Using ontology in query answering systems: Scenarios, requirements and challenges

Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of such a system, each component being designed to solve some one part of the total problem and at the same time reflect well-defined needs on the prat of our customers. We compare our strategy with the research roadmap proposed by the Question Answering Committee of the National Institute of Standards and Technology (NIST), paying special attention to the role of ontology

Saying Hello World with GROOVE - A Solution to the TTC 2011 Instructive Case

This report presents a solution to the Hello World case study of TTC 2011 using GROOVE. We provide and explain the grammar that we used to solve the case study. Every requested question of the case study was solved by a single rule application.Comment: In Proceedings TTC 2011, arXiv:1111.440

Design characteristics of studies on medical practice variation of caesarean section rates : A scoping review

Peer reviewedPublisher PD

Samen de lat hoger leggen: Onderzoek naar de governance en het tuchtrecht voor veilige en integere sport

Veiligheid in de sport staat steeds meer in de aandacht. Zaken rond machtsmisbruik en (seksuele) intimidatie hebben grote impact op betrokkenen. Daarnaast heeft de sport te maken met integriteitsproblemen rond doping, matchfixing en criminele inmenging. Het blijkt moeilijk om misstanden effectief aan te pakken: er zijn veel partijen en belangen betrokken, die elk hun rol moeten pakken binnen hun deel van het stelsel. Daarom heeft het ministerie van Volksgezondheid, Welzijn en Sport (VWS) gevraagd om een onderzoek naar de governance en het tuchtrecht van veiligheid en integriteit in de sport. Dit onderzoek is uitgevoerd door Andersson Elffers Felix (AEF) in samenwerking met Mulier Instituut, de Universiteit Utrecht, en Kennedy Van der Laan. Doel van het onderzoek is om in beeld te krijgen hoe taken, rollen en verantwoordelijkheden zijn verdeeld in het landschap van sport en overheid. Wie draagt welke verantwoordelijkheid om veiligheid en integriteit te bevorderen? En hoe kan dit stelsel effectiever georganiseerd worden, zodat misstanden beter kunnen worden aangepakt en waar mogelijk voorkomen? Als specifiek onderdeel hiervan hebben de onderzoekers gekeken naar de rol van het tuchtrecht in de sport, en het functioneren van het Instituut Sportrechtspraak (ISR). Aanbevelingen worden gedaan voor het versterken van de uitvoering en de ontwikkeling van het ISR. Bij dit onderzoek zijn veel partijen betrokken vanuit zowel de georganiseerde sport, de ondernemende sport, justitiële partijen, en de overheid (rijk en gemeenten). Ook is gesproken met slachtoffers van grensoverschrijdend gedrag. Met al deze gesprekspartners is nagedacht over hoe het stelsel verbeterd kan worden en wat daarvoor nodig is

Qualitative aspects and validation of a screening method for pesticides in vegetables and fruits based on liquid chromatography coupled to full scan high resolution (Orbitrap) mass spectrometry

The analytical capabilities of liquid chromatography with single-stage high-resolution mass spectrometry have been investigated with emphasis on qualitative aspects related to selective detection during screening and to identification. The study involved 21 different vegetable and fruit commodities, a screening database of 556 pesticides for evaluation of false positives, and a test set of 130 pesticides spiked to the commodities at 0.01, 0.05, and 0.20 mg/kg for evaluation of false negatives. The final method involved a QuEChERS-based sample preparation (without dSPE clean up) and full scan acquisition using alternating scan events without/with fragmentation, at a resolving power of 50,000. Analyte detection was based on extraction of the exact mass (±5 ppm) of the major adduct ion at the database retention time ±30 s and the presence of a second diagnostic ion. Various options for the additional ion were investigated and compared (other adduct ions, M + 1 or M + 2 isotopes, fragments). The two-ion approach for selective detection of the pesticides in the full scan data was compared with two alternative approaches based on response thresholds. Using the two-ion approach, the number of false positives out of 11,676 pesticide/commodity combinations targeted was 36 (0.3 %). The percentage of false negatives, assessed for 2,730 pesticide/commodity combinations, was 13 %, 3 %, and 1 % at the 0.01-, 0.05-, and 0.20-mg/kg level, respectively (slightly higher with fully automated detection). Following the SANCO/12495/2011 protocol for validation of screening methods, the screening detection limit was determined for 130 pesticides and found to be 0.01, 0.05, and ≥0.20 mg/kg for 86, 30, and 14 pesticides, respectively. For the detected pesticides in the spiked samples, the ability for unambiguous identification according to EU criteria was evaluated. A proposal for adaption of the criteria was made

Serum-based measurements of stromal activation through ADAM12 associate with poor prognosis in colorectal cancer.

BACKGROUND Recently it has been recognized that stromal markers could be used as a clinically relevant biomarker for therapy response and prognosis. Here, we report on a serum marker for stromal activation, A Disintegrin and Metalloprotease 12 (ADAM12) in colorectal cancer (CRC). METHODS Using gene expression databases we investigated ADAM12 expression in CRC and delineated the source of ADAM12 expression. The clinical value of ADAM12 was retrospectively assessed in the CAIRO2 trial in metastatic CRC with 235 patients (31% of total cohort), and an independent rectal cancer cohort (n = 20). RESULTS ADAM12 is expressed by activated CRC associated fibroblasts. In the CAIRO2 trial cohort, ADAM12 serum levels were prognostic (ADAM12 low versus ADAM12 high; median OS 25.3 vs. 17.1 months, HR 1.48 [95% CI 1.11-1.96], P = 0.007). The prognostic potential was specifically high for metastatic rectal cancer (HR 1.78 [95% CI 1.06-3.00], P = 0.030) and mesenchymal subtype tumors (HR 2.12 [95% CI 1.25-3.60], P = 0.004). ADAM12 also showed potential for predicting recurrence in an exploratory analysis of non-metastatic rectal cancers. CONCLUSIONS Here we describe a non-invasive marker for activated stroma in CRC which associates with poor outcome, especially for primary cancers located in the rectum

Somatic genomic alterations in retinoblastoma beyond RB1 are rare and limited to copy number changes

Retinoblastoma is a rare childhood cancer initiated by RB1 mutation or MYCN amplification, while additional alterations may be required for tumor development. However, the view on single nucleotide variants is very limited. To better understand oncogenesis, we determined the genomic landscape of retinoblastoma. We performed exome sequencing of 71 retinoblastomas and matched blood DNA. Next, we determined the presence of single nucleotide variants, copy number alterations and viruses. Aside from RB1, recurrent gene mutations were very rare. Only a limited fraction of tumors showed BCOR (7/71, 10%) or CREBBP alterations (3/71, 4%). No evidence was found for the presence of viruses. Instead, specific somatic copy number alterations were more common, particularly in patients diagnosed at later age. Recurrent alterations of chromosomal arms often involved less than one copy, also in highly pure tumor samples, suggesting within-tumor heterogeneity. Our results show that retinoblastoma is among the least mutated cancers and signify the extreme sensitivity of the childhood retina for RB1 loss. We hypothesize that retinoblastomas arising later in retinal development benefit more from subclonal secondary alterations and therefore, these alterations are more selected for in these tumors. Targeted therapy based on these subclonal events might be insufficient for complete tumor control