Sample records for large clinical database
-
National Databases for Neurosurgical Outcomes Research: Options, Strengths, and Limitations.
Karhade, Aditya V; Larsen, Alexandra M G; Cote, David J; Dubois, Heloise M; Smith, Timothy R
2017-08-05
Quality improvement, value-based care delivery, and personalized patient care depend on robust clinical, financial, and demographic data streams of neurosurgical outcomes. The neurosurgical literature lacks a comprehensive review of large national databases. To assess the strengths and limitations of various resources for outcomes research in neurosurgery. A review of the literature was conducted to identify surgical outcomes studies using national data sets. The databases were assessed for the availability of patient demographics and clinical variables, longitudinal follow-up of patients, strengths, and limitations. The number of unique patients contained within each data set ranged from thousands (Quality Outcomes Database [QOD]) to hundreds of millions (MarketScan). Databases with both clinical and financial data included PearlDiver, Premier Healthcare Database, Vizient Clinical Data Base and Resource Manager, and the National Inpatient Sample. Outcomes collected by databases included patient-reported outcomes (QOD); 30-day morbidity, readmissions, and reoperations (National Surgical Quality Improvement Program); and disease incidence and disease-specific survival (Surveillance, Epidemiology, and End Results-Medicare). The strengths of large databases included large numbers of rare pathologies and multi-institutional nationally representative sampling; the limitations of these databases included variable data veracity, variable data completeness, and missing disease-specific variables. The improvement of existing large national databases and the establishment of new registries will be crucial to the future of neurosurgical outcomes research. Copyright © 2017 by the Congress of Neurological Surgeons
-
Use of large healthcare databases for rheumatology clinical research.
Desai, Rishi J; Solomon, Daniel H
2017-03-01
Large healthcare databases, which contain data collected during routinely delivered healthcare to patients, can serve as a valuable resource for generating actionable evidence to assist medical and healthcare policy decision-making. In this review, we summarize use of large healthcare databases in rheumatology clinical research. Large healthcare data are critical to evaluate medication safety and effectiveness in patients with rheumatologic conditions. Three major sources of large healthcare data are: first, electronic medical records, second, health insurance claims, and third, patient registries. Each of these sources offers unique advantages, but also has some inherent limitations. To address some of these limitations and maximize the utility of these data sources for evidence generation, recent efforts have focused on linking different data sources. Innovations such as randomized registry trials, which aim to facilitate design of low-cost randomized controlled trials built on existing infrastructure provided by large healthcare databases, are likely to make clinical research more efficient in coming years. Harnessing the power of information contained in large healthcare databases, while paying close attention to their inherent limitations, is critical to generate a rigorous evidence-base for medical decision-making and ultimately enhancing patient care.
-
Medical data mining: knowledge discovery in a clinical data warehouse.
Prather, J. C.; Lobach, D. F.; Goodwin, L. K.; Hales, J. W.; Hage, M. L.; Hammond, W. E.
1997-01-01
Clinical databases have accumulated large quantities of information about patients and their medical conditions. Relationships and patterns within this data could provide new medical knowledge. Unfortunately, few methodologies have been developed and applied to discover this hidden knowledge. In this study, the techniques of data mining (also known as Knowledge Discovery in Databases) were used to search for relationships in a large clinical database. Specifically, data accumulated on 3,902 obstetrical patients were evaluated for factors potentially contributing to preterm birth using exploratory factor analysis. Three factors were identified by the investigators for further exploration. This paper describes the processes involved in mining a clinical database including data warehousing, data query and cleaning, and data analysis. PMID:9357597
-
Practice databases and their uses in clinical research.
Tierney, W M; McDonald, C J
1991-04-01
A few large clinical information databases have been established within larger medical information systems. Although they are smaller than claims databases, these clinical databases offer several advantages: accurate and timely data, rich clinical detail, and continuous parameters (for example, vital signs and laboratory results). However, the nature of the data vary considerably, which affects the kinds of secondary analyses that can be performed. These databases have been used to investigate clinical epidemiology, risk assessment, post-marketing surveillance of drugs, practice variation, resource use, quality assurance, and decision analysis. In addition, practice databases can be used to identify subjects for prospective studies. Further methodologic developments are necessary to deal with the prevalent problems of missing data and various forms of bias if such databases are to grow and contribute valuable clinical information.
