Patient trial matching using pseudo-siamese network.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e14050-e14050
Author(s):  
Cao Xiao ◽  
Junyi Gao ◽  
Lucas Glass ◽  
Jimeng Sun
Keyword(s):  
Clinical Trials ◽  
Information Retrieval ◽  
Great Success ◽  
Accuracy Score ◽  
Matching Model ◽  
Exclusion Criteria ◽  
Dynamic Memory ◽  
Siamese Network ◽  
The Cross ◽  
Real World Datasets

e14050 Background: Clinical trials suffer from insufficient patient (pt) recruitment. The availability of electronic health records (EHR) and trial eligibility criteria (EC) is promising for data driven pt-trial matching. The objective is to find qualified pt given patients' EHR and trial EC in unstructured text EC. Pseudo-Siamese network is a novel subfield within information retrieval and has shown great success in the cross-modal information retrieval problems such as semantic image-text retrieval (e.g., match images with text descriptions). The objective is to find the match between pts and clinical trials using Pseudo-Siamese network based cross-modal retrieval. Our model addresses the following challenges: (1) How to match unstructured EC text with structured EHR where EC often encode more general disease concepts and EHR represent pt conditions using more specific medical codes. (2) How to capture pts' evolving health conditions. (3) How to explicitly handle the difference for inclusion and exclusion criteria. Methods: Our matching model addresses these challenges as follows: (1) we augment the medical codes in pts’ records with their textual descriptions and hierarchical taxonomies, such that concepts can be embedded in finer and more coarse levels for better concept alignment across pt data and ECs. (2) We include an attentive dynamic memory network that extracts the best matching and more recent pt EHR to match with ECs. (3) We introduce a composite loss term to maximize the similarity between pt records and inclusion criteria while minimizes the similarity between pt records and exclusion criteria. Results: We evaluated our model on a pt-trial match dataset on the ECs collected from 590 clinical trials from ClinicalTrials.gov. We also extract 83,371 pt claims data from IQVIA database collected (2002-2018), where each pt is eligible for at least one trial. We compared our model with leading pt-trial matching models. Our model significantly outperforms the best baseline model by 24.3% relatively higher accuracy score. We also tested these models in 34 oncology trials in 25 cancers. Results will be reported. Conclusions: Pseudo-Siamese network successfully solved the cross-modal information retrieval problems. We therefore propose a new pt-trial matching model based on Pseudo-Siamese network model. Experiments on real-world datasets demonstrated that our model significantly outperforms existing works in pt-trial matching for oncology trials.

Attrition Diagrams for Clinical Trials and Meta-analyses in Stata

2018 ◽  
Vol 18 (2) ◽  
pp. 387-394
Author(s):  
Christiaan H. Righolt ◽  
Salaheddin M. Mahmud
Keyword(s):  
Clinical Trials ◽  
Command Line ◽  
Exclusion Criteria ◽  
Meta Analyses

In this article, we present attrition, a suite of commands to simplify the maintenance and documentation of implemented exclusion criteria and attrition conditions using standard Stata facilities and to generate an attrition diagram. attrition can be used, both from the command line and in do-files, to keep the diagram up to date with the analysis it documents. Six subcommands (set, exclude, count, tab, list, graph) allow the diagram to be constructed in a versatile way.

scholarly journals Critical Appraisal on the Selection Criteria for Evidence-based Healthcare

2021 ◽  
Author(s):  
Paulo Cesar Morales Mayer ◽  
Caroline Amélia Gonçalves ◽  
Franz Porzsolt
Keyword(s):  
Cervical Cancer ◽  
Clinical Trials ◽  
Selection Criteria ◽  
Human Subjects ◽  
Evidence Based ◽  
Inclusion Criteria ◽  
Pragmatic Trials ◽  
Exclusion Criteria ◽  
Policy Makers ◽  
Evidence Based Healthcare

Abstract Background: Evidence-Based healthcare deals basically with published clinical trials to guide the decision making on what treatment to use for any specific conditions.Aims: The present paper assessed the inclusion and exclusion criteria used in clinical trials of cervical cancer aiming at establishing a clear distinction between each criterion.Methods: We performed a bibliographical search in pubmed with the terms cervical cancer and treatment or therapy filtered for clinical trials with human subjects for the last ten years. A total of 30 papers were used extracting and classifying the inclusion and exclusion category according to the characteristic they described. Results: We found no clear parameter to establish which criteria could exclusively serve as inclusion or exclusion across the papers, about 56% of the categories identified were found either listed as inclusion or exclusion criteria or even as both in some cases.Conclusions: The key issue of selection criteria is not in its form but in its function, the first point to consider is if the trial is experimental (focused on efficacy and proof of principle) or observational (pragmatic trials, focused on effectiveness and real world conditions). We suggest, inclusion criteria should be broad, focused on the investigated condition; exclusion criteria should apply only to the subset of this “included” population, and do not take part in observational studies. These conclusions do not serve only for researchers but should affect practitioners and policy makers to correctly compare the results of investigated treatment.

