bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collaborative Music Therapy and Speech-Language Pathology for Pediatric Acquired Communication Impairments: A Phenomenological International Perspective
Authors: Burns James , Keaveney Cecilia , Nieto Natalia , O’Connor Rebecca , Moss Hilary 
Published: November 2024

Abstract
The partnership between music therapy and speech-language pathology is gaining recognition as an effective approach in the rehabilitation of young children with acquired communication impairments (ACIs). Yet, there remains a notable gap in understanding the distinctive contributions and challenges inherent in this collaborative practice. This study explored the perspectives of music therapists (MTs) and speech-language pathologists (SLPs) regarding the unique role of this collaborative effort, the elements of successful collaboration, and the methods implemented by clinicians to evaluate outcomes. Semi-structured interviews were conducted with nine pairs of MTs and SLPs in rehabilitation facilities across seven countries. These interviews were analyzed thematically using Van Manen’s approach to hermeneutic phenomenology. Three themes arose from the data: (a) the role of collaborative music therapy and speech-language pathology, (b) building blocks of successful collaboration, and (c) evaluating collaborative practices. This collaboration fosters a unified strategy aimed at achieving shared language and communication goals. By combining their distinct expertise, MTs and SLPs can address the complex and varied needs of children with ACIs more effectively. However, further research is essential to comprehensively understand the functional outcomes arising from such collaborative endeavors in pediatric ACIs. This is crucial for validating the efficacy and significance of this approach in bolstering language and communication skills and advocating for its wider integration within rehabilitation services.
GTO: a comprehensive gene therapy omnibus
Authors: Meng Xuehang , Du Yujia , Liu Chang , Zhai Zhaoyu , Pan Jianbo 
Published: November 2024

Abstract
Gene therapy, which involves the delivery of genetic material into cells to correct an underlying genetic problem, has emerged as a promising approach for treating various conditions. To promote research in this rapidly evolving field, we developed the Gene Therapy Omnibus (GTO) (http://www.inbirg.com/gto/), a comprehensive resource containing detailed clinical trial data and molecular information related to gene therapy. The GTO includes 6333 clinical trial records and 3466 transcriptome profiles, with information on 614 altered genes and 22 types of gene therapy, including DNA therapies, RNA therapies and genetically-modified cell therapies. For each gene therapy product in a clinical trial, detailed information, such as altered gene name, structural components, indication, vector information, phase of the clinical trial, clinical outcomes and adverse effects, is provided when available. Additionally, 345 comparison datasets, including 29 single-cell RNA-sequencing datasets comprising information on both gene therapy and control samples, were established. Differential gene expression and downstream functional enrichment analyses were performed through standardized pipelines to elucidate the molecular alterations induced by gene therapy. The user-friendly interface of the GTO supports efficient data retrieval, visualization and analysis, making it an invaluable resource for researchers and clinicians performing clinical research on gene therapy and the underlying mechanisms.
The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters
Authors: Udwary Daniel W , Doering Drew T , Foster Bryce , Smirnova Tatyana , Kautsar Satria A , Mouncey Nigel J 
Published: November 2024

Abstract
Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.
Combining neural networks with galaxy light subtraction for discovering strong lenses in the Hyper Suprime-Cam Subaru Strategic Program
Authors: Ishida Yuichiro , Wong Kenneth C , Jaelani Anton T , More Anupreeta 
Published: November 2024

Abstract
Galaxy-scale strong gravitational lenses are valuable objects for a variety of astrophysical and cosmological applications. Strong lensing galaxies are rare, so efficient search methods, such as convolutional neural networks (CNNs), are often used on large imaging datasets. In this work, we apply a new technique to improve the performance of supervised neural networks by subtracting the central (lensing) galaxy light from both the training and test datasets. We use multiband imaging data from the Hyper Suprime-Cam Subaru Strategic Program as our training and test datasets. By subtracting the lensing galaxy light, we increase the contrast of the lensed source compared to the original imaging data. We also apply the light subtraction to non-lenses in order to compare them to the light-subtracted lenses. Residual features resulting from poor light subtraction can adversely affect the performance of networks trained on the subtracted images alone. We find that combining the light-subtracted images with the original $gri$-band images for training and classification can overcome this and improve the overall classification accuracy. We find the area under the receiver operating characteristic curve can be improved to 0.841 using the combination of the fiducial images and light-subtracted images, compared to 0.808 for the fiducial imaging dataset alone. This may be a promising technique for improving future lens searches using CNNs.
Mitochondrial Splicing Efficiency Is Lower in Holoparasites Than in Free-Living Plants
Authors: Garcia Laura E , Sanchez-Puerta M Virginia 
Published: November 2024

