10 results on '"Fogarty R"'
Search Results
2. Molecular dynamics study of structure and reactions at the hydroxylated Mg(0001)/bulk water interface.
- Author
-
Fogarty, R. M. and Horsfield, A. P.
- Subjects
- *
MOLECULAR dynamics , *DENSITY functional theory , *AUTOMOBILE parts , *METASTABLE states , *HYDROGEN bonding - Abstract
A molecular level understanding of the aqueous Mg corrosion mechanism will be essential in developing improved alloys for battery electrodes, automobile parts, and biomedical implants. The structure and reactivity of the hydroxylated surface is expected to be key to the overall mechanism because (i) it is predicted to be the metastable surface state (rather than the bare surface) under a range of conditions and (ii) it provides a reasonable model for the outer corrosion film/water interface. We investigate the structure, interactions, and reactivity at the hydroxylated Mg(0001)/water interface using a combination of static Density Functional Theory calculations and second-generation Car–Parrinello ab initio molecular dynamics. We carry out detailed structural analyses into, among other properties, near-surface water orientations, favored adsorption sites, and near-surface hydrogen bonding behavior. Despite the short timescale (tens of ps) of our molecular dynamics run, we observe a cathodic water splitting event; the rapid timescale for this reaction is explained in terms of near-surface water structuring lowering the reaction barrier. Furthermore, we observe oxidation of an Mg surface atom to effectively generate a univalent Mg species (Mg+). Results are discussed in the context of understanding the Mg corrosion mechanism: For example, our results provide an explanation for the catalytic nature of the Mg corrosion film toward water splitting and a feasible mechanism for the generation of the univalent Mg species often proposed as a key intermediate. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
3. Structure and interactions at the Mg(0001)/water interface: An ab initio study.
- Author
-
Fogarty, R. M., Li, B. X., Harrison, N. M., and Horsfield, A. P.
- Subjects
- *
ATOMIC structure , *METALWORK , *ATOMIC charges , *DENSITY functional theory , *MINIMAL surfaces - Abstract
A molecular level understanding of metal/bulk water interface structure is key for a wide range of processes, including aqueous corrosion, which is our focus, but their buried nature makes experimental investigation difficult and we must mainly rely on simulations. We investigate the Mg(0001)/water interface using second generation Car–Parrinello molecular dynamics (MD) to gain structural information, combined with static density functional theory calculations to probe the atomic interactions and electronic structure (e.g., calculating the potential of zero charge). By performing detailed structural analyses of both metal–surface atoms and the near-surface water, we find that, among other insights: (i) water adsorption causes significant surface roughening (the planar distribution for top-layer Mg has two peaks separated by ≈ 0.6 A ̊ ), (ii) strongly adsorbed water covers only ≈ 1 4 of available surface sites, and (iii) adsorbed water avoids clustering on the surface. Static calculations are used to gain a deeper understanding of the structuring observed in MD. For example, we use an energy decomposition analysis combined with calculated atomic charges to show that adsorbate clustering is unfavorable due to Coulombic repulsion between adsorption site surface atoms. Results are discussed in the context of previous simulations carried out on other metal/water interfaces. The largest differences for the Mg(0001)/water system appear to be the high degree of surface distortion and the minimal difference between the metal work function and metal/water potential of zero charge (at least compared to other interfaces with similar metal–water interaction strengths). The structural information, in this paper, is important for understanding aqueous Mg corrosion, as the Mg(0001)/water interface is the starting point for key reactions. Furthermore, our focus on understanding the driving forces behind this structuring leads to important insights for general metal/water interfaces. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
