bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scalable precision wide-field imaging in radio interferometry – II. AIRI validated on ASKAP data
Authors: Wilber A G , Dabbech A , Terris M , Jackson A , Wiaux Y 
Published: May 2023

ABSTRACT
Accompanying Part I, this sequel delineates a validation of the recently proposed AI for Regularization in radio-interferometric Imaging (AIRI) algorithm on observations from the Australian Square Kilometre Array Pathfinder (ASKAP). The monochromatic AIRI-ASKAP images showcased in this work are formed using the same parallelized and automated imaging framework described in Part I: ‘uSARA validated on ASKAP data’. Using a Plug-and-Play approach, AIRI differs from uSARA by substituting a trained denoising deep neural network (DNN) for the proximal operator in the regularization step of the forward–backward algorithm during deconvolution. We build a trained shelf of DNN denoisers that target the estimated image dynamic ranges of our selected data. Furthermore, we quantify variations of AIRI reconstructions when selecting the nearest DNN on the shelf versus using a universal DNN with the highest dynamic range, opening the door to a more complete framework that not only delivers image estimation but also quantifies epistemic model uncertainty. We continue our comparative analysis of source structure, diffuse flux measurements, and spectral index maps of selected target sources as imaged by AIRI and the algorithms in Part I – uSARA and WSClean. Overall, we see an improvement over uSARA and WSClean in the reconstruction of diffuse components in AIRI images. The scientific potential delivered by AIRI is evident in further imaging precision, more accurate spectral index maps, and a significant acceleration in deconvolution time, whereby AIRI is four times faster than its subiterative sparsity-based counterpart uSARA.
Asteroseismology of the DAV star KUV 08368+4026
Authors: Yang Y H , Chen Y H , Tang M Y 
Published: May 2023

ABSTRACT
As a DAV star, KUV 08368+4026 was observed by Li et al. in 2009 February, 2009 December, 2010 January, and 2012 February. They extracted 30 frequencies from the reported 300 h observation data and identified 17 independent modes. Based on the frequency splitting relationship, 6 l = 1 modes and 1 l = 2 mode are identified. The seven identified modes are reliable and can be used to constrain fitting models. A large sample (7,558,272) DAV star models were established using White Dwarf Evolution Code (wdec; 2018 version). The theoretical modes are calculated and used to fit the observed modes in order to obtain a best-fitting model. The best-fitting model has an average fitting error of σRMS = 0.71 s. The best-fitting model parameters are M* = 0.685 ± 0.005 M⊙, Teff = 11820 ± 40 K, log(MHe/M*) = − 5.00 ± 0.01, and, log(MH/M*) = − 6.90 ± 0.01. The stellar mass M* and effective temperature Teff of the best-fitting model are basically consistent with the results of the spectroscopy. The mass of the He layer is thinner than the results obtained from previous asteroseismic models. The best-fitting model has a small Carbon/Oxygen central core with an oxygen abundance of XO = 0.76. The asteroseismological distance calculated using the luminosity of our best-fitting model is basically consistent with that of the Kiso Schmidt ultraviolet excess survey.
Redefining normal breast cell populations using long noncoding RNAs
Authors: Bitar Mainá , Rivera Isela Sarahi , Almeida Isabela , Shi Wei , Ferguson Kaltin , Beesley Jonathan , Lakhani Sunil R , Edwards Stacey L , French Juliet D 
Published: May 2023

