bluuebunny/crossref_metadata_2025_split huggingface dataset:
Melt electrowritten scaffold architectures to mimic vasculature mechanics and control neo-tissue orientation
Authors: Federici Angelica S. , Tornifoglio Brooke , Lally Caitríona , Garcia Orquidea , Kelly Daniel J. , Hoey David A. 
Published: April 2023

AbstractCardiovascular disease is one of the leading causes of death worldwide, commonly associated with the development of an arteriosclerotic plaque and impairment of blood flow in arteries. Current adopted grafts to bypass the stenosed vessel fail to recapitulate the unique mechanical behaviour of native vessels, particularly in the case of small diameter vessels (<6 mm), leading to graft failure. Therefore, in this study, melt-electrowriting (MEW) was adopted to produce a range of fibrous grafts to mimic the extracellular matrix (ECM) architecture of the tunica media of vessels, in an attempt to match the mechanical and biological behaviour of the native tissue. Initially, the range of collagen architectures within the native vessel was determined, and subsequently replicated using MEW (winding angles (WA) 45°, 26.5°, 18.4°, 11.3°). These scaffolds recapitulated the anisotropic, non-linear mechanical behaviour of native carotid blood vessels. Moreover, these grafts facilitated human mesenchymal stromal/stem cell (hMSC) infiltration, differentiation, and ECM deposition that was independent of WA. The bioinspired MEW fibre architecture promoted cell alignment and preferential neo-tissue orientation in a manner similar to that seen in native tissue, particularly for WA 18.4° and 11.3°, which is a mandatory requirement for long-term survival of the regenerated tissue post-scaffold degradation. Lastly, the WA 18.4° was translated to a tubular graft and was shown to mirror the mechanical behaviour of small diameter vessels within physiological strain. Taken together, this study demonstrates the capacity to use MEW to fabricate bioinspired grafts to mimic the tunica media of vessels and recapitulate vascular mechanics which could act as a framework for small diameter graft development and functional long-term tissue regeneration.
Climate, host and geography shape insect and fungal communities of trees
Authors: Franić Iva , Allan Eric , Prospero Simone , Adamson Kalev , Attorre Fabio , Auger-Rozenberg Marie Anne , Augustin Sylvie , Avtzis Dimitrios , Baert Wim , Barta Marek , Bauters Kenneth , Bellahirech Amani , Boroń Piotr , Bragança Helena , Brestovanská Tereza , Brurberg May Bente , Burgess Treena , Burokienė Daiva , Cleary Michelle , Corley Juan , Coyle David R , Csóka György , Černý Karel , Davydenko Kateryna , de Groot Maarten , Diez Julio Javier , Doğmuş Lehtijärvi H. Tuğba , Drenkhan Rein , Edwards Jacqueline , Elsafy Mohammed , Eötvös Csaba Béla , Falko Roman , Fan Jianting , Feddern Nina , Fürjes-Mikó Ágnes , Gossner Martin M. , Grad Bartłomiej , Hartmann Martin , Havrdova Ludmila , Horáková Miriam Kádasi , Hrabětová Markéta , Justesen Mathias Just , Kacprzyk Magdalena , Kenis Marc , Kirichenko Natalia , Kovač Marta , Kramarets Volodymyr , Lacković Nikola , Lantschner Maria Victoria , Lazarević Jelena , Leskiv Marianna , Li Hongmei , Madsen Corrie Lynne , Malumphy Chris , Matošević Dinka , Matsiakh Iryna , May Tom W. , Meffert Johan , Migliorini Duccio , Nikolov Christo , O’Hanlon Richard , Oskay Funda , Paap Trudy , Parpan Taras , Piškur Barbara , Ravn Hans Peter , Richard John , Ronse Anne , Roques Alain , Ruffner Beat , Santini Alberto , Sivickis Karolis , Soliani Carolina , Talgø Venche , Tomoshevich Maria , Uimari Anne , Ulyshen Michael , Vettraino Anna Maria , Villari Caterina , Wang Yongjun , Witzell Johanna , Zlatković Milica , Eschen René 
Published: April 2023