-
Smeets, Hugo M; de Wit, Niek J; Hoes, Arno W
2011-04-01
Observational studies performed within routine health care databases have the advantage of their large size and, when the aim is to assess the effect of interventions, can offer a completion to randomized controlled trials with usually small samples from experimental situations. Institutional Health Insurance Databases (HIDs) are attractive for research because of their large size, their longitudinal perspective, and their practice-based information. As they are based on financial reimbursement, the information is generally reliable. The database of one of the major insurance companies in the Netherlands, the Agis Health Database (AHD), is described in detail. Whether the AHD data sets meet the specific requirements to conduct several types of clinical studies is discussed according to the classification of the four different types of clinical research; that is, diagnostic, etiologic, prognostic, and intervention research. The potential of the AHD for these various types of research is illustrated using examples of studies recently conducted in the AHD. HIDs such as the AHD offer large potential for several types of clinical research, in particular etiologic and intervention studies, but at present the lack of detailed clinical information is an important limitation. Copyright © 2011 Elsevier Inc. All rights reserved.
-
Design and deployment of a large brain-image database for clinical and nonclinical research
NASA Astrophysics Data System (ADS)
Yang, Guo Liang; Lim, Choie Cheio Tchoyoson; Banukumar, Narayanaswami; Aziz, Aamer; Hui, Francis; Nowinski, Wieslaw L.
2004-04-01
An efficient database is an essential component of organizing diverse information on image metadata and patient information for research in medical imaging. This paper describes the design, development and deployment of a large database system serving as a brain image repository that can be used across different platforms in various medical researches. It forms the infrastructure that links hospitals and institutions together and shares data among them. The database contains patient-, pathology-, image-, research- and management-specific data. The functionalities of the database system include image uploading, storage, indexing, downloading and sharing as well as database querying and management with security and data anonymization concerns well taken care of. The structure of database is multi-tier client-server architecture with Relational Database Management System, Security Layer, Application Layer and User Interface. Image source adapter has been developed to handle most of the popular image formats. The database has a user interface based on web browsers and is easy to handle. We have used Java programming language for its platform independency and vast function libraries. The brain image database can sort data according to clinically relevant information. This can be effectively used in research from the clinicians" points of view. The database is suitable for validation of algorithms on large population of cases. Medical images for processing could be identified and organized based on information in image metadata. Clinical research in various pathologies can thus be performed with greater efficiency and large image repositories can be managed more effectively. The prototype of the system has been installed in a few hospitals and is working to the satisfaction of the clinicians.
-
Very large database of lipids: rationale and design.
Martin, Seth S; Blaha, Michael J; Toth, Peter P; Joshi, Parag H; McEvoy, John W; Ahmed, Haitham M; Elshazly, Mohamed B; Swiger, Kristopher J; Michos, Erin D; Kwiterovich, Peter O; Kulkarni, Krishnaji R; Chimera, Joseph; Cannon, Christopher P; Blumenthal, Roger S; Jones, Steven R
2013-11-01
Blood lipids have major cardiovascular and public health implications. Lipid-lowering drugs are prescribed based in part on categorization of patients into normal or abnormal lipid metabolism, yet relatively little emphasis has been placed on: (1) the accuracy of current lipid measures used in clinical practice, (2) the reliability of current categorizations of dyslipidemia states, and (3) the relationship of advanced lipid characterization to other cardiovascular disease biomarkers. To these ends, we developed the Very Large Database of Lipids (NCT01698489), an ongoing database protocol that harnesses deidentified data from the daily operations of a commercial lipid laboratory. The database includes individuals who were referred for clinical purposes for a Vertical Auto Profile (Atherotech Inc., Birmingham, AL), which directly measures cholesterol concentrations of low-density lipoprotein, very low-density lipoprotein, intermediate-density lipoprotein, high-density lipoprotein, their subclasses, and lipoprotein(a). Individual Very Large Database of Lipids studies, ranging from studies of measurement accuracy, to dyslipidemia categorization, to biomarker associations, to characterization of rare lipid disorders, are investigator-initiated and utilize peer-reviewed statistical analysis plans to address a priori hypotheses/aims. In the first database harvest (Very Large Database of Lipids 1.0) from 2009 to 2011, there were 1 340 614 adult and 10 294 pediatric patients; the adult sample had a median age of 59 years (interquartile range, 49-70 years) with even representation by sex. Lipid distributions closely matched those from the population-representative National Health and Nutrition Examination Survey. The second harvest of the database (Very Large Database of Lipids 2.0) is underway. Overall, the Very Large Database of Lipids database provides an opportunity for collaboration and new knowledge generation through careful examination of granular lipid data on a large scale. © 2013 Wiley Periodicals, Inc.
