bluuebunny/crossref_metadata_2025_split huggingface dataset:
An FUV and optical study of star formation in closely interacting galaxies: star-forming rings, tidal arms, and nuclear outflows
Authors: Yadav Jyoti , Das Mousumi , Barway Sudhanshu , Combes Francoise 
Published: September 2023

ABSTRACT
We present a study of the morphology of star formation and the associated nuclear activity in a sample of eight closely interacting southern galaxies, which are in different stages of interaction, starting with nearly merged nuclei that have one prominent bulge to more widely spaced interacting galaxies. We have used far-ultraviolet (FUV) observations from the Ultraviolet Imaging Telescope (UVIT), near-Infrared observations from the Infrared Survey Facility (IRSF) telescope, and archival optical data from the Very Large Telescope (VLT)/Multi-Unit Spectroscopic Explorer (MUSE) integral field spectrograph. Analysing resolved stellar populations across the disc of the interacting galaxies can provide unique insights into how interactions affect galaxy properties, such as morphology, star formation rates, and chemical composition. We take advantage of the unprecedented capabilities of MUSE and UVIT to carry out a highly detailed spatially and spectrally resolved study of star formation rate, star formation histories, metallicity, and active galactic nucleus activity in the sample of eight interacting galaxies that are in different stages of interaction. Most of our sample galaxies are gas-rich and show evidence of recent, massive star formation in tidal tails, rings, and spiral arms. This is evident from their FUV and Hα emissions, which trace young, massive star-forming regions. We compared the star formation rate in the barred and unbarred galaxies in our sample and found that the barred galaxies do not show significant enhancement in star formation rate or large-scale difference in star formation morphology compared to unbarred galaxies. IC5250 and NGC7733N show extended nuclear outflows of sizes ∼5 and 8 kpc, respectively.
The intrinsic alignment of red galaxies in DES Y1 redMaPPer galaxy clusters
Authors: Zhou C , Tong A , Troxel M A , Blazek J , Lin C , Bacon D , Bleem L , Chang C , Costanzi M , DeRose J , Dietrich J P , Drlica-Wagner A , Gruen D , Gruendl R A , Hoyle B , Jarvis M , MacCrann N , Mawdsley B , McClintock T , Melchior P , Prat J , Pujol A , Rozo E , Rykoff E S , Samuroff S , Sheldon E , Shin T , Rosell A Carnero , Yanny B , Sánchez C , Tucker D L , Sevilla-Noarbe I , Zuntz J , Varga T N , Zhang Y , Alves O , Amon A , Bertin E , Brooks D , Burke D L , Kind M Carrasco , da Costa L N , Davis T M , De Vicente J , Desai S , Diehl H T , Doel P , Everett S , Ferrero I , Flaugher B , Frieman J , Gerdes D W , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , James D J , Jeltema T , Kuehn K , Lahav O , Lima M , Marshall J L , Mena-Fernández J , Menanteau F , Miquel R , Palmese A , Paz-Chinchón F , Pieres A , Malagón A A Plazas , Porredon A , Raveri M , Romer A K , Sanchez E , Smith M , Soares-Santos M , Suchyta E , Swanson M E C , Tarle G , To C , Weaverdyck N , Weller J , Wiseman P 
Published: September 2023

