Integration of object-oriented knowledge representation with the CLIPS rule based system

The paper describes a portion of the work aimed at developing an integrated, knowledge based environment for the development of engineering-oriented applications. An Object Representation Language (ORL) was implemented in C++ which is used to build and modify an object-oriented knowledge base. The ORL was designed in such a way so as to be easily integrated with other representation schemes that could effectively reason with the object base. Specifically, the integration of the ORL with the rule based system C Language Production Systems (CLIPS), developed at the NASA Johnson Space Center, will be discussed. The object-oriented knowledge representation provides a natural means of representing problem data as a collection of related objects. Objects are comprised of descriptive properties and interrelationships. The object-oriented model promotes efficient handling of the problem data by allowing knowledge to be encapsulated in objects. Data is inherited through an object network via the relationship links. Together, the two schemes complement each other in that the object-oriented approach efficiently handles problem data while the rule based knowledge is used to simulate the reasoning process. Alone, the object based knowledge is little more than an object-oriented data storage scheme; however, the CLIPS inference engine adds the mechanism to directly and automatically reason with that knowledge. In this hybrid scheme, the expert system dynamically queries for data and can modify the object base with complete access to all the functionality of the ORL from rules

Do doorways really matter : investigating memory benefits of event segmentation in a virtual learning environment

Event segmentation allows the flow of information experienced in life to be partitioned into distinct episodes, facilitating understanding of the world, action within it, and the ability to store information in memory. One basis on which experiences are segmented is the presence of physical boundaries, such as walking through doorways. Previous findings have shown that event segmentation has a significant influence on memory, with better memory for events occurring within a single boundary (compared to events that cross boundaries). By manipulating the features of boundaries and the amount of information presented between boundaries the present research investigates the nature of event boundaries. We make use of a virtual learning environment to present lists of words in virtual rooms, testing memory for the word lists as a function of the presence or absence of spatial-temporal gaps and physical boundaries during encoding (i.e., by maintaining participants within individual rooms or moving them through doorways between rooms). Across four experiments, we show that segmenting information with spatial-temporal gaps results in an increase in clustering (reflecting the structure imposed at encoding) an increase in the number of words remembered during later tests of episodic recall (a memory benefit) and an increase in recalling the words in the order of presentation. Importantly, however, the data show that the presence of doorways is not required for event segmentation to benefit memory: increases in clustering, memory for temporal order and recall performance were found with temporal gaps alone. Furthermore, the results suggest that episodic memory may be optimised if the amount of information between boundaries can be maintained within working memory. We discuss the implications of the findings for Event Segmentation Theory and propose an alternative theoretical account of the episodic memory benefits based on temporal clustering. [Abstract copyright: Copyright © 2020 Elsevier B.V. All rights reserved.]PostprintPeer reviewe

Widely-tunable mid-infrared ring cavity pump-enhanced OPO and application in photo-thermal interferometric trace ethane detection

Funding: Innovate UK (133076); Engineering and Physical Sciences Research Council (EP//L01596X/1, EP/M01326X/1, EP/M024385/1); European Research Council (ERC-2018-STG 803665).The development of a broadly and accurately tunable single-frequency mid-infrared laser source and its application to a sensitive laser absorption detection method are described. Photo-thermal interferometric spectroscopy is employed as a phase-sensitive method to detect the minute refractive index change caused by the heating of a gas under laser radiation. A separate probe beam allows for the spectrally-interesting mid-infrared region to be examined whilst utilizing low cost, high detectivity photodetectors in the visible/near-infrared region. We also describe the implementation of a Sagnac interferometer to minimize the effects of environmental perturbation and provide inherent passive stability. A continuous-wave ring-cavity pump-enhanced OPO has been developed to provide excitation light from 3–4 µm at 140 mW with the ability to mode-hop tune continuously over 90 cm−1 in 0.07 cm−1 steps. Complementary use of both detection apparatus and excitation source has allowed for presence of ethane to be detected down to 200 parts per billion.developed to provide excitation light from 3–4 µm at 140 mW with the ability to mode-hop tune continuously over 90 cm−1 in 0.07 cm−1 steps. Complementary use of both detection apparatus and excitation source has allowed for presence of ethane to be detected down to 200 parts per billion.Publisher PDFPeer reviewe

A thin layer angiogenesis assay: a modified basement matrix assay for assessment of endothelial cell differentiation

