Automated UML-based ontology generation in OSLO²

In 2015, Flanders Information started the OSLO2 project, aimed at easing the exchange of data and increasing the interoperability of Belgian government services. RDF ontologies were developed to break apart the government data silos and stimulate data reuse. However, ontology design still encounters a number of difficulties. Since domain experts are generally unfamiliar with RDF, a design process is needed that allows these experts to efficiently contribute to intermediate ontology prototypes. We designed the OSLO2 ontologies using UML, a modeling language well known within the government, as a single source specification. From this source, the ontology and other relevant documents are generated. This paper describes the conversion tooling and the pragmatic approaches that were taken into account in its design. While this tooling is somewhat focused on the design principles used in the OSLO2 project, it can serve as the basis for a generic conversion tool. All source code and documentation are available online

Fibre-specific laterality of white matter in left and right language dominant people

Language is the most commonly described lateralised cognitive function, relying more on the left hemisphere compared to the right hemisphere in over 90% of the population. Most research examining the structure-function relationship of language lateralisation only included people showing a left language hemisphere dominance. In this work, we applied a state-of-the-art "fixel-based" analysis approach, allowing statistical analysis of white matter micro- and macrostructure on a fibre-specific level in a sample of participants with left and right language dominance (LLD and RLD). Both groups showed a similar extensive pattern of white matter lateralisation including a comparable leftwards lateralisation of the arcuate fasciculus, regardless of their functional language lateralisation. These results suggest that lateralisation of language functioning and the arcuate fasciculus are driven by independent biases. Finally, a significant group difference of lateralisation was detected in the forceps minor, with a leftwards lateralisation in LLD and rightwards lateralisation for the RLD group

Silicon photonics traveling wave photodiode with integrated star coupler for high-linearity mm-wave applications

Next-generation wireless communication will require increasingly faster data links. To achieve those higher data rates, the shift towards mmWave frequencies and smaller cell sizes will play a major role. Radio-over-Fiber has been proposed as a possible architecture to allow for this shift but is nowadays typically implemented digitally. as CPRI (Common Public Radio Interface). Centralization will be important to keep next-generation architectures cost-effective and therefore shared optical amplification at the central office could be preferable. Unfortunately. limited power handling capabilities of photodetectors still hinder the shift towards centralized optical amplification. Traveling wave photodetectors (TWPDs) have been devised to allow for high-linearity, high-speed opto-electronic conversion. In this paper, an architecture is discussed consisting of such a TWPD implemented on the iSiPP25G silicon photonics platform. A monolithically integrated star coupler is added in the design to provide compact power distribution while preserving the high linearity of the TWPD. The traveling wave structure (using 16 photodetectors) has a measured 3 dB bandwidth of 27.5 GHz and a fairly flat S-21 up to 50 GHz (less than 1 dB extra loss). Furthermore, the output referred third-order intercept point at 28 GHz, is improved from -1.79 dBm for a single Ge photodiode to 20.98 dBm by adopting the traveling wave design. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreemen

Integrated optical frequency shifter on a silicon platform

An integrated optical frequency shifter on a standard silicon photonics platform completely fabricated in a CMOS pilot line and showing MHz frequency shifts with a sideband suppression ratio up to 36 dB is demonstrated

Photonic integrated circuit based FMCW coherent LiDAR

We present the demonstration of an integrated Frequency Modulated Continuous Wave LiDAR on a silicon platform. The waveform calibration, the scanning system and the balanced detectors are implemented on chip. Detection and ranging of a moving hard target at up to 60 m with less than 5 mW of output power is demonstrated here

The enterobacterium <i>Trabulsiella odontotermitis</i> presents novel adaptations related to its association with fungus-growing termites

Fungus-growing termites rely on symbiotic microorganisms to help break down plant material and to obtain nutrients. Their fungal cultivar, Termitomyces, is the main plant degrader and food source for the termites, while gut bacteria complement Termitomyces in the degradation of foodstuffs, fixation of nitrogen, and metabolism of amino acids and sugars. Due to the community complexity and because these typically anaerobic bacteria can rarely be cultured, little is known about the physiological capabilities of individual bacterial members of the gut communities and their associations with the termite host. The bacterium Trabulsiella odontotermitis is associated with fungus-growing termites, but this genus is generally understudied, with only two described species. Taking diverse approaches, we obtained a solid phylogenetic placement of T. odontotermitis among the Enterobacteriaceae, investigated the physiology and enzymatic profiles of T. odontotermitis isolates, determined the localization of the bacterium in the termite gut, compared draft genomes of two T. odontotermitis isolates to those of their close relatives, and examined the expression of genes relevant to host colonization and putative symbiont functions. Our findings support the hypothesis that T. odontotermitis is a facultative symbiont mainly located in the paunch compartment of the gut, with possible roles in carbohydrate metabolism and aflatoxin degradation, while displaying adaptations to association with the termite host, such as expressing genes for a type VI secretion system which has been demonstrated to assist bacterial competition, colonization, and survival within hosts