-
Aegerter, Philippe; Bendersky, Noelle; Tran, Thi-Chien; Ropers, Jacques; Taright, Namik; Chatellier, Gilles
2014-01-01
Recruitment of large samples of patients is crucial for evidence level and efficacy of clinical trials (CT). Clinical Trial Recruitment Support Systems (CTRSS) used to estimate patient recruitment are generally specific to Hospital Information Systems and few were evaluated on a large number of trials. Our aim was to assess, on a large number of CT, the usefulness of commonly available data as Diagnosis Related Groups (DRG) databases in order to estimate potential recruitment. We used the DRG database of a large French multicenter medical institution (1.2 million inpatient stays and 400 new trials each year). Eligibility criteria of protocols were broken down into in atomic entities (diagnosis, procedures, treatments...) then translated into codes and operators recorded in a standardized form. A program parsed the forms and generated requests on the DRG database. A large majority of selection criteria could be coded and final estimations of number of eligible patients were close to observed ones (median difference = 25). Such a system could be part of the feasability evaluation and center selection process before the start of the clinical trial.
-
Use of large electronic health record databases for environmental epidemiology studies.
Background: Electronic health records (EHRs) are a ubiquitous component of the United States healthcare system and capture nearly all data collected in a clinic or hospital setting. EHR databases are attractive for secondary data analysis as they may contain detailed clinical rec...
-
Schell, Scott R
2006-02-01
Enforcement of the Health Insurance Portability and Accountability Act (HIPAA) began in April, 2003. Designed as a law mandating health insurance availability when coverage was lost, HIPAA imposed sweeping and broad-reaching protections of patient privacy. These changes dramatically altered clinical research by placing sizeable regulatory burdens upon investigators with threat of severe and costly federal and civil penalties. This report describes development of an algorithmic approach to clinical research database design based upon a central key-shared data (CK-SD) model allowing researchers to easily analyze, distribute, and publish clinical research without disclosure of HIPAA Protected Health Information (PHI). Three clinical database formats (small clinical trial, operating room performance, and genetic microchip array datasets) were modeled using standard structured query language (SQL)-compliant databases. The CK database was created to contain PHI data, whereas a shareable SD database was generated in real-time containing relevant clinical outcome information while protecting PHI items. Small (< 100 records), medium (< 50,000 records), and large (> 10(8) records) model databases were created, and the resultant data models were evaluated in consultation with an HIPAA compliance officer. The SD database models complied fully with HIPAA regulations, and resulting "shared" data could be distributed freely. Unique patient identifiers were not required for treatment or outcome analysis. Age data were resolved to single-integer years, grouping patients aged > 89 years. Admission, discharge, treatment, and follow-up dates were replaced with enrollment year, and follow-up/outcome intervals calculated eliminating original data. Two additional data fields identified as PHI (treating physician and facility) were replaced with integer values, and the original data corresponding to these values were stored in the CK database. Use of the algorithm at the time of database design did not increase cost or design effort. The CK-SD model for clinical database design provides an algorithm for investigators to create, maintain, and share clinical research data compliant with HIPAA regulations. This model is applicable to new projects and large institutional datasets, and should decrease regulatory efforts required for conduct of clinical research. Application of the design algorithm early in the clinical research enterprise does not increase cost or the effort of data collection.
