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1. Rayleigh-Plateau Instability on an angled and eccentric fiber: An alternative approach

Author

Maity, Dilip Kumar, Wagstaff, Christopher, Dighe, Sandip, and Truscott, Tadd

Subjects
Physics - Fluid Dynamics
Abstract

This research explores the modulation of Rayleigh-Plateau Instability (RPI) by adjusting the orientation angle and eccentricity of a wire within a nozzle. We demonstrate that both the angle and eccentricity significantly influence the RPI regimes. They both also influence characteristics, such as velocity, wavelength, and droplet volume. Notably, when wires are both angled and eccentric, the effect of angle prevails. Our approach includes an empirical scaling analysis, comparing gravity, surface tension, and viscosity forces on a single bead, yielding a unified empirical viscous force law, enhancing understanding of RP regime dynamics. This new framework enriches our understanding of the forces at play in RPI and provides practical insights into the manipulation of fluid dynamics in industrial applications.

Published
2024

2. Generalizing to any diverse distribution: uniformity, gentle finetuning and rebalancing

Author

Loukas, Andreas, Martinkus, Karolis, Wagstaff, Ed, and Cho, Kyunghyun

Subjects
Computer Science - Machine Learning
Abstract

As training datasets grow larger, we aspire to develop models that generalize well to any diverse test distribution, even if the latter deviates significantly from the training data. Various approaches like domain adaptation, domain generalization, and robust optimization attempt to address the out-of-distribution challenge by posing assumptions about the relation between training and test distribution. Differently, we adopt a more conservative perspective by accounting for the worst-case error across all sufficiently diverse test distributions within a known domain. Our first finding is that training on a uniform distribution over this domain is optimal. We also interrogate practical remedies when uniform samples are unavailable by considering methods for mitigating non-uniformity through finetuning and rebalancing. Our theory provides a mathematical grounding for previous observations on the role of entropy and rebalancing for o.o.d. generalization and foundation model training. We also provide new empirical evidence across tasks involving o.o.d. shifts which illustrate the broad applicability of our perspective.

Published
2024

3. Minimal Free Resolutions of Edge Ideals of Edge-Weighted Complete Bipartite Graphs

Author

Kubik, Bethany, Tracy, Denise Rangel, and Sather-Wagstaff, Keri Ann

Subjects
Mathematics - Commutative Algebra
Abstract

We explicitly describe cellular minimal free resolutions of certain classes of edge ideals of weighted complete bipartite graphs based on a construction of Visscher. Specifically, we show that Visscher's construction minimally resolves all edge ideals of undirected vertex-weighted complete bipartite graphs, and we characterize the edge-weighted complete bipartite graphs whose edge ideals are minimally resolved by Visscher's construction.

Published
2024

4. Mapping taste and flavour traits to genetic markers in lettuce Lactuca sativa.

Author

Chadwick, Martin, Swann, Jonathan, Gawthrop, Frances, Michelmore, Richard, Scaglione, Davide, Jose-Truco, Maria, and Wagstaff, Carol

Subjects
Breeding, Flavour, Lactuca sativa, NMR, Quantitative trait loci, Sesquiterpene
Abstract

Lettuce is the most highly consumed raw leafy vegetable crop eaten worldwide, making it nutritionally important in spite of its comparatively low nutrient density in relation to other vegetables. However, the perception of bitterness caused by high levels of sesquiterpenoid lactones and comparatively low levels of sweet tasting sugars limits palatability. To assess variation in nutritional and taste-related metabolites we assessed 104 members of a Lactuca sativa cv. Salinas x L. serriola (accession UC96US23) mapping population. Plants were grown in three distinct environments, and untargeted NMR and HPLC were used as a rapid chemotyping method, from which 63 unique Quantitative Trait Loci (QTL) were identified. We were able to identify putative regulatory candidate genes underlying the QTL for fructose on linkage group 9, which accounted for up to 36 % of our population variation, and which was stable across all three growing environments; and for 15-p-hydroxyyphenylacetyllactucin-8-sulfate on linkage group 5 which has previously been identified for its low bitterness, while retaining anti-herbivory field effects. We also identified a candidate gene for flavonoid 3,5- hydroxylase underlying a polyphenol QTL on linkage group 5, and two further candidate genes in sugar biosynthesis on linkage groups 2 and 5. Collectively these candidate genes and their associated markers can inform a route for plant breeders to improve the palatability and nutritional value of lettuce in their breeding programmes.

Published
2024

5. Evaluating Terrain-Dependent Performance for Martian Frost Detection in Visible Satellite Observations

Author

Doran, Gary, Diniega, Serina, Lu, Steven, Wronkiewicz, Mark, and Wagstaff, Kiri L.

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Seasonal frosting and defrosting on the surface of Mars is hypothesized to drive both climate processes and the formation and evolution of geomorphological features such as gullies. Past studies have focused on manually analyzing the behavior of the frost cycle in the northern mid-latitude region of Mars using high-resolution visible observations from orbit. Extending these studies globally requires automating the detection of frost using data science techniques such as convolutional neural networks. However, visible indications of frost presence can vary significantly depending on the geologic context on which the frost is superimposed. In this study, we (1) present a novel approach for spatially partitioning data to reduce biases in model performance estimation, (2) illustrate how geologic context affects automated frost detection, and (3) propose mitigations to observed biases in automated frost detection., Comment: This is the author's version of the work. It is posted here for your personal use. Not for redistribution. The definitive Version of Record was published in: SIGKDD DeepSpatial '22, August 15, 2022, Washington, DC

Published
2024

6. Diverse RNA viruses of parasitic nematodes can elicit antibody responses in vertebrate hosts

Author

Quek, Shannon, Hadermann, Amber, Wu, Yang, De Coninck, Lander, Hegde, Shrilakshmi, Boucher, Jordan R., Cresswell, Jessica, Foreman, Ella, Steven, Andrew, LaCourse, E. James, Ward, Stephen A., Wanji, Samuel, Hughes, Grant L., Patterson, Edward I., Wagstaff, Simon C., Turner, Joseph D., Parry, Rhys H., Kohl, Alain, Heinz, Eva, Otabil, Kenneth Bentum, Matthijnssens, Jelle, Colebunders, Robert, and Taylor, Mark J.

Published
2024
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8. Interactive Mars Image Content-Based Search with Interpretable Machine Learning

Author

Vasu, Bhavan, Lu, Steven, Dunkel, Emily, Wagstaff, Kiri L., Grimes, Kevin, and McAuley, Michael

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Information Retrieval
Abstract

The NASA Planetary Data System (PDS) hosts millions of images of planets, moons, and other bodies collected throughout many missions. The ever-expanding nature of data and user engagement demands an interpretable content classification system to support scientific discovery and individual curiosity. In this paper, we leverage a prototype-based architecture to enable users to understand and validate the evidence used by a classifier trained on images from the Mars Science Laboratory (MSL) Curiosity rover mission. In addition to providing explanations, we investigate the diversity and correctness of evidence used by the content-based classifier. The work presented in this paper will be deployed on the PDS Image Atlas, replacing its non-interpretable counterpart., Comment: 7 pages, 6 figures

Published
2024

9. Micrococcin cysteine-to-thiazole conversion through transient interactions between the scaffolding protein TclI and the modification enzymes TclJ and TclN.

Author

Calvopina-Chavez, Diana G, Bursey, Devan M, Tseng, Yi-Jie, Patil, Leena M, Bewley, Kathryn D, Bennallack, Philip R, McPhie, Josh M, Wagstaff, Kimberly B, Daley, Anisha, Miller, Susan M, Moody, James D, Price, John C, and Griffitts, Joel S

Subjects
Biochemistry and Cell Biology, Biological Sciences, Antimicrobial Resistance, Emerging Infectious Diseases, Infectious Diseases, Infection, thiazole, thiopeptide, post-translationally modified peptides, Microbiology, Medical microbiology
Abstract

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a broad group of compounds mediating microbial competition in nature. Azole/azoline heterocycle formation in the peptide backbone is a key step in the biosynthesis of many RiPPs. Heterocycle formation in RiPP precursors is often carried out by a scaffold protein, an ATP-dependent cyclodehydratase, and an FMN-dependent dehydrogenase. It has generally been assumed that the orchestration of these modifications is carried out by a stable complex including the scaffold, cyclodehydratase, and dehydrogenase. The antimicrobial RiPP micrococcin begins as a precursor peptide (TclE) with a 35-amino acid N-terminal leader and a 14-amino acid C-terminal core containing six Cys residues that are converted to thiazoles. The putative scaffold protein (TclI) presumably presents the TclE substrate to a cyclodehydratase (TclJ) and a dehydrogenase (TclN) to accomplish the two-step installation of the six thiazoles. In this study, we identify a minimal TclE leader region required for thiazole formation, demonstrate complex formation between TclI, TclJ, and TclN, and further define regions of these proteins required for complex formation. Our results point to a mechanism of thiazole installation in which TclI associates with the two enzymes in a mutually exclusive fashion, such that each enzyme competes for access to the peptide substrate in a dynamic equilibrium, thus ensuring complete modification of each Cys residue in the TclE core.ImportanceThiopeptides are a family of antimicrobial peptides characterized for having sulfur-containing heterocycles and for being highly post-translationally modified. Numerous thiopeptides have been identified; almost all of which inhibit protein synthesis in gram-positive bacteria. These intrinsic antimicrobial properties make thiopeptides promising candidates for the development of new antibiotics. The thiopeptide micrococcin is synthesized by the ribosome and undergoes several post-translational modifications to acquire its bioactivity. In this study, we identify key interactions within the enzymatic complex that carries out cysteine to thiazole conversion in the biosynthesis of micrococcin.