Abstract
Single-cell RNAseq has allowed unprecedented insight into gene expression across different cell populations in normal tissue and disease states. However, almost all studies rely on annotated gene sets to capture gene expression levels and sequencing reads that do not align to known genes are discarded. Here, we discover thousands of long noncoding RNAs (lncRNAs) expressed in human mammary epithelial cells and analyze their expression in individual cells of the normal breast. We show that lncRNA expression alone can discriminate between luminal and basal cell types and define subpopulations of both compartments. Clustering cells based on lncRNA expression identified additional basal subpopulations, compared to clustering based on annotated gene expression, suggesting that lncRNAs can provide an additional layer of information to better distinguish breast cell subpopulations. In contrast, these breast-specific lncRNAs poorly distinguish brain cell populations, highlighting the need to annotate tissue-specific lncRNAs prior to expression analyses. We also identified a panel of 100 breast lncRNAs that could discern breast cancer subtypes better than protein-coding markers. Overall, our results suggest that lncRNAs are an unexplored resource for new biomarker and therapeutic target discovery in the normal breast and breast cancer subtypes.
ChroKit: a Shiny-based framework for interactive analysis, visualization and integration of genomic data
Authors: Croci Ottavio , Campaner Stefano 
Published: May 2023

Abstract
We developed ChroKit (the Chromatin toolKit), an interactive web-based framework written in R that enables intuitive exploration, multidimensional analyses, and visualization of genomic data from ChIP-Seq, DNAse-Seq or any other NGS experiment that reports the enrichment of aligned reads over genomic regions. This program takes preprocessed NGS data and performs operations on genomic regions of interest, including resetting their boundaries, their annotation based on proximity to genomic features, the association to gene ontologies, and signal enrichment calculations. Genomic regions can be further refined or subsetted by user-defined logical operations and unsupervised classification algorithms. ChroKit generates a full range of plots that are easily manipulated by point and click operations, thus allowing ‘on the fly’ re-analysis and fast exploration of the data. Working sessions can be exported for reproducibility, accountability, and easy sharing within the bioinformatics community. ChroKit is multiplatform and can be deployed on a server to enhance computational speed and provide simultaneous access by multiple users. ChroKit is a fast and intuitive genomic analysis tool suited for a wide range of users due to its architecture and its user-friendly graphical interface. ChroKit source code is available at https://github.com/ocroci/ChroKit and the Docker image at https://hub.docker.com/r/ocroci/chrokit.
Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR
Authors: Villemin Jean-Philippe , Bassaganyas Laia , Pourquier Didier , Boissière Florence , Cabello-Aguilar Simon , Crapez Evelyne , Tanos Rita , Cornillot Emmanuel , Turtoi Andrei , Colinge Jacques 
Published: May 2023

Abstract
The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualization methods complement the statistics, including functions dedicated to spatial data. We demonstrate BulkSignalR relevance using different datasets, including new Visium liver metastasis ST data, with experimental validation of protein colocalization. A comparison with other ST packages shows the significantly higher quality of BulkSignalR inferences. BulkSignalR can be applied to any species thanks to its built-in generic ortholog mapping functionality.
Replisome dysfunction upon inducible TIMELESS degradation synergizes with ATR inhibition to trigger replication catastrophe
Authors: Patel Jinal A , Zezelic Camryn , Rageul Julie , Saldanha Joanne , Khan Arafat , Kim Hyungjin 
Published: May 2023

Abstract
The structure of DNA replication forks is preserved by TIMELESS (TIM) in the fork protection complex (FPC) to support seamless fork progression. While the scaffolding role of the FPC to couple the replisome activity is much appreciated, the detailed mechanism whereby inherent replication fork damage is sensed and counteracted during DNA replication remains largely elusive. Here, we implemented an auxin-based degron system that rapidly triggers inducible proteolysis of TIM as a source of endogenous DNA replication stress and replisome dysfunction to dissect the signaling events that unfold at stalled forks. We demonstrate that acute TIM degradation activates the ATR-CHK1 checkpoint, whose inhibition culminates in replication catastrophe by single-stranded DNA accumulation and RPA exhaustion. Mechanistically, unrestrained replisome uncoupling, excessive origin firing, and aberrant reversed fork processing account for the synergistic fork instability. Simultaneous TIM loss and ATR inactivation triggers DNA-PK-dependent CHK1 activation, which is unexpectedly necessary for promoting fork breakage by MRE11 and catastrophic cell death. We propose that acute replisome dysfunction results in a hyper-dependency on ATR to activate local and global fork stabilization mechanisms to counteract irreversible fork collapse. Our study identifies TIM as a point of replication vulnerability in cancer that can be exploited with ATR inhibitors.
Variation in microbial feature perception in the Rutaceae family with immune receptor conservation in citrus
Authors: Trinh Jessica , Li Tianrun , Franco Jessica Y , Toruño Tania Y , Stevens Danielle M , Thapa Shree P , Wong Justin , Pineda Rebeca , de Dios Emmanuel Ávila , Kahn Tracy L , Seymour Danelle K , Ramadugu Chandrika , Coaker Gitta L 
Published: May 2023

