bluuebunny/crossref_metadata_2025_split huggingface dataset:
rworkflows: automating reproducible practices for the R community
Authors: Schilder Brian M. , Murphy Alan E. , Skene Nathan G. 
Published: January 2024

AbstractDespite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have any default built-in checks for minimal coding standards or software usability. This makes it difficult to assess the current quality R packages, or to consistently use them over time and across platforms. While GitHub-native solutions are technically possible, they require considerable time and expertise for each developer to write, implement, and maintain. To address this, we developrworkflows; a suite of tools to make robust continuous integration and deployment (https://github.com/neurogenomics/rworkflows).rworkflowscan be implemented by developers of all skill levels using a one-time R function call which has both sensible defaults and extensive options for customisation. Once implemented, any updates to the GitHub repository automatically trigger parallel workflows that install all software dependencies, run code checks, generate a dedicated documentation website, and deploy a publicly accessible containerised environment. By making therworkflowssuite free, automated, and simple to use, we aim to promote widespread adoption of reproducible practices across a continually growing R community.
Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean
Authors: Deutschmann Ina M. , Delage Erwan , Giner Caterina R. , Sebastián Marta , Poulain Julie , Arístegui Javier , Duarte Carlos M. , Acinas Silvia G. , Massana Ramon , Gasol Josep M. , Eveillard Damien , Chaffron Samuel , Logares Ramiro 
Published: January 2024

AbstractMicrobial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.
A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing
Authors: Feng Ming , Zhang Ai , Nguyen Van , Bisht Anchal , Almqvist Curt , De Veylder Lieven , Carlsbecker Annelie , Melnyk Charles W. 
Published: January 2024

AbstractThe widespread use of plant grafting enables eudicots and gymnosperms to join with closely related species and grow as one. Gymnosperms have dominated forests for over 200 million years, and despite their economic and ecological relevance, we know little about how they graft. Here we developed a micrografting method in conifers using young tissues that allowed efficient grafting with closely related species and between distantly related genera. Conifer graft junctions rapidly connected vasculature and differentially expressed thousands of genes including auxin and cell-wall-related genes. By comparing these genes to those induced during Arabidopsis thaliana graft formation, we found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis in Norway spruce (Picea abies) predicted that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a core regulator of graft healing. This gene was strongly up-regulated during both spruce and Arabidopsis grafting, and Arabidopsis mutants lacking PAT genes failed to attach tissues or successfully graft. Complementing Arabidopsis PAT mutants with the spruce PAT1 homolog rescued tissue attachment and enhanced callus formation. Together, our data show an ability for young tissues to graft with distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration.
Absolute quantification of nicotinamide mononucleotide in biological samples by double isotope-mediated liquid chromatography-tandem mass spectrometry (dimeLC-MS/MS)
Authors: Unno Junya , Mills Kathryn F. , Ogura Tairo , Nishimura Masayuki , Imai Shin-ichiro 
Published: January 2024

AbstractNicotinamide adenine dinucleotide (NAD+) is an essential metabolite for fundamental biological phenomena, including aging. Nicotinamide mononucleotide (NMN) is a key NAD+ intermediate that has been extensively tested as an effective NAD+-boosting compound in mice and humans. However, the accurate measurement of NMN in biological samples has long been a challenge in the field. Here, we have established an accurate, quantitative methodology for measuring NMN by using liquid chromatography-triple quadrupole mass spectrometry (LC-MS/MS) with double isotopic NMN standards. In this new methodology, the matrix effects of biological samples were properly adjusted, and the fate of NMN could be traced during sample processing. We have demonstrated that this methodology can accurately quantitate NMN levels in mouse plasma and confirmed quick, direct NMN uptake into blood circulation and cells. This double isotope-mediated LC-MS/MS (dimeLC-MS/MS) can easily be expanded to other NAD+-related metabolites as a reliable standard methodology for NAD+ biology.
Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer
Authors: Guerriero Jennifer L. , Lin Jia-Ren , Pastorello Ricardo G. , Du Ziming , Chen Yu-An , Townsend Madeline G. , Shimada Kenichi , Hughes Melissa E. , Ren Siyang , Tayob Nabihah , Zheng Kelly , Mei Shaolin , Patterson Alyssa , Taneja Krishan L. , Metzger Otto , Tolaney Sara M. , Lin Nancy U. , Dillon Deborah A. , Schnitt Stuart J. , Sorger Peter K. , Mittendorf Elizabeth A. , Santagata Sandro 
Published: January 2024

