48 results on '"Ozols M"'
Search Results
2. Photoplethysmography Device for Detection of Changes in the Vasomotor Parameters of Small Laboratory Animals
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Paturskis, Juris, Veliks, V., Ozols, M., Svikis, I., Erts, R., Spigulis, J., Magjarevic, R., editor, Nagel, J. H., editor, Katashev, Alexei, editor, Dekhtyar, Yuri, editor, and Spigulis, Janis, editor
- Published
- 2008
- Full Text
- View/download PDF
3. Assessing Trustworthy AI in Times of COVID-19: Deep Learning for Predicting a Multiregional Score Conveying the Degree of Lung Compromise in COVID-19 Patients.
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Allahabadi, H, Amann, J, Balot, I, Beretta, A, Binkley, C, Bozenhard, J, Bruneault, F, Brusseau, J, Candemir, S, Cappellini, LA, Chakraborty, S, Cherciu, N, Cociancig, C, Coffee, M, Ek, I, Espinosa-Leal, L, Farina, D, Fieux-Castagnet, G, Frauenfelder, T, Gallucci, A, Giuliani, G, Golda, A, van Halem, I, Hildt, E, Holm, S, Kararigas, G, Krier, SA, Kuhne, U, Lizzi, F, Madai, VI, Markus, AF, Masis, S, Mathez, EW, Mureddu, F, Neri, E, Osika, W, Ozols, M, Panigutti, C, Parent, B, Pratesi, F, Moreno-Sanchez, PA, Sartor, G, Savardi, M, Signoroni, A, Sormunen, H-M, Spezzatti, A, Srivastava, A, Stephansen, AF, Theng, LB, Tithi, JJ, Tuominen, J, Umbrello, S, Vaccher, F, Vetter, D, Westerlund, M, Wurth, R, Zicari, RV, Allahabadi, H, Amann, J, Balot, I, Beretta, A, Binkley, C, Bozenhard, J, Bruneault, F, Brusseau, J, Candemir, S, Cappellini, LA, Chakraborty, S, Cherciu, N, Cociancig, C, Coffee, M, Ek, I, Espinosa-Leal, L, Farina, D, Fieux-Castagnet, G, Frauenfelder, T, Gallucci, A, Giuliani, G, Golda, A, van Halem, I, Hildt, E, Holm, S, Kararigas, G, Krier, SA, Kuhne, U, Lizzi, F, Madai, VI, Markus, AF, Masis, S, Mathez, EW, Mureddu, F, Neri, E, Osika, W, Ozols, M, Panigutti, C, Parent, B, Pratesi, F, Moreno-Sanchez, PA, Sartor, G, Savardi, M, Signoroni, A, Sormunen, H-M, Spezzatti, A, Srivastava, A, Stephansen, AF, Theng, LB, Tithi, JJ, Tuominen, J, Umbrello, S, Vaccher, F, Vetter, D, Westerlund, M, Wurth, R, and Zicari, RV
- Abstract
This article's main contributions are twofold: 1) to demonstrate how to apply the general European Union's High-Level Expert Group's (EU HLEG) guidelines for trustworthy AI in practice for the domain of healthcare and 2) to investigate the research question of what does "trustworthy AI" mean at the time of the COVID-19 pandemic. To this end, we present the results of a post-hoc self-assessment to evaluate the trustworthiness of an AI system for predicting a multiregional score conveying the degree of lung compromise in COVID-19 patients, developed and verified by an interdisciplinary team with members from academia, public hospitals, and industry in time of pandemic. The AI system aims to help radiologists to estimate and communicate the severity of damage in a patient's lung from Chest X-rays. It has been experimentally deployed in the radiology department of the ASST Spedali Civili clinic in Brescia, Italy, since December 2020 during pandemic time. The methodology we have applied for our post-hoc assessment, called Z-Inspection®, uses sociotechnical scenarios to identify ethical, technical, and domain-specific issues in the use of the AI system in the context of the pandemic.
- Published
- 2022
4. Proof tactics for a theory of state machines in a graphical environment
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Eastaughffe, K. A., Ozols, M. A., Cant, A., and McCune, William, editor
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- 1997
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- View/download PDF
5. XIsabelle: A system description
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Ozols, M. A., Cant, A., Eastaughffe, K. A., and McCune, William, editor
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- 1997
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- View/download PDF
6. Quantum-access security of the Winternitz one-time signature scheme
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Majenz, C., Manfouo, C.M., Ozols, M., Tessaro, S., ILLC (FNWI), Analysis (KDV, FNWI), Quantum Matter and Quantum Information, and Logic and Computation (ILLC, FNWI/FGw)
- Subjects
FOS: Computer and information sciences ,Quantum Physics ,Computer Science - Cryptography and Security ,Security and privacy → Digital signatures ,one-time signature schemes ,Security and privacy → Information-theoretic techniques ,TheoryofComputation_GENERAL ,FOS: Physical sciences ,post-quantum cryptography ,quantum world ,quantum random oracle model ,information-theoretic security ,Theory of computation → Quantum information theory ,quantum cryptography ,Quantum Physics (quant-ph) ,hash-based signatures ,Cryptography and Security (cs.CR) ,Computer Science::Cryptography and Security - Abstract
Quantum-access security, where an attacker is granted superposition access to secret-keyed functionalities, is a fundamental security model and its study has inspired results in post-quantum security. We revisit, and fill a gap in, the quantum-access security analysis of the Lamport one-time signature scheme (OTS) in the quantum random oracle model (QROM) by Alagic et al. (Eurocrypt 2020). We then go on to generalize the technique to the Winternitz OTS. Along the way, we develop a tool for the analysis of hash chains in the QROM based on the superposition oracle technique by Zhandry (Crypto 2019) which might be of independent interest., LIPIcs, Vol. 199, 2nd Conference on Information-Theoretic Cryptography (ITC 2021), pages 21:1-21:22
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- 2021
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7. Predicting Proteolysis in Complex Proteomes Using Deep Learning
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Ozols, M, Eckersley, A, Platt, CI, Stewart-McGuinness, C, Hibbert, SA, Revote, J, Li, F, Griffiths, CEM, Watson, REB, Song, J, Bell, M, Sherratt, MJ, Ozols, M, Eckersley, A, Platt, CI, Stewart-McGuinness, C, Hibbert, SA, Revote, J, Li, F, Griffiths, CEM, Watson, REB, Song, J, Bell, M, and Sherratt, MJ
- Abstract
Both protease- and reactive oxygen species (ROS)-mediated proteolysis are thought to be key effectors of tissue remodeling. We have previously shown that comparison of amino acid composition can predict the differential susceptibilities of proteins to photo-oxidation. However, predicting protein susceptibility to endogenous proteases remains challenging. Here, we aim to develop bioinformatics tools to (i) predict cleavage site locations (and hence putative protein susceptibilities) and (ii) compare the predicted vulnerabilities of skin proteins to protease- and ROS-mediated proteolysis. The first goal of this study was to experimentally evaluate the ability of existing protease cleavage site prediction models (PROSPER and DeepCleave) to identify experimentally determined MMP9 cleavage sites in two purified proteins and in a complex human dermal fibroblast-derived extracellular matrix (ECM) proteome. We subsequently developed deep bidirectional recurrent neural network (BRNN) models to predict cleavage sites for 14 tissue proteases. The predictions of the new models were tested against experimental datasets and combined with amino acid composition analysis (to predict ultraviolet radiation (UVR)/ROS susceptibility) in a new web app: the Manchester proteome susceptibility calculator (MPSC). The BRNN models performed better in predicting cleavage sites in native dermal ECM proteins than existing models (DeepCleave and PROSPER), and application of MPSC to the skin proteome suggests that: compared with the elastic fiber network, fibrillar collagens may be susceptible primarily to protease-mediated proteolysis. We also identify additional putative targets of oxidative damage (dermatopontin, fibulins and defensins) and protease action (laminins and nidogen). MPSC has the potential to identify potential targets of proteolysis in disparate tissues and disease states.