Published
2024

15. CRISPR-edited human ES-derived oligodendrocyte progenitor cells improve remyelination in rodents

Author

Laura J. Wagstaff, Nadine Bestard-Cuche, Maja Kaczmarek, Antonella Fidanza, Lorraine McNeil, Robin J. M. Franklin, and Anna C. Williams

Subjects
Science
Abstract

Abstract In Multiple Sclerosis (MS), inflammatory demyelinated lesions in the brain and spinal cord lead to neurodegeneration and progressive disability. Remyelination can restore fast saltatory conduction and neuroprotection but is inefficient in MS especially with increasing age, and is not yet treatable with therapies. Intrinsic and extrinsic inhibition of oligodendrocyte progenitor cell (OPC) function contributes to remyelination failure, and we hypothesised that the transplantation of ‘improved’ OPCs, genetically edited to overcome these obstacles, could improve remyelination. Here, we edit human(h) embryonic stem cell-derived OPCs to be unresponsive to a chemorepellent released from chronic MS lesions, and transplant them into rodent models of chronic lesions. Edited hOPCs display enhanced migration and remyelination compared to controls, regardless of the host age and length of time post-transplant. We show that genetic manipulation and transplantation of hOPCs overcomes the negative environment inhibiting remyelination, with translational implications for therapeutic strategies for people with progressive MS.

Published
2024
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16. Data-Driven Approaches to Searches for the Technosignatures of Advanced Civilizations

Author

Lazio, T. Joseph W., Djorgovski, S. G., Howard, Andrew, Cutler, Curt, Sheikh, Sofia Z., Cavuoti, Stefano, Herzing, Denise, Wagstaff, Kiri, Wright, Jason T., Gajjar, Vishal, Hand, Kevin, Rebbapragada, Umaa, Allen, Bruce, Cartmill, Erica, Foster, Jacob, Gelino, Dawn, Graham, Matthew J., Longo, Giuseppe, Mahabal, Ashish A., Pachter, Lior, Ravi, Vikram, and Sussman, Gerald

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Physics - Popular Physics
Abstract

Humanity has wondered whether we are alone for millennia. The discovery of life elsewhere in the Universe, particularly intelligent life, would have profound effects, comparable to those of recognizing that the Earth is not the center of the Universe and that humans evolved from previous species. There has been rapid growth in the fields of extrasolar planets and data-driven astronomy. In a relatively short interval, we have seen a change from knowing of no extrasolar planets to now knowing more potentially habitable extrasolar planets than there are planets in the Solar System. In approximately the same interval, astronomy has transitioned to a field in which sky surveys can generate 1 PB or more of data. The Data-Driven Approaches to Searches for the Technosignatures of Advanced Civilizations_ study at the W. M. Keck Institute for Space Studies was intended to revisit searches for evidence of alien technologies in light of these developments. Data-driven searches, being able to process volumes of data much greater than a human could, and in a reproducible manner, can identify *anomalies* that could be clues to the presence of technosignatures. A key outcome of this workshop was that technosignature searches should be conducted in a manner consistent with Freeman Dyson's "First Law of SETI Investigations," namely "every search for alien civilizations should be planned to give interesting results even when no aliens are discovered." This approach to technosignatures is commensurate with NASA's approach to biosignatures in that no single observation or measurement can be taken as providing full certainty for the detection of life. Areas of particular promise identified during the workshop were (*) Data Mining of Large Sky Surveys, (*) All-Sky Survey at Far-Infrared Wavelengths, (*) Surveys with Radio Astronomical Interferometers, and (*) Artifacts in the Solar System., Comment: Final Report prepared for the W. M. Keck Institute for Space Studies (KISS), http://kiss.caltech.edu/workshops/technosignatures/technosignatures.html ; eds. Lazio, Djorgovski, Howard, & Cutler; The study leads gratefully acknowledge the outstanding support of Michele Judd, KISS Executive Director, and her dedicated staff, who made the study experience invigorating and enormously productive

Published
2023
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17. Ring homomorphisms and local rings with quasi-decomposable maximal ideal

Author

Nasseh, Saeed, Sather-Wagstaff, Keri Ann, and Takahashi, Ryo

Subjects
Mathematics - Commutative Algebra, 13D02, 13D05, 13D07, 13H10, 18A30
Abstract

The notion of local rings with quasi-decomposable maximal ideal was formally introduced by Nasseh and Takahashi. In separate works, the authors of the present paper show that such rings have rigid homological properties; for instance, they are both Ext- and Tor-friendly. One point of this paper is to further explore the homological properties of these rings and also introduce new classes of such rings from a combinatorial point of view. Another point is to investigate how far some of these homological properties can be pushed along certain diagrams of local ring homomorphisms., Comment: 21 pages

Published
2023

18. First reports of Beet curly top virus, Citrus yellow vein-associated virus, and Hop latent viroid in industrial hemp (Cannabis sativa) in Washington State.

Author

Jarugula, Sridhar, Wagstaff, Camille, Mitra, Arunabha, Crowder, David W, Gang, David R, and Naidu, Rayapati A

Subjects
Plant Biology, Agricultural, Veterinary and Food Sciences, Biological Sciences, Horticultural Production, Infection, field crops, pathogen detection, viruses and viroids, Causal Agent, Crop Type, Field crops, Pathogen detection, Subject Areas, Viruses and viroids, other, Microbiology, Crop and Pasture Production, Plant Biology & Botany, Crop and pasture production, Plant biology
Abstract

In 2021 and 2022, virus-like symptoms were observed in several cultivars of industrial hemp (Cannabis sativa) in two fields in central Washington, USA. Affected plants had a range of symptoms at different developmental stages, with young plants having severe stunting with shortened internodes and reduced flower mass. Young leaves of infected plants also showed light green to total yellowing, and twirling with twisting margins (Fig. S1). Infections of older plants caused less foliar symptoms that consisted of mosaic, mottling, and mild chlorosis on a few branches with tacoing of older leaves. To assess if symptomatic hemp plants were infected with Beet curly top virus (BCTV) as reported earlier (Giladi et al., 2020; Chiginsky et al., 2021), symptomatic leaves were collected from 38 plants, and the extracted total nucleic acids tested by PCR to amplify a 496-base pair (bp) fragment specific to BCTV coat protein (CP) using primers BCTV2-F 5'-GTGGATCAATTTCCAG-ACAATTATC-3' and BCTV2-R 5'-CCCATAAGAGCCATATCA-AACTTC-3' (Strausbaugh et al. 2008). BCTV was found in 37 of the 38 plants. To further assess the virome of symptomatic hemp plants, total RNA was extracted from symptomatic leaves of four plants using Spectrum total RNA isolation kits (Sigma-Aldrich, St. Louis, MO) and subjected to high-throughput sequencing on an Illumina Novaseq platform in paired-end mode (University of Utah, Salt Lake City, UT). The raw reads (33 to 40 million per sample) were trimmed based on quality and ambiguity and resulting paired-end reads of ≈142 bp length were assembled de novo into a pool of contigs (CLC Genomics Workbench 21, Qiagen Inc.). Virus sequences were identified through BLASTn analysis in GenBank (https://www.ncbi.nlm.nih.gov/blast). One contig of 2,929 nucleotides (nt) obtained from one sample (accession no. OQ068391) showed 99.3% identity with BCTV-Wor strain reported from sugar beet in Idaho (accession no. KX867055 Strausbaugh et al., 2017). Another contig of 1,715 nt from a second sample (accession no. OQ068392) shared 97.3% identity with BCTV-CO strain (accession no. KX867022). Two contig sequences of 2,876 nt (accession no. OQ068388) and 1,399 nt (accession no. OQ068389) obtained from the 3rd and 4th samples showed 97.2% and 98.3% identity, respectively, with Citrus yellow vein-associated virus (CYVaV, accession no. MT893740.1) reported in industrial hemp from Colorado (Chiginsky et al., 2021). Contigs of 256 nt sequence (accession no. OQ068390) obtained from the 3rd and 4th samples also showed 99-100% identity with Hop Latent viroid (HLVd) sequences in GenBank (accessions OK143457 and X07397). These results indicated single infections of BCTV strains and co-infection of CYVaV and HLVd in individual plants. To confirm theagents, symptomatic leaves were collected from 28 randomly selected hemp plants and tested by PCR/RT-PCR using primers specific to BCTV (Strausbaugh et al., 2008), CYVaV (Kwon et al., 2021) and HLVd (Matoušek et al., 2001). Amplicons specific to BCTV (496 bp), CYVaV (658 bp) and HLVd (256 bp) were detected in 28, 25, and 2 samples, respectively. BCTV CP sequences obtained by Sanger sequencing from seven samples showed 100% sequence identity with BCTV-CO and BCTV-Wor strains in six and one samples, respectively. Similarly, sequences of CYVaV- and HLVd-specific amplicons showed 100% identity with corresponding sequences in GenBank. To the best of our knowledge, this is the first report of two strains of BCTV (BCTV-CO and BCTV-Wor), CYVaV, and HLVd infecting industrial hemp in Washington state.