-
Olier, Ivan; Springate, David A; Ashcroft, Darren M; Doran, Tim; Reeves, David; Planner, Claire; Reilly, Siobhan; Kontopantelis, Evangelos
2016-01-01
The use of Electronic Health Records databases for medical research has become mainstream. In the UK, increasing use of Primary Care Databases is largely driven by almost complete computerisation and uniform standards within the National Health Service. Electronic Health Records research often begins with the development of a list of clinical codes with which to identify cases with a specific condition. We present a methodology and accompanying Stata and R commands (pcdsearch/Rpcdsearch) to help researchers in this task. We present severe mental illness as an example. We used the Clinical Practice Research Datalink, a UK Primary Care Database in which clinical information is largely organised using Read codes, a hierarchical clinical coding system. Pcdsearch is used to identify potentially relevant clinical codes and/or product codes from word-stubs and code-stubs suggested by clinicians. The returned code-lists are reviewed and codes relevant to the condition of interest are selected. The final code-list is then used to identify patients. We identified 270 Read codes linked to SMI and used them to identify cases in the database. We observed that our approach identified cases that would have been missed with a simpler approach using SMI registers defined within the UK Quality and Outcomes Framework. We described a framework for researchers of Electronic Health Records databases, for identifying patients with a particular condition or matching certain clinical criteria. The method is invariant to coding system or database and can be used with SNOMED CT, ICD or other medical classification code-lists.
-
[Privacy and public benefit in using large scale health databases].
Yamamoto, Ryuichi
2014-01-01
In Japan, large scale heath databases were constructed in a few years, such as National Claim insurance and health checkup database (NDB) and Japanese Sentinel project. But there are some legal issues for making adequate balance between privacy and public benefit by using such databases. NDB is carried based on the act for elderly person's health care but in this act, nothing is mentioned for using this database for general public benefit. Therefore researchers who use this database are forced to pay much concern about anonymization and information security that may disturb the research work itself. Japanese Sentinel project is a national project to detecting drug adverse reaction using large scale distributed clinical databases of large hospitals. Although patients give the future consent for general such purpose for public good, it is still under discussion using insufficiently anonymized data. Generally speaking, researchers of study for public benefit will not infringe patient's privacy, but vague and complex requirements of legislation about personal data protection may disturb the researches. Medical science does not progress without using clinical information, therefore the adequate legislation that is simple and clear for both researchers and patients is strongly required. In Japan, the specific act for balancing privacy and public benefit is now under discussion. The author recommended the researchers including the field of pharmacology should pay attention to, participate in the discussion of, and make suggestion to such act or regulations.
-
Olier, Ivan; Springate, David A.; Ashcroft, Darren M.; Doran, Tim; Reeves, David; Planner, Claire; Reilly, Siobhan; Kontopantelis, Evangelos
2016-01-01
Background The use of Electronic Health Records databases for medical research has become mainstream. In the UK, increasing use of Primary Care Databases is largely driven by almost complete computerisation and uniform standards within the National Health Service. Electronic Health Records research often begins with the development of a list of clinical codes with which to identify cases with a specific condition. We present a methodology and accompanying Stata and R commands (pcdsearch/Rpcdsearch) to help researchers in this task. We present severe mental illness as an example. Methods We used the Clinical Practice Research Datalink, a UK Primary Care Database in which clinical information is largely organised using Read codes, a hierarchical clinical coding system. Pcdsearch is used to identify potentially relevant clinical codes and/or product codes from word-stubs and code-stubs suggested by clinicians. The returned code-lists are reviewed and codes relevant to the condition of interest are selected. The final code-list is then used to identify patients. Results We identified 270 Read codes linked to SMI and used them to identify cases in the database. We observed that our approach identified cases that would have been missed with a simpler approach using SMI registers defined within the UK Quality and Outcomes Framework. Conclusion We described a framework for researchers of Electronic Health Records databases, for identifying patients with a particular condition or matching certain clinical criteria. The method is invariant to coding system or database and can be used with SNOMED CT, ICD or other medical classification code-lists. PMID:26918439
-
PRIM versus CART in subgroup discovery: when patience is harmful.
Abu-Hanna, Ameen; Nannings, Barry; Dongelmans, Dave; Hasman, Arie
2010-10-01
We systematically compare the established algorithms CART (Classification and Regression Trees) and PRIM (Patient Rule Induction Method) in a subgroup discovery task on a large real-world high-dimensional clinical database. Contrary to current conjectures, PRIM's performance was generally inferior to CART's. PRIM often considered "peeling of" a large chunk of data at a value of a relevant discrete ordinal variable unattractive, ultimately missing an important subgroup. This finding has considerable significance in clinical medicine where ordinal scores are ubiquitous. PRIM's utility in clinical databases would increase when global information about (ordinal) variables is better put to use and when the search algorithm keeps track of alternative solutions.
