UvA-DARE (Digital Academic Repository)

In vivo delayed-type hypersensitivity skin test anergy in human immunodeficiency virus type 1 infection is associated with T cell nonresponsiveness in vitr

Spatio-structural granularity of biological material entities

<p>Abstract</p> <p>Background</p> <p>With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities.</p> <p>Results</p> <p>The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the <it>compositional object perspective </it>as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities.</p> <p>Conclusions</p> <p>The here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different <it>views </it>on its content (i.e. data, knowledge), each organized into different levels of detail.</p

Increasing Clinical Virulence in Two Decades of the Italian HIV Epidemic

The recent origin and great evolutionary potential of HIV imply that the virulence of the virus might still be changing, which could greatly affect the future of the pandemic. However, previous studies of time trends of HIV virulence have yielded conflicting results. Here we used an established methodology to assess time trends in the severity (virulence) of untreated HIV infections in a large Italian cohort. We characterized clinical virulence by the decline slope of the CD4 count (n = 1423 patients) and the viral setpoint (n = 785 patients) in untreated patients with sufficient data points. We used linear regression models to detect correlations between the date of diagnosis (ranging 1984–2006) and the virulence markers, controlling for gender, exposure category, age, and CD4 count at entry. The decline slope of the CD4 count and the viral setpoint displayed highly significant correlation with the date of diagnosis pointing in the direction of increasing virulence. A detailed analysis of riskgroups revealed that the epidemics of intravenous drug users started with an apparently less virulent virus, but experienced the strongest trend towards steeper CD4 decline among the major exposure categories. While our study did not allow us to exclude the effect of potential time trends in host factors, our findings are consistent with the hypothesis of increasing HIV virulence. Importantly, the use of an established methodology allowed for a comparison with earlier results, which confirmed that genuine differences exist in the time trends of HIV virulence between different epidemics. We thus conclude that there is not a single global trend of HIV virulence, and results obtained in one epidemic cannot be extrapolated to others. Comparison of discordant patterns between riskgroups and epidemics hints at a converging trend, which might indicate that an optimal level of virulence might exist for the virus

Functional remission of people with serious mental illness (SMI):Psychometric properties of a new ROM-instrument

BACKGROUND: Instruments are used for routine outcome monitoring of patients with severe mental illness in order to measure psychiatric symptoms, care needs and quality of life. By adding an instrument for measuring functional remission a more complete picture can be given of the complaints, the symptoms and general functioning, which can give direction to providing care for patients with severe mental illness. AIM: To describe the development and testing of a new instrument of functional remission (FR) among people with a psychotic disorder or another serious mental disorder (SMI) as an addition to the symptomatic remission (SR), according to international criteria. METHOD: The FR-assessment involves assessment by a mental health professional who conducts a semi-structured interview with the patient and his or her family and/or uses patient files relating to the three areas of functioning: daily living and self-care; work, study and housekeeping; and social contacts. These areas are rated on a three-point scale of o: independent; 1: partially independent; 2: dependent. The assessment covers a period of six months, in accordance with the measurement of symptomatic remission and should be part of regular routine outcome monitoring (ROM) procedures. The FR-instrument was used in 2012 with 840 patients from eight Dutch mental care institutions and included a one-year follow-up among 523 patients (response 62%). RESULTS: The results showed that the instrument is relatively easily to complete. It was also relevant for clinical practice, although further research is needed because of the raters' low response. Intra- and inter-rater reliability, discriminating and convergent validity, and sensitivity to change were rated sufficient to good. CONCLUSION: If the FR-instrument becomes part of regular ROM-procedures and is used as a measure of societal participation, it could be a useful addition to current measures of symptomatic remission.</p

Functional remission of people with serious mental illness (SMI):Psychometric properties of a new ROM-instrument

BACKGROUND: Instruments are used for routine outcome monitoring of patients with severe mental illness in order to measure psychiatric symptoms, care needs and quality of life. By adding an instrument for measuring functional remission a more complete picture can be given of the complaints, the symptoms and general functioning, which can give direction to providing care for patients with severe mental illness. AIM: To describe the development and testing of a new instrument of functional remission (FR) among people with a psychotic disorder or another serious mental disorder (SMI) as an addition to the symptomatic remission (SR), according to international criteria. METHOD: The FR-assessment involves assessment by a mental health professional who conducts a semi-structured interview with the patient and his or her family and/or uses patient files relating to the three areas of functioning: daily living and self-care; work, study and housekeeping; and social contacts. These areas are rated on a three-point scale of o: independent; 1: partially independent; 2: dependent. The assessment covers a period of six months, in accordance with the measurement of symptomatic remission and should be part of regular routine outcome monitoring (ROM) procedures. The FR-instrument was used in 2012 with 840 patients from eight Dutch mental care institutions and included a one-year follow-up among 523 patients (response 62%). RESULTS: The results showed that the instrument is relatively easily to complete. It was also relevant for clinical practice, although further research is needed because of the raters' low response. Intra- and inter-rater reliability, discriminating and convergent validity, and sensitivity to change were rated sufficient to good. CONCLUSION: If the FR-instrument becomes part of regular ROM-procedures and is used as a measure of societal participation, it could be a useful addition to current measures of symptomatic remission.</p

Classificatory Theory in Data-Intensive Science: The Case of Open Biomedical Ontologies

publication-status: Publishedtypes: ArticleThis is the author's version of a paper that was subsequently published in International Studies in the Philosophy of Science. Please cite the published version by following the DOI link.Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and argue that they constitute an example of classificatory theory. This form of theorizing emerges from classification practices in conjunction with experimental know-how and expresses the knowledge underpinning the analysis and interpretation of data disseminated online.Economic and Social Research Council (ESRC)The British AcademyLeverhulme Trus