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Supporting Parallel R Code in Clinical Trials: A Grid-Based Approach

Dennis Wegener, Thierry Sengstag, Stelios Sfakianakis, Stefan Rüping
2008 2008 IEEE International Symposium on Parallel and Distributed Processing with Applications  
In this paper, we describe an extension to the ACGT GridR environment which allows the parallelization of loops in R scripts in view of their distributed execution on a computational grid.  ...  The use of parallelization directives as special R comments provides users with the potential to accelerate lengthy calculations with changes to preexisting code.  ...  Acknowledgments The authors gratefully acknowledge the financial support of the European Commission for the Project ACGT, FP6/2004/IST-026996. References  ... 
doi:10.1109/ispa.2008.29 dblp:conf/ispa/WegenerSSR08 fatcat:a42ukhvvsvet7cyxr7levl54si

Building a System for Advancing Clinico-Genomic Trials on Cancer

Stelios Sfakianakis, Norbert M. Graf, Alexander Hoppe, Stefan Rüping, Dennis Wegener, Lefteris Koumakis, George Zacharioudakis
2009 Professional Practice in Artificial Intelligence  
In the project ACGT, a grid-based software system to support clinicians and bio-statisticians in their daily work is being developed.  ...  In this paper, results of the initial requirements analysis and approaches to address these requirements are presented.  ...  The R code to be executed can be given directly by the user in the form of a script, but in order to increase the possibility of distributing and re-using code, the intended way to execute R code is by  ... 
dblp:conf/ifip12/SfakianakisGHRWKZ09 fatcat:akpvrowf65fq5juyzxtbnegpq4

Developing Regulatory-compliant Electronic Case Report Forms for Clinical Trials: Experience with The Demand Trial

B. Ene-Iordache, S. Carminati, L. Antiga, N. Rubis, P. Ruggenenti, G. Remuzzi, A. Remuzzi
2009 JAMIA Journal of the American Medical Informatics Association  
A b s t r a c t The use of electronic case report forms (CRF) to gather data in randomized clinical trials has grown to progressively replace paper-based forms.  ...  Here the authors focus on the development of computerized systems for clinical trials implementing FDA and EU recommendations and regulations, and describe a laptop-based electronic CRF used in a randomized  ...  The authors thank Chiesi Farmaceutici Spa, Parma, Italy for their support for the DEMAND trial.  ... 
doi:10.1197/jamia.m2787 pmid:19261946 pmcid:PMC2732224 fatcat:t2meo3thdfbk5kb24ijillohay

A randomised controlled trial investigating the clinical and cost-effectiveness of Alpha-Stim AID cranial electrotherapy stimulation (CES) in patients seeking treatment for moderate severity depression in primary care (Alpha-Stim-D Trial)

Shireen Patel, Clement Boutry, Priya Patel, Michael P. Craven, Boliang Guo, Azhar Zafar, Joe Kai, David Smart, Debbie Butler, Fred Higton, Rebecca McNaughton, Paul M. Briley (+4 others)
2022 Trials  
The study is a multi-centre parallel-group, double-blind, non-commercial, randomised controlled superiority trial.  ...  Methods The aim of this study is to investigate the clinical and cost-effectiveness of Alpha-Stim AID in treatment-seeking patients (aged 16 years upwards) with moderate to moderately severe depressive  ...  We acknowledge the help and support of the NIHR Clinical Research Network in the East Midlands and TVSM. We would like to thank Ashley Duncan and Dr.  ... 
doi:10.1186/s13063-022-06192-1 pmid:35379314 pmcid:PMC8978160 fatcat:hfezm3igpbba5lhyh3cznttgfi

Design of trials for interrupting the transmission of endemic pathogens

Mariabeth Silkey, Tobias Homan, Nicolas Maire, Alexandra Hiscox, Richard Mukabana, Willem Takken, Thomas A. Smith
2016 Trials  
The approach is applicable to a range of infectious diseases transmitted via environmental reservoirs or via arthropod vectors.  ...  Methods: A generic model of disease transmission was used to simulate infections in stepped wedge cluster-randomized trials (SWCRTs) of a transmission-reducing intervention, where the intervention has  ...  Acknowledgments The authors acknowledge financial support from the COmON Foundation, http://www.comonstichting.org.  ... 
doi:10.1186/s13063-016-1378-1 pmid:27266269 pmcid:PMC4895826 fatcat:h6yuwwmuhjazzfetg3mam457ei

