNase P function. However, much remains unknown about the regulation of RNase P expression, the turnover and degradation of the enzyme, and the mechanisms underlying the phenotypes and complementation of specific RNase P mutations. InEscherichia coli, the temperature-sensitivernpA49mutation in the protein subunit of RNase P has arguably been one of the most well-studied and commonly used mutations for examining the enzyme’s activityin vivo. Here we report for the first time naturally-occurring temperature-resistant suppressor mutations ofE. colistrains carrying thernpA49allele. We find thatrnpA49strains can partially compensate the temperature-sensitive defect via gene amplifications of either RNase P subunit (rnpA49orrnpB) or by the acquisition of loss-of-function mutations in Lon protease or RNase R. Our results agree with previous plasmid overexpression and gene deletion complementation studies and importantly suggest the involvement of Lon protease in the degradation and/or regulatory pathway(s) of the mutant protein subunit of RNase P. This work offers novel insight into the behavior and complementation of thernpA49allelein vivoand provides direction for follow-up studies regarding RNase P regulation and turnover.
Altered neural activity in the mesoaccumbens pathway underlies impaired social reward processing inShank3-deficient rats
Authors: Barbier Marie , Thirtamara Rajamani Keerthi , Netser Shai , Wagner Shlomo , Harony-Nicolas Hala 
Published: December 2023

AbstractSocial behaviors are crucial for human connection and belonging, often impacted in conditions like Autism Spectrum Disorder (ASD). The mesoaccumbens pathway (VTA and NAc) plays a pivotal role in social behavior and is implicated in ASD. However, the impact of ASD-related mutations on social reward processing remains insufficiently explored. This study focuses on theShank3mutation, associated with a rare genetic condition and linked to ASD, examining its influence on the mesoaccumbens pathway during behavior, using theShank3-deficient rat model. Our findings indicate thatShank3-deficient rats exhibit atypical social interactions and have difficulty adjusting behavior based on reward values, associated with modified neuronal activity of VTA dopaminergic and GABAergic neurons and reduced dopamine release in the NAc. Moreover, we demonstrate that manipulating VTA neuronal activity can normalize this behavior, providing insights into the effects ofShank3mutations on social reward and behavior, and identify a potential neural pathway for intervention.
Early life stress induces sex-specific changes in behavior and parallel locus coeruleus neuron excitability
Authors: Savannah Brannan , Sarahi Porcayo , Richardson Ben D 
Published: December 2023

AbstractStress-related psychiatric disorders are more common in female clinical populations after adolescence, but the exact mechanism behind this difference is unknown. The locus coeruleus (LC) is a brain area that contains adrenergic norepinephrine (NE)-releasing neurons previously found to display basal sex differences in excitability and stress neuropeptide responses in animal models. Corticotropin releasing factor (CRF), the neuropeptide responsible for stress signaling, has been shown to directly alter LC neuron firing, thereby providing one mechanism by which stress may modulate noradrenergic function in either acute or chronic stress. Such activation of CRF receptor 1 (CRF1) by CRF in the LC is fundamentally different in male and female mice due to increased CRF receptor expression, G-protein coupling, and CRF-stimulated NE release in female compared to males. Despite evidence for an interaction between sex, LC adrenergic neuron activity, and stress, how early life stress affects LC neuronal behavior in parallel to anxiety, activity, and cognition (i.e. components of PTSD and ADHD) in a sexual dimorphic manner has not been explored. The effects of an early life variable stress (ELVS) paradigm inducing stress at both early life and adolescence were assessed in C57 male and female mice using behavioral and electrophysiological measures for hyperactivity, anxiety, short-term memory, repetitive behaviors and LC neuron excitability. Hyperactivity in open field and deficits in Y-maze performance were observed in ELVS female mice when compared to controls. ELVS females, but not males, showed a reduction in LC excitability when compared to controls of the same sex, which was due to hyperpolarization and an increase in the action potential delay time. LC neurons form naïve mice indicated that CRF1receptor-mediated effects on LC neuron excitability were largely due to Gq-mediated (Ca2+-dependent) signaling in male mice and non Ca2+-dependent (likely Gs) in female mice. Through this animal model of early life stress inducing impaired memory and hyperactivity in a sex-specific manner, further investigation to ameliorate these symptoms may benefit more targeted treatment approaches for stress-related disorders based on sex and developmental stage of trauma exposure(s).
Multitask Learning of Biophysically-Detailed Neuron Models
Authors: Verhellen Jonas , Beshkov Kosio , Amundsen Sebastian , Ness Torbjørn V. , Einevoll Gaute T. 
Published: December 2023