- Published
- 2021
8. Hamiltonian simulation with optimal sample complexity
- Author
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Massachusetts Institute of Technology. Department of Physics, Kimmel, S, Lin, CYY, Low, GH, Ozols, M, Yoder, TJ, Massachusetts Institute of Technology. Department of Physics, Kimmel, S, Lin, CYY, Low, GH, Ozols, M, and Yoder, TJ
- Abstract
© 2017 Author(s). We investigate the sample complexity of Hamiltonian simulation: how many copies of an unknown quantum state are required to simulate a Hamiltonian encoded by the density matrix of that state? We show that the procedure proposed by Lloyd, Mohseni, and Rebentrost [Nat. Phys., 10(9):631-633, 2014] is optimal for this task. We further extend their method to the case of multiple input states, showing how to simulate any Hermitian polynomial of the states provided. As applications, we derive optimal algorithms for commutator simulation and orthogonality testing, and we give a protocol for creating a coherent superposition of pure states, when given sample access to those states. We also show that this sample-based Hamiltonian simulation can be used as the basis of a universal model of quantum computation that requires only partial swap operations and simple single-qubit states.
- Published
- 2021
9. Span programs and quantum time complexity
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Cornelissen, A., Jeffery, S., Ozols, M., Piedrafita, A., Esparza, J., Král', D., ILLC (FNWI), Analysis (KDV, FNWI), Logic and Computation (ILLC, FNWI/FGw), IoP (FNWI), Quantum Matter and Quantum Information, and Centrum Wiskunde & Informatica, Amsterdam (CWI), The Netherlands
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FOS: Computer and information sciences ,Quantum Physics ,Computer Science - Computational Complexity ,Span programs ,Theory of computation → Quantum query complexity ,FOS: Physical sciences ,Computer Science::Programming Languages ,Variable-time quantum search ,Theory of computation → Algorithm design techniques ,Computational Complexity (cs.CC) ,Quantum Physics (quant-ph) ,Quantum query algorithms ,Theory of computation → Quantum complexity theory - Abstract
Span programs are an important model of quantum computation due to their tight correspondence with quantum query complexity. For any decision problem $f$, the minimum complexity of a span program for $f$ is equal, up to a constant factor, to the quantum query complexity of $f$. Moreover, this correspondence is constructive. A span program for $f$ with complexity $C$ can be compiled into a bounded error quantum algorithm for $f$ with query complexity $O(C)$, and vice versa. In this work, we prove an analogous connection for quantum time complexity. In particular, we show how to convert a quantum algorithm for $f$ with time complexity $T$ into a span program for $f$ such that it compiles back into a quantum algorithm for $f$ with time complexity $\widetilde{O}(T)$. While the query complexity of quantum algorithms obtained from span programs is well-understood, it is not generally clear how to implement certain query-independent operations in a time-efficient manner. We show that for span programs derived from algorithms with a time-efficient implementation, we can preserve the time efficiency when implementing the span program. This means in particular that span programs not only fully capture quantum query complexity, but also quantum time complexity. One practical advantage of being able to convert quantum algorithms to span programs in a way that preserves time complexity is that span programs compose very nicely. We demonstrate this by improving Ambainis's variable-time quantum search result using our construction through a span program composition for the OR function., 54 pages, 2 figures
- Published
- 2020
10. Span programs and quantum time complexity
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Cornelissen, A.J. (Arjan), Jeffery, S. (Stacey), Ozols, M. (Maris), Piedrafita Postigo, A. (Álvaro), Cornelissen, A.J. (Arjan), Jeffery, S. (Stacey), Ozols, M. (Maris), and Piedrafita Postigo, A. (Álvaro)
- Abstract
Span programs are an important model of quantum computation due to their correspondence with quantum query and space complexity. While the query complexity of quantum algorithms obtained from span programs is well-understood, it is not generally clear how to implement certain query-independent operations in a time-efficient manner. In this work, we prove an analogous connection for quantum time complexity. In particular, we show how to convert a sufficiently-structured quantum algorithm for f with time complexity T into a span program for f such that it compiles back into a quantum algorithm for f with time complexity Õ(T). This shows that for span programs derived from algorithms with a time-efficient implementation, we can preserve the time efficiency when implementing the span program, which means that span programs capture time, query and space complexities and are a complete model of quantum algorithms. One practical advantage of being able to convert quantum algorithms to span programs in a way that preserves time complexity is that span programs compose very nicely. We demonstrate this by improving Ambainis's variable-time quantum search result using our construction through a span program composition for the OR function.
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- 2020
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11. DOVE: A tool for design oriented verification and evaluation
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Ozols, M. A., Eastaughffe, K. A., Cant, A., Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, and Johnson, Michael, editor
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- 1997
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12. On quantum chosen-ciphertext attacks and learning with errors
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Alagic, G. (Gorjan), Jeffery, S. (Stacey), Ozols, M. (Maris), Poremba, A. (Alexander), Alagic, G. (Gorjan), Jeffery, S. (Stacey), Ozols, M. (Maris), and Poremba, A. (Alexander)
- Abstract
Quantum computing is a significant threat to classical public-key cryptography. In strong “quantum access” security models, numerous symmetric-key cryptosystems are also vulnerable. We consider classical encryption in a model which grants the adversary quantum oracle access to encryption and decryption, but where the latter is restricted to non-adaptive (i.e., pre-challenge) queries only. We define this model formally using appropriate notions of ciphertext indistinguishability and semantic security (which are equivalent by standard arguments) and call it QCCA1 in analogy to the classical CCA1 security model. Using a bound on quantum random-access codes, we show that the standard PRF-based encryption schemes are QCCA1-secure when instantiated with quantum-secure primitives. We then revisit standard IND-CPA-secure Learning with Errors (LWE) encryption and show that leaking just one quantum decryption query (and no other queries or leakage of any kind) allows the adversary to recover the full secret key with constant success probability. In the classical setting, by contrast, recovering the key requires a linear number of decryption queries. The algorithm at the core of our attack is a (large-modulus version of) the well-known Bernstein-Vazirani algorithm. We emphasize that our results should not be interpreted as a weakness of these cryptosystems in their stated security setting (i.e., post-quantum chosen-plaintext secrecy). Rather, our results mean that, if these cryptosystems are exposed to chosen-ciphertext attacks (e.g., as a result of deployment in an inappropriate real-world setting) then quantum attacks are even more devastating than classical ones.