Deciphering the morphology of motor evoked potentials

Motor Evoked Potentials (MEPs) are used to monitor disability progression in multiple sclerosis (MS). Their morphology plays an important role in this process. Currently, however, there is no clear definition of what constitutes a normal or abnormal morphology. To address this, five experts independently labeled the morphology (normal or abnormal) of the same set of 1,000 MEPs. The intra- and inter-rater agreement between the experts indicates they agree on the concept of morphology, but differ in their choice of threshold between normal and abnormal morphology. We subsequently performed an automated extraction of 5,943 time series features from the MEPs to identify a valid proxy for morphology, based on the provided labels. To do this, we compared the cross-validation performances of one-dimensional logistic regression models fitted to each of the features individually. We find that the approximate entropy (ApEn) feature can accurately reproduce the majority-vote labels. The performance of this feature is evaluated on an independent test set by comparing to the majority vote of the neurologists, obtaining an AUC score of 0.92. The model slightly outperforms the average neurologist at reproducing the neurologists consensus-vote labels. We can conclude that MEP morphology can be consistently defined by pooling the interpretations from multiple neurologists and that ApEn is a valid continuous score for this. Having an objective and reproducible MEP morphological abnormality score will allow researchers to include this feature in their models, without manual annotation becoming a bottleneck. This is crucial for large-scale, multi-center datasets. An exploratory analysis on a large single-center dataset shows that ApEn is potentially clinically useful. Introducing an automated, objective, and reproducible definition of morphology could help overcome some of the barriers that are currently obstructing broad adoption of evoked potentials in daily care and patient follow-up, such as standardization of measurements between different centers, and formulating guidelines for clinical use

Simultaneous Segmentation and Anatomical Labeling of the Cerebral Vasculature

We present a novel algorithm for the simultaneous segmentation and anatomical labeling of the cerebral vasculature. The method first constructs an over-complete graph capturing the vasculature. It then selects and labels the subset of edges that most likely represents the true vasculature. Unlike existing approaches that first attempt to obtain a good segmentation and then perform labeling, we jointly optimize for both by simultaneously taking into account the image evidence and the prior knowledge about the geometry and connectivity of the vasculature. This results in an Integer Program (IP), which we solve optimally using a branch-and-cut algorithm. We evaluate our approach on a public dataset of 50 cerebral MRA images, and demonstrate that it compares favorably against state-of-the-art methods

2018 EULAR recommendations for physical activity in people with inflammatory arthritis and osteoarthritis

Regular physical activity (PA) is increasingly promoted for people with rheumatic and musculoskeletal diseases as well as the general population. We evaluated if the public health recommendations for PA are applicable for people with inflammatory arthritis (iA; Rheumatoid Arthritis and Spondyloarthritis) and osteoarthritis (hip/knee OA) in order to develop evidence-based recommendations for advice and guidance on PA in clinical practice. The EULAR standardised operating procedures for the development of recommendations were followed. A task force (TF) (including rheumatologists, other medical specialists and physicians, health professionals, patient-representatives, methodologists) from 16 countries met twice. In the first TF meeting, 13 research questions to support a systematic literature review (SLR) were identified and defined. In the second meeting, the SLR evidence was presented and discussed before the recommendations, research agenda and education agenda were formulated. The TF developed and agreed on four overarching principles and 10 recommendations for PA in people with iA and OA. The mean level of agreement between the TF members ranged between 9.8 and 8.8. Given the evidence for its effectiveness, feasibility and safety, PA is advocated as integral part of standard care throughout the course of these diseases. Finally, the TF agreed on related research and education agendas. Evidence and expert opinion inform these recommendations to provide guidance in the development, conduct and evaluation of PA-interventions and promotion in people with iA and OA. It is advised that these recommendations should be implemented considering individual needs and national health systems.EULA

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

<p>Abstract</p> <p>Background</p> <p>Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. <it>Salmonella enterica </it>subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem.</p> <p>Results</p> <p>Here, we describe a community-driven effort, in which more than 20 experts in <it>S</it>. Typhimurium biology and systems biology collaborated to reconcile and expand the <it>S</it>. Typhimurium BiGG knowledge-base. The consensus MR was obtained starting from two independently developed MRs for <it>S</it>. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community-based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi-target drug therapy approaches.</p> <p>Conclusion</p> <p>Taken together, with the growing number of parallel MRs a structured, community-driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.</p