4. RNA Sequencing of Lens Capsular Epithelium Implicates Novel Pathways in Pseudoexfoliation Syndrome.
- Author
-
Mullany, S, Marshall, H, Zhou, T, Thomson, D, Schmidt, JM, Qassim, A, Knight, LSW, Hollitt, G, Berry, EC, Nguyen, T, To, M-S, Dimasi, D, Kuot, A, Dubowsky, J, Fogarty, R, Sun, M, Chehade, L, Kuruvilla, S, Supramaniam, D, Breen, J, Sharma, S, Landers, J, Lake, S, Mills, RA, Hassall, MM, Chan, WO, Klebe, S, Souzeau, E, Siggs, OM, Craig, JE, Mullany, S, Marshall, H, Zhou, T, Thomson, D, Schmidt, JM, Qassim, A, Knight, LSW, Hollitt, G, Berry, EC, Nguyen, T, To, M-S, Dimasi, D, Kuot, A, Dubowsky, J, Fogarty, R, Sun, M, Chehade, L, Kuruvilla, S, Supramaniam, D, Breen, J, Sharma, S, Landers, J, Lake, S, Mills, RA, Hassall, MM, Chan, WO, Klebe, S, Souzeau, E, Siggs, OM, and Craig, JE
- Abstract
PURPOSE: Pseudoexfoliation syndrome (PEX) is a common systemic disease that results in severe and often irreversible vision loss. Despite considerable research effort, PEX remains incompletely understood. This study sought to perform the first RNAseq study in elucidate the pathophysiology of PEX, and contribute a publicly available transcriptomic data resource for future research. METHODS: Human ocular lens capsular epithelium samples were collected from 25 patients with PEX and 39 non-PEX controls undergoing cataract surgery. RNA extracted from these specimens was subjected to polyadenylated (mRNA) selection and deep bulk RNA sequencing. Differential expression analysis investigated protein-coding gene transcripts. Exploratory analyses used pathway analysis tools, and curated class- and disease-specific gene sets. RESULTS: Differential expression analysis demonstrated that 2882 genes were differentially expressed according to PEX status. Genes associated with viral gene expression pathways were among the most upregulated, alongside genes encoding ribosomal and mitochondrial respiratory transport chain proteins. Cell adhesion protein transcripts including type 4 collagen subunits were downregulated. CONCLUSIONS: This comparative transcriptomic dataset highlights novel and previously recognized pathogenic pathways in PEX and provides the first comprehensive transcriptomic resource, adding an additional layer to build further understanding of PEX pathophysiology.
- Published
- 2022
5. 409 The Impact of Level Loading in a Large Academic Medical System
- Author
-
Dilip, M., Su, H., Zhang, W., Meng, L., Tuffuor, K., Pham, L., Fogarty, R., Venkatesh, A., Pinker, E., and Sangal, R.
- Published
- 2024
- Full Text
- View/download PDF
6. Resonant X-ray photoelectron spectroscopy: identification of atomic contributions to valence states
- Author
-
Seymour, J. M., primary, Gousseva, E., additional, Bennett, R. A., additional, Large, A. I., additional, Held, G., additional, Hein, D., additional, Wartner, G., additional, Quevedo, W., additional, Seidel, R., additional, Kolbeck, C., additional, Clarke, C. J., additional, Fogarty, R. M., additional, Bourne, R. A., additional, Palgrave, R. G., additional, Hunt, P. A., additional, and Lovelock, K. R. J., additional
- Published
- 2022
- Full Text
- View/download PDF
7. Navigating challenges and workarounds: A qualitative study of healthcare and support workers' perceptions on providing care to people seeking sanctuary.