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- 2019
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13. DOVE: A tool for design oriented verification and evaluation
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Ozols, M. A., primary, Eastaughffe, K. A., additional, and Cant, A., additional
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- 1997
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14. XIsabelle: A system description
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Ozols, M. A., primary, Cant, A., additional, and Eastaughffe, K. A., additional
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- 1997
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15. Proof tactics for a theory of state machines in a graphical environment
- Author
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Eastaughffe, K. A., primary, Ozols, M. A., additional, and Cant, A., additional
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- 1997
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16. Trading inverses for an irrep in the Solovay-Kitaev theorem
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Bouland, A., Ozols, M., Jeffery, S., Logic and Computation (ILLC, FNWI/FGw), ILLC (FNWI), and Quantum Matter and Quantum Information
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Quantum Physics ,000 Computer science, knowledge, general works ,Computer Science::Emerging Technologies ,Computer Science ,FOS: Mathematics ,FOS: Physical sciences ,Mathematical Physics (math-ph) ,Representation Theory (math.RT) ,Quantum Physics (quant-ph) ,Mathematical Physics ,Mathematics - Representation Theory - Abstract
The Solovay-Kitaev theorem states that universal quantum gate sets can be exchanged with low overhead. More specifically, any gate on a fixed number of qudits can be simulated with error $\epsilon$ using merely $\mathrm{polylog}(1/\epsilon)$ gates from any finite universal quantum gate set $\mathcal{G}$. One drawback to the theorem is that it requires the gate set $\mathcal{G}$ to be closed under inversion. Here we show that this restriction can be traded for the assumption that $\mathcal{G}$ contains an irreducible representation of any finite group $G$. This extends recent work of Sardharwalla et al. [arXiv:1602.07963], and applies also to gates from the special linear group. Our work can be seen as partial progress towards the long-standing open problem of proving an inverse-free Solovay-Kitaev theorem [arXiv:quant-ph/0505030, arXiv:0908.0512]., Comment: 16 pages, TQC 2018 proceedings version
- Published
- 2018
17. The role of fibroblasts in the pathogenesis of linear morphoea: targeting the secretome
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Mellody, K.T., primary, Ozols, M., additional, and Watson, R.E.B., additional
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- 2019
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18. On non-adaptive quantum chosen-ciphertext attacks and Learning with Errors
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Alagic, G. (Gorjan), Jeffery, S. (Stacey), Ozols, M. (Maris), Poremba, A. (Alexander), Alagic, G. (Gorjan), Jeffery, S. (Stacey), Ozols, M. (Maris), and Poremba, A. (Alexander)
- Abstract
Large-scale quantum computing is a significant threat to classical public-key cryptography. In strong “quantum access” security models, numerous symmetric-key cryptosystems are also vulnerable. We consider classical encryption in a model which grants the adversary quantum oracle access to encryption and decryption, but where the latter is restricted to non-adaptive (i.e., pre-challenge) queries only. We define this model formally using appropriate notions of c
- Published
- 2018
19. 659 Identifying novel biomarkers of aging
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Halai, P., primary, Ozols, M., additional, Griffiths, C.E.M., additional, Watson, R.E.B., additional, and Langton, A.K., additional
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- 2018
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20. Multi-spectral optoelectronic device for skin microcirculation analysis
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Asare, L., Kviesis-Kipge, E., Ozols, M., Spigulis, J., and Renars Erts
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General Physics and Astronomy - Published
- 2012
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21. 571 Establishing a ‘gold standard’ skin proteome
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Hibbert, S.A., primary, Ozols, M., additional, Griffiths, C.E., additional, Watson, R.E., additional, and Sherratt, M.J., additional
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- 2016
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22. Unbounded number of channel uses are required to see quantum capacity
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Cubitt, Toby S., Elkouss Coronas, David, Matthews, William, Ozols, M., Pérez García, David, Strelchuk, S., Cubitt, Toby S., Elkouss Coronas, David, Matthews, William, Ozols, M., Pérez García, David, and Strelchuk, S.
- Abstract
Transmitting data reliably over noisy communication channels is one of the most important applications of information theory, and is well understood for channels modelled by classical physics. However, when quantum effects are involved, we do not know how to compute channel capacities. This is because the formula for the quantum capacity involves maximizing the coherent information over an unbounded number of channel uses. In fact, entanglement across channel uses can even increase the coherent information from zero to non-zero. Here we study the number of channel uses necessary to detect positive coherent information. In all previous known examples, two channel uses already sufficed. It might be that only a finite number of channel uses is always sufficient. We show that this is not the case: for any number of uses, there are channels for which the coherent information is zero, but which nonetheless have capacity, Depto. de Análisis Matemático y Matemática Aplicada, Fac. de Ciencias Matemáticas, TRUE, pub
- Published
- 2015
23. Dynamics of an active magnetic particle in a rotating magnetic field
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Cēbers, A., primary and Ozols, M., additional
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- 2006
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24. Optical systems for non-invasive cardiovascular biosensing
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Erts, R., primary, SpigulisSr., J., additional, and Ozols, M., additional
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- 2005
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25. Xlsabelle: A Graphical User Interface to the Isabelle Theorem Prover.
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DEFENCE SCIENCE AND TECHNOLOGY ORGANIZATION CANBERRA (AUSTRALIA), Cant, A., Ozols, M. A., DEFENCE SCIENCE AND TECHNOLOGY ORGANIZATION CANBERRA (AUSTRALIA), Cant, A., and Ozols, M. A.
- Abstract
Interactive theorem provers such as Isabelle are powerful tools, but are difficult and time-consuming to learn. If a suitable Graphical User Interface (GUI) is provided for such a tool, it can speed up the learning process considerably, leading to greater productivity for users of the tool, and increased takeup in industry. In this paper, we discuss the user-interface aspects of Isabelle, and formulate requirements for a GUI. XIsabelle, a GUI for XIsabelle, is described in detail. XIsabelle uses standard, easily available, methods for providing X Windows wrappers to interactive non-GUI programs, namely Tcl/Tk and the program Expect.
- Published
- 1995
26. An Approach to Automated Reasoning About Operational Semantics.
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DEFENCE SCIENCE AND TECHNOLOGY ORGANIZATION CANBERRA (AUSTRALIA), Cant, A., Ozols, M. A., DEFENCE SCIENCE AND TECHNOLOGY ORGANIZATION CANBERRA (AUSTRALIA), Cant, A., and Ozols, M. A.
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The assurance of the safety or security of critical software rests on a clear understanding of the formal semantics of the programming language used. Operational semantics is the most widely used means of formally defining a language. The need for high levels of assurance, along with the complexity of these definitions for real programming languages, means that tool support is essential for carrying out reasoning about code with respect to the language definition. In this paper, we describe a generic approach to automated reasoning about the operational semantics of programming languages. As an application of this approach, we describe the construction of an environment for reasoning about programs written in a functional subset of ML. The system we describe (called Elle) captures the formal operational semantics definition of a large subset of Standard ML within the theorem prover Isabelle, and provides some support for the verification of ML programs. (AN)
- Published
- 1994
27. A portable two-channel PPG cardiovascular sensor device
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Janis Spigulis, Erts, R., and Ozols, M.
28. Hamiltonian simulation with optimal sample complexity
- Author
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Kimmel, S, Lin, CYY, Low, GH, Ozols, M, and Yoder, TJ
- Subjects
quant-ph ,16. Peace & justice - Abstract
© 2017 Author(s). We investigate the sample complexity of Hamiltonian simulation: how many copies of an unknown quantum state are required to simulate a Hamiltonian encoded by the density matrix of that state? We show that the procedure proposed by Lloyd, Mohseni, and Rebentrost [Nat. Phys., 10(9):631-633, 2014] is optimal for this task. We further extend their method to the case of multiple input states, showing how to simulate any Hermitian polynomial of the states provided. As applications, we derive optimal algorithms for commutator simulation and orthogonality testing, and we give a protocol for creating a coherent superposition of pure states, when given sample access to those states. We also show that this sample-based Hamiltonian simulation can be used as the basis of a universal model of quantum computation that requires only partial swap operations and simple single-qubit states., S.K. and C.Y.L. are funded by the Department of Defense. G.H.L. is funded by the NSF CCR and the ARO quantum computing projects. M.O. acknowledges Leverhulme Trust Early Career Fellowship (ECF-2015-256) and European Union project QALGO (Grant Agreement No. 600700) for financial support. T.J.Y. thanks the DoD, Air Force Office of Scientific Research, National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a. The authors are grateful to the University of Maryland Libraries’ Open Access Publishing Fund and the Massachusetts Institute of Technology Open Access Publishing Fund for partial funding for open access.
