Ariadne's Thread - Interactive Navigation in a World of Networked Information

This work-in-progress paper introduces an interface for the interactive visual exploration of the context of queries using the ArticleFirst database, a product of OCLC. We describe a workflow which allows the user to browse live entities associated with 65 million articles. In the on-line interface, each query leads to a specific network representation of the most prevailing entities: topics (words), authors, journals and Dewey decimal classes linked to the set of terms in the query. This network represents the context of a query. Each of the network nodes is clickable: by clicking through, a user traverses a large space of articles along dimensions of authors, journals, Dewey classes and words simultaneously. We present different use cases of such an interface. This paper provides a link between the quest for maps of science and on-going debates in HCI about the use of interactive information visualisation to empower users in their search.Comment: CHI'15 Extended Abstracts, April 18-23, 2015, Seoul, Republic of Korea. ACM 978-1-4503-3146-3/15/0

Contextualization of topics - browsing through terms, authors, journals and cluster allocations

This paper builds on an innovative Information Retrieval tool, Ariadne. The tool has been developed as an interactive network visualization and browsing tool for large-scale bibliographic databases. It basically allows to gain insights into a topic by contextualizing a search query (Koopman et al., 2015). In this paper, we apply the Ariadne tool to a far smaller dataset of 111,616 documents in astronomy and astrophysics. Labeled as the Berlin dataset, this data have been used by several research teams to apply and later compare different clustering algorithms. The quest for this team effort is how to delineate topics. This paper contributes to this challenge in two different ways. First, we produce one of the different cluster solution and second, we use Ariadne (the method behind it, and the interface - called LittleAriadne) to display cluster solutions of the different group members. By providing a tool that allows the visual inspection of the similarity of article clusters produced by different algorithms, we present a complementary approach to other possible means of comparison. More particular, we discuss how we can - with LittleAriadne - browse through the network of topical terms, authors, journals and cluster solutions in the Berlin dataset and compare cluster solutions as well as see their context.Comment: proceedings of the ISSI 2015 conference (accepted

Early respiratory and skin symptoms in relation to ethnic background: the importance of socioeconomic status; the PIAMA study

AIMS: To evaluate ethnic differences in the prevalence of respiratory and skin symptoms in the first two years of life. METHODS: A total of 4146 children participated in the Prevention and Incidence of Asthma and Mite Allergy (PIAMA) study. Parents completed questionnaires on respirato

Minimizing Communication in the Multidimensional FFT

We present a parallel algorithm for the fast Fourier transform (FFT) in higher dimensions. This algorithm generalizes the cyclic-to-cyclic one-dimensional parallel algorithm to a cyclic-to-cyclic multidimensional parallel algorithm while retaining the property of needing only a single all-to-all communication step. This is under the constraint that we use at most √N processors for an FFT on an array with a total of N elements, irrespective of the dimension d or the shape of the array. The only assumption we make is that N is sufficiently composite. Our algorithm starts and ends in the same data distribution. We present our multidimensional implementation FFTU which utilizes the sequential FFTW program for its local FFTs, and which can handle any dimension d. We obtain experimental results for d ≤5 using MPI on up to 4096 cores of the supercomputer Snellius, comparing FFTU with the parallel FFTW program and with PFFT and heFFTe. These results show that FFTU is competitive with the state of the art and that it allows one to use a larger number of processors, while keeping communication limited to a single all-to-all operation. For arrays of size 10243 and 645, FFTU achieves a speedup of a factor 149 and 176, respectively, on 4096 processors

Feasibility and effectiveness of trifluridine/tipiracil in metastatic colorectal cancer: real-life data from The Netherlands