Abstract
Although much is known about the responses of model plants to microbial features, we still lack an understanding of the extent of variation in immune perception across members of a plant family. In this work, we analyzed immune responses in Citrus and wild relatives, surveying 86 Rutaceae genotypes with differing leaf morphologies and disease resistances. We found that responses to microbial features vary both within and between members. Species in 2 subtribes, the Balsamocitrinae and Clauseninae, can recognize flagellin (flg22), cold shock protein (csp22), and chitin, including 1 feature from Candidatus Liberibacter species (csp22CLas), the bacterium associated with Huanglongbing. We investigated differences at the receptor level for the flagellin receptor FLAGELLIN SENSING 2 (FLS2) and the chitin receptor LYSIN MOTIF RECEPTOR KINASE 5 (LYK5) in citrus genotypes. We characterized 2 genetically linked FLS2 homologs from “Frost Lisbon” lemon (Citrus ×limon, responsive) and “Washington navel” orange (Citrus ×aurantium, nonresponsive). Surprisingly, FLS2 homologs from responsive and nonresponsive genotypes were expressed in Citrus and functional when transferred to a heterologous system. “Washington navel” orange weakly responded to chitin, whereas “Tango” mandarin (C. ×aurantium) exhibited a robust response. LYK5 alleles were identical or nearly identical between the 2 genotypes and complemented the Arabidopsis (Arabidopsis thaliana) lyk4/lyk5-2 mutant with respect to chitin perception. Collectively, our data indicate that differences in chitin and flg22 perception in these citrus genotypes are not the results of sequence polymorphisms at the receptor level. These findings shed light on the diversity of perception of microbial features and highlight genotypes capable of recognizing polymorphic pathogen features.
Validation of a patient-reported outcome measure for giant cell arteritis
Authors: Ndosi Mwidimi , Almeida Celia , Dawson Jill , Dures Emma , Greenwood Rosemary , Bromhead Alison , Guly Catherine , Stern Steve , Hill Catherine , Mackie Sarah , Robson Joanna C 
Published: May 2023

Abstract

Objectives
GCA is systemic vasculitis manifesting as cranial, ocular or large vessel vasculitis. A prior qualitative study developed 40 candidate items to assess the impact of GCA on health-related quality of life (HRQoL). This study aimed to determine final scale structure and measurement properties of the GCA patient reported outcome (GCA-PRO) measure.

Methods
Cross-sectional study included UK patients with clinician-confirmed GCA. They completed 40 candidate items for the GCA-PRO at times 1 and 2 (3 days apart), EQ-5D-5L, ICECAP-A, CAT-PROM5 and self-report of disease activity. Rasch and exploratory factor analyses informed item reduction and established structural validity, reliability and unidimensionality of the final GCA-PRO. Evidence of validity was also established with hypothesis testing (GCA-PRO vs other PRO scores, and between participants with ‘active disease’ vs those ‘in remission’) and test–retest reliability.

