bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geography of the Underserved
Authors: Kaufman Elinore J. , Prentice Carter , Williams Devin , Song Jamie , Haddad Diane N. , Brown Joshua B. , Chen Xinwei , Colling Kristin , Chatterjee Paula 
Published: September 2024

Objective:
To determine the proportion and characteristics of injured rural residents treated at urban trauma centers (TCs), urban non-trauma centers (NTCs), rural TCs, and rural NTCs.

Summary Background Data:
Timely treatment at a designated trauma center improves outcomes for patients with serious injuries, but rural residents have limited access to designated trauma centers. Rural non-trauma centers may constitute an underrecognized source of trauma care.

Methods:
We used the National Emergency Department Sample to conduct a retrospective, pooled cross-sectional study of ED visits among rural residents with injury severity score (ISS) ≥ 9 (indicating at least moderate injury). Hospitals were designated as a trauma (TC) or non-trauma center (NTC) and as rural or urban. We compared management, disposition, and outcomes among hospital types.

Results:
Of 748,587 injured rural residents from 2016-2020, 384,113 (51.3%) were treated in rural NTCs, 232,845 (31.1%) in urban TCs, 116,493 (15.6%) in urban NTCs, and 15,137 (2.0%) in rural TCs. Injuries treated at rural NTCs were moderate in severity (ISS 9-15) in 76.6% of visits, severe (ISS 16-25) in 15.7%, and very severe (ISS > 25) in 1.1%. Urban TCs saw the highest proportion of very severe injuries (17.3%). Rural NTCs managed 77.5% of visits definitively, discharging 72.8%. They transferred 21.9% of patients. Length of stay was longest and hospital charges highest for patients treated in urban TCs, which also performed the most procedures. Rural NTCs had the shortest length of stay and lowest mean charges.

Conclusions:
Rural non-trauma centers provided initial care for more than half of injured rural residents, including 2 in 5 of those with the most severe injuries, and managed more than 3 in 4 definitively. These hospitals may be an under-recognized component of the US trauma system.
Care bundle for preventing intraventricular hemorrhage in premature infants: a best practice implementation project
Authors: Solaz García Álvaro , Ros Navarret Rosario , Aguar Carrascosa Marta , Valles Murcia Nerea , Llorens Roberto , Torrejón Rodríguez Laura , Pinilla González Alejandro , Albornos-Muñoz Laura , Escrig Fernández Raquel 
Published: September 2024

ABSTRACT

Introduction:
Intraventricular hemorrhages remain a major problem in neonatology, because their complications affect neonatal morbidity, mortality, and long-term neurodevelopmental outcomes.

Aim:
The aim of this project was to prevent intraventricular hemorrhage in premature infants during their first days of life in a neonatal intensive care unit (NICU).

Methods:
This pre- and post-implementation clinical audit project used the JBI Evidence Implementation Framework and was conducted in a tertiary-level Spanish NICU with a consecutive sample. A baseline audit was conducted using 13 audit criteria derived from JBI summaries of the best available evidence. This was followed by the implementation of an action plan, which included a care bundle and health care professionals’ education. These improvement strategies were then evaluated using a follow-up audit.

Results:
The baseline and follow-up audits evaluated 54 and 56 infants, respectively. The follow-up audit showed 100% improvement for Criteria 2, 3, 6, and 7, which covered sleep safety and noise. Criteria 12 and 13, which covered cord clamping and positioning the infant, improved by 25.99%. Criterion 9, on antenatal corticosteroids, showed a slight improvement of 5.56%.

Conclusions:
This study increased compliance with an evidence-based, family-centered care approach to preventing intraventricular hemorrhage in premature infants. This was achieved by conducting a baseline and follow-up audit, implementing a training program, and keeping more comprehensive nursing records. Further studies could assess the long-term effectiveness of interventions and/or the incidence of intraventricular hemorrhage and neurodevelopmental disorders in premature infants.