ABSTRACT
Clusters of galaxies trace the most non-linear peaks in the cosmic density field. The weak gravitational lensing of background galaxies by clusters can allow us to infer their masses. However, galaxies associated with the local environment of the cluster can also be intrinsically aligned due to the local tidal gradient, contaminating any cosmology derived from the lensing signal. We measure this intrinsic alignment in Dark Energy Survey (DES) Year 1 redMaPPer clusters. We find evidence of a non-zero mean radial alignment of galaxies within clusters between redshifts 0.1–0.7. We find a significant systematic in the measured ellipticities of cluster satellite galaxies that we attribute to the central galaxy flux and other intracluster light. We attempt to correct this signal, and fit a simple model for intrinsic alignment amplitude (AIA) to the measurement, finding AIA = 0.15 ± 0.04, when excluding data near the edge of the cluster. We find a significantly stronger alignment of the central galaxy with the cluster dark matter halo at low redshift and with higher richness and central galaxy absolute magnitude (proxies for cluster mass). This is an important demonstration of the ability of large photometric data sets like DES to provide direct constraints on the intrinsic alignment of galaxies within clusters. These measurements can inform improvements to small-scale modelling and simulation of the intrinsic alignment of galaxies to help improve the separation of the intrinsic alignment signal in weak lensing studies.
Evolution in the orbital structure of quiescent galaxies from MAGPI, LEGA-C, and SAMI surveys: direct evidence for merger-driven growth over the last 7 Gyr
Authors: D’Eugenio Francesco , van der Wel Arjen , Piotrowska Joanna M , Bezanson Rachel , Taylor Edward N , van de Sande Jesse , Baker William M , Bell Eric F , Bellstedt Sabine , Bland-Hawthorn Joss , Bluck Asa F L , Brough Sarah , Bryant Julia J , Colless Matthew , Cortese Luca , Croom Scott M , Derkenne Caro , van Dokkum Pieter , Fisher Deanne , Foster Caroline , Gallazzi Anna , de Graaff Anna , Groves Brent , van Houdt Josha , del P. Lagos Claudia , Looser Tobias J , Maiolino Roberto , Maseda Michael , Mendel J Trevor , Nersesian Angelos , Pacifici Camilla , Poci Adriano , Remus Rhea-Silvia , Sweet Sarah M , Thater Sabine , Tran Kim-Vy , Übler Hannah , Valenzuela Lucas M , Wisnioski Emily , Zibetti Stefano 
Published: September 2023

ABSTRACT
We present the first study of spatially integrated higher-order stellar kinematics over cosmic time. We use deep rest-frame optical spectroscopy of quiescent galaxies at redshifts z = 0.05, 0.3, and 0.8 from the SAMI, MAGPI, and LEGA-C surveys to measure the excess kurtosis h4 of the stellar velocity distribution, the latter parametrized as a Gauss-Hermite series. Conservatively using a redshift-independent cut in stellar mass ($M_\star = 10^{11}\, \mathrm{M_\odot }$) and matching the stellar-mass distributions of our samples, we find 7σ evidence of h4 increasing with cosmic time, from a median value of 0.019 ± 0.002 at z = 0.8 to 0.059 ± 0.004 at z = 0.06. Alternatively, we use a physically motivated sample selection based on the mass distribution of the progenitors of local quiescent galaxies as inferred from numerical simulations; in this case, we find 10σ evidence. This evolution suggests that, over the last 7 Gyr, there has been a gradual decrease in the rotation-to-dispersion ratio and an increase in the radial anisotropy of the stellar velocity distribution, qualitatively consistent with accretion of gas-poor satellites. These findings demonstrate that massive galaxies continue to accrete mass and increase their dispersion support after becoming quiescent.
Relaxation of Natural Selection in the Evolution of the Giant Lungfish Genomes
Authors: Fuselli Silvia , Greco Samuele , Biello Roberto , Palmitessa Sergio , Lago Marta , Meneghetti Corrado , McDougall Carmel , Trucchi Emiliano , Rota Stabelli Omar , Biscotti Assunta Maria , Schmidt Daniel J , Roberts David T , Espinoza Thomas , Hughes Jane Margaret , Ometto Lino , Gerdol Marco , Bertorelle Giorgio 
Published: September 2023

Abstract
Nonadaptive hypotheses on the evolution of eukaryotic genome size predict an expansion when the process of purifying selection becomes weak. Accordingly, species with huge genomes, such as lungfish, are expected to show a genome-wide relaxation signature of selection compared with other organisms. However, few studies have empirically tested this prediction using genomic data in a comparative framework. Here, we show that 1) the newly assembled transcriptome of the Australian lungfish, Neoceratodus forsteri, is characterized by an excess of pervasive transcription, or transcriptional leakage, possibly due to suboptimal transcriptional control, and 2) a significant relaxation signature in coding genes in lungfish species compared with other vertebrates. Based on these observations, we propose that the largest known animal genomes evolved in a nearly neutral scenario where genome expansion is less efficiently constrained.
RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures
Authors: Malhotra Sony , Mulvaney Thomas , Cragnolini Tristan , Sidhu Haneesh , Joseph Agnel P , Beton Joseph G , Topf Maya 
Published: September 2023