BACKGROUND: Basement matrices such as Matrigel™ and Geltrex™ are used in a variety of cell culture assays of anchorage-dependent differentiation including endothelial cell tube formation assays. The volumes of matrix recommended for these assays (approximately 150 μl/cm(2)) are costly, limit working distances for microscopy, and require cell detachment for subsequent molecular analysis. Here we describe the development and validation of a thin-layer angiogenesis (TLA) assay for assessing the angiogenic potential of endothelial cells that overcomes these limitations. RESULTS: Geltrex™ basement matrix at 5 μl/cm(2) in 24-well (10 μl) or 96-well (2 μl) plates supports endothelial cell differentiation into tube-like structures in a comparable manner to the standard larger volumes of matrix. Since working distances are reduced, high-resolution single cell microscopy, including DIC and confocal imaging, can be used readily. Using MitoTracker dye we now demonstrate, for the first time, live mitochondrial dynamics and visualise the 3-dimensional network of mitochondria present in differentiated endothelial cells. Using a standard commercial total RNA extraction kit (Qiagen) we also show direct RNA extraction and RT-qPCR from differentiated endothelial cells without the need to initially detach cells from their supporting matrix. CONCLUSIONS: We present here a new thin-layer assay (TLA) for measuring the anchorage-dependent differentiation of endothelial cells into tube-like structures which retains all the characteristics of the traditional approach but with the added benefit of a greatly lowered cost and better compatibility with other techniques, including RT-qPCR and high-resolution microscopy. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12860-014-0041-5) contains supplementary material, which is available to authorized users

Do case-only designs yield consistent results across design and different databases? A case study of hip fractures and benzodiazepines.

BACKGROUND: The case-crossover (CXO) and self-controlled case series (SCCS) designs are increasingly used in pharmacoepidemiology. In both, relative risk estimates are obtained within persons, implicitly controlling for time-fixed confounding variables. OBJECTIVES: To examine the consistency of relative risk estimates of hip/femur fractures (HFF) associated with the use of benzodiazepines (BZD) across case-only designs in two databases (DBs), when a common protocol was applied. METHODS: CXO and SCCS studies were conducted in BIFAP (Spain) and CPRD (UK). Exposure to BZD was divided into non-use, current, recent and past use. For CXO, odds ratios (OR; 95%CI) of current use versus non-use/past were estimated using conditional logistic regression adjusted for co-medications (AOR). For the SCCS, conditional Poisson regression was used to estimate incidence rate ratios (IRR; 95%CI) of current use versus non/past-use, adjusted for age. To investigate possible event-exposure dependence the relative risk in the 30 days prior to first BZD exposure was also evaluated. RESULTS: In the CXO current use of BZD was associated with an increased risk of HFF in both DBs, AORBIFAP = 1.47 (1.29-1.67) and AORCPRD = 1.55 (1.41-1.70). In the SCCS, IRRs for current exposure was 0.79 (0.72-0.86) in BIFAP and 1.21 (1.13-1.30) in CPRD. However, when we considered separately the 30-day pre-exposure period, the IRR for current period was 1.43 (1.31-1.57) in BIFAP and 1.37 (1.27-1.47) in CPRD. CONCLUSIONS: CXO designs yielded consistent results across DBs, while initial SCCS analyses did not. Accounting for event-exposure dependence, estimates derived from SCCS were more consistent across DBs and designs

Integrative GWAS and co-localisation analysis suggests novel genes associated with age-related multimorbidity

Abstract Advancing age is the greatest risk factor for developing multiple age-related diseases. Therapeutic approaches targeting the underlying pathways of ageing, rather than individual diseases, may be an effective way to treat and prevent age-related morbidity while reducing the burden of polypharmacy. We harness the Open Targets Genetics Portal to perform a systematic analysis of nearly 1,400 genome-wide association studies (GWAS) mapped to 34 age-related diseases and traits, identifying genetic signals that are shared between two or more of these traits. Using locus-to-gene (L2G) mapping, we identify 995 targets with shared genetic links to age-related diseases and traits, which are enriched in mechanisms of ageing and include known ageing and longevity-related genes. Of these 995 genes, 128 are the target of an approved or investigational drug, 526 have experimental evidence of binding pockets or are predicted to be tractable, and 341 have no existing tractability evidence, representing underexplored genes which may reveal novel biological insights and therapeutic opportunities. We present these candidate targets for exploration and prioritisation in a web application

An operational workflow for producing periodic estimates of species occupancy at national scales