- Author
-
Khanom A, Evans BA, Alanazy W, Couzens L, Fagan L, Fogarty R, John A, Khan T, Kingston MR, Moyo S, Porter A, Richardson G, Rungua G, Williams V, and Snooks H
- Subjects
- Humans, Wales, Female, Male, Attitude of Health Personnel, State Medicine, Adult, Qualitative Research, Health Personnel psychology, Interviews as Topic
- Abstract
Background: Healthcare and support workers play a pivotal role in delivering quality services and support to people seeking sanctuary who have experienced poor physical and mental health linked to previous trauma, relocation and loss of freedoms. However, they often encounter various challenges in their daily work, ranging from communication barriers to resource constraints. This qualitative study seeks to delve into the perspectives of healthcare and support workers' experience of workarounds, employed to overcome barriers to providing care., Aim: This study aims to describe healthcare providers', practitioners' and health and third sector support workers' views on barriers and workarounds to providing care for people seeking sanctuary, to inform policy and practice., Design: A qualitative study was carried out using semi-structured telephone interviews., Setting: This study focused on primary, secondary, community and specialist National Health Service (NHS) support services for people seeking sanctuary in Wales, United Kingdom (2018)., Method: We interviewed 32 healthcare providers, practitioners and support workers employed by primary care and third sector organisations. Our approach involved obtaining verbal informed consent before digitally recording and transcribing all interviews. To analyse the data, we used the Four Levels of Change for Improving Quality model as a guiding framework for interpretation., Results: Our study findings reveal that certain respondents expressed challenges in meeting the needs of people seeking sanctuary; notably, their experience of delivering care differed by care settings. Specifically, those involved in providing specialist NHS care believed that there was room for improvement. Mainstream primary, secondary and community health practitioners faced limitations due to resource constraints and lacked tailored information to address the unique circumstances and needs of sanctuary seekers. To address these gaps, workarounds emerged at both individual and local levels (team/departmental and organisational level). These included establishing informal communication channels between providers, fostering cross service collaboration to fill gaps and adapting existing services to enhance accessibility., Conclusion: Understanding healthcare providers', practitioners' and support workers' perspectives offers invaluable insights into ways to enhance healthcare delivery to sanctuary seekers. Acknowledging challenges and harnessing innovative workarounds can foster a more effective and compassionate service for this vulnerable population., Patient or Public Contribution: The HEAR study actively involved public contributors in the design, delivery and dissemination of the research. Two public contributors (S. M. and G. R.) who had personal experience of seeking asylum served as study co-applicants. They played pivotal roles in shaping the research by participating in its development and securing funding. Alongside other co-applicants, S. M. and G. R. formed the Research Management Group, overseeing study delivery. Their contributions extended to strategic decision-making and specific feedback at critical junctures, including participant recruitment, data collection, analysis and reporting. Additionally, S. M. and G. R. were instrumental in recruiting and supporting a team of peer researchers, enhancing respondent participation among people seeking sanctuary. To facilitate effective public involvement, we provided named contacts for support (A. K. and R. F.), research training, honoraria, reimbursement of expenses and accessible information in line with best practice., (© 2024 The Authors. Health Expectations published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
8. Classifying Malignancy in Prostate Glandular Structures from Biopsy Scans with Deep Learning.
- Author
-
Fogarty R, Goldgof D, Hall L, Lopez A, Johnson J, Gadara M, Stoyanova R, Punnen S, Pollack A, Pow-Sang J, and Balagurunathan Y
- Abstract
Histopathological classification in prostate cancer remains a challenge with high dependence on the expert practitioner. We develop a deep learning (DL) model to identify the most prominent Gleason pattern in a highly curated data cohort and validate it on an independent dataset. The histology images are partitioned in tiles (14,509) and are curated by an expert to identify individual glandular structures with assigned primary Gleason pattern grades. We use transfer learning and fine-tuning approaches to compare several deep neural network architectures that are trained on a corpus of camera images (ImageNet) and tuned with histology examples to be context appropriate for histopathological discrimination with small samples. In our study, the best DL network is able to discriminate cancer grade (GS3/4) from benign with an accuracy of 91%, F
1 -score of 0.91 and AUC 0.96 in a baseline test (52 patients), while the cancer grade discrimination of the GS3 from GS4 had an accuracy of 68% and AUC of 0.71 (40 patients).- Published
