bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pilot study of device-assessed physical activity and ecological momentary assessment among adolescent and young adult survivors of childhood cancer
Authors: King-Dowling Sara , Harris Sheereen , Daniel Lauren C , Kwan Matthew Y W , Ginsberg Jill P , Goldmuntz Elizabeth , Szalda Dava , Schwartz Lisa A 
Published: February 2025

Abstract

Background
Adolescent and young adult survivors of childhood cancer (AYA) are at risk for treatment-related late effects (eg, heart and lung problems) which may be mitigated by physical activity (PA). To design effective, tailored PA interventions for this population, predictors and benefits of PA behavior need to be measured in real-time.

Purpose
To examine the feasibility and acceptability of ecological momentary assessment (EMA) combined with accelerometry and explore the dynamic associations between PA and real-time physical and psychosocial factors among AYA.

Methods
AYA (N = 20, mean age = 18.9 years) recently off cancer treatment participated in a 2-week intensive monitoring protocol in which they completed up to 4 EMA surveys/day assessing current mood, pain, fatigue, arousal, PA intentions and motivation, and social-environmental context, while PA levels were passively monitored using a wrist-worn ActiGraph GT9X accelerometer. Acceptability was measured via self-report.

Results
EMA and accelerometry were feasible and acceptable (≥70% compliance and study endorsement) for AYA. Multilevel models showed that AYA engaged in more PA when they were away from home, with others, in a better mood, less fatigued, more energetic, and more motivated than their own average levels. Further, when AYA engaged in more PA than their usual levels in the hour before completing an EMA survey, they subsequently reported less fatigue, less pain, more energy, and a more positive mood.

Conclusions
EMA and accelerometry are acceptable and feasible among AYA survivors of childhood cancer. This methodology can be utilized for understanding the real-time barriers, facilitators, and benefits of PA behaviors in this at-risk population to design effective, dynamic PA interventions.
Exacerbation of racial disparities in COVID-19 outcomes by Alzheimer’s Disease and Related Dementias among nursing home residents
Authors: Zullo Andrew R , Gravenstein Stefan , Howe Chanelle J 
Published: February 2025

Abstract
The coronavirus disease 2019 (COVID-19) pandemic has disproportionately impacted Black nursing home (NH) residents. Alzheimer’s Disease and Related Dementias (ADRD) may exacerbate disparities, however little empirical evidence exists on the degree to which race and ADRD intersect to impact COVID-19-related outcomes. We conducted a cohort study (April-December 2020) leveraging electronic health records from 12 United States NH corporations. We used parametric g-formula to obtain standardized estimates of incident COVID-19 infection and 30-day COVID-19-associated hospitalization or death by race, both overall and within strata of ADRD status. The cohort comprised 127,913 resident-episodes, including 15,379 incident COVID-19 infections, 1,522 deaths, and 2,548 hospitalizations. Black residents were more likely than White residents to experience incident COVID-19 and subsequent hospitalization, but not more likely to subsequently die. Disparities in hospitalization and a combined endpoint of hospitalization or death were more pronounced among residents with ADRD compared to residents without ADRD. These results suggest the presence of disparities in COVID-19 outcomes by race and provide evidence that ADRD status may exacerbate racial disparities in COVID-19 outcomes among nursing home residents. Our findings offer valuable insights for current and future preparedness efforts in NHs in the United States and countries with similarly under-resourced long-term care settings.
The Effect of Body Expressions on the Learning Process and Facial Recognition among Healthy Participants and Individuals with Traumatic Brain Injury: Examination Using Eye Movements
Authors: Lugasi Natalie , Sachar Yaron , Vakil Eli 
Published: February 2025

Abstract

Objective
Context-dependent effect (CDE) is a process by which reinstating at test the original learning context enhances the recall ability of the material being studied. Although recognition by people with traumatic brain injury (TBI) is poorer than that of healthy controls, both groups show CDE equally. In the current study, we seek to test the effect of body emotional expressions as contextual information, on facial recognition, and eye movements.

