LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 4 of total 4

Search options

  1. Article ; Online: diceR

    Derek S. Chiu / Aline Talhouk

    BMC Bioinformatics, Vol 19, Iss 1, Pp 1-

    an R package for class discovery using an ensemble driven approach

    2018  Volume 4

    Abstract: Abstract Background Given a set of features, researchers are often interested in partitioning objects into homogeneous clusters. In health research, cancer research in particular, high-throughput data is collected with the aim of segmenting patients into ...

    Abstract Abstract Background Given a set of features, researchers are often interested in partitioning objects into homogeneous clusters. In health research, cancer research in particular, high-throughput data is collected with the aim of segmenting patients into sub-populations to aid in disease diagnosis, prognosis or response to therapy. Cluster analysis, a class of unsupervised learning techniques, is often used for class discovery. Cluster analysis suffers from some limitations, including the need to select up-front the algorithm to be used as well as the number of clusters to generate, in addition, there may exist several groupings consistent with the data, making it very difficult to validate a final solution. Ensemble clustering is a technique used to mitigate these limitations and facilitate the generalization and reproducibility of findings in new cohorts of patients. Results We introduce diceR (diverse cluster ensemble in R), a software package available on CRAN: https://CRAN.R-project.org/package=diceR Conclusions diceR is designed to provide a set of tools to guide researchers through a general cluster analysis process that relies on minimizing subjective decision-making. Although developed in a biological context, the tools in diceR are data-agnostic and thus can be applied in different contexts.
    Keywords Data mining ; Cluster analysis ; Ensemble ; Consensus ; Cancer ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 004 ; 006
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Wearable Biosensors in the Workplace

    Lauren C. Tindale / Derek Chiu / Nicole Minielly / Viorica Hrincu / Aline Talhouk / Judy Illes

    Frontiers in Digital Health, Vol

    Perceptions and Perspectives

    2022  Volume 4

    Abstract: ObjectivesWearable body and brain sensors are permeating the consumer market and are increasingly being considered for workplace applications with the goal of promoting safety, productivity, health, and wellness. However, the monitoring of physiologic ... ...

    Abstract ObjectivesWearable body and brain sensors are permeating the consumer market and are increasingly being considered for workplace applications with the goal of promoting safety, productivity, health, and wellness. However, the monitoring of physiologic signals in real-time prompts concerns about benefit and risk, ownership of such digital data, data transfer privacy, and the discovery and disclosure of signals of possible health significance. Here we explore the perceptions and perspectives of employers and employees about key ethical considerations regarding the potential use of sensors in the workplace.MethodsWe distributed a survey developed and refined based on key research questions and past literature to a wide range and size of industries in British Columbia, Canada. Both employers (potential Implementers) and employees (potential Users) were invited to participate.ResultsWe received 344 survey responses. Most responses were from construction, healthcare, education, government, and utilities sectors. Across genders, industries, and workplace sizes, we found a convergence of opinions on perceived benefit and concern between potential Implementers and potential Users regarding the motivation to use biosensors in the workplace. Potential Implementers and Users also agreed on issues pertaining to safety, privacy, disclosure of findings of possible medical significance, risks, data ownership, data sharing, and transfer of data between workplaces. The greatest variability between potential Users and Implementers pertained to data ownership.ConclusionStrong agreement in the perception of biosensor use in the workplace between potential Implementers and Users reflects shared interest, motivation, and responsibility for their use. The use of sensors is rapidly increasing, and transparency about key use factors–both practical and ethical–is essential to maintain the current and desirable level of solidarity.
    Keywords wearable sensor ; wearable electronic devices ; occupational safety ; biosensor ; corporate ethics ; workplace sensor ; Medicine ; R ; Public aspects of medicine ; RA1-1270 ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 170
    Language English
    Publishing date 2022-07-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: From biobank and data silos into a data commons

    Rebecca Asiimwe / Stephanie Lam / Samuel Leung / Shanzhao Wang / Rachel Wan / Anna Tinker / Jessica N. McAlpine / Michelle M. M. Woo / David G. Huntsman / Aline Talhouk

    Journal of Translational Medicine, Vol 19, Iss 1, Pp 1-

    convergence to support translational medicine

    2021  Volume 13

    Abstract: Abstract Background To drive translational medicine, modern day biobanks need to integrate with other sources of data (clinical, genomics) to support novel data-intensive research. Currently, vast amounts of research and clinical data remain in silos, ... ...

    Abstract Abstract Background To drive translational medicine, modern day biobanks need to integrate with other sources of data (clinical, genomics) to support novel data-intensive research. Currently, vast amounts of research and clinical data remain in silos, held and managed by individual researchers, operating under different standards and governance structures; a framework that impedes sharing and effective use of data. In this article, we describe the journey of British Columbia’s Gynecological Cancer Research Program (OVCARE) in moving a traditional tumour biobank, outcomes unit, and a collection of data silos, into an integrated data commons to support data standardization and resource sharing under collaborative governance, as a means of providing the gynecologic cancer research community in British Columbia access to tissue samples and associated clinical and molecular data from thousands of patients. Results Through several engagements with stakeholders from various research institutions within our research community, we identified priorities and assessed infrastructure needs required to optimize and support data collections, storage and sharing, under three main research domains: (1) biospecimen collections, (2) molecular and genomics data, and (3) clinical data. We further built a governance model and a resource portal to implement protocols and standard operating procedures for seamless collections, management and governance of interoperable data, making genomic, and clinical data available to the broader research community. Conclusions Proper infrastructures for data collection, sharing and governance is a translational research imperative. We have consolidated our data holdings into a data commons, along with standardized operating procedures to meet research and ethics requirements of the gynecologic cancer community in British Columbia. The developed infrastructure brings together, diverse data, computing frameworks, as well as tools and applications for managing, analyzing, and sharing data. Our data ...
    Keywords Biobanks ; Biospecimens ; Biobank-technologies ; Precision medicine ; Data commons ; Laboratory Information Management Systems (LIMS) ; Medicine ; R
    Subject code 306
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction.

    Aline Talhouk / Stefan Kommoss / Robertson Mackenzie / Martin Cheung / Samuel Leung / Derek S Chiu / Steve E Kalloger / David G Huntsman / Stephanie Chen / Maria Intermaggio / Jacek Gronwald / Fong C Chan / Susan J Ramus / Christian Steidl / David W Scott / Michael S Anglesio

    PLoS ONE, Vol 11, Iss 4, p e

    2016  Volume 0153844

    Abstract: A major weakness in many high-throughput genomic studies is the lack of consideration of a clinical environment where one patient at a time must be evaluated. We examined generalizable and platform-specific sources of variation from NanoString gene ... ...

    Abstract A major weakness in many high-throughput genomic studies is the lack of consideration of a clinical environment where one patient at a time must be evaluated. We examined generalizable and platform-specific sources of variation from NanoString gene expression data on both ovarian cancer and Hodgkin lymphoma patients. A reference-based strategy, applicable to single-patient molecular testing is proposed for batch effect correction. The proposed protocol improved performance in an established Hodgkin lymphoma classifier, reducing batch-to-batch misclassification while retaining accuracy and precision. We suggest this strategy may facilitate development of NanoString and similar molecular assays by accelerating prospective validation and clinical uptake of relevant diagnostics.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top