Abstract
Mitochondria play a crucial role in eukaryotic organisms, housing their own genome with genes vital for oxidative phosphorylation. Coordination between nuclear and mitochondrial genomes is pivotal for organelle gene expression. Splicing, editing and processing of mitochondrial transcripts are regulated by nuclear-encoded factors. Splicing efficiency (SEf) of the many group II introns present in plant mitochondrial genes is critical for mitochondrial function since a splicing defect or splicing deficiency can severely impact plant growth and development. This study investigates SEf in free-living and holoparasitic plants, focusing on 25 group II introns from 15 angiosperm species. Our comparative analyses reveal distinctive splicing patterns with holoparasites exhibiting significantly lower SEf, potentially linked to their unique evolutionary trajectory. Given the preponderance of horizontal gene transfer (HGT) in parasitic plants, we investigated the effect of HGT on SEf, such as the presence of foreign introns or foreign nuclear-encoded splicing factors. Contrary to expectations, the SEf reductions do not correlate with HGT events, suggesting that other factors are at play, such as the loss of photosynthesis or the transition to a holoparasitic lifestyle. The findings of this study broaden our understanding of the molecular evolution in parasitic plants and shed light on the multifaceted factors influencing organelle gene expression.
Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants
Authors: Wang Xutong , Duan Jingbo , Clark Chancelor B , Feng Wanjie , Ma Jianxin 
Published: November 2024

Abstract
Alternative transcription initiation (ATI) appears to be a ubiquitous regulatory mechanism of gene expression in eukaryotes. However, the extent to which it affects the products of gene expression and how it evolves and is regulated remain unknown. Here, we report genome-wide identification and analysis of transcription start sites (TSSs) in various soybean (Glycine max) tissues using a survey of transcription initiation at promoter elements with high-throughput sequencing (STRIPE-seq). We defined 193,579 TSS clusters/regions (TSRs) in 37,911 annotated genes, with 56.5% located in canonical regulatory regions and 43.5% from start codons to 3′ untranslated regions, which were responsible for changes in open reading frames of 24,131 genes. Strikingly, 6,845 genes underwent ATI within coding sequences (CDSs). These CDS-TSRs were tissue-specific, did not have TATA-boxes typical of canonical promoters, and were embedded in nucleosome-free regions flanked by nucleosomes with enhanced levels of histone marks potentially associated with intragenic transcriptional initiation, suggesting that ATI within CDSs was epigenetically tuned and associated with tissue-specific functions. Overall, duplicated genes possessed more TSRs, exhibited lower degrees of tissue specificity, and underwent stronger purifying selection than singletons. This study highlights the significance of ATI and the genomic and epigenomic factors shaping the distribution of ATI in CDSs in a paleopolyploid eukaryote.
How reliance on Spanish-language social media predicts beliefs in false political narratives amongst Latinos
Authors: Abrajano Marisa , Garcia Marianna , Pope Aaron , Vidigal Robert , Tucker Joshua A , Nagler Jonathan 
Published: November 2024

Abstract
False political narratives are nearly inescapable on social media in the United States. They are a particularly acute problem for Latinos, and especially for those who rely on Spanish-language social media for news and information. Studies have shown that Latinos are vulnerable to misinformation because they rely more heavily on social media and messaging platforms than non-Hispanic whites. Moreover, fact-checking algorithms are not as robust in Spanish as they are in English, and social media platforms put far more effort into combating misinformation on English-language media than Spanish-language media, which compounds the likelihood of being exposed to misinformation. As a result, we expect that Latinos who use Spanish-language social media to be more likely to believe in false political narratives when compared with Latinos who primarily rely on English-language social media for news. To test this expectation, we fielded the largest online survey to date of social media usage and belief in political misinformation of Latinos. Our study, fielded in the months leading up to and following the 2022 midterm elections, examines a variety of false political narratives that were circulating in both Spanish and English on social media. We find that social media reliance for news predicts one’s belief in false political stories, and that Latinos who use Spanish-language social media have a higher probability of believing in false political narratives, compared with Latinos using English-language social media.
Online Graded Motor Imagery Is Effective in Women Diagnosed With Pelvic Pain: A Randomized Controlled Trial
Authors: Lopez-Brull Aida , Perez-Dominguez Borja , Plaza-Carrasco Maria , Blasco-Ortiz Cristina , Navarro-Ribera Blanca , Casaña Jose , Mohedo Esther Diaz , Nahon Irmina 
Published: November 2024

Abstract

Objective
Effective therapeutic strategies are crucial for managing genito-pelvic pain/penetration disorder (GPPPD), a condition presenting challenges for both patients and health care providers. This study aims to assess the effectiveness of an online graded motor imagery (GMI) program in alleviating pain intensity and improving sexual function in women diagnosed with GPPPD.