- 2023
- Full Text
- View/download PDF
9. RNA Sequencing of Lens Capsular Epithelium Implicates Novel Pathways in Pseudoexfoliation Syndrome.
- Author
-
Mullany S, Marshall H, Zhou T, Thomson D, Schmidt JM, Qassim A, Knight LSW, Hollitt G, Berry EC, Nguyen T, To MS, Dimasi D, Kuot A, Dubowsky J, Fogarty R, Sun M, Chehade L, Kuruvilla S, Supramaniam D, Breen J, Sharma S, Landers J, Lake S, Mills RA, Hassall MM, Chan WO, Klebe S, Souzeau E, Siggs OM, and Craig JE
- Subjects
- Epithelium metabolism, Humans, Sequence Analysis, RNA, Cataract Extraction, Exfoliation Syndrome genetics, Exfoliation Syndrome pathology, Lens, Crystalline metabolism
- Abstract
Purpose: Pseudoexfoliation syndrome (PEX) is a common systemic disease that results in severe and often irreversible vision loss. Despite considerable research effort, PEX remains incompletely understood. This study sought to perform the first RNAseq study in elucidate the pathophysiology of PEX, and contribute a publicly available transcriptomic data resource for future research., Methods: Human ocular lens capsular epithelium samples were collected from 25 patients with PEX and 39 non-PEX controls undergoing cataract surgery. RNA extracted from these specimens was subjected to polyadenylated (mRNA) selection and deep bulk RNA sequencing. Differential expression analysis investigated protein-coding gene transcripts. Exploratory analyses used pathway analysis tools, and curated class- and disease-specific gene sets., Results: Differential expression analysis demonstrated that 2882 genes were differentially expressed according to PEX status. Genes associated with viral gene expression pathways were among the most upregulated, alongside genes encoding ribosomal and mitochondrial respiratory transport chain proteins. Cell adhesion protein transcripts including type 4 collagen subunits were downregulated., Conclusions: This comparative transcriptomic dataset highlights novel and previously recognized pathogenic pathways in PEX and provides the first comprehensive transcriptomic resource, adding an additional layer to build further understanding of PEX pathophysiology.
- Published
- 2022
- Full Text
- View/download PDF
10. Asylum seekers' and refugees' experiences of accessing health care: a qualitative study.
- Author
-
Khanom A, Alanazy W, Couzens L, Evans BA, Fagan L, Fogarty R, John A, Khan T, Kingston MR, Moyo S, Porter A, Rhydderch M, Richardson G, Rungua G, Russell I, and Snooks H
- Abstract
Background: Asylum seekers and refugees (ASRs) often experience poor health in host countries. The United Nations High Commissioner for Refugees (UNHCR) requires hosts to ensure these sanctuary seekers have access to basic health care., Aim: To identify barriers and facilitators that affect access to health care by ASRs in Wales., Design & Setting: Participatory research approach using qualitative focus groups across Wales, which hosts 10 000 refugees., Method: Eight focus groups were undertaken with ASRs, support workers, and volunteers ( n = 57)., Results: Specialist NHS-funded services and grant-aided non-governmental organisations (NGOs) facilitated access to health care, including primary care. Most ASRs understood the role of general practice in providing and coordinating care, but were unaware of out-of-hours services. Reported barriers included: language difficulties, health literacy, unrecognised needs, and the cost of travel to appointments. Participants recognised the importance of mental health, but were disappointed by the state of mental health care. Some feared seeking support for mental health from their GP, and few were aware they had the right to move practice if they were unhappy. Written information about health care was not as accessible to refugees as to asylum seekers (ASs). While some participants read such material before consulting, others struggled to access information when in need. Few participants were aware of health prevention services. Even when they knew about services, such as smoking cessation, these services' difficulty in accommodating ASRs was a barrier., Conclusion: The main barriers identified were: availability of interpreters; knowledge about entitlements; and access to specialist services., (Copyright © 2021, The Authors.)
- Published
- 2021
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.