Published
2023

23. Barriers and facilitators to healthy eating in disadvantaged adults living in the UK: a scoping review

Author

Raluca A. Briazu, Fatima Masood, Louise Hunt, Clare Pettinger, Carol Wagstaff, and Rachel McCloy

Subjects
Socioeconomic deprivation, Dietary intake, Environmental barriers, Scoping review, Theoretical domains framework, Public aspects of medicine, RA1-1270
Abstract

Abstract In the UK people living in disadvantaged communities are less likely than those with higher socio-economic status to have a healthy diet. To address this inequality, it is crucial scientists, practitioners and policy makers understand the factors that hinder and assist healthy food choice in these individuals. In this scoping review, we aimed to identify barriers and facilitators to healthy eating among disadvantaged individuals living in the UK. Additionally, we used the Theoretical Domains Framework (TDF) to synthesise results and provide a guide for the development of theory-informed behaviour change interventions. Five databases were searched, (CINAHL, Embase, MEDLINE, PsycINFO, and Web of Science) for articles assessing healthy dietary intake of disadvantaged adults living in the UK. A total of 50 papers (34 quantitative; 16 qualitative) were included in this review. Across all studies we identified 78 barriers and 49 facilitators found to either impede and/or encourage healthy eating. Both barriers and facilitators were more commonly classified under the Environmental, Context and Resources TDF domain, with 74% of studies assessing at least one factor pertaining to this domain. Results thus indicate that context related factors such as high cost and accessibility of healthy food, rather than personal factors, such as lack of efficiency in healthy lifestyle drive unhealthy eating in disadvantaged individuals in the UK. We discuss how such factors are largely overlooked in current interventions and propose that more effort should be directed towards implementing interventions that specifically target infrastructures rather than individuals.

Published
2024
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24. Tumour-specific phosphorylation of serine 419 drives alpha-enolase (ENO1) nuclear export in triple negative breast cancer progression

Author

Morgan L Marshall, Kim YC Fung, David A Jans, and Kylie M Wagstaff

Subjects
Alpha-enolase, Triple negative breast cancer, Protein phosphorylation, Tumour-specific localisation, Nuclear transport, Biotechnology, TP248.13-248.65, Biology (General), QH301-705.5, Biochemistry, QD415-436
Abstract

Abstract Background The glycolytic enzyme alpha-enolase is a known biomarker of many cancers and involved in tumorigenic functions unrelated to its key role in glycolysis. Here, we show that expression of alpha-enolase correlates with subcellular localisation and tumorigenic status in the MCF10 triple negative breast cancer isogenic tumour progression model, where non-tumour cells show diffuse nucleocytoplasmic localisation of alpha-enolase, whereas tumorigenic cells show a predominantly cytoplasmic localisation. Alpha-enolase nucleocytoplasmic localisation may be regulated by tumour cell-specific phosphorylation at S419, previously reported in pancreatic cancer. Results Here we show ENO1 phosphorylation can also be observed in triple negative breast cancer patient samples and MCF10 tumour progression cell models. Furthermore, prevention of alpha-enolase-S419 phosphorylation by point mutation or a casein kinase-1 specific inhibitor D4476, induced tumour-specific nuclear accumulation of alpha-enolase, implicating S419 phosphorylation and casein kinase-1 in regulating subcellular localisation in tumour cell-specific fashion. Strikingly, alpha-enolase nuclear accumulation was induced in tumour cells by treatment with the specific exportin-1-mediated nuclear export inhibitor Leptomycin B. This suggests that S419 phosphorylation in tumour cells regulates alpha-enolase subcellular localisation by inducing its exportin-1-mediated nuclear export. Finally, as a first step to analyse the functional consequences of increased cytoplasmic alpha-enolase in tumour cells, we determined the alpha-enolase interactome in the absence/presence of D4476 treatment, with results suggesting clear differences with respect to interaction with cytoskeleton regulating proteins. Conclusions The results suggest for the first time that tumour-specific S419 phosphorylation may contribute integrally to alpha-enolase cytoplasmic localisation, to facilitate alpha-enolase’s role in modulating cytoskeletal organisation in triple negative breast cancer. This new information may be used for development of triple negative breast cancer specific therapeutics that target alpha-enolase.

Published
2024
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26. Cosmic Microwave Background Recovery: A Graph-Based Bayesian Convolutional Network Approach

Author

Adams, Jadie, Lu, Steven, Gorski, Krzysztof M., Rocha, Graca, and Wagstaff, Kiri L.

Subjects
Computer Science - Machine Learning, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

The cosmic microwave background (CMB) is a significant source of knowledge about the origin and evolution of our universe. However, observations of the CMB are contaminated by foreground emissions, obscuring the CMB signal and reducing its efficacy in constraining cosmological parameters. We employ deep learning as a data-driven approach to CMB cleaning from multi-frequency full-sky maps. In particular, we develop a graph-based Bayesian convolutional neural network based on the U-Net architecture that predicts cleaned CMB with pixel-wise uncertainty estimates. We demonstrate the potential of this technique on realistic simulated data based on the Planck mission. We show that our model accurately recovers the cleaned CMB sky map and resulting angular power spectrum while identifying regions of uncertainty. Finally, we discuss the current challenges and the path forward for deploying our model for CMB recovery on real observations., Comment: Published at the Thirty-fifth Annual Conference on Innovative Applications of Artificial Intelligence (IAAI-23). 7 pages, 6 figures

Published
2023

27. Contrastive Learning for Self-Supervised Pre-Training of Point Cloud Segmentation Networks With Image Data

Author

Janda, Andrej, Wagstaff, Brandon, Ng, Edwin G., and Kelly, Jonathan

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Reducing the quantity of annotations required for supervised training is vital when labels are scarce and costly. This reduction is particularly important for semantic segmentation tasks involving 3D datasets, which are often significantly smaller and more challenging to annotate than their image-based counterparts. Self-supervised pre-training on unlabelled data is one way to reduce the amount of manual annotations needed. Previous work has focused on pre-training with point clouds exclusively. While useful, this approach often requires two or more registered views. In the present work, we combine image and point cloud modalities by first learning self-supervised image features and then using these features to train a 3D model. By incorporating image data, which is often included in many 3D datasets, our pre-training method only requires a single scan of a scene and can be applied to cases where localization information is unavailable. We demonstrate that our pre-training approach, despite using single scans, achieves comparable performance to other multi-scan, point cloud-only methods., Comment: In Proceedings of the Conference on Robots and Vision (CRV'23), Montreal, Canada, Jun. 6-8, 2023. arXiv admin note: substantial text overlap with arXiv:2211.11801

Published
2023
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39. GAPDH suppresses adenovirus-induced oxidative stress and enables a superfast production of recombinant adenovirus

Author

Guozhi Zhao, Piao Zhao, Yonghui Wang, Hui Zhang, Yi Zhu, Jiamin Zhong, Wulin You, Guowei Shen, Changqi Luo, Ou Mei, Xingye Wu, Jingjing Li, Yi Shu, Hongwei Wang, William Wagstaff, Hue H. Luu, Yang Bi, Lewis L. Shi, Russell R. Reid, Tong-Chuan He, Li Jiang, Wei Tang, Jiaming Fan, and Ziwei Tang

Subjects
GAPDH, Gene therapy, Oxidative stress, Packaging cell line, Reactive oxygen species, Recombinant adenovirus, Medicine (General), R5-920, Genetics, QH426-470
Abstract

Recombinant adenovirus (rAdV) is a commonly used vector system for gene transfer. Efficient initial packaging and subsequent production of rAdV remains time-consuming and labor-intensive, possibly attributable to rAdV infection-associated oxidative stress and reactive oxygen species (ROS) production. Here, we show that exogenous GAPDH expression mitigates adenovirus-induced ROS-associated apoptosis in HEK293 cells, and expedites adenovirus production. By stably overexpressing GAPDH in HEK293 (293G) and 293pTP (293GP) cells, respectively, we demonstrated that rAdV-induced ROS production and cell apoptosis were significantly suppressed in 293G and 293GP cells. Transfection of 293G cells with adenoviral plasmid pAd-G2Luc yielded much higher titers of Ad-G2Luc at day 7 than that in HEK293 cells. Similarly, Ad-G2Luc was amplified more efficiently in 293G than in HEK293 cells. We further showed that transfection of 293GP cells with pAd-G2Luc produced much higher titers of Ad-G2Luc at day 5 than that of 293pTP cells. 293GP cells amplified the Ad-G2Luc much more efficiently than 293pTP cells, indicating that exogenous GAPDH can further augment pTP-enhanced adenovirus production. These results demonstrate that exogenous GAPDH can effectively suppress adenovirus-induced ROS and thus accelerate adenovirus production. Therefore, the engineered 293GP cells represent a superfast rAdV production system for adenovirus-based gene transfer and gene therapy.