Methods
Eighty-seven women were randomly assigned to either an online GMI group or a control group. The online GMI protocol involved engaging participants in 2-week segments of left/right judgment exercises, mental simulation of movements, and gradual exposure therapy. After 6 weeks, we assessed pain intensity and sexual function. The control group gained access to the program upon study completion.

Results
The online GMI group demonstrated a significant reduction in pain intensity, coupled with improvements in sexual function. Notably, participants with enhanced movement imagery abilities experienced greater improvements, while those with negative beliefs and thoughts regarding vaginal penetration showed lower sexual function scores.

Conclusion
An online GMI program is effective in alleviating the pain burden faced by women dealing with GPPPD.

Impact
Effectively addressing pelvic pain in patients remains a daunting challenge for physical therapists. Therefore, implementing efficient and easily accessible strategies is crucial. The incorporation of GMI intervention proves to be an effective approach for improving both pain and sexual functioning in women with GPPPD.
A Dynamic Model of Authoritarian Social Control
Authors: Lagunoff Roger 
Published: November 2024

Abstract
Authoritarian regimes often use targeted social control—unequal application of the law to limit expressive freedom and enforce social conformity. At the same time, their methods appear less draconian than in the past. In this model, an authority structures punishments and rewards to compel adherence to its preferred norm. The authority’s commitment is time-limited and depends on imperfectly informative signals of a citizen’s behaviour. Given two citizens with the same observed behaviour, the authority imposes harsher punishments on the poorer and/or ex ante dissident individual. Lighter punishments are imposed on the wealthier citizen to prevent “over-compliance”. Wealth inequality increases over time. Some citizens become prosperous “lackeys” while others become destitute from confiscation. In stable regimes with high state capacity, the authority reduces punishments and/or increases rewards to allow citizens to accumulate wealth, leading to social conformity and balanced growth in the long run. In unstable regimes with low capacity, the citizenry splits into groups of wealthy lackeys and destitute proles.
The diffusion of industrial robots in Europe: regional or country effect?
Authors: Nuccio Massimiliano , Guerzoni Marco , Cappelli Riccardo , Geuna Aldo 
Published: November 2024

Abstract
The paper investigates whether the penetration of advanced manufacturing technologies can be better explained at the regional or national level. If regional effects prevail, policy actions would focus on local investments, while if country effects make regional covariates redundant, they should be redirected to more structural reform of the national systems of innovation. In this respect, the contribution is 2-fold. First, data on acquisitions of industrial robots in the five largest European economies are rescaled at regional levels to draw a clear picture of winners and losers in the robotics race after the 2008 financial crisis. Second, we explain differential of growth rates in robot adoption with (1) traditional measures of industrial variety, (2) an unsupervised machine learning approach classifying a region’s industry profile (3) usual determinants of innovation and, thereafter test the robustness of the results when country effects are added. As the main result, we highlight a process of regional convergence in which country-fixed effects hold greater explanatory power, although related variety and the number of skilled people are statistically significant regional explanatory factors. We do not discover a specific industry mix associated with the rise of adoption, but we highlight the one associated with its decline.
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
Authors: Nanduri Sravani , Black Allison , Bedford Trevor , Huddleston John 
Published: November 2024