29. Extracellular matrix fragmentation in young, healthy cartilaginous tissues
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Craddock, R.J., Hodson, N.W., Ozols, M., Shearer, T., Hoyland, J.A., Sherratt, M.J., Craddock, R.J., Hodson, N.W., Ozols, M., Shearer, T., Hoyland, J.A., and Sherratt, M.J.
- Abstract
Although the composition and structure of cartilaginous tissues is complex, collagen II fibrils and aggrecan are the most abundant assemblies in both articular cartilage (AC) and the nucleus pulposus (NP) of the intervertebral disc (IVD). Whilst structural heterogeneity of intact aggrecan (containing three globular domains) is well characterised, the extent of aggrecan fragmentation in healthy tissues is poorly defined. Using young, yet skeletally mature (18-30 months), bovine AC and NP tissues, it was shown that, whilst the ultrastructure of intact aggrecan was tissue-dependent, most molecules (AC: 95 %; NP: 99.5 %) were fragmented (lacking one or more globular domains). Fragments were significantly smaller and more structurally heterogeneous in the NP compared with the AC (molecular area; AC: 8543 nm^2; NP: 4625 nm^2; p < 0.0001). In contrast, fibrillar collagen appeared structurally intact and tissue-invariant. Molecular fragmentation is considered indicative of a pathology; however, these young, skeletally mature tissues were histologically and mechanically (reduced modulus: AC: ≈ 500 kPa; NP: ≈ 80 kPa) comparable to healthy tissues and devoid of notable gelatinase activity (compared with rat dermis). As aggrecan fragmentation was prevalent in neonatal bovine AC (99.5 % fragmented, molecular area: 5137 nm^2) as compared with mature AC (95.0 % fragmented, molecular area: 8667 nm^2), it was hypothesised that targeted proteolysis might be an adaptive process that modified aggrecan packing (as simulated computationally) and, hence, tissue charge density, mechanical properties and porosity. These observations provided a baseline against which pathological and/or age-related fragmentation of aggrecan could be assessed and suggested that new strategies might be required to engineer constructs that mimic the mechanical properties of native cartilaginous tissues.
30. Prediction, screening and characterization of novel bioactive tetrapeptide matrikines for skin rejuvenation.
- Author
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Jariwala N, Ozols M, Eckersley A, Mambwe B, Watson REB, Zeef L, Gilmore A, Debelle L, Bell M, Bradley EJ, Doush Y, Keenan A, Courage C, Leroux R, Peschard O, Mondon P, Ringenbach C, Bernard L, Pitois A, and Sherratt MJ
- Subjects
- Humans, Skin drug effects, Skin pathology, Skin metabolism, Cells, Cultured, Female, Middle Aged, Cell Proliferation drug effects, Extracellular Matrix metabolism, Male, Extracellular Matrix Proteins metabolism, Adult, Aged, Proteomics methods, Fibroblasts metabolism, Fibroblasts drug effects, Skin Aging drug effects, Rejuvenation, Oligopeptides pharmacology
- Abstract
Background: Extracellular matrices play a critical role in tissue structure and function and aberrant remodelling of these matrices is a hallmark of many age-related diseases. In skin, loss of dermal collagens and disorganization of elastic fibre components are key features of photoageing. Although the application of some small matrix-derived peptides to aged skin has been shown to beneficially affect in vitro cell behaviour and, in vivo, molecular architecture and clinical appearance, the discovery of new peptides has lacked a guiding hypothesis., Objectives: To identify, using protease cleavage site prediction, novel putative matrikines with beneficial activities for skin composition and structure., Methods: Here, we present an in silico (peptide cleavage prediction) to in vitro (proteomic and transcriptomic activity testing in cultured human dermal fibroblasts) to in vivo (short-term patch test and longer-term split-face clinical study) discovery pipeline, which enables the identification and characterization of peptides with differential activities., Results: Using this pipeline we showed that cultured fibroblasts were responsive to all applied peptides, but their associated bioactivity was sequence-dependent. Based on bioactivity, toxicity and protein source, we further characterized a combination of two novel peptides, GPKG (glycine-proline-lysine-glycine) and LSVD (leucine-serine-valine-aspartate), that acted in vitro to enhance the transcription of matrix -organization and cell proliferation genes and in vivo (in a short-term patch test) to promote processes associated with epithelial and dermal maintenance and remodelling. Prolonged use of a formulation containing these peptides in a split-face clinical study led to significantly improved measures of crow's feet and firmness in a mixed population., Conclusions: This approach to peptide discovery and testing can identify new synthetic matrikines, providing insights into biological mechanisms of tissue homeostasis and repair and new pathways to clinical intervention., Competing Interests: Conflicts of interest M.B., E.J.B., Y.D., C.C. and A.K. are employees of No7 Beauty Company, Walgreens Boots Alliance; O.P., P.M., C.R., L.B., R.L. and A.P. are employees of Sederma and are bound by confidentiality agreements that prevent them from disclosing their competing interests in this work. N.J., M.O., A.E. and B.M. were supported by a programme grant awarded by No7 Beauty Company, Walgreens Boots Alliance to M.J.S. and R.E.B.W. L.D., A.G. and L.Z. declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Association of Dermatologists.)
- Published
- 2024
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- View/download PDF
31. Oxidative DNA damage promotes vascular aging associated with changes in extracellular matrix-regulating proteins.
- Author
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Foote K, Rienks M, Schmidt L, Theofilatos K, Yasmin, Ozols M, Eckersley A, Shah A, Figg N, Finigan A, O'Shaughnessy K, Wilkinson IB, Mayr M, and Bennett M
- Abstract
Aims: Vascular aging is characterized by vessel stiffening, with increased deposition of extracellular matrix (ECM) proteins including collagens. Oxidative DNA damage occurs in vascular aging, but how it regulates ECM proteins and vascular stiffening is unknown. We sought to determine the relationship between oxidative DNA damage and ECM regulatory proteins in vascular aging., Methods and Results: We examined oxidative DNA damage, the major base excision repair (BER) enzyme 8-Oxoguanine DNA Glycosylase (Ogg1) and its regulators, multiple physiological markers of aging, and ECM proteomics in mice from 22-72w. Vascular aging was associated with increased oxidative DNA damage, and decreased expression of Ogg1, its active acetylated form, its acetylation regulatory proteins P300 and CBP, and the transcription factor Foxo3a. Vascular stiffness was examined in vivo in control, Ogg1-/-, or mice with vascular smooth muscle cell-specific expression of Ogg1+ (Ogg1) or an inactive mutation (Ogg1KR). Ogg1-/- and Ogg1KR mice showed reduced arterial compliance and distensibility, and increased stiffness and pulse pressure, whereas Ogg1 expression normalised all parameters to 72w. ECM proteomics identified major changes in collagens with aging, and downregulation of the ECM regulatory proteins Protein 6-lysyl oxidase (LOX) and WNT1-inducible-signaling pathway protein 2 (WISP2). Ogg1 overexpression upregulated LOX and WISP2 both in vitro and in vivo, and downregulated Transforming growth factor β1 (TGFb1) and Collagen 4α1 in vivo compared with Ogg1KR. Foxo3a activation induced Lox, while Wnt3 induction of Wisp2 also upregulated LOX and Foxo3a, and downregulated TGFβ1 and fibronectin 1. In humans, 8-oxo-G increased with vascular stiffness, while active OGG1 reduced with both age and stiffness., Conclusions: Vascular aging is associated with oxidative DNA damage, downregulation of major BER proteins, and changes in multiple ECM structural and regulatory proteins. Ogg1 protects against vascular aging, associated with changes in ECM regulatory proteins including LOX and WISP2., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Cardiology.)