AbstractNon-native pests, climate change, and their interactions are likely to alter relationships between trees and tree-associated organisms with consequences for forest health. To understand and predict such changes, factors structuring tree-associated communities need to be determined. Here, we analysed the data consisting of records of insects and fungi collected from dormant twigs from 155 tree species at 51 botanical gardens or arboreta in 32 countries. Generalized dissimilarity models revealed similar relative importance of studied climatic, host-related and geographic factors on differences in tree-associated communities. Mean annual temperature, phylogenetic distance between hosts and geographic distance between locations were the major drivers of dissimilarities. The increasing importance of high temperatures on differences in studied communities indicate that climate change could affect tree-associated organisms directly and indirectly through host range shifts. Insect and fungal communities were more similar between closely related vs. distant hosts suggesting that host range shifts may facilitate the emergence of new pests. Moreover, dissimilarities among tree-associated communities increased with geographic distance suggesting that human-mediated transport may facilitate the introductions of new pests. The results of this study highlight the need to limit the establishment of tree pests and increase the resilience of forest ecosystems to changes in climate.
Spatially repeatable components from ultrafast ultrasound are associated with motor unit activity in human isometric contractions
Authors: Rohlén Robin , Carbonaro Marco , Cerone Giacinto L. , Meiburger Kristen M. , Botter Alberto , Grönlund Christer 
Published: April 2023

AbstractObjectiveUltrafast ultrasound imaging has been used to measure intramuscular mechanical dynamics associated with single motor unit (MU) activations. Detecting MU activity from ultrasound sequences requires decomposing a displacement velocity field into components consisting of spatial maps and temporal displacement signals. These components can be associated with putative MU activity or spurious movements (noise). The differentiation between putative MUs and noise has been accomplished by comparing the temporal displacement signals with MU firings obtained from needle EMG. Here, we examined whether the repeatability of the spatial maps over brief time intervals can serve as a criterion for distinguishing putative MUs from noise in low-force isometric contractions.ApproachIn five healthy subjects, ultrafast ultrasound images and high-density surface EMG (HDsEMG) were recorded simultaneously from biceps brachii. MUs identified through HDsEMG decomposition were used as a reference to assess the outcomes of the ultrasound-based decomposition. For each contraction, displacement velocity sequences from the same eight-second ultrasound recording were separated into consecutive two-second epochs and decomposed. The Jaccard Similarity Coefficient (JSC) was employed to evaluate the repeatability of components’ spatial maps across epochs. Finally, the association between the ultrasound components and the MUs decomposed from HDsEMG was assessed.Main resultsAll the MU-matched components had JSC > 0.38, indicating they were repeatable and accounted for about one-third of the HDsEMG-detected MUs (1.8 ± 1.6 matches over 4.9 ± 1.8 MUs). The repeatable components (with JSC over the empirical threshold of 0.38) represented 14% of the total components (6.5 ± 3.3 components). These findings align with our hypothesis that intra-sequence repeatability can differentiate putative MUs from spurious components and can be used for data reduction.SignificanceThe results of our study provide the foundation for developing stand-alone methods to identify MU in ultrafast ultrasound sequences and represent a step forward towards real-time imaging of active MU territories. These methods are relevant for studying muscle neuromechanics and designing novel neural interfaces.
The genomic landscape of adaptation to a new host plant
Authors: Steward Rachel A. , Nilsson Kalle J. , Ortega Giménez Jesús , Nolen Zachary J. , Yan Chao , Huang Yajuan , Ayala López Julio , Runemark Anna 
Published: April 2023