Spanish abstract:

http://links.lww.com/IJEBH/A262
Intravital imaging of pulmonary lymphatics in inflammation and metastatic cancer
Authors: Cleary Simon J. , Qiu Longhui , Seo Yurim , Baluk Peter , Liu Dan , Serwas Nina K. , Cyster Jason G. , McDonald Donald M. , Krummel Matthew F. , Looney Mark R. 
Published: September 2024

AbstractIntravital microscopy has enabled the study of immune dynamics in the pulmonary microvasculature, but many key events remain unseen because they occur in deeper lung regions. We therefore developed a technique for stabilized intravital imaging of bronchovascular cuffs and collecting lymphatics surrounding pulmonary veins in mice. Intravital imaging of pulmonary lymphatics revealed ventilation-dependence of steady-state lung lymph flow and ventilation-independent lymph flow during inflammation. We imaged the rapid exodus of migratory dendritic cells through lung lymphatics following inflammation and measured effects of pharmacologic and genetic interventions targeting chemokine signaling. Intravital imaging also captured lymphatic immune surveillance of lung-metastatic cancers and lymphatic metastasis of cancer cells. To our knowledge, this is the first imaging of lymph flow and leukocyte migration through intact pulmonary lymphatics. This approach will enable studies of protective and maladaptive processes unfolding within the lungs and in other previously inaccessible locations.Graphical abstract
Implementation of Ribo-BiFC method to plant systems using a split mVenus approach
Authors: Raabe Karel , Náprstková Alena , Pieters Janto , Torutaeva Elnura , Jirásková Veronika , Kahrizi Zahra , Michailidis Christos , Honys David 
Published: September 2024

AbstractTranslation is a fundamental process for every living organism. In plants, the rate of translation is tightly modulated during development and in response to environmental cues. However, it is difficult to measure the actual translation state of the tissuesin vivo. Here, we report the implementation of anin vivotranslation marker based on bimolecular fluorescence complementation, the Ribo-BiFC. We combined method originally developed for fruit-fly with an improved low background split-mVenus BiFC system previously described in plants. We labelledArabidopsis thalianasmall subunit ribosomal protein (RPS) and large subunit ribosomal protein (RPL) with fragments of the mVenus fluorescent protein. Upon the assembly of the 80S ribosome, the mVenus fragments complemented and were detected by fluorescent microscopy. We show that these recombinant proteins are in close proximity in the tobacco epidermal cells, although the signal is reduced when compared to BiFC signal from known interactors. This Ribo-BiFC method system can be used in stable transgenic lines to enable visualisation of translational rate in plant tissues and could be used to study translation dynamics and its changes during plant development, under abiotic stress or in different genetic backgrounds.
Conserved Evolutionary Response to Whole Genome Duplication in Angiosperms Revealed Using High Resolution Gene Expression Profiling
Authors: Leal J. Luis , Hodková Eva , Billhardt Anja , Eklund D. Magnus , Granath Gustaf , Egoavil Pilar Herrera , Chen Jun , Milesi Pascal , Salojärvi Jarkko , Lascoux Martin 
Published: September 2024

ABSTRACTAutopolyploidy, the result of genome duplication within a single species, is widespread among plant lineages and believed to have played a major role in angiosperm evolution and diversification. Whole genome duplication often triggers significant morphological and ecological changes in autopolyploids vis-a-vis their diploid progenitors, which are induced by subtle changes in gene expression patterns, often of a stochastic nature. Recent results have nonetheless identified specific changes in meiotic, metabolic, and defense response pathways that seem to be commonly shared among autopolyploid species, hinting at convergent evolution. Notably, a set of 12 core meiotic genes, including several genes involved in meiotic crossover formation, has been found to undergo strong selective pressure in the aftermath of autopolyploidization. For the most part these findings have been based on the study ofArabidopsis arenosaandA. lyrataautotetraploids and the question has remained as to whether the evolutionary forces shaping the establishment and evolution of autopolyploidy in the Arabidopsis model system extend more broadly across angiosperms, an area where our knowledge is still limited. In order to address these questions, we conducted a comparative transcriptome analysis ofBetula pubescens, a highly introgressed autotetraploid, and its diploid sister species,B. pendula, two birch species belonging to the Fagales order that diverged from Brassicales 120-140 Mya. Our results reveal significant changes in the expression patterns ofB. pubescensin genes involved in secondary metabolic processes and the regulation of stress response to pathogens, in agreement with results obtained in other autopolyploid plant complexes. Allele-specific expression analysis identified 16 meiotic genes inB. pubescenswith constrained expression patterns, strongly favoring alleles introgressed fromB. humilisorB. nana, a set that includes 8 meiotic genes −ASY1,ASY3,PDS5B,PRD3,SYN1,SMC3, SHOC1andSCC4− previously found to be under selection in Arabidopsis autopolyploids. These results provide support to the hypothesis that whole genome duplication triggers similar genomic responses across flowering plants, and that the evolutionary path available to autopolyploids for regaining meiotic stability is highly conserved and dependent on a small group of core meiotic genes.
Precision Repair of Zone-Specific Meniscal Injuries Using a Tunable Extracellular Matrix-Based Hydrogel System
Authors: Lee Se-Hwan , Li Zizhao , Zhang Ellen Y. , Kim Dong Hwa , Huang Ziqi , Lee Sang Jin , Kang Hyun-Wook , Burdick Jason A. , Mauck Robert L. , Heo Su Chin 
Published: September 2024