Published
2024
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40. Stratified analyses refine association between TLR7 rare variants and severe COVID-19

Author

Jannik Boos, Caspar I. van der Made, Gayatri Ramakrishnan, Eamon Coughlan, Rosanna Asselta, Britt-Sabina Löscher, Luca V.C. Valenti, Rafael de Cid, Luis Bujanda, Antonio Julià, Erola Pairo-Castineira, J. Kenneth Baillie, Sandra May, Berina Zametica, Julia Heggemann, Agustín Albillos, Jesus M. Banales, Jordi Barretina, Natalia Blay, Paolo Bonfanti, Maria Buti, Javier Fernandez, Sara Marsal, Daniele Prati, Luisa Ronzoni, Nicoletta Sacchi, Joachim L. Schultze, Olaf Riess, Andre Franke, Konrad Rawlik, David Ellinghaus, Alexander Hoischen, Axel Schmidt, Kerstin U. Ludwig, Valeria Rimoldi, Elvezia M. Paraboschi, Alessandra Bandera, Flora Peyvandi, Giacomo Grasselli, Francesco Blasi, Francesco Malvestiti, Serena Pelusi, Cristiana Bianco, Lorenzo Miano, Angela Lombardi, Pietro Invernizzi, Alessio Gerussi, Giuseppe Citerio, Andrea Biondi, Maria Grazia Valsecchi, Marina Elena Cazzaniga, Giuseppe Foti, Ilaria Beretta, Mariella D'Angiò, Laura Rachele Bettini, Xavier Farré, Susana Iraola-Guzmán, Manolis Kogevinas, Gemma Castaño-Vinyals, Koldo Garcia-Etxebarria, Beatriz Nafria, Mauro D'Amato, Adriana Palom, Colin Begg, Sara Clohisey, Charles Hinds, Peter Horby, Julian Knight, Lowell Ling, David Maslove, Danny McAuley, Johnny Millar, Hugh Montgomery, Alistair Nichol, Peter J.M. Openshaw, Alexandre C. Pereira, Chris P. Ponting, Kathy Rowan, Malcolm G. Semple, Manu Shankar-Hari, Charlotte Summers, Timothy Walsh, Latha Aravindan, Ruth Armstrong, Heather Biggs, Ceilia Boz, Adam Brown, Richard Clark, Audrey Coutts, Judy Coyle, Louise Cullum, Sukamal Das, Nicky Day, Lorna Donnelly, Esther Duncan, Angie Fawkes, Paul Fineran, Max Head Fourman, Anita Furlong, James Furniss, Bernadette Gallagher, Tammy Gilchrist, Ailsa Golightly, Fiona Griffiths, Katarzyna Hafezi, Debbie Hamilton, Ross Hendry, Andy Law, Dawn Law, Rachel Law, Sarah Law, Rebecca Lidstone-Scott, Louise Macgillivray, Alan Maclean, Hanning Mal, Sarah McCafferty, Ellie Mcmaster, Jen Meikle, Shona C. Moore, Kirstie Morrice, Lee Murphy, Sheena Murphy, Mybaya Hellen, Wilna Oosthuyzen, Chenqing Zheng, Jiantao Chen, Nick Parkinson, Trevor Paterson, Katherine Schon, Andrew Stenhouse, Mihaela Das, Maaike Swets, Helen Szoor-McElhinney, Filip Taneski, Lance Turtle, Tony Wackett, Mairi Ward, Jane Weaver, Nicola Wrobel, Marie Zechner, Gill Arbane, Aneta Bociek, Sara Campos, Neus Grau, Tim Owen Jones, Rosario Lim, Martina Marotti, Marlies Ostermann, Christopher Whitton, Zoe Alldis, Raine Astin-Chamberlain, Fatima Bibi, Jack Biddle, Sarah Blow, Matthew Bolton, Catherine Borra, Ruth Bowles, Maudrian Burton, Yasmin Choudhury, David Collier, Amber Cox, Amy Easthope, Patrizia Ebano, Stavros Fotiadis, Jana Gurasashvili, Rosslyn Halls, Pippa Hartridge, Delordson Kallon, Jamila Kassam, Ivone Lancoma-Malcolm, Maninderpal Matharu, Peter May, Oliver Mitchelmore, Tabitha Newman, Mital Patel, Jane Pheby, Irene Pinzuti, Zoe Prime, Oleksandra Prysyazhna, Julian Shiel, Melanie Taylor, Carey Tierney, Suzanne Wood, Anne Zak, Olivier Zongo, Stephen Bonner, Keith Hugill, Jessica Jones, Steven Liggett, Evie Headlam, Nageswar Bandla, Minnie Gellamucho, Michelle Davies, Christopher Thompson, Marwa Abdelrazik, Dhanalakshmi Bakthavatsalam, Munzir Elhassan, Arunkumar Ganesan, Anne Haldeos, Jeronimo Moreno-Cuesta, Dharam Purohit, Rachel Vincent, Kugan Xavier, Kumar Rohit, Frater Alasdair, Malik Saleem, Carter David, Jenkins Samuel, Zoe Lamond, Wall Alanna, Jaime Fernandez-Roman, David O. Hamilton, Emily Johnson, Brian Johnston, Maria Lopez Martinez, Suleman Mulla, David Shaw, Alicia A.C. Waite, Victoria Waugh, Ingeborg D. Welters, Karen Williams, Anna Cavazza, Maeve Cockrell, Eleanor Corcoran, Maria Depante, Clare Finney, Ellen Jerome, Mark McPhail, Monalisa Nayak, Harriet Noble, Kevin O'Reilly, Evita Pappa, Rohit Saha, Sian Saha, John Smith, Abigail Knighton, David Antcliffe, Dorota Banach, Stephen Brett, Phoebe Coghlan, Ziortza Fernandez, Anthony Gordon, Roceld Rojo, Sonia Sousa Arias, Maie Templeton, Megan Meredith, Lucy Morris, Lucy Ryan, Amy Clark, Julia Sampson, Cecilia Peters, Martin Dent, Margaret Langley, Saima Ashraf, Shuying Wei, Angela Andrew, Archana Bashyal, Neil Davidson, Paula Hutton, Stuart McKechnie, Jean Wilson, David Baptista, Rebecca Crowe, Rita Fernandes, Rosaleen Herdman-Grant, Anna Joseph, Denise O'Connor, Meryem Allen, Adam Loveridge, India McKenley, Eriko Morino, Andres Naranjo, Richard Simms, Kathryn Sollesta, Andrew Swain, Harish Venkatesh, Jacyntha Khera, Jonathan Fox, Gillian Andrew, Lucy Barclay, Marie Callaghan, Rachael Campbell, Sarah Clark, Dave Hope, Lucy Marshall, Corrienne McCulloch, Kate Briton, Jo Singleton, Sohphie Birch, Lutece Brimfield, Zoe Daly, David Pogson, Steve Rose, Ceri Battle, Elaine Brinkworth, Rachel Harford, Carl Murphy, Luke Newey, Tabitha Rees, Marie Williams, Sophie Arnold, Petra Polgarova, Katerina Stroud, Eoghan Meaney, Megan Jones, Anthony Ng, Shruti Agrawal, Nazima Pathan, Deborah White, Esther Daubney, Kay Elston, Lina Grauslyte, Musarat Hussain, Mandeep Phull, Tatiana Pogreban, Lace Rosaroso, Erika Salciute, George Franke, Joanna Wong, Aparna George, Laura Ortiz-Ruiz de Gordoa, Emily Peasgood, Claire Phillips, Michelle Bates, Jo Dasgin, Jaspret Gill, Annette Nilsson, James Scriven, Carlos Castro Delgado, Deborah Dawson, Lijun Ding, Georgia Durrant, Obiageri Ezeobu, Sarah Farnell-Ward, Abiola Harrison, Rebecca Kanu, Susannah Leaver, Elena Maccacari, Soumendu Manna, Romina Pepermans Saluzzio, Joana Queiroz, Tinashe Samakomva, Christine Sicat, Joana Texeira, Edna Fernandes Da Gloria, Ana Lisboa, John Rawlins, Jisha Mathew, Ashley Kinch, William James Hurt, Nirav Shah, Victoria Clark, Maria Thanasi, Nikki Yun, Kamal Patel, Sara Bennett, Emma Goodwin, Matthew Jackson, Alissa Kent, Clare Tibke, Wiesia Woodyatt, Ahmed Zaki, Azmerelda Abraheem, Peter Bamford, Kathryn Cawley, Charlie Dunmore, Maria Faulkner, Rumanah Girach, Helen Jeffrey, Rhianna Jones, Emily London, Imrun Nagra, Farah Nasir, Hannah Sainsbury, Clare Smedley, Tahera Patel, Matthew Smith, Srikanth Chukkambotla, Aayesha Kazi, Janice Hartley, Joseph Dykes, Muhammad Hijazi, Sarah Keith, Meherunnisa Khan, Janet Ryan-Smith, Philippa Springle, Jacqueline Thomas, Nick Truman, Samuel Saad, Dabheoc Coleman, Christopher Fine, Roseanna Matt, Bethan Gay, Jack Dalziel, Syamlan Ali, Drew Goodchild, Rhiannan Harling, Ravi Bhatterjee, Wendy Goddard, Chloe Davison, Stephen Duberly, Jeanette Hargreaves, Rachel Bolton, Miriam Davey, David Golden, Rebecca Seaman, Shiney Cherian, Sean Cutler, Anne Emma Heron, Anna Roynon-Reed, Tamas Szakmany, Gemma Williams, Owen Richards, Yusuf Cheema, Hollie Brooke, Sarah Buckley, Jose Cebrian Suarez, Ruth Charlesworth, Karen Hansson, John Norris, Alice Poole, Alastair Rose, Rajdeep Sandhu, Brendan Sloan, Elizabeth Smithson, Muthu Thirumaran, Veronica Wagstaff, Alexandra Metcalfe, Mark Brunton, Jess Caterson, Holly Coles, Matthew Frise, Sabi Gurung Rai, Nicola Jacques, Liza Keating, Emma Tilney, Shauna Bartley, Parminder Bhuie, Sian Gibson, Amanda Lyle, Fiona McNeela, Jayachandran Radhakrishnan, Alistair Hughes, Bryan Yates, Jessica Reynolds, Helen Campbell, Maria Thompsom, Steve Dodds, Stacey Duffy, Sandra Greer, Karen Shuker, Ascanio Tridente, Reena Khade, Ashok Sundar, George Tsinaslanidis, Isobel Birkinshaw, Joseph Carter, Kate Howard, Joanne Ingham, Rosie Joy, Harriet Pearson, Samantha Roche, Zoe Scott, Hollie Bancroft, Mary Bellamy, Margaret Carmody, Jacqueline Daglish, Faye Moore, Joanne Rhodes, Mirriam Sangombe, Salma Kadiri, Maria Croft, Ian White, Victoria Frost, Maia Aquino, Rajeev Jha, Vinodh Krishnamurthy, Lai Lim, Li Lim, Edward Combes, Teishel Joefield, Sonja Monnery, Valerie Beech, Sallyanne Trotman, Christine Almaden-Boyle, Pauline Austin, Louise Cabrelli, Stephen Cole, Matt Casey, Susan Chapman, Clare Whyte, Yolanda Baird, Aaron Butler, Indra Chadbourn, Linda Folkes, Heather Fox, Amy Gardner, Raquel Gomez, Gillian Hobden, Luke Hodgson, Kirsten King, Michael Margarson, Tim Martindale, Emma Meadows, Dana Raynard, Yvette Thirlwall, David Helm, Jordi Margalef, Kristine Criste, Rebecca Cusack, Kim Golder, Hannah Golding, Oliver Jones, Samantha Leggett, Michelle