- Published
- 2024
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32. hadge: a comprehensive pipeline for donor deconvolution in single-cell studies.
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Curion F, Wu X, Heumos L, André MMG, Halle L, Ozols M, Grant-Peters M, Rich-Griffin C, Yeung HY, Dendrou CA, Schiller HB, and Theis FJ
- Subjects
- Humans, Brain metabolism, Brain cytology, Software, Genotype, Single-Cell Analysis methods
- Abstract
Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue., (© 2024. The Author(s).)
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- 2024
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33. Peptide location fingerprinting identifies structural alterations within basement membrane components in ageing kidney.
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Eckersley A, Morais MR, Ozols M, and Lennon R
- Subjects
- Mice, Animals, Humans, Aged, Basement Membrane metabolism, Kidney pathology, Extracellular Matrix Proteins metabolism, Collagen Type IV genetics, Collagen Type IV metabolism, Laminin genetics, Laminin metabolism, Proteomics, Kidney Diseases metabolism
- Abstract
During ageing, the glomerular and tubular basement membranes (BM) of the kidney undergo a progressive decline in function that is underpinned by histological changes, including glomerulosclerosis and tubular interstitial fibrosis and atrophy. This BM-specific ageing is thought to result from damage accumulation to long-lived extracellular matrix (ECM) protein structures. Determining which BM proteins are susceptible to these structure-associated changes, and the possible mechanisms and downstream consequences, is critical to understand age-related kidney degeneration and to identify markers for therapeutic intervention. Peptide location fingerprinting (PLF) is an emerging proteomic mass spectrometry analysis technique capable of identifying ECM proteins with structure-associated differences that may occur by damage modifications in ageing. Here, we apply PLF as a bioinformatic screening tool to identify BM proteins with structure-associated differences between young and aged human glomerular and tubulointerstitial compartments. Several functional regions within key BM components displayed alterations in tryptic peptide yield, reflecting potential age-dependent shifts in molecular (e.g. laminin-binding regions in agrin) and cellular (e.g. integrin-binding regions in laminins 521 and 511) interactions, oxidation (e.g. collagen IV) and the fragmentation and release of matrikines (e.g. canstatin and endostatin from collagens IV and XVIII). Furthermore, we found that periostin and the collagen IV α2 chain exhibited structure-associated differences in ageing that were conserved between human kidney and previously analysed mouse lung, revealing BM components that harbour shared susceptibilities across species and organs., Competing Interests: Declaration of Competing Interest The authors declare no conflicts of interest., (Copyright © 2023. Published by Elsevier B.V.)
- Published
- 2023
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34. Peptide location fingerprinting identifies species- and tissue-conserved structural remodelling of proteins as a consequence of ageing and disease.
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Eckersley A, Ozols M, Chen P, Tam V, Ward LJ, Hoyland JA, Trafford A, Yuan XM, Schiller HB, Chan D, and Sherratt MJ
- Subjects
- Mice, Animals, Humans, Fibronectins metabolism, Filamins analysis, Filamins metabolism, Proteomics methods, Collagen metabolism, Aging metabolism, Laminin metabolism, Peptides metabolism, Macroglobulins analysis, Macroglobulins metabolism, Intervertebral Disc metabolism, Intervertebral Disc Degeneration metabolism, Atherosclerosis genetics, Atherosclerosis metabolism
- Abstract
Extracellular matrices (ECMs) in the intervertebral disc (IVD), lung and artery are thought to undergo age-dependant accumulation of damage by chronic exposure to mechanisms such as reactive oxygen species, proteases and glycation. It is unknown whether this damage accumulation is species-dependant (via differing lifespans and hence cumulative exposures) or whether it can influence the progression of age-related diseases such as atherosclerosis. Peptide location fingerprinting (PLF) is a new proteomic analysis method, capable of the non-targeted identification of structure-associated changes within proteins. Here we applied PLF to publicly available ageing human IVD (outer annulus fibrosus), ageing mouse lung and human arterial atherosclerosis datasets and bioinformatically identified novel target proteins alongside common age-associated differences within protein structures which were conserved between three ECM-rich organs, two species, three IVD tissue regions, sexes and in an age-related disease. We identify peptide yield differences across protein structures which coincide with biological regions, potentially reflecting the functional consequences of ageing or atherosclerosis for macromolecular assemblies (collagen VI), enzyme/inhibitor activity (alpha-2 macroglobulin), activation states (complement C3) and interaction states (laminins, perlecan, fibronectin, filamin-A, collagen XIV and apolipoprotein-B). Furthermore, we show that alpha-2 macroglobulin and collagen XIV exhibit possible shared structural consequences in IVD ageing and arterial atherosclerosis, providing novel links between an age-related disease and intrinsic ageing. Crucially, we also demonstrate that fibronectin, laminin beta chains and filamin-A all exhibit conserved age-associated structural differences between mouse lung and human IVD, providing evidence that ECM, and their associating proteins, may be subjected to potentially similar mechanisms or consequences of ageing across both species, irrespective of differences in lifespan and tissue function., Competing Interests: Declaration of Competing Interest The authors declare no conflicts of interest. WBA approved manuscript submission but exerted no editorial control., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)
- Published
- 2022
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35. Assessing Trustworthy AI in Times of COVID-19: Deep Learning for Predicting a Multiregional Score Conveying the Degree of Lung Compromise in COVID-19 Patients.
- Author
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Allahabadi H, Amann J, Balot I, Beretta A, Binkley C, Bozenhard J, Bruneault F, Brusseau J, Candemir S, Cappellini LA, Chakraborty S, Cherciu N, Cociancig C, Coffee M, Ek I, Espinosa-Leal L, Farina D, Fieux-Castagnet G, Frauenfelder T, Gallucci A, Giuliani G, Golda A, van Halem I, Hildt E, Holm S, Kararigas G, Krier SA, Kuhne U, Lizzi F, Madai VI, Markus AF, Masis S, Mathez EW, Mureddu F, Neri E, Osika W, Ozols M, Panigutti C, Parent B, Pratesi F, Moreno-Sanchez PA, Sartor G, Savardi M, Signoroni A, Sormunen HM, Spezzatti A, Srivastava A, Stephansen AF, Theng LB, Tithi JJ, Tuominen J, Umbrello S, Vaccher F, Vetter D, Westerlund M, Wurth R, and Zicari RV
- Abstract
This article's main contributions are twofold: 1) to demonstrate how to apply the general European Union's High-Level Expert Group's (EU HLEG) guidelines for trustworthy AI in practice for the domain of healthcare and 2) to investigate the research question of what does "trustworthy AI" mean at the time of the COVID-19 pandemic. To this end, we present the results of a post-hoc self-assessment to evaluate the trustworthiness of an AI system for predicting a multiregional score conveying the degree of lung compromise in COVID-19 patients, developed and verified by an interdisciplinary team with members from academia, public hospitals, and industry in time of pandemic. The AI system aims to help radiologists to estimate and communicate the severity of damage in a patient's lung from Chest X-rays. It has been experimentally deployed in the radiology department of the ASST Spedali Civili clinic in Brescia, Italy, since December 2020 during pandemic time. The methodology we have applied for our post-hoc assessment, called Z-Inspection®, uses sociotechnical scenarios to identify ethical, technical, and domain-specific issues in the use of the AI system in the context of the pandemic.