AbstractAdaptation to novel ecological niches is known to be rapid. However, how the loci underlying ecological divergence are coupled to traits reproductively isolating populations, ultimately enabling the formation of persistent species, remains a consequential question in speciation research. Here, we investigated the genomic differences underpinning colonization of a new niche and formation of two partly sympatric host races ofTephritis conurapeacock flies. We took advantage of two independent sympatric zones west and east of the Baltic Sea, where host plant specialists using the thistle speciesCirsium heterophyllumandC. oleraceumco-occur, and address what regions of the genome maintain the host races in parallel. Using genome-wide association, differentiation and divergence statistics, we identified a large, highly divergent region associated with host use among western and eastern populations. Within this region, we identified unique haplotypes associated with each host race, indicative of a large inversion, adding to the growing body of evidence that structural changes to the genome are important for adaptations to persist in the face of gene flow. We further showed strong signatures of selection in this region, especially in populations of the derivedC. oleraceumspecialist host race. The region also had reduced introgression, especially in western populations, while the rest of the genome showed signs of extensive gene flow. Genes within highly differentiated windows within the putative inversion were not only enriched for functions involved in host adaptation, including phenology and metabolic responses to different metabolites in the two host plants, but also enriched for gametogenesis, fertilization and embryological development, all of which suggest sequence divergence could have large consequences on reproductive isolation between the host races. In conclusion, this study suggests that structural changes in the genome may facilitate the formation of persistent host races, and ultimately speciation, in face of gene flow.
NucleosomeDB - a database of 3D nucleosome structures and their complexes with comparative analysis toolkit
Authors: Armeev Grigoriy A. , Gribkova Anna K. , Shaytan Alexey K. 
Published: April 2023

AbstractNucleosomes are basic building blocks of chromatin, comprising DNA wrapped around an octamer of eight histone proteins. They play key roles in DNA compaction, epigenetic mark up of the genome and actively participate in chromatin dynamics. X-ray and later cryo-EM studies have contributed greatly to our understanding of nucleosome structure, their interactions and dynamics. With over 470 nucleosome containing structures in the Protein Data Bank there is a wealth of information to be gleaned from these structures, especially through comparative analysis. However, due to the variability in their representation (chain naming, residue numbering, other artifacts), these structures cannot be systematically analyzed “as is”. To address this issue, we developed a framework for analyzing and classifying nucleosome structures and their complexes, resulting in the creation of the NucleosomeDB database and the corresponding web-service. NucleosomeDB allows researchers to search, explore, and compare nucleosomes with each other, despite differences in composition and peculiarities of their representation. By utilizing the information contained within the NucleosomeDB, researchers can gain valuable insights into how nucleosomes interact with DNA and other proteins, assess the implications of mutations and protein binding on nucleosome structure. The detailed information contained within NucleosomeDB can contribute to a better understanding of the structure and function of nucleosomes, and ultimately, the functioning of chromatin and gene regulation. NucleosmeDB is freely available athttps://nucldb.intbio.org.
Identifying variants associated with dwarfism via long read sequencing of theDdw1locus in winter rye
Authors: Haardt Rowena C. , Schmiedchen Brigitta , Gordillo-Rodriguez Andres , Eifler Jakob 
Published: April 2023

AbstractDwarfism or semi-dwarfism is an established characteristic in the European cereal market, for example semi-dwarf barley and wheat are commonplace. However, dwarf winter rye is still atypical commercially and fundamental research into the underlying genes influencing plant height is still in its relative infancy. In this study, association between two independent dwarf donors are established asDdw1carriers and variants within theDdw1locus are identified using long read sequencing. Here over 20,000 variants are identified as having putative association with the dwarf phenotype by using twoDdw1genotypes and four representative (non-dwarf) elite lines for exclusion. Consequently, the sequence data presented here provides rye breeders and researchers a resource to develop KASP markers to track the allelic status ofDdw1and to select for dwarf material.
A single-dose of intranasal vaccination with a live-attenuated SARS-CoV-2 vaccine candidate promotes protective mucosal and systemic immunity
Authors: Adam Awadalkareem , Kalveram Birte , Chen John Yun-Chung , Yeung Jason , Rodriguez Leslie , Singh Ankita , Shi Pei-Yong , Xie Xuping , Wang Tian 
Published: April 2023