Male, Martyna Marani, Kirsty Prager, Toran Williams, Belinda Roberts, Karen Salmon, Peter Anderson, Katie Archer, Karen Austin, Caroline Davis, Alison Durie, Olivia Kelsall, Jessica Thrush, Charlie Vigurs, Laura Wild, Hannah-Louise Wood, Helen Tranter, Alison Harrison, Nicholas Cowley, Michael McAlindon, Andrew Burtenshaw, Stephen Digby, Emma Low, Aled Morgan, Naiara Cother, Tobias Rankin, Sarah Clayton, Alex McCurdy, Cecilia Ahmed, Balvinder Baines, Sarah Clamp, Julie Colley, Risna Haq, Anne Hayes, Jonathan Hulme, Samia Hussain, Sibet Joseph, Rita Kumar, Zahira Maqsood, Manjit Purewal, Leonie Benham, Zena Bradshaw, Joanna Brown, Melanie Caswell, Jason Cupitt, Sarah Melling, Stephen Preston, Nicola Slawson, Emma Stoddard, Scott Warden, Bethan Deacon, Ceri Lynch, Carla Pothecary, Lisa Roche, Gwenllian Sera Howe, Jayaprakash Singh, Keri Turner, Hannah Ellis, Natalie Stroud, Jodie Hunt, Joy Dearden, Emma Dobson, Andy Drummond, Michelle Mulcahy, Sheila Munt, Grainne O'Connor, Jennifer Philbin, Chloe Rishton, Redmond Tully, Sarah Winnard, Susanne Cathcart, Katharine Duffy, Alex Puxty, Kathryn Puxty, Lynne Turner, Jane Ireland, Gary Semple, Kate Long, Simon Whiteley, Elizabeth Wilby, Bethan Ogg, Amanda Cowton, Andrea Kay, Melanie Kent, Kathryn Potts, Ami Wilkinson, Suzanne Campbell, Ellen Brown, Julie Melville, Jay Naisbitt, Rosane Joseph, Maria Lazo, Olivia Walton, Alan Neal, Peter Alexander, Schvearn Allen, Joanne Bradley-Potts, Craig Brantwood, Jasmine Egan, Timothy Felton, Grace Padden, Luke Ward, Stuart Moss, Susannah Glasgow, Lynn Abel, Michael Brett, Brian Digby, Lisa Gemmell, James Hornsby, Patrick MacGoey, Pauline O'Neil, Richard Price, Natalie Rodden, Kevin Rooney, Radha Sundaram, Nicola Thomson, Bridget Hopkins, Laura Thrasyvoulou, Heather Willis, Martyn Clark, Martina Coulding, Edward Jude, Jacqueline McCormick, Oliver Mercer, Darsh Potla, Hafiz Rehman, Heather Savill, Victoria Turner, Charlotte Downes, Kathleen Holding, Katie Riches, Mary Hilton, Mel Hayman, Deepak Subramanian, Priya Daniel, Oluronke Adanini, Nikhil Bhatia, Maines Msiska, Rebecca Collins, Ian Clement, Bijal Patel, A. Gulati, Carole Hays, K. Webster, Anne Hudson, Andrea Webster, Elaine Stephenson, Louise McCormack, Victoria Slater, Rachel Nixon, Helen Hanson, Maggie Fearby, Sinead Kelly, Victoria Bridgett, Philip Robinson, Julie Camsooksai, Charlotte Humphrey, Sarah Jenkins, Henrik Reschreiter, Beverley Wadams, Yasmin Death, Victoria Bastion, Daphene Clarke, Beena David, Harriet Kent, Rachel Lorusso, Gamu Lubimbi, Sophie Murdoch, Melchizedek Penacerrada, Alastair Thomas, Jennifer Valentine, Ana Vochin, Retno Wulandari, Brice Djeugam, Gillian Bell, Katy English, Amro Katary, Louise Wilcox, Michelle Bruce, Karen Connolly, Tracy Duncan, Helen T-Michael, Gabriella Lindergard, Samuel Hey, Claire Fox, Jordan Alfonso, Laura Jayne Durrans, Jacinta Guerin, Bethan Blackledge, Jade Harris, Martin Hruska, Ayaa Eltayeb, Thomas Lamb, Tracey Hodgkiss, Lisa Cooper, Joanne Rothwell, Angela Allan, Felicity Anderson, Callum Kaye, Jade Liew, Jasmine Medhora, Teresa Scott, Erin Trumper, Adriana Botello, Liana Lankester, Nikitas Nikitas, Colin Wells, Bethan Stowe, Kayleigh Spencer, Craig Brandwood, Lara Smith, Katie Birchall, Laurel Kolakaluri, Deborah Baines, Anila Sukumaran, Elena Apetri, Cathrine Basikolo, Laura Catlow, Bethan Charles, Paul Dark, Reece Doonan, Alice Harvey, Daniel Horner, Karen Knowles, Stephanie Lee, Diane Lomas, Chloe Lyons, Tracy Marsden, Danielle McLaughlan, Liam McMorrow, Jessica Pendlebury, Jane Perez, Maria Poulaka, Nicola Proudfoot, Melanie Slaughter, Kathryn Slevin, Vicky Thomas, Danielle Walker, Angiy Michael, Matthew Collis, Tracey Cosier, Gemma Millen, Neil Richardson, Natasha Schumacher, Heather Weston, James Rand, Nicola Baxter, Steven Henderson, Sophie Kennedy-Hay, Christopher McParland, Laura Rooney, Malcolm Sim, Gordan McCreath, Louise Akeroyd, Shereen Bano, Matt Bromley, Lucy Gurr, Tom Lawton, James Morgan, Kirsten Sellick, Deborah Warren, Brian Wilkinson, Janet McGowan, Camilla Ledgard, Amelia Stacey, Kate Pye, Ruth Bellwood, Michael Bentley, Jeremy Bewley, Zoe Garland, Lisa Grimmer, Bethany Gumbrill, Rebekah Johnson, Katie Sweet, Denise Webster, Georgia Efford, Karen Convery, Deirdre Fottrell-Gould, Lisa Hudig, Jocelyn Keshet-Price, Georgina Randell, Katie Stammers, Maria Bokhari, Vanessa Linnett, Rachael Lucas, Wendy McCormick, Jenny Ritzema, Amanda Sanderson, Helen Wild, Anthony Rostron, Alistair Roy, Lindsey Woods, Sarah Cornell, Fiona Wakinshaw, Kimberley Rogerson, Jordan Jarmain, Robert Parker, Amie Reddy, Ian Turner-Bone, Laura Wilding, Peter Harding, Caroline Abernathy, Louise Foster, Andrew Gratrix, Vicky Martinson, Priyai Parkinson, Elizabeth Stones, Llucia Carbral-Ortega, Georgia Bercades, David Brealey, Ingrid Hass, Niall MacCallum, Gladys Martir, Eamon Raith, Anna Reyes, Deborah Smyth, Letizia Zitter, Sarah Benyon, Suzie Marriott, Linda Park, Samantha Keenan, Elizabeth Gordon, Helen Quinn, Kizzy Baines, Lenka Cagova, Adama Fofano, Lucie Garner, Helen Holcombe, Sue Mepham, Alice Michael Mitchell, Lucy Mwaura, Krithivasan Praman, Alain Vuylsteke, Julie Zamikula, Bally Purewal, Vanessa Rivers, Stephanie Bell, Hayley Blakemore, Borislava Borislavova, Beverley Faulkner, Emma Gendall, Elizabeth Goff, Kati Hayes, Matt Thomas, Ruth Worner, Kerry Smith, Deanna Stephens, Louise Mew, Esther Mwaura, Richard Stewart, Felicity Williams, Lynn Wren, Sara-Beth Sutherland, Emily Bevan, Jane Martin, Dawn Trodd, Geoff Watson, Caroline Wrey Brown, Amy Collins, Waqas Khaliq, Estefania Treus Gude, Olugbenga Akinkugbe, Alasdair Bamford, Emily Beech, Holly Belfield, Michael Bell, Charlene Davies, Gareth A.L. Jones, Tara McHugh, Hamza Meghari, Lauran O'Neill, Mark J. Peters, Samiran Ray, Ana Luisa Tomas, Iona Burn, Geraldine Hambrook, Katarina Manso, Ruth Penn, Pradeep Shanmugasundaram, Julie Tebbutt, Danielle Thornton, Jade Cole, Rhys Davies, Donna Duffin, Helen Hill, Ben Player, Emma Thomas, Angharad Williams, Denise Griffin, Nycola Muchenje, Mcdonald Mupudzi, Richard Partridge, Jo-Anna Conyngham, Rachel Thomas, Mary Wright, Maria Alvarez Corral, Reni Jacob, Cathy Jones, Craig Denmade, Sarah Beavis, Katie Dale, Rachel Gascoyne, Joanne Hawes, Kelly Pritchard, Lesley Stevenson, Amanda Whileman, Patricia Doble, Joanne Hutter, Corinne Pawley, Charmaine Shovelton, Marius Vaida, Deborah Butcher, Susie O'Sullivan, Nicola Butterworth-Cowin, Norfaizan Ahmad, Joann Barker, Kris Bauchmuller, Sarah Bird, Kay Cawthron, Kate Harrington, Yvonne Jackson, Faith Kibutu, Becky Lenagh, Shamiso Masuko, Gary H. Mills, Ajay Raithatha, Matthew Wiles, Jayne Willson, Helen Newell, Alison Lye, Lorenza Nwafor, Claire Jarman, Sarah Rowland-Jones, David Foote, Joby Cole, Roger Thompson, James Watson, Lisa Hesseldon, Irene Macharia, Luke Chetam, Jacqui Smith, Amber Ford, Samantha Anderson, Kathryn Birchall, Kay Housley, Sara Walker, Leanne Milner, Helena Hanratty, Helen Trower, Patrick Phillips, Simon Oxspring, Ben Donne, Catherine Jardine, Dewi Williams, Alasdair Hay, Rebecca Flanagan, Gareth Hughes, Scott Latham, Emma McKenna, Jennifer Anderson, Robert Hull, Kat Rhead, Carina Cruz, Natalie Pattison, Rob Charnock, Denise McFarland, Denise Cosgrove, Ashar Ahmed, Anna Morris, Srinivas Jakkula, Asifa Ali, Megan Brady, Sam Dale, Annalisa Dance, Lisa Gledhill, Jill Greig, Kathryn Hanson, Kelly Holdroyd, Marie Home, Diane Kelly, Ross Kitson, Lear Matapure, Deborah Melia, Samantha Mellor, Tonicha Nortcliffe, Jez Pinnell, Matthew Robinson, Lisa Shaw, Ryan Shaw, Lesley Thomis, Alison Wilson, Tracy Wood, Lee-Ann Bayo, Ekta Merwaha, Tahira Ishaq, Sarah Hanley, Meg Hibbert, Dariusz Tetla, Chrsitopher Woodford, Latha Durga, Gareth Kennard-Holden, Debbie Branney, Jordan Frankham, Sally Pitts, Nigel White, Shondipon Laha, Mark Verlander, Alexandra Williams, Abdelhakim Altabaibeh, Ana Alvaro, Kayleigh Gilbert, Louise Ma, Loreta Mostoles, Chetan Parmar, Kathryn Simpson, Champa Jetha, Lauren Booker, Anezka Pratley, Colene Adams, Anita Agasou, Tracie Arden, Amy Bowes, Pauline Boyle, Mandy Beekes, Heather Button, Nigel Capps, Mandy Carnahan, Anne Carter, Danielle Childs, Denise Donaldson, Kelly Hard, Fran Hurford, Yasmin Hussain, Ayesha Javaid, James Jones, Sanal Jose, Michael Leigh, Terry Martin, Helen Millward, Nichola