- Published
- 2022
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36. Matrikines as mediators of tissue remodelling.
- Author
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Jariwala N, Ozols M, Bell M, Bradley E, Gilmore A, Debelle L, and Sherratt MJ
- Subjects
- Cytokines metabolism, Extracellular Matrix metabolism, Humans, Peptides metabolism, Skin metabolism, Collagen chemistry, Wound Healing
- Abstract
Extracellular matrix (ECM) proteins confer biomechanical properties, maintain cell phenotype and mediate tissue repair (via release of sequestered cytokines and proteases). In contrast to intracellular proteomes, where proteins are monitored and replaced over short time periods, many ECM proteins function for years (decades in humans) without replacement. The longevity of abundant ECM proteins, such as collagen I and elastin, leaves them vulnerable to damage accumulation and their host organs prone to chronic, age-related diseases. However, ECM protein fragmentation can potentially produce peptide cytokines (matrikines) which may exacerbate and/or ameliorate age- and disease-related ECM remodelling. In this review, we discuss ECM composition, function and degradation and highlight examples of endogenous matrikines. We then critically and comprehensively analyse published studies of matrix-derived peptides used as topical skin treatments, before considering the potential for improvements in the discovery and delivery of novel matrix-derived peptides to skin and internal organs. From this, we conclude that while the translational impact of matrix-derived peptide therapeutics is evident, the mechanisms of action of these peptides are poorly defined. Further, well-designed, multimodal studies are required., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2022
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37. Defining the Protease and Protease Inhibitor (P/PI) Proteomes of Healthy and Diseased Human Skin by Modified Systematic Review.
- Author
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Stewart-McGuinness C, Platt CI, Ozols M, Goh B, Griffiths TW, and Sherratt MJ
- Subjects
- Antiviral Agents, Humans, Peptide Hydrolases, Proteomics, Protease Inhibitors pharmacology, Proteome
- Abstract
Proteases and protease inhibitors (P/PIs) are involved in many biological processes in human skin, yet often only specific families or related groups of P/PIs are investigated. Proteomics approaches, such as mass spectrometry, can define proteome signatures (including P/PIs) in tissues; however, they struggle to detect low-abundance proteins. To overcome these issues, we aimed to produce a comprehensive proteome of all P/PIs present in normal and diseased human skin, in vivo, by carrying out a modified systematic review using a list of P/PIs from MEROPS and combining this with key search terms in Web of Science. Resulting articles were manually reviewed against inclusion/exclusion criteria and a dataset constructed. This study identified 111 proteases and 77 protease inhibitors in human skin, comprising the serine, metallo-, cysteine and aspartic acid catalytic families of proteases. P/PIs showing no evidence of catalytic activity or protease inhibition, were designated non-peptidase homologs (NPH), and no reported protease inhibitory activity (NRPIA), respectively. MMP9 and TIMP1 were the most frequently published P/PIs and were reported in normal skin and most skin disease groups. Normal skin and diseased skin showed significant overlap with respect to P/PI profile; however, MMP23 was identified in several skin disease groups, but was absent in normal skin. The catalytic profile of P/PIs in wounds, scars and solar elastosis was distinct from normal skin, suggesting that a different group of P/PIs is responsible for disease progression. In conclusion, this study uses a novel approach to provide a comprehensive inventory of P/PIs in normal and diseased human skin reported in our database. The database may be used to determine either which P/PIs are present in specific diseases or which diseases individual P/PIs may influence.
- Published
- 2022
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38. Peptide Location Fingerprinting Reveals Tissue Region-Specific Differences in Protein Structures in an Ageing Human Organ.
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Eckersley A, Ozols M, Chen P, Tam V, Hoyland JA, Trafford A, Chan D, and Sherratt MJ
- Subjects
- Aged, Extracellular Matrix, Humans, Proteomics, Aging metabolism, Collagen metabolism, Intervertebral Disc metabolism, Peptide Mapping
- Abstract
In ageing tissues, long-lived extracellular matrix (ECM) proteins are susceptible to the accumulation of structural damage due to diverse mechanisms including glycation, oxidation and protease cleavage. Peptide location fingerprinting (PLF) is a new mass spectrometry (MS) analysis technique capable of identifying proteins exhibiting structural differences in complex proteomes. PLF applied to published young and aged intervertebral disc (IVD) MS datasets (posterior, lateral and anterior regions of the annulus fibrosus) identified 268 proteins with age-associated structural differences. For several ECM assemblies (collagens I, II and V and aggrecan), these differences were markedly conserved between degeneration-prone (posterior and lateral) and -resistant (anterior) regions. Significant differences in peptide yields, observed within collagen I α2, collagen II α1 and collagen V α1, were located within their triple-helical regions and/or cleaved C-terminal propeptides, indicating potential accumulation of damage and impaired maintenance. Several proteins (collagen V α1, collagen II α1 and aggrecan) also exhibited tissue region (lateral)-specific differences in structure between aged and young samples, suggesting that some ageing mechanisms may act locally within tissues. This study not only reveals possible age-associated differences in ECM protein structures which are tissue-region specific, but also highlights the ability of PLF as a proteomic tool to aid in biomarker discovery.
- Published
- 2021
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39. Peptide location fingerprinting reveals modification-associated biomarker candidates of ageing in human tissue proteomes.
- Author
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Ozols M, Eckersley A, Mellody KT, Mallikarjun V, Warwood S, O'Cualain R, Knight D, Watson REB, Griffiths CEM, Swift J, and Sherratt MJ
- Subjects
- Aged, Biomarkers chemistry, Chromatography, Liquid, Extracellular Matrix chemistry, Hemidesmosomes chemistry, Humans, Keratins metabolism, Middle Aged, Peptides analysis, Protein Biosynthesis, Proteome chemistry, Software, Tandem Mass Spectrometry, Peptide Mapping methods, Proteomics methods, Skin chemistry, Skin Aging radiation effects
- Abstract
Although dysfunctional protein homeostasis (proteostasis) is a key factor in many age-related diseases, the untargeted identification of structurally modified proteins remains challenging. Peptide location fingerprinting is a proteomic analysis technique capable of identifying structural modification-associated differences in mass spectrometry (MS) data sets of complex biological samples. A new webtool (Manchester Peptide Location Fingerprinter), applied to photoaged and intrinsically aged skin proteomes, can relatively quantify peptides and map statistically significant differences to regions within protein structures. New photoageing biomarker candidates were identified in multiple pathways including extracellular matrix organisation (collagens and proteoglycans), protein synthesis and folding (ribosomal proteins and TRiC complex subunits), cornification (keratins) and hemidesmosome assembly (plectin and integrin α6β4). Crucially, peptide location fingerprinting uniquely identified 120 protein biomarker candidates in the dermis and 71 in the epidermis which were modified as a consequence of photoageing but did not differ significantly in relative abundance (measured by MS1 ion intensity). By applying peptide location fingerprinting to published MS data sets, (identifying biomarker candidates including collagen V and versican in ageing tendon) we demonstrate the potential of the MPLF webtool for biomarker discovery., (© 2021 The Authors. Aging Cell published by Anatomical Society and John Wiley & Sons Ltd.)
