| 1. |
- Agirre, Jon, et al.
(author)
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The CCP4 suite: integrative software for macromolecular crystallography
- 2023
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In: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 79, s. 449-461
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Journal article (peer-reviewed)abstract
- The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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| 2. |
- Triebner, K., et al.
(author)
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Menopause Is Associated with Accelerated Lung Function Decline
- 2017
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In: American Journal of Respiratory and Critical Care Medicine. - : AMER THORACIC SOC. - 1073-449X .- 1535-4970. ; 195:8, s. 1058-1065
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Journal article (peer-reviewed)abstract
- Rationale: Menopause is associated with changes in sex hormones, which affect immunity, inflammation, and osteoporosis and may impair lung function. Lung function decline has not previously been investigated in relation to menopause. Objectives: To study whether lung function decline, assessed by FVC and FEV1, is accelerated in women who undergo menopause. Methods: The population-based longitudinal European Community Respiratory Health Survey provided serum samples, spirometry, and questionnaire data about respiratory and reproductive health from three study waves (n = 1,438). We measured follicle-stimulating hormone and luteinizing hormone and added information on menstrual patterns to determine menopausal status using latent class analysis. Associations with lung function decline were investigated using linear mixed effects models, adjusting for age, height, weight, pack-years, current smoking, age at completed full-time education, spirometer, and including study center as random effect. Measurements and Main Results: Menopausal status was associated with accelerated lung function decline. The adjusted mean FVC decline was increased by -10.2 ml/yr (95% confidence interval [CI], -13.1 to -7.2) in transitional women and -12.5 ml/yr (95% CI, -16.2 to -8.9) in post-menopausal women, compared with women menstruating regularly. The adjusted mean FEV1 decline increased by -3.8 ml/yr (95% CI, -6.3 to -2.9) in transitional women and -5.2 ml/yr (95% CI, -8.3 to -2.0) in post-menopausal women. Conclusions: Lung function declined more rapidly among transitional and post-menopausal women, in particular for FVC, beyond the expected age change. Clinicians should be aware that respiratory health often deteriorates during reproductive aging.
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| 3. |
- Triebner, K., et al.
(author)
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Describing the status of reproductive ageing simply and precisely: A reproductive ageing score based on three questions and validated with hormone levels
- 2020
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:6
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Journal article (peer-reviewed)abstract
- Equation 6. Quadratic logistic function approximating the function mu(B)(with age in years). Equation 1. Proportion of women who have regular menstruation for each number of reported menstruations in the last year(with period = number of periods per year, x = number of women answering "Yes" to the question: "Do you have regular periods?", y = number of women answering "No, they have been irregular for a few months" and z = number of women answering "No, my periods have stopped", e.g. x(11) = number of women reporting regular menstruation among those who report 11 menstruations in the last 12 months). Equation 5. Biquadratic exponential function mu(A)depending of the number of periods. Equation 3. Age modification by smoking and oophorectomy. Equation 2. Proportion of women whose menstruations have already stopped, for each reported year of age(with age = age in years, x = number of women answering "Yes" to the question: "Do you have regular periods?", y = number of women answering "No, they have been irregular for a few months", z = number of women answering "No, my periods have stopped", e.g. x(40) = number of women reporting regular menstruations among those who are 40 years old). Equation 7. Final formula to calculate the reproductive ageing score (RAS)(with period being the number of periods per year and age as the age in years, modified according to smoking status and oophorectomy). Objective Most women live to experience menopause and will spend 4-8 years transitioning from fertile age to full menstrual stop. Biologically, reproductive ageing is a continuous process, but by convention, it is defined categorically as pre-, peri- and postmenopause; categories that are sometimes supported by measurements of sex hormones in blood samples. We aimed to develop and validate a new tool, a reproductive ageing score (RAS), that could give a simple and yet precise description of the status of reproductive ageing, without hormone measurements, to be used by health professionals and researchers. Methods Questionnaire data on age, menstrual regularity and menstrual frequency was provided by the large multicentre population-based RHINE cohort. A continuous reproductive ageing score was developed from these variables, using techniques of fuzzy mathematics, to generate a decimal number ranging from 0.00 (nonmenopausal) to 1.00 (postmenopausal). The RAS was then validated with sex hormone measurements (follicle stimulating hormone and 17 beta-estradiol) and interview-data provided by the large population-based ECRHS cohort, using receiver-operating characteristics (ROC). Results The RAS, developed from questionnaire data of the RHINE cohort, defined with high precision and accuracy the menopausal status as confirmed by interview and hormone data in the ECRHS cohort. The area under the ROC curve was 0.91 (95% Confidence interval (CI): 0.90-0.93) to distinguish nonmenopausal women from peri- and postmenopausal women, and 0.85 (95% CI: 0.83-0.88) to distinguish postmenopausal women from nonmenopausal and perimenopausal women. Conclusions The RAS provides a useful and valid tool for describing the status of reproductive ageing accurately, on a continuous scale from 0.00 to 1.00, based on simple questions and without requiring blood sampling. The score allows for a more precise differentiation than the conventional categorisation in pre-, peri- and postmenopause. This is useful for epidemiological research and clinical trials. Equation 4. The reproductive ageing score as an aggregation function of mu(A)and mu(B).