Abstract
Molecular structures are often fitted into cryo-EM maps by flexible fitting. When this requires large conformational changes, identifying rigid bodies can help optimize the model-map fit. Tools for identifying rigid bodies in protein structures exist, however an equivalent for nucleic acid structures is lacking. With the increase in cryo-EM maps containing RNA and progress in RNA structure prediction, there is a need for such tools. We previously developed RIBFIND, a program for clustering protein secondary structures into rigid bodies. In RIBFIND2, this approach is extended to nucleic acid structures. RIBFIND2 can identify biologically relevant rigid bodies in important groups of complex RNA structures, capturing a wide range of dynamics, including large rigid-body movements. The usefulness of RIBFIND2-assigned rigid bodies in cryo-EM model refinement was demonstrated on three examples, with two conformations each: Group II Intron complexed IEP, Internal Ribosome Entry Site and the Processome, using cryo-EM maps at 2.7–5 Å resolution. A hierarchical refinement approach, performed on progressively smaller sets of RIBFIND2 rigid bodies, was clearly shown to have an advantage over classical all-atom refinement. RIBFIND2 is available via a web server with structure visualization and as a standalone tool.
Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP
Authors: Lyu Zhihui , Villanueva Patricia , O’Malley Liam , Murphy Parker , Augenstreich Jacques , Briken Volker , Singh Abhyudai , Ling Jiqiang 
Published: September 2023

Abstract
Translational fidelity is critical for microbial fitness, survival and stress responses. Much remains unknown about the genetic and environmental control of translational fidelity and its single-cell heterogeneity. In this study, we used a high-throughput fluorescence-based assay to screen a knock-out library of Escherichia coli and identified over 20 genes critical for stop-codon readthrough. Most of these identified genes were not previously known to affect translational fidelity. Intriguingly, we show that several genes controlling metabolism, including cyaA and crp, enhance stop-codon readthrough. CyaA catalyzes the synthesis of cyclic adenosine monophosphate (cAMP). Combining RNA sequencing, metabolomics and biochemical analyses, we show that deleting cyaA impairs amino acid catabolism and production of ATP, thus repressing the transcription of rRNAs and tRNAs to decrease readthrough. Single-cell analyses further show that cAMP is a major driver of heterogeneity in stop-codon readthrough and rRNA expression. Our results highlight that carbon metabolism is tightly coupled with stop-codon readthrough.
The Application of CT Radiomics in the Diagnosis of Vein Wall Invasion in Patients With Renal Cell Carcinoma Combined With Tumor Thrombus
Authors: Zhao Xun , Yan Ye , Xie Wanfang , Zhao Litao , Zhang Shudong , Liu Jiangang , Liu Cheng , Ma Lulin 
Published: September 2023

Abstract

Objective
The objective of this study was to explore the application of radiomics combined with machine learning to establish different models to assist in the diagnosis of venous wall invasion in patients with renal cell carcinoma and venous tumor thrombus and to evaluate the diagnostic efficacy.

Materials and Methods
We retrospectively reviewed the data of 169 patients in Peking University Third Hospital from March 2015 to January 21, who was diagnosed as renal mass with venous invasion. According to the intraoperative findings, 111 patients were classified to the venous wall invasion group and 58 cases in the non-invasion group. ITK-snap was used for tumor segmentation and PyRadiomics 3.0.1 package was used for feature extraction. A total of 1598 features could be extracted from each CT image. The patients were divided into training set and testing set by time. The elastic-net regression with 4-fold cross-validation was used as a dimension-reduction method. After feature selection, a support vector machines (SVM) model, a logistic regression (LR) model, and an extra trees (ET) model were established. Then the sensitivity, specificity, accuracy, and the area under the curve (AUC) were calculated to evaluate the diagnostic performance of each model on the testing set.