AbstractEmerging data suggests that HER2 intratumoral heterogeneity (ITH) is associated with therapy resistance, highlighting the need for new strategies to assess HER2 ITH. A promising approach is leveraging multiplexed tissue analysis techniques such as cyclic immunofluorescence (CyCIF), which enable visualization and quantification of 10–60 antigens at single-cell resolution from individual tissue sections. In this study, we qualified a breast cancer-specific antibody panel, including HER2, ER, and PR, for multiplexed tissue imaging. We then compared the performance of these antibodies against established clinical standards using pixel-, cell- and tissue-level analyses, utilizing 866 tissue cores (representing 294 patients). To ensure reliability, the CyCIF antibodies were qualified against HER2 immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) data from the same samples. Our findings demonstrate the successful qualification of a breast cancer antibody panel for CyCIF, showing high concordance with established clinical antibodies. Subsequently, we employed the qualified antibodies, along with antibodies for CD45, CD68, PD-L1, p53, Ki67, pRB, and AR, to characterize 567 HER2+ invasive breast cancer samples from 189 patients. Through single-cell analysis, we identified four distinct cell clusters within HER2+ breast cancer exhibiting heterogeneous HER2 expression. Furthermore, these clusters displayed variations in ER, PR, p53, AR, and PD-L1 expression. To quantify the extent of heterogeneity, we calculated heterogeneity scores based on the diversity among these clusters. Our analysis revealed expression patterns that are relevant to breast cancer biology, with correlations to HER2 ITH and potential relevance to clinical outcomes.
cGAS-STING pathway expression correlates with genomic instability and immune cell infiltration in breast cancer
Authors: Chen Mengting , Yu Shibo , van der Sluis Tineke , Zwager Mieke C. , Schröder Carolien P. , van der Vegt Bert , van Vugt Marcel A. T. M. 
Published: January 2024

AbstractGenomic instability, as caused by oncogene-induced replication stress, can lead to the activation of inflammatory signaling, involving the cGAS-STING and JAK-STAT pathways. Inflammatory signaling has been associated with pro-tumorigenic features, but also with favorable response to treatment, including to immune checkpoint inhibition. In this study, we aim to explore relations between inflammatory signaling, markers of replication stress, and immune cell infiltration in breast cancer. Expression levels of cGAS-STING signaling components (STING, phospho-TBK1, and phospho-STAT1), replication stress markers (γH2AX and pRPA), replication stress-related proto-oncogenes (Cyclin E1 and c-Myc) and immune cell markers (CD20, CD4, and CD57) are determined immunohistochemically on primary breast cancer samples (n = 380). RNA-sequencing data from TCGA (n = 1082) and METABRIC (n = 1904) are used to calculate cGAS-STING scores. pTBK1, pSTAT1 expression and cGAS-STING pathway scores are all increased in triple-negative breast cancers compared to other subtypes. Expression of γH2AX, pRPA, Cyclin E1, c-Myc, and immune cell infiltration positively correlate with p-STAT1 expression (P < 0.001). Additionally, we observe significant positive associations between expression of pTBK1 and γH2AX, pRPA, c-Myc, and number of CD4+ cells and CD20+ cells. Also, cGAS-STING scores are correlated with genomic instability metrics, such as homologous recombination deficiency (P < 0.001) and tumor mutational burden (P < 0.01). Moreover, data from the I-SPY2 clinical trial (n = 71) confirms that higher cGAS-STING scores are observed in breast cancer patients who responded to immunotherapy combined with chemotherapy. In conclusion, the cGAS-STING pathway is highly expressed in TNBCs and is correlated with genomic instability and immune cell infiltration.
Linking acetylated α-Tubulin redistribution to α-Synuclein pathology in brain of Parkinson’s disease patients
Authors: Mazzetti Samanta , Giampietro Federica , Calogero Alessandra Maria , Isilgan Huseyin Berkcan , Gagliardi Gloria , Rolando Chiara , Cantele Francesca , Ascagni Miriam , Bramerio Manuela , Giaccone Giorgio , Isaias Ioannis Ugo , Pezzoli Gianni , Cappelletti Graziella 
Published: January 2024