Results
The study population consisted of 428 patients: mean (s.d.) age 74.2 (7.2), 285 (67%) female; 327 (76%) cranial GCA, 114 (26.6%) large vessel vasculitis and 142 (33.2%) ocular involvement. Rasch analysis eliminated 10 candidate GCA items and informed restructuring of response categories into four-point Likert scales. Factor analysis confirmed four domains: acute symptoms (eight items), activities of daily living (seven items), psychological (seven items) and participation (eight items). The overall scale had adequate Rasch model fit (χ2 = 25.219, degrees of freedom = 24, P = 0.394). Convergent validity with EQ5D-5L, ICECAP-A and Cat-PROM5 was confirmed through hypothesis testing. Internal consistency and test–retest reliability were excellent.

Conclusion
The final GCA-PRO is a 30-item, four-domain scale with robust evidence of validity and reliability in measuring HRQoL in people with GCA.
The experimentation–accountability trade-off in innovation and industrial policy: are learning networks the solution?
Authors: Radosevic Slavo , Kanellou Despina , Tsekouras George 
Published: May 2023

Abstract
The exact nature of industrial/innovation (I/I) policy challenges and the best way to address them are unknown ex ante. This requires a degree of experimentation, which can be problematic in the context of an accountable public administration and leaves the question of how to reconcile the experimental nature of I/I policy with the need for public accountability, a crucial but unresolved issue. The trade-off between experimentation and accountability requires a governance model that will allow continuous feedback loops among the various stakeholders and ongoing evaluation of and adjustments to activities as programmes are implemented. We propose an ‘action learning’ approach, incorporating the governance mechanism of ‘learning networks’ to handle the problems of implementing experimental governance of new and untried I/I policies. We resolve the issue of accountability by drawing on the literature on network governance in public policy. By integrating control and learning dimensions of accountability, this approach enables us to resolve conceptually and empirically trade-offs between the need for experimentation and accountability in I/I policy.
Tyrannosaurus rex runs again: a theoretical analysis of the hypothesis that full-grown large theropods had a locomotory advantage to hunt in a shallow-water environment
Authors: Blanco R Ernesto 
Published: May 2023

Abstract
Biomechanical analyses suggest that adult large theropods, such as Tyrannosaurus rex, could not run, and its top speed probably was at most 10 m/s. This probably implied a speed disadvantage of adult T. rex compared with some smaller potential prey. Living predators at a disadvantage owing to speed or manoeuvrability sometimes use the environment or special techniques to minimize those differences. Here, I made a theoretical analysis of the possibility that adult large theropods, such as T. rex, could occasionally pursue prey in water to take advantage of their body size. There are arguments based on scaling laws to support this hypothesis. To give an example, I applied a biomechanical model to estimate the speed in a shallow-water environment of adult T. rex and two smaller dinosaurs, a juvenile Edmontosaurus annectens and Struthiomimus sedens. I conclude that by wading or swimming, the adult T. rex would have been faster than smaller prey in water. I also suggest that in water, adult large theropods, such as T. rex, were able to use a running gait that was probably precluded on land. Finally, I propose a near-shore hunting scenario for adult T. rex and other full-grown large theropods.
Deletion of MGF‐110‐9L gene from African swine fever virus weakens autophagic degradation of TBK1 as a mechanism for enhancing type I interferon production
Authors: Ren Jingjing , Li Dan , Zhu Guoqiang , Yang Wenping , Ru Yi , Feng Tao , Qin Xiaodong , Hao Rongzeng , Duan Xianghan , Liu Xiangtao , Zheng Haixue 
Published: May 2023