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| 4. |
- Abella, J., et al.
(author)
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SAFEXPLAIN : Safe and Explainable Critical Embedded Systems Based on AI
- 2023
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In: Proceedings -Design, Automation and Test in Europe, DATE. - : Institute of Electrical and Electronics Engineers Inc.. - 9783981926378
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Conference paper (peer-reviewed)abstract
- Deep Learning (DL) techniques are at the heart of most future advanced software functions in Critical Autonomous AI-based Systems (CAIS), where they also represent a major competitive factor. Hence, the economic success of CAIS industries (e.g., automotive, space, railway) depends on their ability to design, implement, qualify, and certify DL-based software products under bounded effort/cost. However, there is a fundamental gap between Functional Safety (FUSA) requirements on CAIS and the nature of DL solutions. This gap stems from the development process of DL libraries and affects high-level safety concepts such as (1) explainability and traceability, (2) suitability for varying safety requirements, (3) FUSA-compliant implementations, and (4) real-time constraints. As a matter of fact, the data-dependent and stochastic nature of DL algorithms clashes with current FUSA practice, which instead builds on deterministic, verifiable, and pass/fail test-based software. The SAFEXPLAIN project tackles these challenges and targets by providing a flexible approach to allow the certification - hence adoption - of DL-based solutions in CAIS building on: (1) DL solutions that provide end-to-end traceability, with specific approaches to explain whether predictions can be trusted and strategies to reach (and prove) correct operation, in accordance to certification standards; (2) alternative and increasingly sophisticated design safety patterns for DL with varying criticality and fault tolerance requirements; (3) DL library implementations that adhere to safety requirements; and (4) computing platform configurations, to regain determinism, and probabilistic timing analyses, to handle the remaining non-determinism.
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| 5. |
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| 6. |
- Agirre, J. A., et al.
(author)
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The VALU3S ECSEL project : Verification and validation of automated systems safety and security
- 2021
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In: Microprocessors and microsystems. - : Elsevier BV. - 0141-9331 .- 1872-9436. ; 87, s. 104349-
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Journal article (peer-reviewed)abstract
- Manufacturers of automated systems and their components have been allocating an enormous amount of time and effort in R&D activities, which led to the availability of prototypes demonstrating new capabilities as well as the introduction of such systems to the market within different domains. Manufacturers need to make sure that the systems function in the intended way and according to specifications. This is not a trivial task as system complexity rises dramatically the more integrated and interconnected these systems become with the addition of automated functionality and features to them. This effort translates into an overhead on the V&V (verification and validation) process making it time-consuming and costly. In this paper, we present VALU3S, an ECSEL JU (joint undertaking) project that aims to evaluate the state-of-the-art V&V methods and tools, and design a multi-domain framework to create a clear structure around the components and elements needed to conduct the V&V process. The main expected benefit of the framework is to reduce time and cost needed to verify and validate automated systems with respect to safety, cyber-security, and privacy requirements. This is done through identification and classification of evaluation methods, tools, environments and concepts for V&V of automated systems with respect to the mentioned requirements. VALU3S will provide guidelines to the V&V community including engineers and researchers on how the V&V of automated systems could be improved considering the cost, time and effort of conducting V&V processes. To this end, VALU3S brings together a consortium with partners from 10 different countries, amounting to a mix of 25 industrial partners, 6 leading research institutes, and 10 universities to reach the project goal.