AbstractHighly specialized microtubules in neurons are crucial to both health and disease of the nervous system, and their properties are strictly regulated by different post-translational modifications, including α-Tubulin acetylation. An imbalance in the levels of acetylated α-Tubulin has been reported in experimental models of Parkinson’s disease (PD) whereas pharmacological or genetic modulation that leads to increased acetylated α-Tubulin successfully rescues axonal transport defects and inhibits α-Synuclein aggregation. However, the role of acetylation of α-Tubulin in the human nervous system is largely unknown as most studies are based on in vitro evidence. To capture the complexity of the pathological processes in vivo, we analysedpost-mortemhuman brain of PD patients and control subjects. In the brain of PD patients at Braak stage 6, we found a redistribution of acetylated α-Tubulin, which accumulates in the neuronal cell bodies in subcortical structures but not in the cerebral cortex, and decreases in the axonal compartment, both in putamen bundles of fibres and in sudomotor fibres. High-resolution and 3D reconstruction analysis linked acetylated α-Tubulin redistribution to α-Synuclein oligomerization and to phosphorylated Ser 129 α-Synuclein, leading us to propose a model for Lewy body (LB) formation. Finally, inpost-mortemhuman brain, we observed threadlike structures, resembling tunnelling nanotubes that contain α-Synuclein oligomers and are associated with acetylated α-Tubulin enriched neurons. In conclusion, we support the role of acetylated α-Tubulin in PD pathogenesis and LB formation.
Quantum key distribution using deterministic single-photon sources over a field-installed fibre link
Authors: Zahidy Mujtaba , Mikkelsen Mikkel T. , Müller Ronny , Da Lio Beatrice , Krehbiel Martin , Wang Ying , Bart Nikolai , Wieck Andreas D. , Ludwig Arne , Galili Michael , Forchhammer Søren , Lodahl Peter , Oxenløwe Leif K. , Bacco Davide , Midolo Leonardo 
Published: January 2024

AbstractQuantum-dot-based single-photon sources are key assets for quantum information technology, supplying on-demand scalable quantum resources for computing and communication. However, long-lasting issues such as limited long-term stability and source brightness have traditionally impeded their adoption in real-world applications. Here, we realize a quantum key distribution field trial using true single photons across an 18-km-long dark fibre, located in the Copenhagen metropolitan area, using an optimized, state-of-the-art, quantum-dot single-photon source frequency-converted to the telecom wavelength. A secret key generation rate of > 2 kbits/s realized over a 9.6 dB channel loss is achieved with a polarization-encoded BB84 scheme, showing remarkable stability for more than 24 hours of continuous operation. Our results highlight the maturity of deterministic single-photon source technology while paving the way for advanced single-photon-based communication protocols, including fully device-independent quantum key distribution, towards the goal of a quantum internet.
Myeloid cell-associated aromatic amino acid metabolism facilitates CNS myelin regeneration
Authors: Hu Jingwen , Melchor George S. , Ladakis Dimitrios , Reger Joan , Kim Hee Won , Chamberlain Kelly A. , Shults Nataliia V. , Oft Helena C. , Smith Victoria N. , Rosko Lauren M. , Li Erqiu , Baydyuk Maryna , Fu Meng-Meng , Bhargava Pavan , Huang Jeffrey K. 
Published: January 2024