AbstractMeniscus injuries present significant therapeutic challenges due to their limited self-healing capacity and diverse biological and mechanical properties across meniscal tissue. Conventional repair strategies neglect to replicate the complex zonal characteristics within the meniscus, resulting in suboptimal outcomes. In this study, we introduce an innovative, age- and stiffness-tunable meniscus decellularized extracellular matrix (DEM)-based hydrogel system designed for precision repair of heterogeneous, zonal-dependent meniscus injuries. By synthesizing age-dependent DEM hydrogels, we identified distinct cellular responses: fetal bovine meniscus-derived DEM promoted chondrogenic differentiation, while adult meniscus-derived DEM supported fibrochondrogenic phenotypes. The incorporation of methacrylate hyaluronic acid (MeHA) further refined the mechanical properties and injectability of the DEM-based hydrogels. The combination of age-dependent DEM with MeHA allowed for precise stiffness tuning, influencing cell differentiation and closely mimicking native tissue environments.In vivotests confirmed the biocompatibility of hydrogels and their integration with native meniscus tissues. Furthermore, advanced 3D bioprinting techniques enabled the fabrication of hybrid hydrogels with biomaterial and mechanical gradients, effectively emulating the zonal properties of meniscus tissue and enhancing cell integration. This study represents a significant advancement in meniscus tissue engineering, providing a promising platform for customized regenerative therapies across a range of heterogeneous fibrous connective tissues.
Local adaptation to climate facilitates a global invasion
Authors: Gamba Diana , Vahsen Megan L. , Maxwell Toby M. , Pirtel Nikki , Romero Seth , Van Ee Justin J. , Penn Amanda , Das Aayudh , Ben-Zeev Rotem , Baughman Owen , Blaney C. Sean , Bodkins Randy , Budha-Magar Shanta , Copeland Stella M. , Davis-Foust Shannon L. , Diamond Alvin , Donnelly Ryan C. , Dunwiddie Peter W. , Ensing David J. , Everest Thomas A. , Hoitink Holly , Holdrege Martin C. , Hufbauer Ruth A. , Juzėnas Sigitas , Kalwij Jesse M. , Kashirina Ekaterina , Kim Sangtae , Klisz Marcin , Klyueva Alina , Langeveld Michel , Lutfy Samuel , Martin Daniel , Merkord Christopher L. , Morgan John W. , Nagy Dávid U. , Ott Jacqueline P. , Puchalka Radoslaw , Pyle Lysandra A. , Rasran Leonid , Rector Brian G. , Rosche Christoph , Sadykova Marina , Shriver Robert K. , Stanislavschi Alexandr , Starzomski Brian M. , Stone Rachel L. , Turner Kathryn G. , Urza Alexandra K. , VanWallendael Acer , Wegenschimmel Carl-Adam , Zweck Justin , Brown Cynthia S. , Leger Elizabeth A. , Blumenthal Dana M. , Germino Matthew J. , Porensky Lauren M. , Hooten Mevin B. , Adler Peter B. , Lasky Jesse R. 
Published: September 2024