Results
Patients before September 2019 were divided into the training set, of which 88 patients were in the invasion group and 42 patients were in the non-invasion group. The others were in the testing set, of which 32 patients were in the invasion group and 16 patients were in the non-invasion group. A total of 34 radiomics features were obtained by the elastic-net regression. The SVM model had an AUC value of 0.641 (95% CI, 0.463-0.769), a sensitivity of 1.000, and a specificity of 0.062. The LR model had an AUC value of 0.769 (95% CI, 0.620-0.877), a sensitivity of 0.913, and a specificity of 0.312. The ET model had an AUC value of 0.853 (95% CI, 0.734-0.948), a sensitivity of 0.783, and a specificity of 0.812. Among the 3 models, the ET model had the best diagnostic effect, with a good balance of sensitivity and specificity. And the higher the tumor thrombus grade, the better the diagnostic efficacy of the ET model. In inferior vena cava tumor thrombus, the sensitivity, specificity, accuracy, and AUC of ET model can be improved to 0.889, 0.800, 0.857, 0.878 (95% CI, 0.745-1.000).

Conclusion
Machine learning combined with radiomics method can effectively identify whether venous wall was invaded by tumor thrombus and has high diagnostic efficacy with an AUC of 0.853 (95% CI, 0.734-0.948).
Impact of dark energy on the equation of state in light of the latest cosmological data
Authors: Myrzakulov N , Koussour M , Alfedeel Alnadhief H A , Hassan E I 
Published: September 2023

Abstract
We reconstruct the effective equation of state (EoS) within the framework of the general theory of relativity in a homogeneous and isotropic Friedmann–Lemaître–Robertson–Walker universe, which is assumed to be composed of matter and dark energy (DE). Our analysis employs a dataset consisting of 31 cosmic chronometer data points, six data points of baryon acoustic oscillations, and 1048 type Ia supernovae from the Pantheon sample, and we determine the best-fitting values of the model parameters through Markov chain Monte Carlo simulation. We then use these parameter values to calculate various cosmological parameters, such as the DE EoS parameter, the energy density, the deceleration parameter, the state-finder parameters, and the Om(z) diagnostic. All the analyzed cosmological parameters show behavior consistent with the accelerated universe scenario.
Systematic Development of Standards for Mixed Methods Reporting in Rehabilitation Health Sciences Research
Authors: Tovin Melissa M , Wormley Michelle E 
Published: September 2023

Abstract

Objective
Mixed methods research (MMR) integrates quantitative and qualitative methods throughout the research process to answer complex research questions. MMR designs align with the guiding frameworks of patient-centered care and social determinants of health by effectively examining the role of contextual factors and human experiences in influencing health and rehabilitation outcomes. Reporting standards and critical appraisal tools ensure the quality and transparency of the research process. MMR standards exist; yet, there is a need for reporting guidelines and an appraisal tool that meets field standards, is applicable across rehabilitation fields of study, and can accommodate the range of possibilities for combining research approaches and methods.

Methods
Mixed Methods Reporting in Rehabilitation & Health Sciences (MMR-RHS) was developed using a systematic consensus-building process in accordance with published guidance and was preregistered with the Enhancing the Quality and Transparency of Health Research Network. MMR-RHS evolved through a sequence of steps, including extensive literature review, expert consultation, stakeholder feedback, pilot testing, and tool refinement.

Results
MMR-RHS consists of 20 criteria that align with field standards for rigor and transparency, with an emphasis on integration throughout the research process, a key component of MMR.

Conclusions
A systematic process was utilized to develop the reporting standards and an appraisal tool for MMR in rehabilitation and health science. The tool is comprehensive, includes a set of criteria grounded in MMR literature, and is flexible for application to a range of MMR designs commonly seen in rehabilitation research.

Impact
The MMR-RHS may improve the quality and transparency of MMR by supporting investigators, authors, reviewers, and editors during project development, manuscript preparation, and critical review. The tool may assist readers in critical appraisal, knowledge translation, and application of published MMR findings. Ultimately, the MMR-RHS may help legitimize mixed methods in rehabilitation and health research, an important step toward understanding the complexities of health care, patient outcomes, and evolving societal health needs.
Outcomes following switching from etanercept originator to etanercept biosimilar in 1024 patients with RA: a matched-analysis of the BSRBR-RA
Authors: Kearsley-Fleet Lianne , Rokad Aasiyah , Tsoi Man-Fung , Zhao Sizheng Steven , Lunt Mark , Watson Kath D ,   BSRBR-RA Contributors Group, Hyrich Kimme L 
Published: September 2023

Abstract

Objectives
Adults with RA are being switched from etanercept originator to biosimilar in non-medical/cost-saving switching. This analysis aims to investigate outcomes in these patients, including (i) drug survival and (ii) disease activity at 6 months and 12 months, compared with those who remain on the originator.