AbstractThe human brain operates at multiple levels, from molecules to circuits, and understanding these complex processes requires integrated research efforts. Simulating biophysically-detailed neuron models is a computationally expensive but effective method for studying local neural circuits. Recent innovations have shown that artificial neural networks (ANNs) can accurately predict the behaviour of these detailed models in terms of spikes, electrical potentials, and optical readouts. While these methods have the potential to accelerate large network simulations by several orders of magnitude compared to conventional differential equation based modelling, they currently only predict voltage outputs for the soma or a select few neuron compartments. Our novel approach, based on enhanced state-of-the-art architectures for multitask learning (MTL), allows for the simultaneous prediction of membrane potentials in each compartment of a neuron model, at a speed of up to two orders of magnitude faster than classical simulation methods. By predicting all membrane potentials together, our approach not only allows for comparison of model output with a wider range of experimental recordings (patch-electrode, voltage-sensitive dye imaging), it also provides the first stepping stone towards predicting local field potentials (LFPs), electroencephalogram (EEG) signals, and magnetoencephalography (MEG) signals from ANN-based simulations. It further presents a challenging benchmark for MTL architectures due to the large amount of data involved, the presence of correlations between neighbouring compartments, and the non-Gaussian distribution of membrane potentials.
Protocol using similarity score and improved shrink-wrap algorithm for better convergence of phase-retrieval calculation in X-ray diffraction imaging
Authors: Yoshida Syouyo , Harada Kosei , Uezu So , Takayama Yuki , Nakasako Masayoshi 
Published: December 2023

In X-ray diffraction imaging (XDI), electron density maps of a targeted particle are reconstructed computationally from the diffraction pattern alone using phase-retrieval (PR) algorithms. However, the PR calculations sometimes fail to yield realistic electron density maps that approximate the structure of the particle. This occurs due to the absence of structure amplitudes at and near the zero-scattering angle and the presence of Poisson noise in weak diffraction patterns. Consequently, the PR calculation becomes a bottleneck for XDI structure analyses. Here, a protocol to efficiently yield realistic maps is proposed. The protocol is based on the empirical observation that realistic maps tend to yield low similarity scores, as suggested in our prior study [Sekiguchi et al. (2017), J. Synchrotron Rad.
24, 1024–1038]. Among independently and concurrently executed PR calculations, the protocol modifies all maps using the electron-density maps exhibiting low similarity scores. This approach, along with a new protocol for estimating particle shape, improved the probability of obtaining realistic maps for diffraction patterns from various aggregates of colloidal gold particles, as compared with PR calculations performed without the protocol. Consequently, the protocol has the potential to reduce computational costs in PR calculations and enable efficient XDI structure analysis of non-crystalline particles using synchrotron X-rays and X-ray free-electron laser pulses.
Organizational factors determining LGBT disclosure: an analysis of the Brazilian context
Authors: Pinheiro Alan Bandeira , do Prado Nágela Bianca , Moraes Gustavo Hermínio Salati Marcondes de , Carraro Wendy Beatriz Witt Haddad 
Published: December 2023

PurposeThis study investigated the impact of some determinant organizational factors on disseminating LGBT information in Brazilian companies in 2019.Design/methodology/approachThe study is exploratory and has a quantitative approach, which uses secondary data from the CSR Hub database 2019 of publicly traded Brazilian companies. For constructing the LGBT disclosure metric, the authors took the study by Parizek and Evangelinos (2021). The independent variables were the social responsibility, financial and governance characteristics of the companies. Analysis was conducted by combining a symmetric method (multiple linear regression analysis with econometric models) and an asymmetric approach (fuzzy-set qualitative comparative analysis).FindingsThe research findings showed that companies with higher performance in CSR have greater LGBT disclosure. Findings also show that companies with higher financial performance tend to have greater LGBT disclosure. This is because larger companies have more resources to invest in CSR practices and sexual diversity policies, as well as a greater number of stakeholders pressing them to act more responsibly. Additional results showed that companies that signed the UN Global Compact and publish an environmental report annually have greater engagement in LGBT disclosure.Originality/valueThis study's novelty emerges from applying the fsQCA technique, which helps to a broaden understanding of the conditions necessary to achieve greater LGBT disclosure. Furthermore, this study initiates the debate on LGBT disclosure in emerging economies, a recent topic and still little explored empirically.
Economics of ChatGPT: a labor market view on the occupational impact of artificial intelligence
Authors: Zarifhonarvar Ali 
Published: December 2023