Method
Twenty-four healthy individuals and 27 patients with moderate-to-severe TBI participated in the study. Participants were exposed to photos of people with neutral facial and body expressions and were asked to remember the people for a subsequent memory test. In the testing session, they were asked to determine whether the person presented to them had appeared before, under two conditions: (1) where the context remains constant (facial and body expressions remained neutral–Repeat condition) and (2) where the context changes (facial expression remained neutral but the body expression changed to angry or happy–Re-pair condition).

Results
While the memory of the individuals with TBI was poorer than that of the controls, both groups exhibited equal CDE. We found that both groups, controls more than TBI, spent most of their time looking at the head. Furthermore, longer dwell time was associated with better recognition in the study phase.

Conclusions
These findings are consistent with previous studies showing that despite impaired memory following TBI compared to a control group, CDE was preserved. The current study extends the context effect to body postures that express emotion.
Embed-Search-Align: DNA Sequence Alignment using Transformer models
Authors: Holur Pavan , Enevoldsen K C , Rajesh Shreyas , Mboning Lajoyce , Georgiou Thalia , Bouchard Louis-S , Pellegrini Matteo , Roychowdhury Vwani 
Published: February 2025

Abstract

Motivation
DNA sequence alignment, an important genomic task, involves assigning short DNA reads to the most probable locations on an extensive reference genome. Conventional methods tackle this challenge in two steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models (LLM) in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have encoded DNA sequences into vectors using Transformers and have shown promising results in tasks involving classification of short DNA sequences. Performance at sequence classification tasks does not, however, guarantee sequence alignment, where it is necessary to conduct a genome-wide search to align every read successfully, a significantly longer-range task by comparison.

Results
We bridge this gap by developing a “Embed-Search-Align” (ESA) framework, where a novel Reference-Free DNA Embedding (RDE) Transformer model generates vector embeddings of reads and fragments of the reference in a shared vector space; read-fragment distance metric is then used as a surrogate for sequence similarity. ESA introduces: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. RDE is 99% accurate when aligning 250-length reads onto a human reference genome of 3 gigabases (single-haploid), rivaling conventional algorithmic sequence alignment methods such as Bowtie and BWA-Mem. RDE far exceeds the performance of 6 recent DNA-Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Availability and Information
Please see https://anonymous.4open.science/r/dna2vec-7E4E/readme.md.

Supplementary Information
Please see attached file.
Four-year Loneliness Trajectory and Its Predictors in Older Adults
Authors: Huang Yan , Martire Lynn M , Jones Damon 
Published: February 2025

Abstract

Background and Objectives
Loneliness is a modifiable risk factor for health decline in older adults and its level may change over time. This study aimed to explore how loneliness changes across four years in older adults and investigate potential between-person and within-person predictors of this trajectory.

Research Design and Methods
Using growth curve modeling, we analyzed data collected annually between 2017 and 2020 from 128 older adults (Mage = 77.91) in independent-living or retirement communities.

Results
A quadratic model best fit the loneliness trajectory, showing loneliness decreased first and then increased over four years. At baseline, social relationship factors and health status, especially depressive symptoms, were correlated with the level of loneliness. None of the baseline variables had significant associations with the linear rate of change in loneliness. Increases in depressive symptoms and decreases in physical functioning were separately related to an increased level of loneliness. A secondary analysis showed the COVID-19 pandemic influenced the rate of change in loneliness.

Discussion and Implications
Findings suggest the loneliness trajectory for older adults follows a nonlinear trend, and that within-person variability exists in this trajectory. Social relationships and health indicators contribute to the trajectory of loneliness, and depressive symptoms were the most salient predictor of change in loneliness. The COVID-19 pandemic also influenced the uptick in loneliness in 2020. More attention and support should be offered to older adults who are less socially connected or experience health declines, to prevent loneliness and thus increase the healthy longevity of our older population.
Genetic architecture of cherry leaf spot (Blumeriella jaapii) resistance in sour cherry (P. Cerasus L.) uncovered by QTL analyses in a biparental population genotyped with the 6+9K SNP array
Authors: Emeriewen Ofere Francis , Wöhner Thomas Wolfgang , Braun Vincent , Schröpfer Susan , Schuster Mirko , Peil Andreas , Flachowsky Henryk 
Published: February 2025