Methods
Using BSRBR-RA, those who switched directly from etanercept originator to biosimilar were identified and matched to patients receiving the originator, based on gender, age, disease duration and originator start year. Drug survival was calculated; Cox-proportional hazard models assessed differences in drug persistence between those who switched vs remaining on originator. Change in DAS28 after 6 months and 12 months was compared between cohorts. Multiple imputation was used.

Results
A total of 1024 adults with RA switching from etanercept originator to biosimilar were included, with a matched cohort of patients remaining on the originator. Patients who switched onto a biosimilar product were no more likely to discontinue etanercept treatment vs those who remained on the originator; hazard ratio 1.06 (95%CI 0.89–1.26), with 65% of patients remaining on treatment at three years. Ninety-five (9%) patients switched back to the originator within the first year. After 6 months and 12 months, biosimilar patients were no more likely to have a worsening of DAS28 (&gt;0.6 units) compared with those who remained on the originator.

Conclusions
This is the largest matched comparative effectiveness analysis showing patients switching from etanercept originator to biosimilar appearing to do just as well with regard to disease activity and drug persistence compared with those who remained on the originator. These data will be reassuring to clinicians and patients regarding non-medical switching.
Labour market digitalization and social class: evidence of mobility and reproduction from a European survey of online platform workers
Authors: Martindale Nicholas , Lehdonvirta Vili 
Published: September 2023

Abstract
The type of work we do as adults is significantly influenced by our parents’ social class. However, digital technologies are transforming the way labour markets work. Candidates are screened using algorithmic decision-making systems. Skills are validated with online tests and feedback ratings. Communications take place online. Could these transformations undermine the advantages that have accrued to workers with privileged backgrounds or reproduce this privilege through digital divides? We examine this question with survey evidence from the online (remote) platform economy, a labour market segment where these digital transformations have progressed furthest (N = 1,001). The results reveal that online platform workers come predominantly from privileged class backgrounds, but we find less evidence of parental class shaping what types of online work they do. We conclude that digital transformations of labour markets may reproduce disparities in access to work but attenuate some class-based differences in the selection of workers by employers.
Sleep apnea, hypoxia, and late-onset epilepsy: the Atherosclerosis Risk in Communities study
Authors: Carosella Christopher M , Gottesman Rebecca F , Kucharska-Newton Anna , Lutsey Pamela L , Spira Adam P , Punjabi Naresh M , Schneider Andrea L C , Full Kelsie M , Johnson Emily L 
Published: September 2023

Abstract

Study Objective
Sleep apnea is associated with unexplained epilepsy in older adults in small studies. We sought to determine the relationship between sleep apnea and additional sleep characteristics and late-onset epilepsy (LOE), adjusting for comorbidities, using data from the large, prospective Atherosclerosis Risk in Communities (ARIC) Study cohort.

Methods
We used Medicare claims to identify cases of LOE in ARIC participants. We used polysomnography data from 1309 ARIC participants who also participated in the Sleep Heart Health Study in 1995–1998, and demographic and comorbidity data from ARIC. Later risk of LOE was evaluated using survival analysis with a competing risk of death. We also used survival analysis in 2672 ARIC participants to identify the association between self-reported obstructive sleep apnea (2011–2013), and the risk of subsequent LOE.

Results
Late-midlife oxygen desaturation to less than 80% during sleep was associated with subsequent development of LOE, adjusted subhazard ratio 3.28 (1.18–9.08), but the apnea–hypopnea index was not related. Participant report of diagnosis of sleep apnea in 2011–2013 was also associated with subsequent LOE, adjusted subhazard ratio 2.59 (1.24–5.39).

Conclusions
Sleep apnea and oxygen saturation nadir during sleep are associated with LOE, independently of hypertension and other comorbidities. These potentially modifiable risk factors could have large clinical implications for LOE.