AbstractRegulation of myeloid cell activity is critical for successful myelin regeneration (remyelination) in demyelinating diseases, such as multiple sclerosis (MS). Here, we show aromatic alpha-keto acids (AKAs) generated from the amino acid oxidase, interleukin-4 induced 1 (IL4I1), promote efficient remyelination in mouse models of MS. During remyelination, myeloid cells upregulated the expression of IL4I1. Conditionally knocking out IL4I1 in myeloid cells impaired remyelination efficiency. Mice lacking IL4I1 expression exhibited a reduction in the AKAs, phenylpyruvate, indole-3-pyruvate, and 4-hydroxyphenylpyruvate, in remyelinating lesions. Decreased AKA levels were also observed in people with MS, particularly in the progressive phase when remyelination is impaired. Oral administration of AKAs modulated myeloid cell-associated inflammation, promoted oligodendrocyte maturation, and enhanced remyelination in mice with focal demyelinated lesions. Transcriptomic analysis revealed AKA treatment induced a shift in metabolic pathways in myeloid cells and upregulated aryl hydrocarbon receptor activity in lesions. Our results suggest myeloid cell-associated aromatic amino acid metabolism via IL4I1 produces AKAs in demyelinated lesions to enable efficient remyelination. Increasing AKA levels or targeting related pathways may serve as a strategy to facilitate the regeneration of myelin in inflammatory demyelinating conditions.
Immunogenicity and reactogenicity of intradermal mRNA-1273 SARS-CoV-2 vaccination: a non-inferiority, randomized-controlled trial
Authors: Prins Manon L. M. , Roozen Geert V. T. , Pothast Cilia. R. , Huisman Wesley , van Binnendijk Rob , den Hartog Gerco , Kuiper Vincent P. , Prins Corine , Janse Jacqueline J. , Lamers Olivia. A. C. , Koopman Jan Pieter R. , Kruithof Annelieke C. , Kamerling Ingrid M. C. , Dijkland Romy C. , de Kroon Alicia. C. , Azimi Shohreh , Feltkamp Mariet C. W. , Kuijer Marjan , Jochems Simon P. , Heemskerk Mirjam H. M. , Rosendaal Frits R. , Roestenberg Meta , Visser Leo G. , Roukens Anna H. E. 
Published: January 2024

AbstractFractional dosing can be a cost-effective vaccination strategy to accelerate individual and herd immunity in a pandemic. We assessed the immunogenicity and safety of primary intradermal (ID) vaccination, with a 1/5th dose compared with the standard intramuscular (IM) dose of mRNA-1273 in SARS-CoV-2 naïve persons. We conducted an open-label, non-inferiority, randomized controlled trial in the Netherlands between June and December 2021. One hundred and fifty healthy and SARS-CoV-2 naïve participants, aged 18–30 years, were randomized (1:1:1) to receive either two doses of 20 µg mRNA-1273 ID with a standard needle (SN) or the Bella-mu® needle (BM), or two doses of 100 µg IM, 28 days apart. The primary outcome was non-inferiority in seroconversion rates at day 43 (D43), defined as a neutralizing antibody concentration threshold of 465 IU/mL, the lowest response in the IM group. The non-inferiority margin was set at −15%. Neutralizing antibody concentrations at D43 were 1789 (95% CI: 1488–2150) in the IM and 1263 (951–1676) and 1295 (1020–1645) in the ID-SN and ID-BM groups, respectively. The absolute difference in seroconversion proportion between fractional and standard-dose groups was −13.95% (−24.31 to −3.60) for the ID-SN and −13.04% (−22.78 to −3.31) for the ID-BM group and exceeded the predefined non-inferiority margin. Although ID vaccination with 1/5th dose of mRNA-1273 did not meet the predefined non-inferior criteria, the neutralizing antibody concentrations in these groups are far above the proposed proxy for protection against severe disease (100 IU/mL), justifying this strategy in times of vaccine scarcity to accelerate mass protection against severe disease.
A quest for universal anti-SARS-CoV-2 T cell assay: systematic review, meta-analysis, and experimental validation
Authors: Binayke Akshay , Zaheer Aymaan , Vishwakarma Siddhesh , Singh Savita , Sharma Priyanka , Chandwaskar Rucha , Gosain Mudita , Raghavan Sreevatsan , Murugesan Deepika Rathna , Kshetrapal Pallavi , Thiruvengadam Ramachandran , Bhatnagar Shinjini , Pandey Anil Kumar , Garg Pramod Kumar , Awasthi Amit 
Published: January 2024