Japan Unified Protocol Clinical Trial for Depressive and Anxiety Disorders (JUNP study): study protocol for a randomized controlled trial

Masaya Ito, Yasuyuki Okumura, Masaru Horikoshi, Noriko Kato, Yuki Oe, Mitsuhiro Miyamae, Naotsugu Hirabayashi, Ayako Kanie, Atsuo Nakagawa, Yutaka Ono
2016 BMC Psychiatry  
Methods/design: The trial was designed as a single-center, assessor-blinded, randomized, 20-week, parallel-group superiority study in order to compare the efficacy of the combination of unified protocol  ...  If its efficacy can be confirmed, the unified protocol may be of high clinical value for Japan, a country in which cognitive behavioral treatment has not yet been widely adopted.  ...  Acknowledgements This study was supported by a National Center of Neurology and Psychiatry (NCNP) Intramural Research Grant for Neurological and Psychiatric Disorders, and a Grant-in-Aid for Young Scientists  ... 
doi:10.1186/s12888-016-0779-8 pmid:26987315 pmcid:PMC4797168 fatcat:oxav2qcg6zg7ner6o6qq5k6wcm

Cost talk: protocol for a stepped-wedge cluster randomized trial of an intervention helping patients and urologic surgeons discuss costs of care for slow-growing prostate cancer during shared decision-making

Mary C. Politi, Rachel C. Forcino, Katelyn Parrish, Marie-Anne Durand, A. James O'Malley, Glyn Elwyn
2021 Trials  
Methods We will conduct a stepped-wedge cluster randomized trial in outpatient urology practices affiliated with a large academic medical center in the USA.  ...  Establishing the effectiveness of the strategy under study will allow for its replication in other clinical decision contexts. Trial registration ClinicalTrials.govNCT04397016.  ...  The sponsor has no role in the design, execution, or reporting of the study.  ... 
doi:10.1186/s13063-021-05369-4 pmid:34187547 fatcat:smlvvt6gsndojncbcnopc6lfkm

Individualised sensory intervention to improve quality of life in people with dementia and their companions (SENSE-Cog trial): study protocol for a randomised controlled trial

Jemma Regan, Eric Frison, Fidéline Collin, Piers Dawes, Mark Hann, Ines Himmelsbach, Emma Hooper, David Reeves, Zoe Simkin, Chryssoula Thodi, Fan Yang, Iracema Leroi
2019 Trials  
The SENSE-Cog trial will test whether a home-based multi-part sensory intervention is effective in improving quality of life and other key outcomes in people with dementia and hearing or vision problems  ...  A parallel and complementary process evaluation will be described elsewhere.  ...  We thank the Greater Manchester NIHR Clinical Research Network for supporting the study.  ... 
doi:10.1186/s13063-018-2973-0 fatcat:io72wxnu5bhfzn6bi473tsmb3e

Meeting abstracts from the 4th International Clinical Trials Methodology Conference (ICTMC) and the 38th Annual Meeting of the Society for Clinical Trials

2017 Trials  
Acknowledgements Funded by the MRC North West Hub in Trials Methodological Research (MR/K025635/1) and the NIHR Health Technology Assessment programme (08/14/39).  ...  Pros This approach uses well-supported public domain software, so little in-house coding is required.  ...  Methods EXPONATE was a two-arm parallel cluster randomised trial of a primary care-based intervention for perinatal depression delivered by community midwives in Nigeria.  ... 
doi:10.1186/s13063-017-1902-y fatcat:yt477zyq4vbi7cm6f3sozyl42u

DICOM structured reporting and cancer clinical trials results

David A Clunie
2007 Cancer Informatics  
The use of DICOM Structured Reporting for the encoding and interchange of clinical trial results in a standard manner is reviewed.  ...  The use of biomarkers derived from radiological images as surrogate end-points in therapeutic cancer clinical trials is well established.  ...  In the context of recording measurements of lesions in clinical trials, the question arises as to whether or not the context of use in a template specifi cally designed for clinical trials use is sufficient  ... 
pmid:19390663 pmcid:PMC2666949 fatcat:yfpvov5krrgajebnnxb5lhjrmi