scholarly journals Key Barriers to Clinical Trial Enrolment: A Survey of Clinical Trial Staff at an NCI Designated Cancer Center

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 5864-5864
Author(s):  
Amany R. Keruakous ◽  
Adam S. Asch
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Cultural Bias ◽  
Cancer Center ◽  
Exclusion Criteria ◽  
Strict Inclusion ◽  
Trial Protocols ◽  
Trial Staff ◽  
Disease Site ◽  
Patient Enrolment

Background: Clinical trials, key elements of the processes that account for many of the recent advances in cancer care, are becoming more complex and challenging to conduct. The Stephenson Cancer Center (SCC) has been the lead accruer to NCI-LAP trials over the past three years, and in addition, fields investigator initiated and industry sponsored trials. To identify opportunities for continued improvement in clinical trial enrolment, we sought to identify the obstacles encountered by our clinical trial staff in these activities. Method: We conducted a survey of our research staff including all research nurses and disease site coordinators who participate in recruitment, screening, consenting, data collection and compliance. The survey, sent by email to the clinical trial list-serve at SCC (90 staff member), invited respondents to enumerate obstacles to patient participation in clinical trials. We then performed a follow up meeting with our research coordinators to clarify responses. A total of 26 responses from 90 respondents were received and tabulated by disease site. Results: The most commonly reported obstacles to enrolment were, in descending order: communication/language barriers, cultural bias, time/procedure commitment, and complexity of the trial protocol, financial logistics, comorbidities, and stringent trial criteria. Respondents identified 83 obstacles as frequently encountered obstacles to enrolment. The 83 reported obstacles were classified into 9 categories and organized by disease site as presented in tabular format (below). The most commonly identified obstacles to patient enrolment were communication and language barriers. In patients for whom Spanish is the primary language this was a universal obstacle, as there is a lack of consistent Spanish consents across the clinical trial portfolio. Cultural bias, as an obstacle was manifested as a general mistrust by prospective trial participants of experimental therapies and clinical trials. After communication and cultural bias as barriers, travel requirements and the associated expenses playing a role in patients from rural areas were identified as the most commonly encountered barrier. The complexity of trial protocols and the associated large number of clinic visits, frequent laboratory and imaging tests were also identified as common obstacles. Clinical trial complexity with strict inclusion and exclusion criteria and trial-specified biopsies were frequently cited. Implications: In this descriptive study, common barriers to patient enrolment in clinical trials were identified by clinical trial staff. Assessing barriers encountered by clinical trial staff is infrequently used as a metric for improving clinical trial enrolment, but provides important perspective. In our study, some obstacles are inherent in our patient populations, others appear to be actionable. Development of Spanish language consents and specific programs to overcome negative bias regarding clinical trials are potential areas for improvement. The complexity of clinical trial protocols and the increasingly strict inclusion/exclusion criteria, are issues that will require consideration and action at the level of the cooperative groups and industry. Disclosures No relevant conflicts of interest to declare.

Repurposing Ruxolitinib in Combating COVID-19: a mini review

2021 ◽  
Vol 02 ◽  
Author(s):  
Inshia Begum ◽  
Fathima Murthuza ◽  
Juwairiya Syed Iqbaluddin ◽  
Hafsah Fatima Arsal
Keyword(s):  
Clinical Trials ◽  
Severity Of Illness ◽  
Current Evidence ◽  
Public Healthcare ◽  
Inclusion Criteria ◽  
Research Papers ◽  
Exclusion Criteria ◽  
Mixed Treatment ◽  
Marked Selectivity ◽  
Insight Into