AbstractMeasuring SARS-CoV-2-specific T cell responses is crucial to understanding an individual’s immunity to COVID-19. However, high inter- and intra-assay variability make it difficult to define T cells as a correlate of protection against COVID-19. To address this, we performed systematic review and meta-analysis of 495 datasets from 94 original articles evaluating SARS-CoV-2-specific T cell responses using three assays – Activation Induced Marker (AIM), Intracellular Cytokine Staining (ICS), and Enzyme-Linked Immunospot (ELISPOT), and defined each assay’s quantitative range. We validated these ranges using samples from 193 SARS-CoV-2-exposed individuals. Although IFNγ ELISPOT was the preferred assay, our experimental validation suggested that it under-represented the SARS-CoV-2-specific T cell repertoire. Our data indicate that a combination of AIM and ICS or FluoroSpot assay would better represent the frequency, polyfunctionality, and compartmentalization of the antigen-specific T cell responses. Taken together, our results contribute to defining the ranges of antigen-specific T cell assays and propose a choice of assay that can be employed to better understand the cellular immune response against viral diseases.
An mRNA vaccine encoding the SARS-CoV-2 receptor-binding domain protects mice from various Omicron variants
Authors: Uraki Ryuta , Imai Masaki , Ito Mutsumi , Yamayoshi Seiya , Kiso Maki , Jounai Nao , Miyaji Kazuki , Iwatsuki-Horimoto Kiyoko , Takeshita Fumihiko , Kawaoka Yoshihiro 
Published: January 2024

AbstractHere, we assessed the efficacy of a lipid nanoparticle-based mRNA vaccine candidate encoding the receptor-binding domain (LNP-mRNA-RBD) in mice. Mice immunized with LNP-mRNA-RBD based on the ancestral strain (ancestral-type LNP-mRNA-RBD) showed similar cellular responses against the ancestral strain and BA.5, but their neutralizing activity against BA.5 was lower than that against the ancestral strain. The ancestral-type LNP-mRNA-RBD protected mice from the ancestral strain or BA.5 challenge; however, its ability to reduce the viral burdens after BA.5 challenge was limited. In contrast, immunization with bivalent LNP-mRNA-RBD consisting of the ancestral-type and BA.4/5-type LNP-mRNA-RBD or monovalent BA.4/5-type LNP-mRNA-RBD elicited robust cellular responses, as well as high and moderate neutralizing titers against BA.5 and XBB.1.5, respectively. Furthermore, the vaccines containing BA.4/5-type LNP-mRNA-RBD remarkably reduced the viral burdens following BA.5 or XBB.1.5 challenge. Overall, our findings suggest that LNP-mRNA-RBD is effective against SARS-CoV-2 infection.
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion
Authors: Schmok Jonathan C. , Jain Manya , Street Lena A. , Tankka Alex T. , Schafer Danielle , Her Hsuan-Lin , Elmsaouri Sara , Gosztyla Maya L. , Boyle Evan A. , Jagannatha Pratibha , Luo En-Ching , Kwon Ester J. , Jovanovic Marko , Yeo Gene W. 
Published: January 2024

AbstractRNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification–mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.