Motherwell, Rachel Rikunenko, Jo Stickley, Julie Summers, Louise Ting, Helen Tivenan, Louise Tonks, Rebecca Wilcox, Maureen Holland, Natalie Keenan, Marc Lyons, Helen Wassall, Chris Marsh, Mervin Mahenthran, Emma Carter, Thomas Kong, Helen Blackman, Ben Creagh-Brown, Sinead Donlon, Natalia Michalak-Glinska, Sheila Mtuwa, Veronika Pristopan, Armorel Salberg, Eleanor Smith, Sarah Stone, Charles Piercy, Jerik Verula, Dorota Burda, Rugia Montaser, Lesley Harden, Irving Mayangao, Cheryl Marriott, Paul Bradley, Celia Harris, Susan Anderson, Eleanor Andrews, Janine Birch, Emma Collins, Kate Hammerton, Ryan O'Leary, Michele Clark, Sarah Purvis, Russell Barber, Claire Hewitt, Annette Hilldrith, Karen Jackson-Lawrence, Sarah Shepardson, Maryanne Wills, Susan Butler, Silvia Tavares, Amy Cunningham, Julia Hindale, Sarwat Arif, Sarah Bean, Karen Burt, Michael Spivey, Carrie Demetriou, Charlotte Eckbad, Sarah Hierons, Lucy Howie, Sarah Mitchard, Lidia Ramos, Alfredo Serrano-Ruiz, Katie White, Fiona Kelly, Daniele Cristiano, Natalie Dormand, Zohreh Farzad, Mahitha Gummadi, Kamal Liyanage, Brijesh Patel, Sara Salmi, Geraldine Sloane, Vicky Thwaites, Mathew Varghese, Anelise C. Zborowski, John Allan, Tim Geary, Gordon Houston, Alistair Meikle, Peter O'Brien, Miranda Forsey, Agilan Kaliappan, Anne Nicholson, Joanne Riches, Mark Vertue, Elizabeth Allan, Kate Darlington, Ffyon Davies, Jack Easton, Sumit Kumar, Richard Lean, Daniel Menzies, Richard Pugh, Xinyi Qiu, Llinos Davies, Hannah Williams, Jeremy Scanlon, Gwyneth Davies, Callum Mackay, Joannne Lewis, Stephanie Rees, Metod Oblak, Monica Popescu, Mini Thankachen, Andrew Higham, Kerry Simpson, Jayne Craig, Rosie Baruah, Sheila Morris, Susie Ferguson, Amy Shepherd, Luke Stephen Prockter Moore, Marcela Paola Vizcaychipi, Laura Gomes de Almeida Martins, Jaime Carungcong, Inthakab Ali Mohamed Ali, Karen Beaumont, Mark Blunt, Zoe Coton, Hollie Curgenven, Mohamed Elsaadany, Kay Fernandes, Sameena Mohamed Ally, Harini Rangarajan, Varun Sarathy, Sivarupan Selvanayagam, Dave Vedage, Matthew White, Mandy Gill, Paul Paul, Valli Ratnam, Sarah Shelton, Inez Wynter, Siobhain Carmody, Valerie Joan Page, Claire Marie Beith, Karen Black, Suzanne Clements, Alan Morrison, Dominic Strachan, Margaret Taylor, Michelle Clarkson, Stuart D'Sylva, Kathryn Norman, Fiona Auld, Joanne Donnachie, Ian Edmond, Lynn Prentice, Nikole Runciman, Dario Salutous, Lesley Symon, Anne Todd, Patricia Turner, Abigail Short, Laura Sweeney, Euan Murdoch, Dhaneesha Senaratne, Michaela Hill, Thogulava Kannan, Wild Laura, Rikki Crawley, Abigail Crew, Mishell Cunningham, Allison Daniels, Laura Harrison, Susan Hope, Ken Inweregbu, Sian Jones, Nicola Lancaster, Jamie Matthews, Alice Nicholson, Gemma Wray, Helen Langton, Rachel Prout, Malcolm Watters, Catherine Novis, Anthony Barron, Ciara Collins, Sundeep Kaul, Heather Passmore, Claire Prendergast, Anna Reed, Paula Rogers, Rajvinder Shokkar, Meriel Woodruff, Hayley Middleton, Oliver Polgar, Claire Nolan, Kanta Mahay, Dawn Collier, Anil Hormis, Victoria Maynard, Cheryl Graham, Rachel Walker, Ellen Knights, Alicia Price, Alice Thomas, Chris Thorpe, Teresa Behan, Caroline Burnett, Jonathan Hatton, Elaine Heeney, Atideb Mitra, Maria Newton, Rachel Pollard, Rachael Stead, Vishal Amin, Elena Anastasescu, Vikram Anumakonda, Komala Karthik, Rizwana Kausar, Karen Reid, Jacqueline Smith, Janet Imeson-Wood, Denise Skinner, Jane Gaylard, Dee Mullan, Julie Newman, Alison Brown, Vikki Crickmore, Gabor Debreceni, Joy Wilkins, Liz Nicol, Rosie Reece-Anthony, Mark Birt, Alison Ghosh, Emma Williams, Louise Allen, Eva Beranova, Nikki Crisp, Joanne Deery, Tracy Hazelton, Alicia Knight, Carly Price, Sorrell Tilbey, Salah Turki, Sharon Turney, Joshua Cooper, Cheryl Finch, Sarah Liderth, Alison Quinn, Natalia Waddington, Tina Coventry, Susan Fowler, Michael MacMahon, Amanda McGregor, Anne Cowley, Judith Highgate, Jane Gregory, Susan O'Connell, Tim Smith, Luigi Barberis, Shameer Gopal, Nichola Harris, Victoria Lake, Stella Metherell, Elizabeth Radford, Amelia Daniel, Joanne Finn, Rajnish Saha, Nikki White, Phil Donnison, Fiona Trim, Beena Eapen, Jenny Birch, Laura Bough, Josie Goodsell, Rebecca Tutton, Patricia Williams, Sarah Williams, Barbara Winter-Goodwin, Ailstair Nichol, Kathy Brickell, Michelle Smyth, Lorna Murphy, Samantha Coetzee, Alistair Gales, Igor Otahal, Meena Raj, Craig Sell, Paula Hilltout, Jayne Evitts, Amanda Tyler, Joanne Waldron, Kate Beesley, Sarah Board, Agnieszka Kubisz-Pudelko, Alison Lewis, Jess Perry, Lucy Pippard, Di Wood, Clare Buckley, Peter Barry, Neil Flint, Patel Rekha, Dawn Hales, Lara Bunni, Claire Jennings, Monica Latif, Rebecca Marshall, Gayathri Subramanian, Peter J. McGuigan, Christopher Wasson, Stephanie Finn, Jackie Green, Erin Collins, Bernadette King, Andy Campbell, Sara Smuts, Joseph Duffield, Oliver Smith, Lewis Mallon, Watkins Claire, Liam Botfield, Joanna Butler, Catherine Dexter, Jo Fletcher, Atul Garg, Aditya Kuravi, Poonam Ranga, Emma Virgilio, Zakaula Belagodu, Bridget Fuller, Anca Gherman, Olumide Olufuwa, Remi Paramsothy, Carmel Stuart, Naomi Oakley, Charlotte Kamundi, David Tyl, Katy Collins, Pedro Silva, June Taylor, Laura King, Charlotte Coates, Maria Crowley, Phillipa Wakefield, Jane Beadle, Laura Johnson, Janet Sargeant, Madeleine Anderson, Ailbhe Brady, Rebekah Chan, Jeff Little, Shane McIvor, Helena Prady, Helen Whittle, Bijoy Mathew, Ben Attwood, Penny Parsons, Geraldine Ward, Pamela Bremmer, West Joe, Baird Tracy, Ruddy Jim, Ellie Davies, Sonia Sathe, Catherine Dennis, Alastair McGregor, Victoria Parris, Sinduya Srikaran, Anisha Sukha, Noreen Clarke, Jonathan Whiteside, Mairi Mascarenhas, Avril Donaldson, Joanna Matheson, Fiona Barrett, Marianne O'Hara, Laura Okeefe, Clare Bradley, Christine Eastgate-Jackson, Helder Filipe, Daniel Martin, Amitaa Maharajh, Sara Mingo Garcia, Glykeria Pakou, Mark De Neef, Kathy Dent, Elizabeth Horsley, Muhmmad Nauman Akhtar, Sandra Pearson, Dorota Potoczna, Sue Spencer, Melanie Clapham, Rosemary Harper, Una Poultney, Polly Rice, Rachel Mutch, Lisa Armstrong, Hayley Bates, Emma Dooks, Fiona Farquhar, Brigid Hairsine, Chantal McParland, Sophie Packham, Rehana Bi, Barney Scholefield, Lydia Ashton, Linsha George, Sophie Twiss, David Wright, Manish Chablani, Amy Kirkby, Kimberley Netherton, Kim Davies, Linda O'Brien, Zohra Omar, Emma Perkins, Tracy Lewis, Isobel Sutherland, Karen Burns, Dr Ben Chandler, Kerry Elliott, Janine Mallinson, Alison Turnbull, Prisca Gondo, Bernard Hadebe, Abdul Kayani, Bridgett Masunda, Taya Anderson, Dan Hawcutt, Laura O'Malley, Laura Rad, Naomi Rogers, Paula Saunderson, Kathryn Sian Allison, Deborah Afolabi, Jennifer Whitbread, Dawn Jones, Rachael Dore, Matthew Halkes, Pauline Mercer, Lorraine Thornton, Joy Dawson, Sweyn Garrioch, Melanie Tolson, Jonathan Aldridge, Ritoo Kapoor, David Loader, Karen Castle, Sally Humphreys, Ruth Tampsett, Katherine Mackintosh, Amanda Ayers, Wendy Harrison, Julie North, Suzanne Allibone, Roman Genetu, Vidya Kasipandian, Amit Patel, Ainhi Mac, Anthony Murphy, Parisa Mahjoob, Roonak Nazari, Lucy Worsley, Andrew Fagan, Thomas Bemand, Ethel Black, Arnold Dela Rosa, Ryan Howle, Shaman Jhanji, Ravishankar Rao Baikady, Kate Colette Tatham, Benjamin Thomas, Dina Bell, Rosalind Boyle, Katie Douglas, Lynn Glass, Emma Lee, Liz Lennon, Austin Rattray, Abigail Taylor, Rachel Anne Hughes, Helen Thomas, Alun Rees, Michaela Duskova, Janet Phipps, Suzanne Brooks, Michelle Edwards, Sheena Quaid, Ekaterina Watson, Adam Brayne, Emma Fisher, Jane Hunt, Peter Jackson, Duncan Kaye, Nicholas Love, Juliet Parkin, Victoria Tuckey, Lynne Van Koutrik, Sasha Carter, Benedict Andrew, Louise Findlay, Katie Adams, Jen Service, Alison Williams, Claire Cheyne, Anne Saunderson, Sam Moultrie, Miranda Odam, Kathryn Hall, Isheunesu Mapfunde, Charlotte Willis, Alex Lyon, Chunda Sri-Chandana, Joslan Scherewode, Lorraine Stephenson, Sarah Marsh, John Hardy, Henry Houlden, Eleanor Moncur, Ambreen Tariq, Arianna Tucci, Maria Hobrok, Ronda Loosley, Heather McGuinness, Helen Tench, Rebecca Wolf-Roberts, Val Irvine, Benjamin Shelley, Claire Gorman, Abhinav Gupta, Elizabeth Timlick, Rebecca Brady, Barry Milligan, Arianna Bellini, Jade Bryant, Anton Mayer, Amy Pickard, Nicholas Roe, Jason Sowter, Alex Howlett, Katy Fidler, Emma Tagliavini, and Kevin Donnelly