Abstract
Sour cherry (Prunus cerasus L.) is an economically significant species in the Rosaceae family. Hitherto, there had been limited genetic and genomic resources to elucidate important horticultural traits in this species mainly because of the complex polyploid nature of its genome, a hybrid between Prunus avium and Prunus fruticosa. An important trait that has not been well studied in sour cherry is resistance to cherry leaf spot (CLS), caused by the fungus Blumeriella jaapii. This work took advantage of the RosBREED 6+9K SNP array to study the genetic basis of CLS resistance and inheritance in sour cherry. We established an F1 segregating population by crossing two cultivars, ‘Schattenmorelle’ and ‘Pc 2’ and genotyped both parents and the progeny with the cherry 6+9K SNP array and SSR markers. We evaluated both parents and progeny for resistance and susceptibility to CLS under field conditions. The applied marker systems facilitated the development of parental genetic maps, and the identification of two stable QTLs associated with CLS resistance, CLSR_1f in ‘Pc 2’ and susceptibility, CLSS_1f, in ‘Schattenmorelle’ explaining 40.9% and 21.5%, respectively of the phenotypic variation within the population. The mechanism of resistance in sour cherry appears to be independent of the CLS resistance QTL, CLSR_G4, previously identified in P. canescens, as the CLSR_G4-QTL and associated allele were not identified. Based on our findings, we propose a two-gene model for CLS resistance in sour cherry involving a susceptibility QTL, which might explain why some CLSR_G4-resistant plants in previous studies were susceptible.
Mammography Home Workstations and Remote Diagnostic Breast Imaging: Current Practice Patterns and Planned Future Directions
Authors: Dawar Ria , Grimm Lars J , Sonnenblick Emily B , Dontchos Brian N , Coffey Kristen , Goudreau Sally , Reig Beatriu , Jacobs Sarah A , Shah Zeeshan , Mullen Lisa , Dialani Vandana , Dawar Reema , Sayre James , Dodelzon Katerina , Parikh Jay R , Milch Hannah S 
Published: February 2025

Abstract

Objective
Assess current practices and plans regarding home workstations and remote diagnostic breast imaging in the United States.

Methods
A 43-question survey relating to remote breast imaging was distributed to Society of Breast Imaging members from July 6, 2023, through August 2, 2023. A descriptive summary of responses was performed. Pearson’s chi-squared test was used to compare demographic variables of respondents and questions of interest.

Results
In total, 424 surveys were completed (response rate 13%, 424/3244). One-third of breast imaging radiologists (31%, 132/424) reported reading examinations from home or a personal remote site for a median of 25% of their clinical time. The most common types of examinations read from home were screening mammography (90%, 119/132), screening US (58%, 77/132), diagnostic mammography and MRI (both 53%, 70/132), and diagnostic US (49%, 65/132). Respondents from private practices were more likely than those from academic practices to read diagnostic imaging from home (67%, 35/52 vs 29%, 15/52; P &lt;.001). Respondents practicing in the West were less likely to read breast imaging examinations from home compared with those in other geographic regions (18%, 12/67 vs 28%-43% for other regions; P = .023). No differences were found among respondents’ overall use of home workstations based on age, gender, or having dependents. Most respondents (75%, 318/424) felt that remote breast reading would be a significant practice pattern in the future.

Conclusion
Home workstations for mammography and remote diagnostic breast imaging are a considerable U.S. practice pattern. Further research should explore radiologist preferences regarding remote breast imaging and its impact on clinical care and radiologist well-being.
Changes in time-to-treatment initiation for breast, non-small cell lung, colon, or rectal cancers throughout the COVID-19 pandemic in the United States
Authors: Fan Qinjin , Dong Weichuan , Schafer Elizabeth J , Wagle Nikita Sandeep , Zhao Jingxuan , Shi Kewei Sylvia , Han Xuesong , Yabroff K Robin , Nogueira Leticia M 
Published: February 2025

