Does smoking, age or gender affect the protein phenotype of extracellular vesicles in plasma?

AbstractExtracellular vesicles (EVs) are involved in several diseases, which have formed the basis for the potential use of EV analyses in a clinical setting. The protein phenotype of EVs can provide information on the functionality of the vesicles and may be used for identification of disease-related biomarkers.With this extensive study of 161 healthy individuals it was elucidated that certain markers of plasma EVs are influenced by demographic variations such as gender, age and smoking status. When the purpose is to use EVs as a diagnostic tool, it should be emphasized how important it is to choose the correct demographic group when comparing marker levels of plasma EVs

The impact of various preanalytical treatments on the phenotype of small extracellular vesicles in blood analyzed by protein microarray

AbstractThe research field of extracellular vesicles (EVs) is increasing immensely and the potential uses of EVs seem endless. They are found in large numbers in various body fluids, and blood samples may well serve as liquid biopsies. However, these small membrane-derived entities of cellular origin are not straightforward to work with in regard to isolation and characterization.A broad range of relevant preanalytical issues was tested, with a focus on the phenotypic impact of smaller EVs. The influences of the i) blood collection tube used, ii) incubation time before the initial centrifugation, iii) transportation/physical stress, iv) storage temperature and time (short term and long term), v) choice of centrifugation protocol, vi) freeze-thaw cycles, and vii) exosome isolation procedure (ExoQuick™) were examined. To identify the impact of the preanalytical treatments, the relative amounts (detected signal intensities of CD9-, CD63- and/or CD81-positive) and phenotypes of small EVs were analyzed using the multiplexed antibody-based microarray technology, termed the EV Array. The analysis encompassed 15 surface- or surface-related markers, including CD9, CD63, CD81, CD142, and Annexin V.This study revealed that samples collected in different blood collection tubes suffered to varying degrees from the preanalytical treatments tested here. There is no unequivocal answer to the questions asked. However, in general, the period of time and prospective transportation before the initial centrifugation, choice of centrifugation protocol, and storage temperature were observed to have major impacts on the samples. On the contrary, long-term storage and freeze-thawing seemed to not have a critical influence. Hence, there are pros and cons of any choice regarding sample collection and preparation and may very well be analysis dependent. However, to compare samples and results, it is important to ensure that all samples are of the same type and have been handled similarly

Verifying object-oriented programs with higher-order separation logic in Coq

We present a shallow Coq embedding of a higher-order separation logic with nested triples for an object-oriented programming language. Moreover, we develop novel specification and proof patterns for reasoning in higher-order separation logic with nested triples about programs that use interfaces and interface inheritance. In particular, we show how to use the higher-order features of the Coq formalisation to specify and reason modularly about programs that (1) depend on some unknown code satisfying a specification or that (2) return objects conforming to a certain specification. All of our results have been formally verified in the interactive theorem prover Coq

Eocene (Stronsay Group) post-rift stratigraphy of the Faroe-Shetland region

A preliminary stratigraphic framework for the post-rift Eocene Stronsay Group succession in the Faroe–Shetland region has been constructed, which incorporates lithological information from over fifty wells, boreholes and dredge sites, biostratigraphic data provided by Ichron Limited, and seismic stratigraphy. A stratigraphic-range chart was compiled using released UK and Faroese commercial well data, together with BGS and other public domain information. This chart details the chronological range, general lithology and correlation of the post-rift Eocene record for each commercial well, BGS borehole and other data point, e.g. DSDP site. This dataset was used to construct a set of timeslice maps utilising the Ichron Limited T-sequence biozonation scheme, which were used to interpret the spatial and temporal variation of Eocene post-rift sedimentation across the region. Seismic profiles further provided an insight into the large-scale stratigraphic architecture of the Stronsay Group which, in combination with the geological database, provides a context for several regional unconformities and other significant surfaces identified in the study. On the basis of our provisional assessment of the Stronsay Group in the Faroe–Shetland region we have retained the use of the Horda Formation as the main lithostratigraphic unit, as this shelfmargin to basinal unit – defined originally in the North Sea – is consistent with the character of the Eocene succession that we observe preserved offshore NW Britain. Nonetheless, informal subdivision of the Horda Formation is proposed that reflects several discrete phases of sedimentary input into the Faroe-Shetland Basin. Four unconformity-bounded depositional packages have been tentatively identified, and provisionally assigned ages of Ypresian–early Lutetian (phase 1), Lutetian–early Bartonian (phase 2), Bartonian–Priabonian (phase 3), and late Priabonian (phase 4). The phase 1 and 2 depositional packages are separated by the Mid-Eocene (T2d) unconformity which reflects subaerial exposure and channel incision up to 200 m deep during its formation in the Lutetian. The early Bartonian Base-slope-apron (T2c) unconformity separates the phase 2 and 3 depositional packages, and is similarly erosive along the southern and eastern basin margin. Seismic-stratigraphic evidence suggests that synsedimentary deformation may have been active during depositional phases 1 and 2, including growth and uplift of the Munkagrunnur Ridge, and the Judd and Westray anticlines, as well as uplift of the Flett High. The phase 3 depositional package marks a large-scale progradation of the West Shetland margin, which may reflect uplift and rejuvenation of the hinterland. The phase 3 and 4 depositional packages are separated by the Base-marginal-fan (T2b) reflector, which may be a consequence of renewed uplift of the margin and/or further growth of the inversion anticlines during the Priabonian. This stratigraphic framework provides new insights into the early post-rift tectonic and sedimentary history of the Faroe–Shetland region, identifying a sequence of unconformitybounded units. Comparison with the wider NE Atlantic region indicates broad coincidence between the timing of formation of the unconformities in the Faroe–Shetland region and plate reorganisation events in the adjacent Norway Basin; as well as orogenic and related compressional deformation in western Europe. This raises the possibility that plate boundary forcing may be a key mechanism in passive margin development. It is hoped that this framework will form a useful foundation for future studies of the tectonostratigraphic development of the Faroe–Shetland region