AbstractLocal adaptation may facilitate range expansion during invasions, but the mechanisms promoting destructive invasions remain unclear. Cheatgrass (Bromus tectorum), native to Eurasia and Africa, has invaded globally, with particularly severe impacts in western North America. We sequenced 307 genotypes and conducted controlled experiments. We found that diverse lineages invaded North America, where long-distance gene flow is common. Ancestry and phenotypic clines in the native range predicted those in the invaded range, indicating pre-adapted genotypes colonized different regions. Common gardens showed directional selection on flowering time that reversed between warm and cold sites, potentially maintaining clines. In the Great Basin, genomic predictions of strong local adaptation identified sites where cheatgrass is most dominant. Preventing new introductions that may fuel adaptation is critical for managing ongoing invasions.
Machine-learning convergent melanocytic morphology despite noisy archival slides
Authors: Tada M , Gaskins G , Ghandian S , Mew N , Keiser MJ , Keiser ES 
Published: September 2024

AbstractMelanocytic atypia, ranging from benign to malignant, often leads to diagnostic discordance, complicating its prediction by machine learning models. To overcome this, we paired H&E-stained histology images with contiguous or serial sections immunohistochemically (IHC) stained for melanocytic cells via antibodies for MelanA, MelPro, or SOX10. We developed a deep-learning pipeline to identify melanocytic atypia by digitizing a real-world archival dataset of 122 paired whole slide images from 61 confirmed melanoma in situ (MIS) cases at two institutions. Only 37.7% of the cases contained tissue pairs that matched well enough for deep learning. Nonetheless, the MelanA+MelPro models achieved an average area under the receiver-operating characteristic (AUROC) of 0.948 and an average area under the precision-recall curve (AUPRC) of 0.611, while the SOX10 models had an average of 0.867 AUROC and 0.433 AUPRC. Despite learning from biologically different IHC stains, the convolutional neural network (CNN) models independently exhibited an intuitive convergent rationale by explainable AI saliency calculations. Different antibodies, with nuclear versus cytoplasmic staining, provided complementary yet consistent information, which the CNNs integrated effectively. The resulting multi-antibody virtual stains identified morphologic cytologic and small-scale architectural features directly from H&E-stained histology images, which can assist pathologists in assessing cutaneous MIS.
CRAK-Velo: Chromatin Accessibility Kinetics integration improves RNA Velocity estimation
Authors: El Kazwini Nour , Gao Mingze , Boudjelthia Idris Kouadri , Cai Fangxin , Huang Yuanhua , Sanguinetti Guido 
Published: September 2024

AbstractRNA velocity has recently emerged as a key tool in the analysis of single-cell transcriptomic data, yet connecting RNA velocity analyses to underlying regulatory processes has proved challenging. Here we propose CRAK-Velo, a semi-mechanistic model which integrates chromatin accessibility data in the estimation of RNA velocities. CRAK-Velo provides biologically consistent estimates of developmental flows and enables accurate cell-type deconvolution, while additionally shining light on regulatory processes at the level of interactions between genes and chromatin regions.
The Precise Basecalling of Short-Read Nanopore Sequencing
Authors: Wang Ziyuan , Tu Mei-Juan , Song Chengcheng , Liu Ziyang , Wang Katherine K. , Chen Shuibing , Yu Ai-Ming , Ding Hongxu 
Published: September 2024

ABSTRACTThe nanopore sequencing of short sequences, whose lengths are typically less than 0.3kb therefore comparable with Illumina sequencing techniques, has recently gained wide attention. Here, we design a scheme for training nanopore basecallers that are specialized for short biomolecules. With bioengineered RNA (BioRNA) molecules as examples, we demonstrate the superior accuracy of basecallers trained by our scheme.
Identification of SPP1-positive macrophages by single-cell spatial analysis in human lung tissues with mycobacterial infection
Authors: Katano Harutaka , Hebisawa Akira , Sato Yuko , Hoshino Yoshihiko 
Published: September 2024