Abstract
The COVID-19 pandemic disrupted health care and reduced cancer diagnoses in the United States, raising concerns about its impact on time-to-treatment initiation (TTI), a critical factor for survival. This study examined the changes in TTI for 1 213 481 individuals newly diagnosed with female breast, nonsmall cell lung, colon, or rectal cancer between 2019 and 2022, using the National Cancer Database. We compared TTI in 2020-2022 with 2019 by cancer site, diagnosis time of year, stage, and treatment modality. In 2020, TTI statistically significantly decreased for all cancers compared to 2019, especially in the second quarter (2.97-4.29 days). However, TTI increased across sites in 2021 (0.31-2.15 days) and in 2022 (1.43-5.07 days). Reduced diagnoses and efforts to prioritize cancer care during the pandemic may partly explain observed TTI decreases, whereas workforce constraints likely contributed to the later increases. Ongoing evaluation of TTI and associations with patient outcomes is warranted.
Genome-wide association study and Mendelian randomization analyses reveal insights into bladder cancer etiology
Authors: Larsson Susanna C , Chen Jie , Ruan Xixian , Li Xue , Yuan Shuai 
Published: February 2025

Abstract

Background
The causes of bladder cancer are not completely understood. Our objective was to identify blood proteins and modifiable causal risk factors for bladder cancer by combining genome-wide association studies (GWAS) and Mendelian randomization (MR) analyses.

Methods
We first performed a GWAS meta-analysis of 6984 bladder cancer cases and 708 432 controls from three European databases. Next, we conducted two-sample MR and colocalization analyses using data from the present GWAS and published GWAS meta-analyses on plasma proteins and modifiable factors.

Results
GWAS meta-analysis uncovered 17 bladder cancer susceptibility loci, of which 3 loci were novel. Genes were enriched in pathways related to the metabolic and catabolic processes of xenobiotics and cellular detoxification. Proteome-wide MR analysis based on cis-acting genetic variants revealed that higher plasma levels of glutathione S-transferases were strongly associated with a reduced risk of bladder cancer. There is strong evidence of colocalization between GSTM1 and bladder cancer. Finally, multivariable MR analyses of suspected risk factors for bladder cancer revealed independent causal associations between smoking and adiposity, particularly abdominal obesity, and risk of bladder cancer.

Conclusions
Findings from this large-scale GWAS and multivariable MR analyses highlight the key role of detoxification processes, particularly glutathione S-transferase 1, as well as smoking and abdominal obesity in bladder cancer etiology.
William Gladstone’s Attitude Towards Islam
Authors: Yıldızeli Fahriye Begüm 
Published: February 2025

Abstract
During the heyday of British imperialism in the nineteenth century, perceptions and attitudes towards Islam were derived from the British Empire’s special relationship with the Eastern Question and long-standing trends in Victorian culture. This article explores the views of William Gladstone towards Islam, which have been the subject of a series of controversial debates among scholars. Although most studies of Gladstone have explored the links between his political development and his Christian faith, they have not analysed the grounds of his doctrines towards the Islamic world. In light of the inflammatory rhetoric that Gladstone employed in the ‘Bulgarian Horrors’ pamphlet, his indignation over Turkish rulers, and key elements of his policies towards Christian minorities, some historians have presented the view that he was antagonistic towards Muslims. This study argues that Gladstone had always regarded the Ottoman nation states with ethnic-religious differences independently from the Sublime Porte’s Islamic character of the state. The origins of his thoughts on Islamic civilization, self-government, and cumulative disillusionment with Ottoman reforms reveal the extent to which his humanitarian feelings, ‘religious nationality’, and moral foreign policy influenced his thinking about Islamic governance. It further considers how Gladstone’s liberal mindset and perceptions of Islam developed since his early life and how these later influenced his connections with other Muslim communities—Afghans, Bosnians, Egyptians, Indians, and Albanians.
A Preliminary Analysis of Psychological Strengths: Service Members’ Well-being Post-deployment
Authors: Bowles Stephen V , Neumaier Eric R , Hughes Evan R , Guberman Lucas , Cozzi Francesca M , Bartone Paul T , Switzer Paul , Mallonee Sybil D , Goyette Anna S , Seidler Dustin A , Kelly Julia , Hoyt Tim 
Published: February 2025