Cenozoic pre- and post-breakup compression in the Faroe-Shetland area, within the context of the NE Atlantic

This report is primarily based upon the interpretation of oil industry 2D seismic data, and aims to elucidate aspects of Cenozoic tectonostratigraphic development in the Faroe–Shetland region, especially with regard to post-breakup compression. Evidence of Cenozoic and Late Cretaceous pre-breakup compression and deformation is briefly reviewed. We have utilised established seismo-stratigraphic frameworks and a recently updated scheme for the post-breakup Eocene (Stronsay Group) succession, which are largely based upon the recognition of units bounded by regional unconformities. The seismic expression, extent and thickness of the seismo-stratigraphic units are illustrated by geoseismic profiles, structure contour maps and isochore maps, which are used to analyse the spatial and temporal development of post-breakup compression and deformation within the Faroe-Shetland region. The Faroe-Shetland region records a complex spatial and temporal pattern of departures from the thermal subsidence normally associated with passive margins, including broad uplifts and accelerated basinal subsidence together with fold development up to kilometre scale. The phases of latest Eocene / earliest Oligocene ‘sagging’ (accelerated subsidence) and early Pliocene uplift and exhumation (tilting) appear to be coeval with compression. Indeed, compression appears to have been active throughout post-breakup times, although the loci of deformation have varied both spatially and temporally. Conceivably, some of the large scale sagging, tilting and uplift may be associated with lithospheric folding. Much of the intra-Eocene folding appears to be focused in the southwestern part of the Faroe-Shetland region, around the Munkagrunnur Ridge and Judd area, where phases of shelf progradation are preserved and may be associated with contemporaneous uplift. However, there also appears to be evidence of episodic intra-Eocene and younger uplift in the area around the northern Fugloy Ridge. The overall shaping of the Faroe-Shetland Channel appears to have been initiated at the end of the Eocene, associated with uplift on the Fugloy Ridge and Faroe Platform areas, and with accelerated subsidence in the Faroe-Shetland Basin; this shaping was further developed during the Neogene. A Neogene opening of the ‘Faroe Conduit’ oceanic gateway is favoured on the basis of regional evidence of faunal isolation and restricted environment of deposition together with uncertainty regarding the nature of the ‘Southeast Faroes drift’. A significant phase of Miocene folding is associated with the Intra-Miocene Unconformity (IMU), whereas the Mid Miocene Unconformity (MMU) represents a relatively minor break with a restricted distribution in the NE Faroe-Shetland region. Seabed relief on some folds and late Neogene seismic onlaps may indicate that fold development persisted into Recent times. Lateral offsets and local basin inversion associated with the folding, suggest a strong structural inheritance from the underlying rift architecture. A broad coincidence between the timing of formation of the unconformities and plate reorganisation events in the adjacent Norway Basin and wider region may suggest that these events made important contributions to the forces shaping the margin. The development of Miocene and younger folds may have been influenced by gravitational potential energy / body forces associated with the density structure of the Iceland Insular Margin and the Southern Scandes, or with modulations to ridge-push resulting from transient changes in ridge elevation associated with plume-related temperature (buoyancy) variations in the underlying asthenosphere. Far field stresses associated with, for example, collision between Eurasia and Iberia may also have exerted significant influence on deformation within the Faroe-Shetland region

Structural and dynamics studies of a truncated variant of CI repressor from bacteriophage TP901-1