Abstract
Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or recombine, respectively: seasonal influenza A/H3N2 and SARS-CoV-2. We applied principal component analysis, multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection to sequences with well-defined phylogenetic clades and either reassortment (H3N2) or recombination (SARS-CoV-2). For each low-dimensional embedding of sequences, we calculated the correlation between pairwise genetic and Euclidean distances in the embedding and applied a hierarchical clustering method to identify clusters in the embedding. We measured the accuracy of clusters compared to previously defined phylogenetic clades, reassortment clusters, or recombinant lineages. We found that MDS embeddings accurately represented pairwise genetic distances including the intermediate placement of recombinant SARS-CoV-2 lineages between parental lineages. Clusters from t-SNE embeddings accurately recapitulated known phylogenetic clades, H3N2 reassortment groups, and SARS-CoV-2 recombinant lineages. We show that simple statistical methods without a biological model can accurately represent known genetic relationships for relevant human pathogenic viruses. Our open source implementation of these methods for analysis of viral genome sequences can be easily applied when phylogenetic methods are either unnecessary or inappropriate.
Isofraxidin alleviated radiation-induced testicular damage via the Nrf2/HO-1-NLRP3/ASC Axis
Authors: Hu Changkun , Wu Zekun , Zhang Liangliang , Ma Zengchun , Liao Zebin , Gao Yue 
Published: November 2024

OBJECTIVE:
Radiotherapy is used to treat patients with tumors; however, radiation (IR)-induced testicular injury, which has no effective treatment approved in clinical practice, significantly influences their prognosis and quality of life. The protective effects and underlying mechanisms of action of isofraxidin (IF) against IR-induced testicular injury were investigated.

Methods:
A mouse testis injury model was established using 5 Gy irradiation. H&E staining, immunofluorescence staining, and enzyme-linked immunosorbent assay were used to measure DNA damage, apoptosis, inflammatory reactions, and oxidative stress in the testes of mice after irradiation. The effectiveness of IF irradiation on testicular injury was evaluated, and the mechanisms of the related oxidative stress and inflammatory response pathways are discussed.

Results:
IF can improve IR-induced testicular injury by inhibiting the increased levels of DNA damage, apoptosis rate, oxidative stress, and inflammatory factors. The radioprotective effects of IF on testicular injury are mediated by the stimulation of Nrf2/HO-1 or suppression of NLRP3 inflammasome signaling pathways. In addition, crosstalk between the Nrf2/HO-1 and NLRP3 inflammasome signaling pathways was elucidated, in which the inhibition of the NLRP3 inflammasome was mediated by the activation of Nrf2 signaling with IF upon IR exposure.

Conclusion:
IF can be a potent radioprotective agent to mitigate testicular damage, and may provide a new therapeutic option to alleviate the side effects of radiotherapy in male patients with tumors.
Hospital Medicare Spending per Beneficiary: A Longitudinal Study
Authors: Xu Jing , Hamadi Hanadi , Zhao Mei , Boamah Sheila A. , Tafili Aurora , Spaulding Aaron 
Published: November 2024

SUMMARY

Goal
While studies have examined quality and health outcomes related to the Centers for Medicare & Medicaid Services’ (CMS’s) Hospital Value-Based Purchasing (HVBP) Program, a significant gap exists in the literature regarding the relationship between pay-for-performance initiatives and hospital financial performance in the program’s Efficiency and Cost Reduction domain. This study examined the association between hospitals’ cost inefficiency and participation in the HVBP Program by estimating the probability and magnitude of improvement or achievement in the program’s Efficiency and Cost Reduction domain.

Methods
The 2014–2019 Efficiency and Cost Reduction domain data were obtained from CMS and merged with the American Hospital Association’s Annual Survey Database. We conducted a zero-inflated negative binomial regression to account for the excessive number of zeros in the data.

Principal Findings
The negative binomial component of the model assessed the magnitude of the impact on the Efficiency and Cost Reduction improvement from each covariate, while the zero-inflated component assessed the odds of being in the “certain-zero” group, meaning no chance to improve or achieve. Hospital ownership, location, size, safety-net status, percentage of Medicare patients, and the number of registered nurses per bed were statistically significant. Additionally, the Herfindahl-Hirschman Index and teaching status significantly influenced efficiency performance.

Practical Applications
Changes in hospital performance in this domain exist and have evolved. Hospitals might be at a disadvantage with this performance measure because of their inherent organizational structure. The HVBP Program may not provide clear enough direction or actionable incentive to address the needs of stakeholders influenced primarily by measures of Medicare spending per beneficiary. This study’s findings hold practical value for policymakers, healthcare administrators, and researchers. Policymakers can use this information to tailor future pay-for-performance programs and effectively allocate resources. Healthcare administrators can identify areas for improvement and benchmark their performance against similar institutions. Researchers can explore the program’s long-term sustainability and investigate cost drivers within different hospital groups. By understanding the link between hospital characteristics and cost reduction, all stakeholders can contribute to a more efficient healthcare system.