Subjects
SARS-CoV-2, host genetics, toll-like receptor 7, targeted sequencing, rare variants, variant collapsing analysis, Genetics, QH426-470
Abstract

Summary: Despite extensive global research into genetic predisposition for severe COVID-19, knowledge on the role of rare host genetic variants and their relation to other risk factors remains limited. Here, 52 genes with prior etiological evidence were sequenced in 1,772 severe COVID-19 cases and 5,347 population-based controls from Spain/Italy. Rare deleterious TLR7 variants were present in 2.4% of young (

Published
2024
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41. 'Wait, Do I Need More Fiber?' Exploring UK Consumers’ Dietary Fiber-Related Awareness and White Bread as a Viable Solution to Promote Subsequent Intake

Author

Victoria Norton, Carol Wagstaff, Julia Rodriguez Garcia, Alison Lovegrove, Peter Shewry, Mark Charlton, Nicola Gillett, Marcus John Tindall, and Stella Lignou

Subjects
dietary fiber, focus groups, consumer engagement, staple foods, white bread, Nutrition. Foods and food supply, TX341-641, Nutritional diseases. Deficiency diseases, RC620-627
Abstract

Background: Sufficient dietary fiber consumption is associated with well-established health benefits, yet such intake is currently suboptimal globally. Thus, there is interest in developing strategies to improve dietary fiber intake. One such approach is to increase the dietary fiber content of staple foods, but this needs relevant investigation. Methods: Forty-two United Kingdom (UK) based consumers (18–76 y) were recruited to take part in seven focus group sessions investigating: (i) key factors in food choice; (ii) dietary fiber-related knowledge, awareness, consumption habits, and engagement levels; (iii) willingness to consume dietary fiber-rich staple foods; and (iv) gain initial feedback on dietary fiber-rich breads. Results: Overall, key dietary fiber themes emerged such as knowledge (benefits, foods, recommendations and labeling), consumption (not measuring intake), barriers (convenience and knowledge), resources (education and public appeal), and topics (food examples and cooking). Consumers were positive per se to the idea of dietary fiber-rich staple foods but with various caveats (no changes in appearance, taste, and cost). White bread trends were centered around context (sandwich and toast), habit (comfort food), preferences (soft and fresh), and consumption is variable (daily to less often). In addition, consumers’ preferred labeling strategy for dietary fiber-rich breads was predominately focused on transparency and visibility. Overall, the newly developed breads were well received demonstrating the potential of our prototypes to fit into the white bread market; however, additional consumer insights are needed. Conclusion: Our findings recommend combining education with a personalized element of advice, coupled with a collective effort from the government and food industry, as essential to help encourage a step-change in dietary fiber consumption in the UK population.