International audienceThe CI repressor from the temperate bacteriophage TP901-1 consists of two folded domains, an N-terminal helix-turn-helix DNA-binding domain (NTD) and a C-terminal oligomerization domain (CTD), which we here suggest to be further divided into CTD1 and CTD2. Full-length CI is a hexameric protein, whereas a truncated version, CI∆58, forms dimers. We identify the dimerization region of CI∆58 as CTD1 and determine its secondary structure to be helical both within the context of CI∆58 and in isolation. To our knowledge this is the first time that a helical dimerization domain has been found in a phage repressor. We also precisely determine the length of the flexible linker connecting the NTD to the CTD. Using electrophoretic mobility shift assays and native mass spectrometry, we show that CI∆58 interacts with the OL operator site as one dimer bound to both half-sites, and with much higher affinity than the isolated NTD domain thus demonstrating cooperativity between the two DNA binding domains. Finally, using small angle X-ray scattering data and state-of-the-art ensemble selection techniques, we delineate the conformational space sampled by CI∆58 in solution, and we discuss the possible role that the dynamics play in CI-repressor function

Copenhagen Diabetes Consensus (CODIAC) 2021: user involvement in diabetes care, prevention and research

Aims User involvement is pivotal for health development, but there are significant gaps in our understanding of the concept. The Copenhagen Diabetes Consensus on User Involvement in Diabetes Care, Prevention and Research (CODIAC) was established to address these gaps, share knowledge and develop best practices. Methods A literature review of user involvement was undertaken in diabetes care, prevention and research. Moreover, a Group Concept Mapping (GCM) survey synthesized the knowledge and opinions of researchers, healthcare professionals and people with diabetes and their carers to identify gaps between what is important for user involvement and what is being done in practice. Finally, a consensus conference discussed the main gaps in knowledge and practice while developing plans to address the shortcomings. Results The literature review demonstrated that user involvement is an effective strategy for diabetes care, prevention and research, given the right support and conditions, but gaps and key challenges regarding the value and impact of user involvement approaches were found. The GCM process identified 11 major gaps, where important issues were not being sufficiently practised. The conference considered these gaps and opportunities to develop new collaborative initiatives under eight overall themes. Conclusions User involvement is effective and adds value to diabetes care, prevention and research when used under the right circumstances. CODIAC developed new learning about the way in which academic and research knowledge can be transferred to more practice-oriented knowledge and concrete collaborative initiatives. This approach may be a potential new framework for initiatives in which coherence of process can lead to coherent outputs

Stratified Abstraction of Access Control Policies

The shift to cloud-based APIs has made application security critically depend on understanding and reasoning about policies that regulate access to cloud resources. We present stratified predicate abstraction, a new approach that summarizes complex security policies into a compact set of positive and declarative statements that precisely state who has access to a resource. We have implemented stratified abstraction and deployed it as the engine powering AWS’s IAM Access Analyzer service, and hence, demonstrate how formal methods and SMT can be used for security policy explanation

What works for whom in the management of diabetes in people living with dementia: a realist review

Background Dementia and diabetes mellitus are common long-term conditions and co-exist in a large number of older people. People living with dementia (PLWD) may be less able to manage their diabetes, putting them at increased risk of complications such as hypoglycaemia. The aim of this review was to identify key mechanisms within different interventions that are likely to improve diabetes outcomes in PLWD. Methods This is a realist review involving scoping of the literature and stakeholder interviews to develop theoretical explanations of how interventions might work, systematic searches of the evidence to test and develop the theories and their validation with a purposive sample of stakeholders. Twenty-six stakeholders — user/patient representatives, dementia care providers, clinicians specialising in diabetes or dementia and researchers — took part in interviews, and 24 participated in a consensus conference. Results We included 89 papers. Ten focused on PLWD and diabetes, and the remainder related to people with either dementia, diabetes or other long-term conditions. We identified six context-mechanism-outcome configurations which provide an explanatory account of how interventions might work to improve the management of diabetes in PLWD. This includes embedding positive attitudes towards PLWD, person-centred approaches to care planning, developing skills to provide tailored and flexible care, regular contact, family engagement and usability of assistive devices. An overarching contingency emerged concerning the synergy between an intervention strategy, the dementia trajectory and social and environmental factors, especially family involvement. Conclusions Evidence highlighted the need for personalised care, continuity and family-centred approaches, although there was limited evidence that this happens routinely. This review suggests there is a need for a flexible service model that prioritises quality of life, independence and patient and carer priorities. Future research on the management of diabetes in older people with complex health needs, including those with dementia, needs to look at how organisational structures and workforce development can be better aligned to their needs. Trial registration PROSPERO, CRD42015020625. Registered on 18 May 2015