SummaryAn attenuated SARS-CoV-2 virus with modified viral transcriptional regulatory sequences and deletion of open-reading frames 3, 6, 7 and 8 (∆3678) was previously reported to protect hamsters from SARS-CoV-2 infection and transmission. Here we report that a single-dose intranasal vaccination of ∆3678 protects K18-hACE2 mice from wild-type or variant SARS-CoV-2 challenge. Compared with wild-type virus infection, the ∆3678 vaccination induces equivalent or higher levels of lung and systemic T cell, B cell, IgA, and IgG responses. The results suggest ∆3678 as an attractive mucosal vaccine candidate to boost pulmonary immunity against SARS-CoV-2.
Transcriptome Complexity Disentangled: A Regulatory Molecules Approach
Authors: Asiaee Amir , Abrams Zachary B. , Pua Heather H. , Coombes Kevin R. 
Published: April 2023

AbstractTranscription factors (TFs) and microRNAs (miR-NAs) are fundamental regulators of gene expression, cell state, and biological processes. This study investigated whether a small subset of TFs and miRNAs could accurately predict genome-wide gene expression. We analyzed 8895 samples across 31 cancer types from The Cancer Genome Atlas and identified 28 miRNA and 28 TF clusters using unsupervised learning. Medoids of these clusters could differentiate tissues of origin with 92.8% accuracy, demonstrating their biological relevance. We developed Tissue-Agnostic and Tissue-Aware models to predict 20,000 gene expressions using the 56 selected medoid miR-NAs and TFs. The Tissue-Aware model attained anR2of 0.70 by incorporating tissue-specific information. Despite measuring only 1/400th of the transcriptome, the prediction accuracy was comparable to that achieved by the 1000 landmark genes. This suggests the transcriptome has an intrinsically low-dimensional structure that can be captured by a few regulatory molecules. Our approach could enable cheaper transcriptome assays and analysis of low-quality samples. It also provides insights into genes that are heavily regulated by miRNAs/TFs versus alternative mechanisms. However, model transportability was impacted by dataset discrepancies, especially in miRNA distribution. Overall, this study demonstrates the potential of a biology-guided approach for robust transcriptome representation.
Cysteine tRNA acts as a stop codon readthrough-inducing rti-tRNA in the human HEK293T cell line
Authors: Valášek Leoš Shivaya , Kučerová Michaela , Zeman Jakub , Beznosková Petra 
Published: April 2023

ABSTRACTUnder certain circumstances, any of the three termination codons can be read through by its near-cognate tRNA; i.e. a tRNA whose two out of three anticodon nucleotides base-pair with those of the stop codon. Unless programmed to synthetize C-terminally extended protein variants with expanded physiological roles, readthrough represents an undesirable translational error. On the other side of a coin, a significant number of human genetic diseases is associated with the introduction of nonsense mutations (premature termination codons - PTCs) into coding sequences, where stopping is not desirable. Here, the tRNA’s ability to induce readthrough opens up the intriguing possibility of mitigating the deleterious effects of PTCs on human health. In yeast, the UGA and UAR stop codons were described to be read through by four readthrough-inducing rti-tRNAs – tRNATrpand tRNACys, and tRNATyrand tRNAGln, respectively. The readthrough-inducing potential of tRNATrpand tRNATyrwas also observed in human cell lines. Here, we investigated the readthrough-inducing potential of human tRNACysin the HEK293T cell line. The tRNACysfamily consists of two isoacceptors, one with ACA and the other with GCA anticodons. We selected nine representative tRNACysisodecoders (differing in primary sequence and expression level) and tested them using dual luciferase reporter assays. We found that at least two tRNACyscan significantly elevate UGA readthrough when overexpressed. This indicates a mechanistically conserved nature of rti-tRNAs between yeast and human, supporting the idea that they could be utilized in the PTC-associated RNA therapies.
Separating phases of allopolyploid evolution with resynthesized and naturalCapsella bursa-pastoris
Authors: Duan Tianlin , Sicard Adrien , Glémin Sylvain , Lascoux Martin 
Published: April 2023

SummaryAllopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Telling apart the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesizedCapsellaallotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression level dominance, transgressive expression, and homoeolog expression bias.We found that selfing syndrome, high pollen and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, transgressive expression and most down-regulated expression-level dominance were only found in natural allopolyploids. Natural allotetraploids also had more expression-level dominance toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of expression-level dominance in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of homoeolog expression bias among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids.In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.
Do people with disabilities experience disparities in cancer care? A systematic review
Authors: Tosetti Irene , Kuper Hannah 
Published: April 2023

AbstractBackgroundOver 1.3 billion people, or 16% of the world’s population, live with some form of disability. Recent studies have reported that people with disabilities (PwD) might not be receiving state-of-the-art treatment for cancer as their non-disabled peers; our objective was to systematically review this topic.MethodsA systematic review was undertaken to compare cancer outcomes and quality of cancer care between adults with and without disabilities (NIHR Prospero register ID number: CRD42022281506). A search of the literature was performed in July 2022 across five databases: EMBASE, Medline, Cochrane Library, Web of Science and CINAHL databases. Peer-reviewed quantitative research articles, published in English from 2000 to 2022, with interventional or observational study designs, comparing cancer outcomes between a sample of adult patients with disabilities and a sample without disabilities were included. Studies focused on cancer screening and not treatment were excluded, as well as editorials, commentaries, opinion papers, reviews, case reports, case series under 10 patients and conference abstracts Studies were evaluated by one reviewer for risk of bias based on a set of criteria according to the SIGN 50 guidelines. A narrative synthesis was conducted according to the Cochrane SWiM guidelines, with tables summarizing study characteristics and outcomes. This research received no external funding.ResultsThirty-one studies were included in the systematic review. Compared to people without disabilities, PwD had worse cancer outcomes, in terms of poorer survival and higher overall and cancer-specific mortality. There was also evidence that PwD received poorer quality cancer care, including: lower access to state-of-the-art care or curative-intent therapies, treatment delays, undertreatment or excessively invasive treatment, worse access to in-hospital services, less specialist healthcare utilization, less access to pain medications and inadequate end-of-life quality of care.DiscussionLimitations of this work include the exclusion of qualitative research, no assessment of publication bias, selection performed by only one reviewer, results from high-income countries only, no meta-analysis and a high risk of bias in 15% of included studies. In spite of these limitations, our results show that PwD often experience severe disparities in cancer care with less guideline-consistent care and higher mortality than people without disabilities. These findings raise urgent questions about how to ensure equitable care for PwD; in order to prevent avoidable morbidity and mortality, cancer care programs need to be evaluated and urgently improved, with specific training of clinical staff, more disability inclusive research, better communication and shared decision-making with patients and elimination of physical, social and cultural barriers.
Faithful AI in Medicine: A Systematic Review with Large Language Models and Beyond
Authors: Xie Qianqian , Schenck Edward J. , Yang He S. , Chen Yong , Peng Yifan , Wang Fei 
Published: April 2023

ABSTRACTArtificial intelligence (AI), especially the most recent large language models (LLMs), holds great promise in healthcare and medicine, with applications spanning from biological scientific discovery and clinical patient care to public health policymaking. However, AI methods have the critical concern for generating factually incorrect or unfaithful information, posing potential long-term risks, ethical issues, and other serious consequences. This review aims to provide a comprehensive overview of the faithfulness problem in existing research on AI in healthcare and medicine, with a focus on the analysis of the causes of unfaithful results, evaluation metrics, and mitigation methods. We systematically reviewed the recent progress in optimizing the factuality across various generative medical AI methods, including knowledge-grounded LLMs, text-to-text generation, multimodality-to-text generation, and automatic medical fact-checking tasks. We further discussed the challenges and opportunities of ensuring the faithfulness of AI-generated information in these applications. We expect that this review will assist researchers and practitioners in understanding the faithfulness problem in AI-generated information in healthcare and medicine, as well as the recent progress and challenges in related research. Our review can also serve as a guide for researchers and practitioners who are interested in applying AI in medicine and healthcare.