ABSTRACT
Deployments are stressful for both service members and their families. To promote the overall health and welfare of those impacted by military deployment, it is important to identify individual resilience-building resources that service members can employ to strengthen their own well-being, the well-being of their families, and the readiness of the force. This pilot study examines different resilience-building skills that may impact individual well-being, relationship quality, and family satisfaction post-deployment. A cross-sectional sample of 78 married U.S. military enlisted service members (n = 24) and commissioned officers (n = 54) completed the Coping Self-Efficacy Scale, Resilience Scale for Adults, Humor Styles Questionnaire, Mindful Attention Awareness Scale, Dispositional Resilience Scale, the emotional well-being and spirituality subscales of the Work-Life Well-Being Inventory, and the Social Problem-Solving Inventory-Revised. The use of a positive humor style was significantly associated with individual well-being. Spirituality and religious practices were significantly predictive of a service member’s family satisfaction. Responding to qualitative open-ended questions, service members identified their top 6 subcategories of stress, which were communication, moving, finances, family separation, children, and future employment during post-deployment. The strengths and resources reported as contributing the most to family effectiveness and well-being were personal character traits, external relationship skills, emotional maturity, and the ability to work. The results identified unique individual resilience-building resources for service members, which contribute to their well-being and the well-being of their families. Findings suggest that training on individual resilience-building resources for service members can offer support to the entire family system following military deployment.
Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments
Authors: Liu Jie , Gore Steven K , Heyer Wolf-Dietrich 
Published: February 2025

Abstract
Homologous recombination (HR) is a high-fidelity repair mechanism for double-strand breaks. Rad51 is the key enzyme that forms filaments on single-stranded DNA (ssDNA) to catalyze homology search and DNA strand exchange in recombinational DNA repair. In this study, we employed single-particle cryogenic electron microscopy (cryo-EM) to ascertain the density map of the wild-type budding yeast Rad51-ssDNA filament bound to ADP-AlF3, achieving a resolution of 2.35 Å without imposing helical symmetry. The model assigned 6 Rad51 protomers, 24 nt of DNA, and 6 bound ADP-AlF3. It shows 6-fold symmetry implying monomeric building blocks, unlike the structure of the Rad51-I345T mutant filament with three-fold symmetry implying dimeric building blocks, for which the structural comparisons provide a satisfying mechanistic explanation. This image analysis enables comprehensive comparisons of individual Rad51 protomers within the filament and reveals local conformational movements of amino acid side chains. Notably, R293 in Loop 1 adopts multiple conformations to facilitate L296 and V331 in separating and twisting the DNA triplets. We also analyzed the crystal structure of Rad51-I345T and the predicted structure of yeast Rad51–K342E using the Rad51–ssDNA structure from this study as a reference.
The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation
Authors: Ranjan Amitabh , Mattijssen Sandy , Charlly Nithin , Gallardo Isabel Cruz , Pitman Leah F , Coleman Jennifer C , Conte Maria R , Maraia Richard J 
Published: February 2025

Abstract
LARP4 interacts with poly(A)-binding protein (PABP) to protect messenger RNAs (mRNAs) from deadenylation and decay, and recent data indicate it can direct the translation of functionally related mRNA subsets. LARP4 was known to bind RACK1, a ribosome-associated protein, although the specific regions involved and relevance had been undetermined. Here, through a combination of in-cell and in vitro methodologies, we identified positions 615–625 in conserved region-2 (CR2) of LARP4 (and 646–656 in LARP4B) as directly binding RACK1. Consistent with these results, AlphaFold2-Multimer predicted high-confidence interaction of CR2 with RACK1 propellers 5 and 6. CR2 mutations strongly decreased LARP4 association with cellular RACK1 and ribosomes by multiple assays, whereas PABP association was less affected, consistent with independent interactions. The CR2 mutations decreased LARP4’s ability to stabilize a β-globin mRNA reporter containing an AU-rich element (ARE) to higher degree than β-globin and GFP (green fluorescent protein) mRNAs lacking the ARE. We show LARP4 robustly increases translation of β-glo-ARE mRNA, whereas the LARP4 CR2 mutant is impaired. Analysis of nanoLuc-ARE mRNA for production of luciferase activity confirmed LARP4 promotes translation efficiency, while CR2 mutations are disabling. Thus, LARP4 CR2-mediated interaction with RACK1 can promote translational efficiency of some mRNAs.