DICOM Structured Reporting and Cancer Clinical Trials Results

David A. Clunie
2007 Cancer Informatics  
The use of DICOM Structured Reporting for the encoding and interchange of clinical trial results in a standard manner is reviewed.  ...  The use of biomarkers derived from radiological images as surrogate end-points in therapeutic cancer clinical trials is well established.  ...  In the context of recording measurements of lesions in clinical trials, the question arises as to whether or not the context of use in a template specifi cally designed for clinical trials use is sufficient  ... 
doi:10.4137/cin.s37032 fatcat:6c26bwqbmnahjoytp4oww2a23m

A Configurable Deep Network for high-dimensional clinical trial data

Jim O' Donoghue, Mark Roantree, Martin Van Boxtel
2015 2015 International Joint Conference on Neural Networks (IJCNN)  
In this paper, we present our framework for a configurable deep learning machine and our evaluation and analysis of two shallow approaches: regression and multi-layer perceptron, as a platform to a deep  ...  The purpose of our research is to build a framework which allows easy reconfiguration for the performance of experiments across a number of deep learning approaches.  ...  ACKNOWLEDGMENT This research is carried out under In-MINDD, which is funded by the European Union Seventh Framework Programme, Grant Agreement Number 304979  ... 
doi:10.1109/ijcnn.2015.7280841 dblp:conf/ijcnn/ODonoghueRB15 fatcat:djb6tfquzzbvbjzognihyst7mm

Pragmatic cluster randomized trial to evaluate effectiveness and implementation of enhanced EHR-facilitated cancer symptom control (E2C2)

Lila J. Finney Rutten, Kathryn J. Ruddy, Linda L. Chlan, Joan M. Griffin, Jeph Herrin, Aaron L. Leppin, Deirdre R. Pachman, Jennifer L. Ridgeway, Parvez A. Rahman, Curtis B. Storlie, Patrick M. Wilson, Andrea L. Cheville
2020 Trials  
By surveying and interviewing clinical staff, we will also evaluate whether the use of a multifaceted, evidence-based implementation strategy to support adoption and use of the E2C2 technologies improves  ...  The E2C2 intervention offers a pragmatic, scalable approach to delivering guideline-based symptom and function management for cancer patients.  ...  Trial design {8} E2C2 will be evaluated through a pragmatic cluster randomized stepped wedge trial in which clinics and disease-specific teams are randomized in multiple steps.  ... 
doi:10.1186/s13063-020-04335-w pmid:32503661 fatcat:cyaiq6quo5ahhh374smqjafq7m

The CancerGrid experience: Metadata-based model-driven engineering for clinical trials

Jim Davies, Jeremy Gibbons, Steve Harris, Charles Crichton
2014 Science of Computer Programming  
. • Four case studies. a b s t r a c t The CancerGrid approach to software support for clinical trials is based on two principles: careful curation of semantic metadata about clinical observations, to  ...  In other words, clinical trials management is crying out for a model-driven approach.  ...  The CONSORT trials metamodel and the forms-based approach to model-driven engineering are described in a couple of conference papers [24, 18] .  ... 
doi:10.1016/j.scico.2013.02.010 fatcat:xkbamlmonffspc5wxgf7zbg6vi

Intervention Comparative Effectiveness for Adult Cognitive Training (ICE-ACT) Trial: Rationale, design, and baseline characteristics

Jong-Sung Yoon, Nelson A. Roque, Ronald Andringa, Erin R. Harrell, Katharine G. Lewis, Thomas Vitale, Neil Charness, Walter R. Boot
2019 Contemporary Clinical Trials  
A one-year follow-up from training completion is also scheduled. The baseline results support that randomization was successful across the intervention conditions.  ...  Participants (N = 230, Mean age = 72) were randomly assigned to one of four training conditions: broad training using either (1) a web-based brain game suite, Brain HQ, or (2) a strategy video game, Rise  ...  Nelson A. Roque was also supported by National Institute on Aging Grant T32 AG049676 to The Pennsylvania State University.  ... 
doi:10.1016/j.cct.2019.01.014 pmid:30711665 pmcid:PMC6485952 fatcat:fdxr4l4xprbmbbsv5ka5qb72zm
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