Policy makers require high-level summaries of biodiversity change. However, deriving such summaries from raw biodiversity data is a complex process involving several intermediary stages. In this paper, we describe an operational workflow for generating annual estimates of species occupancy at national scales from raw species occurrence data, which can be used to construct a range of policy-relevant biodiversity indicators. We describe the workflow in detail: from data acquisition, data assessment and data manipulation, through modelling, model evaluation, application and dissemination. At each stage, we draw on our experience developing and applying the workflow for almost a decade to outline the challenges that analysts might face. These challenges span many areas of ecology, taxonomy, data science, computing and statistics. In our case, the principal output of the workflow is annual estimates of occupancy, with measures of uncertainty, for over 5000 species in each of several defined ‘regions’ (e.g. countries, protected areas, etc.) of the UK from 1970 to 2019. This data product corresponds closely to the notion of a species distribution Essential Biodiversity Variable (EBV). Throughout the paper, we highlight methodologies that might not be applicable outside of the UK and suggest alternatives. We also highlight areas where the workflow can be improved; in particular, methods are needed to mitigate and communicate the risk of bias arising from the lack of representativeness that is typical of biodiversity data. Finally, we revisit the ‘ideal’ and ‘minimal’ criteria for species distribution EBVs laid out in previous contributions and pose some outstanding questions that should be addressed as a matter of priority. Going forward, we hope that this paper acts as a template for research groups around the world seeking to develop similar data products

An Asymmetric Eclipse Seen toward the Pre-main-sequence Binary System V928 Tau

K2 observations of the weak-lined T Tauri binary V928 Tau A and B show the detection of a single, asymmetric eclipse, which may be due to a previously unknown substellar companion eclipsing one component of the binary with an orbital period >66 days. Over an interval of about 9 hr, one component of the binary dims by around 60%, returning to its normal brightness about 5 hr later. From modeling of the eclipse shape, we find evidence that the eclipsing companion may be surrounded by a disk or a vast ring system. The modeled disk has a radius of 0.9923 ± 0.0005 R*, with an inclination of 56 78 ± 0 03, a tilt of 41 22 ± 0 05, an impact parameter of −0.2506 ± 0.0002 R*, and an opacity of 1.00. The occulting disk must also move at a transverse velocity of 6.637 ± 0.002 R* day⁻¹, which, depending on whether it orbits V928 Tau A or B, corresponds to approximately 73.53 or 69.26 km s⁻¹. A search in ground-based archival data reveals additional dimming events, some of which suggest periodicity, but no unambiguous period associated with the eclipse observed by K2. We present a new epoch of astrometry that is used to further refine the orbit of the binary, presenting a new lower bound of 67 yr, and constraints on the possible orbital periods of the eclipsing companion. The binary is also separated by 18'' (~2250 au) from the lower-mass CFHT-BD-Tau 7, which is likely associated with V928 Tau A and B. We also present new high-dispersion optical spectroscopy that we use to characterize the unresolved stellar binary

KELT-23Ab: A Hot Jupiter Transiting a Near-solar Twin Close to the TESS and JWST Continuous Viewing Zones

We announce the discovery of KELT-23Ab, a hot Jupiter transiting the relatively bright (V = 10.3) star BD+66 911 (TYC 4187-996-1), and characterize the system using follow-up photometry and spectroscopy. A global fit to the system yields host-star properties of K, , , , (cgs), and . KELT-23Ab is a hot Jupiter with a mass of , radius of , and density of g cm-3. Intense insolation flux from the star has likely caused KELT-23Ab to become inflated. The time of inferior conjunction is and the orbital period is days. There is strong evidence that KELT-23A is a member of a long-period binary star system with a less luminous companion, and due to tidal interactions, the planet is likely to spiral into its host within roughly a gigayear. This system has one of the highest positive ecliptic latitudes of all transiting planet hosts known to date, placing it near the Transiting Planet Survey Satellite and James Webb Space Telescope continuous viewing zones. Thus we expect it to be an excellent candidate for long-term monitoring and follow up with these facilities

Resistance to the impact of interruptions during multitasking by healthy adults and dysexecutive patients

Two experiments (one with healthy adult volunteers and the other with controls and dysexecutive patients) assessed the impact of interruptions on a novel test of multitasking. The test involved switching repeatedly between four tasks (block construction, bead threading, paper folding, alphabetical searching) over a 10 minute period. In Experiment 1, there were 4 groups of 20 healthy participants. One group attempted multitasking with no interruption, a second group was interrupted early in the test, a third group late in the test and a fourth group was interrupted both early and late. Interruption involved carrying out a fifth, unexpected task for a period of one minute before returning to the four main tasks. There was no difference in multitasking performance between the groups. In Experiment 2 the participants were seven dysexecutive patients and 14 age-matched controls. A repeated measures approach was employed to assess the impact of two interruptions (early and late) for both groups. Contrary to predictions, the patients as well as controls were resistant to the effects of interruptions, despite their clearly impaired multitasking performance. These results suggest that the ability to deal with interruptions may be separable from the ability to organise and execute multiple tasks within a limited time frame