Background: The pandemic caused by Coronavirus Disease 2019 (COVID-19), also known as Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV-2), is believed to be one of the greatest threats to global health in the 21st century. Recent collective evidence has warranted Ruxolitinib as a potential agent in recovery. Ruxolitinib is a potent and selective inhibitor of Jack kinase (JAK) 1 and 2 with modest to marked selectivity against tyrosine kinase two and JAK3. Objective: The review aims to outline the current evidence regarding the repurposed treatment for COVID- 19 and give insight into the clinical trials. There has been considerable interest in introducing existing therapeutic agents against COVID-19 to reduce the severity of illness and ease the burden on public healthcare systems. Method: A literature search was conducted using keywords like ‘Ruxolitinib trial’ and ‘COVID-19 Ruxolitinib’ on PubMed, Google Scholar, Science Direct, and Cochrane databases to select research papers and articles on the topic published from January to October 2020. Inclusion criteria were restricted to articles on Ruxolitinib and COVID. In contrast, the exclusion criteria stipulated that any study done on COVID-19 involving a mixed treatment regimen with Ruxolitinib and other drug/s or any studies not pertinent to the purpose of the study would be omitted. Conclusion: Based on the successful outcomes of various researches conducted and clinical trials performed, the use of Ruxolitinib has shown significant improvement and faster clinical recovery among COVID-19 patients of varying severity of infection, advanced age, and multiple comorbidities. This review provides an overview of various such studies with their promising outcomes.

scholarly journals Be Relevant, Non-Redundant, and Timely: Deep Reinforcement Learning for Real-Time Event Summarization

2020 ◽  
Vol 34 (05) ◽  
pp. 9410-9417
Author(s):  
Min Yang ◽  
Chengming Li ◽  
Fei Sun ◽  
Zhou Zhao ◽  
Ying Shen ◽  
...  
Keyword(s):  
Reinforcement Learning ◽  
Real Time ◽  
Language Processing ◽  
Semantic Features ◽  
Unified Framework ◽  
Time Step ◽  
Dynamic Memory ◽  
The Arts ◽  
Real World Datasets ◽  
Event Summarization

Real-time event summarization is an essential task in natural language processing and information retrieval areas. Despite the progress of previous work, generating relevant, non-redundant, and timely event summaries remains challenging in practice. In this paper, we propose a Deep Reinforcement learning framework for real-time Event Summarization (DRES), which shows promising performance for resolving all three challenges (i.e., relevance, non-redundancy, timeliness) in a unified framework. Specifically, we (i) devise a hierarchical cross-attention network with intra- and inter-document attentions to integrate important semantic features within and between the query and input document for better text matching. In addition, relevance prediction is leveraged as an auxiliary task to strengthen the document modeling and help to extract relevant documents; (ii) propose a multi-topic dynamic memory network to capture the sequential patterns of different topics belonging to the event of interest and temporally memorize the input facts from the evolving document stream, avoiding extracting redundant information at each time step; (iii) consider both historical dependencies and future uncertainty of the document stream for generating relevant and timely summaries by exploiting the reinforcement learning technique. Experimental results on two real-world datasets have demonstrated the advantages of DRES model with significant improvement in generating relevant, non-redundant, and timely event summaries against the state-of-the-arts.

scholarly journals Extraction of primary canines for interceptive orthodontic treatment of palatally displaced permanent canines: A systematic review

2017 ◽  
Vol 87 (6) ◽  
pp. 878-885 ◽  
Author(s):  
Naif N. Almasoud
Keyword(s):  
Systematic Review ◽  
Clinical Trials ◽  
Randomized Clinical Trials ◽  
Web Of Science ◽  
Quality Criteria ◽  
Control Groups ◽  
Exclusion Criteria ◽  
The University ◽  
Study Designs ◽  
Primary Canine

ABSTRACT Objective: To determine whether the successful management of palatally displaced permanent canines (PDCs) can be achieved by the interceptive extraction of primary maxillary canines. Materials and Methods: Digital databases (Medline, Scopus, Web of Science, and Cochrane) were searched to retrieve articles published from 1952 to April 2016. The university librarian developed search strategies for each database. Two calibrated reviewers independently reviewed potentially related titles and abstracts. Papers meeting the inclusion and exclusion criteria were read in full. The selected articles were evaluated and scored according to methodological quality criteria. Results: Four randomized clinical trials (RCTs) were included in the systematic review. Compared with two older studies, two more recent RCTs were found to have better study designs, were better conducted, and involved better reporting of the results. The included studies compared intervention groups (children with PDCs undergoing extraction of primary canines) with controls (subjects with PDCs but no primary canine extractions). In three of the four studies, the interceptive extraction of primary canines facilitated eruption of PDCs in more than 65% of cases. Overall, the intervention groups had a markedly higher incidence of successful eruption of PDCs (50%–69%) compared with the control groups (36%–42%). Conclusions: Based on the available evidence, it is reasonable to conclude that eruption of PDCs can be facilitated by extraction of primary canines. However, further high-quality, randomized clinical trials are warranted in other population groups. It is hoped that this study will help orthodontists make evidence-based decisions about clinically managing PDCs.

scholarly journals Strategy for addressing research-site overlap in pragmatic clinical trials: lessons learned from the NIH-DOD-VA Pain Management Collaboratory (PMC)