AbstractAfrican swine fever (ASF) caused by African swine fever virus (ASFV) is a devastating disease for the global pig industry and economic benefit. The limited knowledge on the pathogenesis and infection mechanisms of ASF restricts progress toward vaccine development and ASF control. Previously, we illustrated that deletion of the MGF‐110‐9L gene from highly virulent ASFV CN/GS/2018 strains (ASFV∆9L) results in attenuated virulence in swine, but the underlying mechanism remains unclear. In this study, we found that the difference in virulence between wild‐type ASFV (wt‐ASFV) and ASFV∆9L strains was mainly caused by the difference in TANK Binding Kinase 1 (TBK1) reduction. TBK1 reduction was further identified to be mediated by the autophagy pathway and this degradative process requires the up‐regulation of a positive autophagy regulation molecule‐ Phosphatidylinositol‐4‐Phosphate 3‐Kinase Catalytic Subunit Type 2 Beta (PIK3C2B). Moreover, TBK1 over‐expression was confirmed to inhibit ASFV replication in vitro. In summary, these results indicate that wt‐ASFV counteracts type I interferon (IFN) production by degrading TBK1, while ASFVΔ9L enhanced type I IFN production by weakening TBK1 reduction, clarifying the mechanism that ASFVΔ9L present the attenuated virulence in vitro.
Wound Care Nursing Education in the Acute Care Setting
Authors: Heerschap Corey , Wiesenfeld Samantha 
Published: May 2023

ABSTRACT

OBJECTIVE
To assess the feasibility of a survey study exploring how nurses in acute care prefer to be educated, particularly regarding wound management in the acute care setting.

METHODS
This pilot study utilized a cross-sectional survey design that included both open-ended and close-ended questions. Participants (N = 47) completed the Index of Learning Styles Questionnaire and provided information regarding their educational preferences related to wound management through use of an online survey.

RESULTS
Participants described the importance of varying educational techniques by topic, ensuring an appropriate time of day for education, and preferring smaller educational sessions over time. Most participants preferred one-on-one bedside education, and the most commonly reported learning styles were active, sensing, visual, and a balanced approach to sequential and global learning. There were few correlations between learning styles and choice of education method, only one of which was expected.

CONCLUSIONS
It would be beneficial to conduct this study on a larger scale to confirm results, improve understanding of the correlations, and determine further potential correlations between study variables.
The Effect of Assessments on Student Motivation for Learning and Its Outcomes in Health Professions Education: A Review and Realist Synthesis
Authors: Kusurkar Rashmi A. , Orsini Cesar , Somra Sunia , Artino Anthony R. , Daelmans Hester E.M. , Schoonmade Linda J. , van der Vleuten Cees 
Published: May 2023

Purpose
In health professions education (HPE), the effect of assessments on student motivation for learning and its consequences have been largely neglected. This is problematic because assessments can hamper motivation and psychological well-being. The research questions guiding this review were: How do assessments affect student motivation for learning in HPE? What outcomes does this lead to in which contexts?

Method
In October 2020, the authors searched PubMed, Embase, APA PsycInfo, ERIC, CINAHL, and Web of Science Core Collection for “assessments” AND “motivation” AND “health professions education/students.” Empirical papers or literature reviews investigating the effect of assessments on student motivation for learning in HPE using quantitative, qualitative, or mixed methods from January 1, 2010, to October 29, 2020, were included. The authors chose the realist synthesis method for data analysis to study the intended and unintended consequences of this complex topic. Assessments were identified as stimulating autonomous or controlled motivation using sensitizing concepts from self-determination theory and data on context–mechanism–outcome were extracted.

Results
Twenty-four of 15,291 articles were ultimately included. Assessments stimulating controlled motivation seemed to have negative outcomes. An example of an assessment that stimulates controlled motivation is one that focuses on factual knowledge (context), which encourages studying only for the assessment (mechanism) and results in surface learning (outcome). Assessments stimulating autonomous motivation seemed to have positive outcomes. An example of an assessment that stimulates autonomous motivation is one that is fun (context), which through active learning (mechanism) leads to higher effort and better connection with the material (outcome).

Conclusions
These findings indicate that students strategically learned what was expected to appear in assessments at the expense of what was needed in practice. Therefore, health professions educators should rethink their assessment philosophy and practices and introduce assessments that are relevant to professional practice and stimulate genuine interest in the content.