AbstractTuberculosis and non-tuberculous mycobacterial (NTM) diseases are infections caused byMycobacterium tuberculosisand non-tuberculous mycobacteria such as theMycobacterium aviumcomplex, leading to the formation of granulomatous lesions with caseous necrosis in the lungs. Although granulomatous tissues are infiltrated by numerous inflammatory cells, including macrophages, lymphocytes, and neutrophils, the mechanisms underlying granuloma formation caused by mycobacteria remain unclear. In this study, we performed single-cell spatial analysis on lung tissue samples from patients with tuberculosis and NTM diseases to investigate the infiltrating cell populations. We analyzed seven lung lesions and identified individual cell types infiltrating the granulomatous tissue. Based on gene expression profiles, at least four macrophage subtypes were identified. Notably, SPP1-positive macrophages predominantly found infiltrating the granulomatous tissue. Langhans giant cells expressed SPP1, and numerous SPP1-positive macrophages without giant cell morphology were also observed around the granulomas. RNA-seq analysis revealed elevated SPP1 expression in mycobacterium-infected tissues. The SPP1-CD44 signaling pathway was active in SPP1-positive macrophages and their neighboring cells in mycobacterium-infected tissues. SPP1-positive macrophages were also observed around granulomas in other granulomatous diseases, such as granulomatosis with polyangiitis and sarcoidosis. These findings suggest that SPP1-CD44 signaling in SPP1-positive macrophages may play a role in the pathology of granulomatous diseases, including mycobacterial infections.Brief summarySPP1-CD44 signaling in SPP1-positive macrophages may play a role in granuloma formation in mycobacterial and other granulomatous diseases.
The ‘very moment’ when UDG recognizes a flipped-out uracil base in dsDNA
Authors: Saravanan Vinnarasi , Raouraoua Nessim , Brysbaert Guillaume , Giordano Stefano , Lensink Marc F. , Cleri Fabrizio , Blossey Ralf 
Published: September 2024

ABSTRACTUracil-DNA glycosylase (UDG) is the first enzyme in the base-excision repair (BER) pathway, acting on uracil bases in DNA. How UDG finds its targets has not been conclusively resolved yet. Based on available structural and other experimental evidence, two possible pathways are under discussion. In one, the action of UDG on the DNA bases is believed to follow a ‘pinch-push-pull’ model, in which UDG generates the base-flip in an active manner. A second scenario is based on the exploitation of bases flipping out thermally from the DNA. Recent molecular dynamics (MD) studies of DNA in trinucleosome arrays have shown that base-flipping can be readily induced by the action of mechanical forces on DNA alone. This alternative mechanism could possibly enhance the probability for the second scnenario of UDG-uracil interaction via the formation of a recognition complex of UDG with flipped-out base. In this work we describe DNA structures with flipped-out uracil bases generated by MD simulations which we then subject to docking simulations with the UDG enzyme. Our results for the UDG-uracil recognition complex support the view that base-flipping induced by DNA mechanics can be a relevant mechanism of uracil base recognition by the UDG glycosylase in chromatin.
Characterization of nuclear mitochondrial insertions in canine genome assemblies
Authors: Schall Peter Z. , Meadows Jennifer R.S. , Ramos-Almodovar Fabian , Kidd Jeffrey M. 
Published: September 2024

AbstractBackgroundThe presence of mitochondrial sequences in the nuclear genome (Numts) confounds analyses of mitochondrial sequence variation and is a potential source of false positives in disease studies. To improve the analysis of mitochondrial variation in canines, we completed a systematic assessment of Numt content across genome assemblies, canine populations and the carnivore lineage.ResultsCentering our analysis on the UU_Cfam_GSD_1.0/canFam4/Mischka assembly, a commonly used reference in dog genetic variation studies, we find a total of 321 Numts, located throughout the nuclear genome and encompassing the entire sequence of the mitochondria. Comparison to 14 canine genome assemblies identified 63 Numts with presence-absence dimorphism among dogs, wolves, and a coyote. Further, a subset of Numts were maintained across carnivore evolutionary time (arctic fox, polar bear, cat), with 8 sequences likely more than 10 million years old, and shared with the domestic cat. On a population level, using structural variant data from the Dog10K Consortium for 1,879 dogs and wolves, we identified 11 Numts that are absent in at least one sample as well as 53 Numts that are absent from the Mischka assembly.ConclusionsWe highlight scenarios where the presence of Numts is a potentially confounding factor and provide an annotation of these sequences in canine genome assemblies. This resource will aid the identification and interpretation of polymorphisms in both somatic and germline mitochondrial studies in canines.