Published
2024
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42. Occupational exposure and new-onset asthma in the population-based Telemark study: a 5-year follow-up

Author

Kjell Torén, Anne Kristin Moeller Fell, Regine Abrahamsen, Paul K Henneberger, Johny Kongerud, Geir Klepaker, Nikola Zivadinovic, Anthony Wagstaff, and Keson Jaoiun

Subjects
Medicine
Abstract

Objectives This study aimed to estimate the incidence of asthma and assess the association between job exposure matrix (N-JEM) assigned occupational exposure, self-reported occupational exposure to vapour, gas, dust and fumes (VGDF), mould, damages from moisture and cold, and new-onset asthma. We also aimed to assess the corresponding population attributable fraction (PAF) for ever exposure to VGDF.Design Longitudinal population-based respiratory health study.Setting Responders from the baseline Telemark Study in south-eastern Norway were followed up from 2013 to 2018.Participants 7120 participants, aged 16–55, were followed during a 5-year period.Main outcome measures New-onset asthma and its association with self-reported occupational exposure to VGDF, data from the N-JEM and self-reported workplace conditions were assessed using logistic regression adjusted for gender, age, smoking and body mass index. The PAF was calculated using the PUNAF command in STATA.Results There were 266 (3.7%) cases of new-onset asthma and an incidence density of 7.5 cases per 1000 person-years. A statistically significant association was found for ever exposed to VGDF with an OR of 1.49 (95% CI 1.15 to 1.94), weekly OR 2.00 (95% CI 1.29 to 3.11) and daily OR 2.46 (95% CI 1.39 to 4.35) exposure to VGDF. The corresponding PAF for ever exposed to VGDF was 17% (95% CI 5.4% to 27.8%) and the risk of asthma onset increased with frequent VGDF exposure, indicating a possible exposure–response relationship (p=0.002 for trend). The N-JEM exposure group, accidental peak exposure to irritants had an increased risk of new-onset asthma, OR 2.43 (95% CI 1.21 to 4.90). A significant association was also found for self-reported exposure to visible damages due to moisture 1.51 (95% CI 1.08 to 2.11), visible and smell of mould 1.88 (95% CI 1.32 to 2.68), 1.55 (95% CI 1.12 to 2.16) and cold environment 1.41 (95% CI 1.07 to 1.86).Conclusion Participants had elevated ORs for asthma associated with self-reported and N-JEM-assigned exposures. A PAF of 17% indicates that work-related asthma is still common. The possible exposure–response relationship suggests that reducing occupational VGDF exposure frequency could prevent the onset of asthma.

Published
2024
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43. Mental health of children with epilepsy compared to their peers: population-based cohort from linked primary and secondary healthcare record in England

Author

Millie Wagstaff, Ania Zylbersztejn, and Sophie Bennett

Subjects
Demography. Population. Vital events, HB848-3697
Abstract

Background Children with epilepsy have higher rates of internalising mental health (MH) conditions compared to their peers, although available evidence is limited by small and selective samples. We used linked primary care and hospital admission records covering approximately 4.42% of English population to describe incidence of mental health problems in children with epilepsy compared to their peers. Methods We developed a cohort of young people aged 7-17 years old between 2010-2019, with minimum 1 year of follow-up until death, 18th birthday or 2020 using linked data from the Clinical Practice Research Datalink and Hospital Episodes Statistics. Epilepsy (exposure), depression and anxiety (outcomes) were identified using a combination of diagnostic codes, and primary care prescribing records. We estimated incident rate ratios (IRR) for anxiety/depression/any MH condition for children with epilepsy compared to their peers using negative binomial regression adjusted for sex, age, and area-level deprivation. Results Study cohort included 510,177 children and young people, of whom 3,011 (0.59%) had epilepsy. Children with epilepsy had higher incidence of any MH condition (IRR: 1.39, 95% CI: 1.11–1.73) and anxiety (IRR: 1.38, 95% CI: 1.06–1.77), with differences in depression being non-significant (IRR: 1.25, 95% CI: 0.92–1.66). Discussion Children with epilepsy have higher rates of MH problems than their peers. Further work will examine if this can be partially explained by increased opportunity for MH diagnosis due to more healthcare contacts. Our findings emphasise the importance of integrated care models that address both neurological and psychological aspects of epilepsy management.

Published
2024
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46. Self-Supervised Pre-training of 3D Point Cloud Networks with Image Data

Author

Janda, Andrej, Wagstaff, Brandon, Ng, Edwin G., and Kelly, Jonathan

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Reducing the quantity of annotations required for supervised training is vital when labels are scarce and costly. This reduction is especially important for semantic segmentation tasks involving 3D datasets that are often significantly smaller and more challenging to annotate than their image-based counterparts. Self-supervised pre-training on large unlabelled datasets is one way to reduce the amount of manual annotations needed. Previous work has focused on pre-training with point cloud data exclusively; this approach often requires two or more registered views. In the present work, we combine image and point cloud modalities, by first learning self-supervised image features and then using these features to train a 3D model. By incorporating image data, which is often included in many 3D datasets, our pre-training method only requires a single scan of a scene. We demonstrate that our pre-training approach, despite using single scans, achieves comparable performance to other multi-scan, point cloud-only methods., Comment: In Proceedings of the Conference on Robot Learning (CoRL'22) Workshop on Pre-Training Robot Learning, Auckland, New Zealand, December 15, 2022

Published
2022

47. Athletic Mobile Manipulator System for Robotic Wheelchair Tennis

Author

Zaidi, Zulfiqar, Martin, Daniel, Belles, Nathaniel, Zakharov, Viacheslav, Krishna, Arjun, Lee, Kin Man, Wagstaff, Peter, Naik, Sumedh, Sklar, Matthew, Choi, Sugju, Kakehi, Yoshiki, Patil, Ruturaj, Mallemadugula, Divya, Pesce, Florian, Wilson, Peter, Hom, Wendell, Diamond, Matan, Zhao, Bryan, Moorman, Nina, Paleja, Rohan, Chen, Letian, Seraj, Esmaeil, and Gombolay, Matthew

Subjects
Computer Science - Robotics
Abstract

Athletics are a quintessential and universal expression of humanity. From French monks who in the 12th century invented jeu de paume, the precursor to modern lawn tennis, back to the K'iche' people who played the Maya Ballgame as a form of religious expression over three thousand years ago, humans have sought to train their minds and bodies to excel in sporting contests. Advances in robotics are opening up the possibility of robots in sports. Yet, key challenges remain, as most prior works in robotics for sports are limited to pristine sensing environments, do not require significant force generation, or are on miniaturized scales unsuited for joint human-robot play. In this paper, we propose the first open-source, autonomous robot for playing regulation wheelchair tennis. We demonstrate the performance of our full-stack system in executing ground strokes and evaluate each of the system's hardware and software components. The goal of this paper is to (1) inspire more research in human-scale robot athletics and (2) establish the first baseline for a reproducible wheelchair tennis robot for regulation singles play. Our paper contributes to the science of systems design and poses a set of key challenges for the robotics community to address in striving towards robots that can match human capabilities in sports., Comment: 8 pages, accepted at RA-L, will also be presented at IROS 2023

Published
2022

49. Cultivating Effective Marketing Student Teams: Making Instructors' Tacit Theories Visible

Author

Lindsay, Sophie, Wagstaff, Peter, Jevons, Colin, and Cruz, Angela Gracia B.

Abstract

Teamwork skills are important contributors to classroom learning outcomes and graduate employability. Although much has been reported in the literature about the components and characteristics of effective marketing student teams, less is known about how such knowledge is conceptualized and cultivated by frontline marketing instructors. This study applies a perspective of tacit theory to in-depth interviews with frontline instructors in undergraduate marketing courses. Our findings, summarized in a framework of adaptive cultivation of effective teams (ACET), highlight how instructors perceive effective teamwork as a dynamic interaction between three interwoven components of team effectiveness (team composition, team member behavior, and team culture) and adjust their interventions across these components. Overall, this study uncovers instructors' tacit theories of cultivating effective marketing student teams, and how these tacit theories impact in-class practices.

Published
2023
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50. Does PQIP change how data are used for local quality improvement? : an evaluation of the national Perioperative Quality Improvement Programme

Author

Wagstaff, Duncan

Abstract

This Thesis investigated whether and how the Perioperative Quality Improvement Programme (PQIP) supported local teams to use data for quality improvement of major elective surgery in the NHS. This complex intervention was challenging because of the difficulties local teams faced in collecting, sharing and using data within the multidisciplinary context of perioperative care. A scoping review identified gaps in the existing literature of how data from national perioperative programmes had been used for local quality improvement, and hence informed three interacting mixed-methods empirical workstreams: non-participatory qualitative fieldwork in two case study NHS Trusts before and after they engaged with PQIP data; a national survey of perioperative clinicians and managers; and participatory qualitative fieldwork with the central PQIP Project Team. Perioperative teams were motivated to use local data for improvement, but lacked the time, support or resources to do so. This did not change after engaging with PQIP. Local staff agreed with PQIP's aims to improve perioperative complications but struggled to collect sufficient data to effect change. However, this study only covered the early part of PQIP's implementation which may yet gain greater traction. Successful strategies to support the use of data for improvement were identified at the micro, meso and macro levels. Data collection was more effective in local contexts which dedicated resources to this activity. Local 'champions' spanning professional boundaries were influential in coordinating data collection, analysis and sharing. Organisational-level strategies successfully supported the training, implementation and coordination of QI at the micro level. Financial incentives attached to national clinical audits catalysed greater local multidisciplinary collaboration to use these data for improvement. Future research should investigate how to navigate these contextual influences in order to make best use of the considerable resources invested in national quality improvement programmes.

Published
2023

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