Trials ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Mary Geda ◽  
◽  
Steven Z. George ◽  
Diana J. Burgess ◽  
Dylan V. Scarton ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Pain Management ◽  
Research Effort ◽  
Health Care Systems ◽  
Lessons Learned ◽  
Exclusion Criteria ◽  
Eligibility Criteria ◽  
Recruitment Methods ◽  
Research Site ◽  
Pragmatic Clinical Trials

Abstract Background The Pain Management Collaboratory (PMC) is a multi-site network of pragmatic clinical trials (PCTs) focused on nonpharmacological approaches to pain management, conducted in health care systems of the US Department of Defense (DoD) and Department of Veterans Affairs (VA) and co-funded by the National Institutes of Health (NIH). Concerns about potential research-site overlap prompted the PMC investigator community to consider strategies to avert this problem that could negatively affect recruitment and contaminate interventions and thus pose a threat to trial integrity. Methods We developed a two-step strategy to identify and remediate research-site overlap by obtaining detailed recruitment plans across all PMC PCTs that addressed eligibility criteria, recruitment methods, trial settings, and timeframes. The first, information-gathering phase consisted of a 2-month period for data collection from PIs, stakeholders, and ClinicalTrials.gov. The second, remediation phase consisted of a series of moderated conference calls over a 1-month time period to develop plans to address overlap. Remediation efforts focused on exclusion criteria and recruitment strategies, and they involved collaboration with sponsors and stakeholder groups such as the Military Treatment Facility Engagement Committee (MTFEC). The MTFEC is comprised of collaborating DoD and university-affiliated PIs, clinicians, and educators devoted to facilitating successful pragmatic trials in DoD settings. Results Of 61 recruitment sites for the 11 PMC PCTs, 17 (28%) overlapped. Four PCTs had five overlapping Military Treatment Facilities (MTFs), and eight PCTs had 12 overlapping VA Medical Centers (VAMCs). We developed three general strategies to avoid research-site overlap: (i) modify exclusion criteria, (ii) coordinate recruitment efforts, and/or (iii) replace or avoid any overlapping sites. Potential overlap from competing studies outside of the PMC was apparent at 26 sites, but we were not able to confirm them as true conflicts. Conclusion Proactive strategies can be used to resolve the issue of overlapping research sites in the PMC. These strategies, combined with open and impartial mediation approaches that include researchers, sponsors, and stakeholders, provide lessons learned from this large and complex pragmatic research effort.

scholarly journals Treatment of chikungunya chronic arthritis: A systematic review

2018 ◽  
Vol 64 (1) ◽  
pp. 63-70 ◽  
Author(s):  
Gabriella Maria Pitt Gameiro Sales ◽  
Izabel Crystine Pereira Barbosa ◽  
Laura Maia Sampaio Canejo Neta ◽  
Paloma Lopes de Melo ◽  
Raphael de Azevedo Leitão ◽  
...  
Keyword(s):  
Systematic Review ◽  
Clinical Trials ◽  
Case Reports ◽  
Case Control ◽  
Sudden Onset ◽  
Chronic Arthritis ◽  
Exclusion Criteria ◽  
Daily Life Activities ◽  
Expert Opinions ◽  
Inflammatory Drugs

Summary Introduction: Chikungunya (CHIK) is a tropical arbovirus, transmitted by the female mosquito Aedes aegypti and Aedes albopictus. In Brazil, there have been cases reported since 2014. The initial manifestations of this virus are sudden onset high fever, headache, chills, rashes, myalgia and intense joint pain. Usually, CHIK presents the acute and chronic phases, the latter characterized by bilateral polyarthralgia, which can last for months or even years. During this period, autoimmune diseases can be triggered, making the picture even more complicated. Method: A systematic review was performed on the PubMed and Scielo databases in January 2017. Clinical trials, cohorts, case-control and case reports were included in the study. Expert opinions, societal consensuses and literary reviews were exclusion criteria. Studies were conducted in English, Spanish and Portuguese. The studies were descriptively analyzed and the data was grouped according to methodological similarity. Results: Twenty-four (24) articles were selected and, in compliance with the inclusion and exclusion criteria, 18 were eliminated, with six studies remaining in the present review: five clinical trials and one case report. Conclusion: When the manifestations of CHIK become chronic and, the longer they last, more complications arise. Polyarthralgia can be immaterial, distancing individuals from their daily-life activities. Anti-inflammatory drugs (either steroid or not), in addition to immunosuppressants, homeopathy and physiotherapy are measures of treatment that, according to the literature, have been successful in relieving or extinguishing symptoms. However, it is fundamental that studies of CHIK treatment be further developed.

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