Background: The RECOURSE trial showed clinical efficacy for trifluridine/tipiracil for refractory metastatic colorectal cancer patients. We assessed the feasibility and effectiveness of trifluridine/tipiracil in daily clinical practice in The Netherlands. Methods: Medical records of patients from 17 centers treated in the trifluridine/tipiracil compassionate use program were reviewed and checked for RECOURSE eligibility criteria. Baseline characteristics, safety, and survival times were compared, and prespecified baseline characteristics were tested in multivariate analyses for prognostic significance on overall survival (OS). Results: A total of 136 patients with a median age of 62 years were analyzed. Forty-three patients (32%) did not meet the RECOURSE eligibility criteria for not having received all prior standard treatments (n = 35, 26%) and/or ECOG performance status (PS) 2 (n = 12, 9%). The most common grade ≥3 toxicities were neutropenia (n = 44, 32%), leukopenia (n = 8, 6%), anemia (n = 7, 5%), and fatigue (n = 7, 5%). Median progression-free survival (PFS) and median OS were 2.1 (95% CI, 1.8–2.3) and 5.4 months (95% CI, 4.0–6.9), respectively. Patients with ECOG PS 2 had a worse median OS (3.2 months) compared to patients with ECOG PS 0–1 (5.9 months). ECOG PS, KRAS-mutation status, white blood cell count, serum lactate dehydrogenase, and alkaline phosphatase were prognostic factors for OS. Conclusions: Our data show that treatment with trifluridine/tipiracil in daily clinical practice is feasible and safe. Differences in patient characteristics between our population and the RECOURSE study population should be taken into account in the interpretation of survival data. Our results argue against the use of trifluridine/tipiracil in patients with ECOG PS 2. Funding: Johannes J.M. Kwakman received an unrestricted research grant from Servier

Mite and pet allergen levels in homes of children born to allergic and nonallergic parents: the PIAMA study.

The Prevention and Incidence of Asthma and Mite Allergy (PIAMA) study is a birth cohort study that investigates the influence of allergen exposure on the development of allergy and asthma in the first several years of life. The objectives of this study were to investigate the relationship between a family history of allergy and/or asthma and exposure of newborn children to mite and pet allergen and to study the influence of different home and occupant characteristics on mite allergen exposure. Dust was sampled from the child's mattress and the parental mattress at 3 months after birth of the index child and analyzed for mite and pet allergens. Subjects were divided in groups according to history of asthma and allergy in their parents, and allergen exposure was studied in the different groups. Cat allergen exposure was significantly lower on parental mattresses in families with allergic mothers, but dog allergen exposure was not different. Mite allergen exposure was lower on parental mattresses in families with allergic mothers. Use of mite allergen-impermeable mattress covers reduced mite allergen exposure. Some other characteristics such as age of home and mattress were also found to influence mite allergen exposure. Parental mattresses in homes of allergic mothers had lower cat and mite (but not dog) allergen loadings than mattresses in homes of nonallergic parents. Paternal (as opposed to maternal) allergy seemed to have little influence

The Trial within Cohorts (TwiCs) study design in oncology: experience and methodological reflections

A Trial within Cohorts (TwiCs) study design is a trial design that uses the infrastructure of an observational cohort study to initiate a randomized trial. Upon cohort enrollment, the participants provide consent for being randomized in future studies without being informed. Once a new treatment is available, eligible cohort participants are randomly assigned to the treatment or standard of care. Patients randomized to the treatment arm are offered the new treatment, which they can choose to refuse. Patients who refuse will receive standard of care instead. Patients randomized to the standard of care arm receive no information about the trial and continue receiving standard of care as part of the cohort study. Standard cohort measures are used for outcome comparisons. The TwiCs study design aims to overcome some issues encountered in standard Randomized Controlled Trials (RCTs). An example of an issue in standard RCTs is the slow patient accrual. A TwiCs study aims to improve this by selecting patients using a cohort and only offering the intervention to patients in the intervention arm. In oncology, the TwiCs study design has gained increasing interest during the last decade. Despite its potential advantages over RCTs, the TwiCs study design has several methodological challenges that need careful consideration when planning a TwiCs study. In this article, we focus on these challenges and reflect on them using experiences from TwiCs studies initiated in oncology. Important methodological challenges that are discussed are the timing of randomization, the issue of non-compliance (refusal) after randomization in the intervention arm, and the definition of the intention-to-treat effect in a TwiCs study and how this effect is related to its counterpart in standard RCTs