- Published
- 2021
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40. Predicting Proteolysis in Complex Proteomes Using Deep Learning.
- Author
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Ozols M, Eckersley A, Platt CI, Stewart-McGuinness C, Hibbert SA, Revote J, Li F, Griffiths CEM, Watson REB, Song J, Bell M, and Sherratt MJ
- Subjects
- Amino Acids metabolism, Extracellular Matrix Proteins metabolism, Humans, Neural Networks, Computer, Peptide Hydrolases metabolism, Reactive Oxygen Species metabolism, Reproducibility of Results, Software, Ultraviolet Rays, Deep Learning, Proteolysis radiation effects, Proteome metabolism
- Abstract
Both protease- and reactive oxygen species (ROS)-mediated proteolysis are thought to be key effectors of tissue remodeling. We have previously shown that comparison of amino acid composition can predict the differential susceptibilities of proteins to photo-oxidation. However, predicting protein susceptibility to endogenous proteases remains challenging. Here, we aim to develop bioinformatics tools to (i) predict cleavage site locations (and hence putative protein susceptibilities) and (ii) compare the predicted vulnerabilities of skin proteins to protease- and ROS-mediated proteolysis. The first goal of this study was to experimentally evaluate the ability of existing protease cleavage site prediction models (PROSPER and DeepCleave) to identify experimentally determined MMP9 cleavage sites in two purified proteins and in a complex human dermal fibroblast-derived extracellular matrix (ECM) proteome. We subsequently developed deep bidirectional recurrent neural network (BRNN) models to predict cleavage sites for 14 tissue proteases. The predictions of the new models were tested against experimental datasets and combined with amino acid composition analysis (to predict ultraviolet radiation (UVR)/ROS susceptibility) in a new web app: the Manchester proteome susceptibility calculator (MPSC). The BRNN models performed better in predicting cleavage sites in native dermal ECM proteins than existing models (DeepCleave and PROSPER), and application of MPSC to the skin proteome suggests that: compared with the elastic fiber network, fibrillar collagens may be susceptible primarily to protease-mediated proteolysis. We also identify additional putative targets of oxidative damage (dermatopontin, fibulins and defensins) and protease action (laminins and nidogen). MPSC has the potential to identify potential targets of proteolysis in disparate tissues and disease states.
- Published
- 2021
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41. Simulating Large Quantum Circuits on a Small Quantum Computer.
- Author
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Peng T, Harrow AW, Ozols M, and Wu X
- Abstract
Limited quantum memory is one of the most important constraints for near-term quantum devices. Understanding whether a small quantum computer can simulate a larger quantum system, or execute an algorithm requiring more qubits than available, is both of theoretical and practical importance. In this Letter, we introduce cluster parameters K and d of a quantum circuit. The tensor network of such a circuit can be decomposed into clusters of size at most d with at most K qubits of inter-cluster quantum communication. We propose a cluster simulation scheme that can simulate any (K,d)-clustered quantum circuit on a d-qubit machine in time roughly 2^{O(K)}, with further speedups possible when taking more fine-grained circuit structure into account. We show how our scheme can be used to simulate clustered quantum systems-such as large molecules-that can be partitioned into multiple significantly smaller clusters with weak interactions among them. By using a suitable clustered ansatz, we also experimentally demonstrate that a quantum variational eigensolver can still achieve the desired performance for estimating the energy of the BeH_{2} molecule while running on a physical quantum device with half the number of required qubits.
- Published
- 2020
- Full Text
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42. Proteomic fingerprints of damage in extracellular matrix assemblies.
- Author
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Eckersley A, Ozols M, O'Cualain R, Keevill EJ, Foster A, Pilkington S, Knight D, Griffiths CEM, Watson REB, and Sherratt MJ
- Abstract
In contrast to the dynamic intracellular environment, structural extracellular matrix (ECM) proteins with half-lives measured in decades, are susceptible to accumulating damage. Whilst conventional approaches such as histology, immunohistochemistry and mass spectrometry are able to identify age- and disease-related changes in protein abundance or distribution, these techniques are poorly suited to characterising molecular damage. We have previously shown that mass spectrometry can detect tissue-specific differences in the proteolytic susceptibility of protein regions within fibrillin-1 and collagen VI alpha-3. Here, we present a novel proteomic approach to detect damage-induced "peptide fingerprints" within complex multi-component ECM assemblies (fibrillin and collagen VI microfibrils) following their exposure to ultraviolet radiation (UVR) by broadband UVB or solar simulated radiation (SSR). These assemblies were chosen because, in chronically photoaged skin, fibrillin and collagen VI microfibril architectures are differentially susceptible to UVR. In this study, atomic force microscopy revealed that fibrillin microfibril ultrastructure was significantly altered by UVR exposure whereas the ultrastructure of collagen VI microfibrils was resistant. UVR-induced molecular damage was further characterised by proteolytic peptide generation with elastase followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Peptide mapping revealed that UVR exposure increased regional proteolytic susceptibility within the protein structures of fibrillin-1 and collagen VI alpha-3. This allowed the identification of UVR-induced molecular changes within these two key ECM assemblies. Additionally, similar changes were observed within protein regions of co-purifying, microfibril-associated receptors integrins αv and β1. This study demonstrates that LC-MS/MS mapping of peptides enables the characterisation of molecular post-translational damage (via direct irradiation and radiation-induced oxidative mechanisms) within a complex in vitro model system. This peptide fingerprinting approach reliably allows both the identification of UVR-induced molecular damage in and between proteins and the identification of specific protein domains with increased proteolytic susceptibility as a result of photo-denaturation. This has the potential to serve as a sensitive method of identifying accumulated molecular damage in vivo using conventional mass spectrometry data-sets., Competing Interests: The authors declare that they have no conflicts of interest with the contents of this article. Walgreens Boots Alliance has approved this manuscript submission but exerted no editorial control over the content., (© 2020 The Authors.)
- Published
- 2020
- Full Text
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43. Circadian rhythms in skin and other elastic tissues.
- Author
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Sherratt MJ, Hopkinson L, Naven M, Hibbert SA, Ozols M, Eckersley A, Newton VL, Bell M, and Meng QJ
- Subjects
- Animals, Elastic Tissue metabolism, Extracellular Matrix metabolism, Homeostasis, Humans, Circadian Rhythm, Extracellular Matrix Proteins metabolism, Skin metabolism
- Abstract
Circadian rhythms are daily oscillations that, in mammals, are driven by both a master clock, located in the brain, and peripheral clocks in cells and tissues. Approximately 10% of the transcriptome, including extracellular matrix components, is estimated to be under circadian control. Whilst it has been established that certain collagens and extracellular matrix proteases are diurnally regulated (for example in tendon, cartilage and intervertebral disc) the role played by circadian rhythms in mediating elastic fiber homeostasis is poorly understood. Skin, arteries and lungs are dynamic, resilient, elastic fiber-rich organs and tissues. In skin, circadian rhythms influence cell migration and proliferation, wound healing and susceptibility of the tissues to damage (from protease activity, oxidative stress and ultraviolet radiation). In the cardiovascular system, blood pressure and heart rate also follow age-dependent circadian rhythms whilst the lungs exhibit diurnal variations in immune response. In order to better understand these processes it will be necessary to characterise diurnal changes in extracellular matrix biology. In particular, given the sensitivity of peripheral clocks to external factors, the timed delivery of interventions (chronotherapy) has the potential to significantly improve the efficacy of treatments designed to repair and regenerate damaged cutaneous, vascular and pulmonary tissues., (Copyright © 2019 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.)