PurposeThe study investigates the influence of ChatGPT on the labor market dynamics, aiming to provide a structured understanding of the changes induced by generative AI technologies.Design/methodology/approachAn analysis of existing literature serves as the foundation for understanding the impact, while the supply and demand model helps assess the effects of ChatGPT. A text-mining approach is utilized to analyze the International Standard Occupation Classification, identifying occupations most susceptible to disruption by ChatGPT.FindingsThe study reveals that 32.8% of occupations could be fully impacted by ChatGPT, while 36.5% might experience a partial impact and 30.7% are likely to remain unaffected.Research limitations/implicationsWhile this study offers insights into the potential influence of ChatGPT and other generative AI services on the labor market, it is essential to note that these findings represent potential implications rather than realized labor market effects. Further research is needed to track actual changes in employment patterns and job market dynamics where these AI services are widely adopted.Originality/valueThis paper contributes to the field by systematically categorizing the level of impact on different occupations, providing a nuanced perspective on the short- and long-term implications of ChatGPT and similar generative AI services on the labor market.
Evaluation of ecological restoration effects and diagnosis of obstacle factors in coastal zones: a case study of Qinhuangdao city
Authors: Yan Yuxia , Wang Na , Cao Yun 
Published: December 2023

PurposeCoastal zone ecological restoration project is of great significance to alleviate marine ecological degradation. Evaluating the effect of coastal ecological restoration projects and identifying the obstacle factors affecting their restoration level can provide an empirical basis for future Marine ecological restoration projects.Design/methodology/approachHowever, due to the initial stage of coastal zone ecological restoration projects, the actual monitoring data of coastal zone ecological restoration is relatively lacking. Based on the CRITIC-TOPSIS (combination of CRITIC method and TOPSIS method) method, combined with the subjective perception of the public and the actual data of the restoration project, this paper proposes an evaluation method of the coastal zone ecological restoration effect to obtain the specific implementation effect of the coastal zone ecological restoration project. The main obstacle factors affecting the evaluation of coastal ecological restoration effect are identified by using the obstacle degree model.FindingsThis paper conducted an empirical study on the restoration of sandy shoreline and coastal wetland in Qinhuangdao city. Based on the data of restoration projects and the subjective perception of ecological restoration by the public in Qinhuangdao city, the research results showed that the coastal zone ecological restoration effect of Qinhuangdao city was general. The quality of the restoration project and the public perception have an important influence on the evaluation of the restoration effect. Improving the quality of the restoration project, strengthening the public's participation in ecological restoration and allowing the public to better participate in the ecological restoration of the coastal zone can improve the effect of ecological restoration of the coastal zone in an all-round way.Originality/valueThe research results of this paper have a guiding role in the ecological restoration of coastal cities in the future, and also have a demonstration and reference role for the assessment of the effect of ecological restoration of coastal zones.
From scarcity to security: Participant well‐being in the first 2 years of a basic income pilot
Authors: Hamilton Leah , Choplin Victoria , Paputseanos Taylor 
Published: December 2023

AbstractThis article describes the mental well‐being outcomes of participants in the HudsonUP pilot, a 5‐year basic income initiative for low to mid‐income residents of Hudson, NY. The study employs a mixed‐methods approach, including both quantitative surveys and qualitative phenomenological interviews, to better understand participants' experiences 2 years into the pilot. Through the lens of the psychological theory of scarcity, findings indicate that the HudsonUP program has improved the overall mental well‐being of the participants by reducing the stress and anxiety associated with financial insecurity and helping them to meet their basic needs, pursue further education, and career opportunities. Despite the challenges of the ongoing pandemic and inflation, participants expressed gratitude for the “undercurrent of stability” provided by the program.