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| 7. |
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| 8. |
- Bonetti, A, et al.
(author)
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RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
- 2020
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1, s. 1018-
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Journal article (peer-reviewed)abstract
- Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed; however, these methods have some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA–chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared with existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type–specific RNA-chromatin interactions, and highlights the role of transcription in the establishment of chromatin structure.
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| 9. |
- Abella, Jaume, et al.
(author)
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SAFEXPLAIN : Safe and Explainable Critical Embedded Systems Based on AI
- 2023
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In: DATE 23: Design, Automation And Test In Europe. - 9783981926378 ; , s. 1-6
-
Conference paper (peer-reviewed)abstract
- Deep Learning (DL) techniques are at the heart of most future advanced software functions in Critical Autonomous AI-based Systems (CAIS), where they also represent a major competitive factor. Hence, the economic success of CAIS industries (e.g., automotive, space, railway) depends on their ability to design, implement, qualify, and certify DL-based software products under bounded effort/cost. However, there is a fundamental gap between Functional Safety (FUSA) requirements on CAIS and the nature of DL solutions. This gap stems from the development process of DL libraries and affects high-level safety concepts such as (1) explainability and traceability, (2) suitability for varying safety requirements, (3) FUSA-compliant implementations, and (4) real-time constraints. As a matter of fact, the data-dependent and stochastic nature of DL algorithms clashes with current FUSA practice, which instead builds on deterministic, verifiable, and pass/fail test-based software. The SAFEXPLAIN project tackles these challenges and targets by providing a flexible approach to allow the certification - hence adoption - of DL-based solutions in CAIS building on: (1) DL solutions that provide end-to-end traceability, with specific approaches to explain whether predictions can be trusted and strategies to reach (and prove) correct operation, in accordance to certification standards; (2) alternative and increasingly sophisticated design safety patterns for DL with varying criticality and fault tolerance requirements; (3) DL library implementations that adhere to safety requirements; and (4) computing platform configurations, to regain determinism, and probabilistic timing analyses, to handle the remaining non-determinism. © 2023 EDAA.
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| 10. |
- Ayerdi, J., et al.
(author)
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Towards a Taxonomy for Eliciting Design-Operation Continuum Requirements of Cyber-Physical Systems
- 2020
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In: Proceedings of the IEEE International Conference on Requirements Engineering. - : IEEE Computer Society. - 9781728174389 ; , s. 280-290
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Conference paper (other academic/artistic)abstract
- Software systems that are embedded in autonomous Cyber-Physical Systems (CPSs) usually have a large life-cycle, both during its development and in maintenance. This software evolves during its life-cycle in order to incorporate new requirements, bug fixes, and to deal with hardware obsolescence. The current process for developing and maintaining this software is very fragmented, which makes developing new software versions and deploying them in the CPSs extremely expensive. In other domains, such as web engineering, the phases of development and operation are tightly connected, making it possible to easily perform software updates of the system, and to obtain operational data that can be analyzed by engineers at development time. However, in spite of the rise of new communication technologies (e.g., 5G) providing an opportunity to acquire Design-Operation Continuum Engineering methods in the context of CPSs, there are still many complex issues that need to be addressed, such as the ones related with hardware-software co-design. Therefore, the process of Design-Operation Continuum Engineering for CPSs requires substantial changes with respect to the current fragmented software development process. In this paper, we build a taxonomy for Design-Operation Continuum Engineering of CPSs based on case studies from two different industrial domains involving CPSs (elevation and railway). This taxonomy is later used to elicit requirements from these two case studies in order to present a blueprint on adopting Design-Operation Continuum Engineering in any organization developing CPSs.
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