- Published
- 2019
- Full Text
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44. Extracellular matrix fragmentation in young, healthy cartilaginous tissues.
- Author
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Craddock RJ, Hodson NW, Ozols M, Shearer T, Hoyland JA, and Sherratt MJ
- Subjects
- Adsorption, Aggrecans chemistry, Aggrecans metabolism, Aggrecans ultrastructure, Amino Acid Sequence, Animals, Biomechanical Phenomena, Cattle, Collagen metabolism, Compressive Strength, Computer Simulation, Gelatinases metabolism, Matrix Metalloproteinases metabolism, Microscopy, Atomic Force, Nanoparticles, Nucleus Pulposus, Organ Specificity, Surface Properties, Cartilage, Articular metabolism, Extracellular Matrix metabolism
- Abstract
Although the composition and structure of cartilaginous tissues is complex, collagen II fibrils and aggrecan are the most abundant assemblies in both articular cartilage (AC) and the nucleus pulposus (NP) of the intervertebral disc (IVD). Whilst structural heterogeneity of intact aggrecan ( containing three globular domains) is well characterised, the extent of aggrecan fragmentation in healthy tissues is poorly defined. Using young, yet skeletally mature (18-30 months), bovine AC and NP tissues, it was shown that, whilst the ultrastructure of intact aggrecan was tissue-dependent, most molecules (AC: 95 %; NP: 99.5 %) were fragmented (lacking one or more globular domains). Fragments were significantly smaller and more structurally heterogeneous in the NP compared with the AC (molecular area; AC: 8543 nm2; NP: 4625 nm2; p < 0.0001). In contrast, fibrillar collagen appeared structurally intact and tissue-invariant. Molecular fragmentation is considered indicative of a pathology; however, these young, skeletally mature tissues were histologically and mechanically (reduced modulus: AC: ≈ 500 kPa; NP: ≈ 80 kPa) comparable to healthy tissues and devoid of notable gelatinase activity (compared with rat dermis). As aggrecan fragmentation was prevalent in neonatal bovine AC (99.5 % fragmented, molecular area: 5137 nm2) as compared with mature AC (95.0 % fragmented, molecular area: 8667 nm2), it was hypothesised that targeted proteolysis might be an adaptive process that modified aggrecan packing (as simulated computationally) and, hence, tissue charge density, mechanical properties and porosity. These observations provided a baseline against which pathological and/or age-related fragmentation of aggrecan could be assessed and suggested that new strategies might be required to engineer constructs that mimic the mechanical properties of native cartilaginous tissues.
- Published
- 2018
- Full Text
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45. Defining tissue proteomes by systematic literature review.
- Author
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Hibbert SA, Ozols M, Griffiths CEM, Watson REB, Bell M, and Sherratt MJ
- Subjects
- Humans, Proteome chemistry, Proteome genetics, Meta-Analysis as Topic, Proteome metabolism, Proteomics methods, Skin metabolism, Software
- Abstract
Defining protein composition is a key step in understanding the function of both healthy and diseased biological systems. There is currently little consensus between existing published proteomes in tissues such as the aorta, cartilage and organs such as skin. Lack of agreement as to both the number and identity of proteins may be due to issues in protein extraction, sensitivity/specificity of detection and the use of disparate tissue/cell sources. Here, we developed a method combining bioinformatics and systematic review to screen >32M articles from the Web of Science for evidence of proteins in healthy human skin. The resulting Manchester Proteome ( www.manchesterproteome.manchester.ac.uk ) collates existing evidence which characterises 2,948 skin proteins, 437 unique to our database and 2011 evidenced by both mass spectrometry and immune-based techniques. This approach circumvents the limitations of individual proteomics studies and can be applied to other species, organs, cells or disease-states. Accurate tissue proteomes will aid development of engineered constructs and offer insight into disease treatments by highlighting differences in proteomic composition.
- Published
- 2018
- Full Text
- View/download PDF
46. Unbounded number of channel uses may be required to detect quantum capacity.
- Author
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Cubitt T, Elkouss D, Matthews W, Ozols M, Pérez-García D, and Strelchuk S
- Abstract
Transmitting data reliably over noisy communication channels is one of the most important applications of information theory, and is well understood for channels modelled by classical physics. However, when quantum effects are involved, we do not know how to compute channel capacities. This is because the formula for the quantum capacity involves maximizing the coherent information over an unbounded number of channel uses. In fact, entanglement across channel uses can even increase the coherent information from zero to non-zero. Here we study the number of channel uses necessary to detect positive coherent information. In all previous known examples, two channel uses already sufficed. It might be that only a finite number of channel uses is always sufficient. We show that this is not the case: for any number of uses, there are channels for which the coherent information is zero, but which nonetheless have capacity.
- Published
- 2015
- Full Text
- View/download PDF
47. Bound entangled states with a private key and their classical counterpart.
- Author
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Ozols M, Smith G, and Smolin JA
- Abstract
Entanglement is a fundamental resource for quantum information processing. In its pure form, it allows quantum teleportation and sharing classical secrets. Realistic quantum states are noisy and their usefulness is only partially understood. Bound-entangled states are central to this question--they have no distillable entanglement, yet sometimes still have a private classical key. We present a construction of bound-entangled states with a private key based on classical probability distributions. From this emerge states possessing a new classical analogue of bound entanglement, distinct from the long-sought bound information. We also find states of smaller dimensions and higher key rates than previously known. Our construction has implications for classical cryptography: we show that existing protocols are insufficient for extracting private key from our distributions due to their "bound-entangled" nature. We propose a simple extension of existing protocols that can extract a key from them.
- Published
- 2014
- Full Text
- View/download PDF
48. Bilateral photoplethysmography studies of the leg arterial stenosis.
- Author
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Erts R, Spigulis J, Kukulis I, and Ozols M
- Subjects
- Adult, Aged, Aged, 80 and over, Blood Pressure, Humans, Leg blood supply, Middle Aged, Arterial Occlusive Diseases diagnosis, Peripheral Vascular Diseases diagnosis, Photoplethysmography methods
- Abstract
A newly developed portable multi-channel photoplethysmography (PPG) device has been used for comparative studies of 20 healthy control subjects and 45 patients with diagnosed arterial stenosis in a leg. The peripheral blood pulsations were detected simultaneously at four body sites-the same fingers and toes of both arms and legs. The PPG pulses recorded at the periphery of the stenotic leg, if compared with those of the healthy leg, were much weaker, with delayed arrival as a consequence of increased pulse wave transit time (PWTT) due to higher vascular resistance. The specific PWTT delays for the occluded legs were in the range of 20-80 ms, while in the case of healthy subjects the leg PPG signals arrived without delays or with smaller time-shifts not exceeding 14 ms. The reference bilateral PPG signals detected at the fingertips did not show any notable PWTT delays in both groups. Parallel measurements of local blood pressures by means of the oscillometry method with subsequent calculation of the ankle-brachial index were performed. Convincing correlation between the bilateral differences in the local blood pressure (a routine tool for diagnostics of leg stenosis) and in the corresponding PWTT delay (Pearson's coefficient r = 0.93), as well as between the PWTT delay and the ankle-brachial index (r = -0.96) has been established. From the point of view of PWTT delay, the average value of leg stenosis diagnostic threshold was established to be in the range of 23 +/- 9 ms, with full reliability above 32 ms. The obtained data may find further applications in alternative methodologies for detection and/or assessment of arterial occlusions in human extremities.
- Published
- 2005
- Full Text
- View/download PDF
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