-
Nishio, Shin-Ya; Usami, Shin-Ichi
2017-03-01
Recent advances in next-generation sequencing (NGS) have given rise to new challenges due to the difficulties in variant pathogenicity interpretation and large dataset management, including many kinds of public population databases as well as public or commercial disease-specific databases. Here, we report a new database development tool, named the "Clinical NGS Database," for improving clinical NGS workflow through the unified management of variant information and clinical information. This database software offers a two-feature approach to variant pathogenicity classification. The first of these approaches is a phenotype similarity-based approach. This database allows the easy comparison of the detailed phenotype of each patient with the average phenotype of the same gene mutation at the variant or gene level. It is also possible to browse patients with the same gene mutation quickly. The other approach is a statistical approach to variant pathogenicity classification based on the use of the odds ratio for comparisons between the case and the control for each inheritance mode (families with apparently autosomal dominant inheritance vs. control, and families with apparently autosomal recessive inheritance vs. control). A number of case studies are also presented to illustrate the utility of this database. © 2016 The Authors. **Human Mutation published by Wiley Periodicals, Inc.
-
Generation of comprehensive thoracic oncology database--tool for translational research.
Surati, Mosmi; Robinson, Matthew; Nandi, Suvobroto; Faoro, Leonardo; Demchuk, Carley; Kanteti, Rajani; Ferguson, Benjamin; Gangadhar, Tara; Hensing, Thomas; Hasina, Rifat; Husain, Aliya; Ferguson, Mark; Karrison, Theodore; Salgia, Ravi
2011-01-22
The Thoracic Oncology Program Database Project was created to serve as a comprehensive, verified, and accessible repository for well-annotated cancer specimens and clinical data to be available to researchers within the Thoracic Oncology Research Program. This database also captures a large volume of genomic and proteomic data obtained from various tumor tissue studies. A team of clinical and basic science researchers, a biostatistician, and a bioinformatics expert was convened to design the database. Variables of interest were clearly defined and their descriptions were written within a standard operating manual to ensure consistency of data annotation. Using a protocol for prospective tissue banking and another protocol for retrospective banking, tumor and normal tissue samples from patients consented to these protocols were collected. Clinical information such as demographics, cancer characterization, and treatment plans for these patients were abstracted and entered into an Access database. Proteomic and genomic data have been included in the database and have been linked to clinical information for patients described within the database. The data from each table were linked using the relationships function in Microsoft Access to allow the database manager to connect clinical and laboratory information during a query. The queried data can then be exported for statistical analysis and hypothesis generation.
-
Forrest, Laura; Mitchell, Gillian; Thrupp, Letitia; Petelin, Lara; Richardson, Kate; Mascarenhas, Lyon; Young, Mary-Anne
2018-01-01
Clinical genetics units hold large amounts of information which could be utilised to benefit patients and their families. In Australia, a national research database, the Inherited Cancer Connect (ICCon) database, is being established that comprises clinical genetic data held for all carriers of mutations in cancer predisposition genes. Consumer input was sought to establish the acceptability of the inclusion of clinical genetic data into a research database. A qualitative approach using a modified nominal group technique was used to collect data through consumer forums conducted in three Australian states. Individuals who had previously received care from Familial Cancer Centres were invited to participate. Twenty-four consumers participated in three forums. Participants expressed positive attitudes about the establishment of the ICCon database, which were informed by the perceived benefits of the database including improved health outcomes for individuals with inherited cancer syndromes. Most participants were comfortable to waive consent for their clinical information to be included in the research database in a de-identified format. As major stakeholders, consumers have an integral role in contributing to the development and conduct of the ICCon database. As an initial step in the development of the ICCon database, the forums demonstrated consumers' acceptance of important aspects of the database including waiver of consent.
-
Iavindrasana, Jimison; Depeursinge, Adrien; Ruch, Patrick; Spahni, Stéphane; Geissbuhler, Antoine; Müller, Henning
2007-01-01
The diagnostic and therapeutic processes, as well as the development of new treatments, are hindered by the fragmentation of information which underlies them. In a multi-institutional research study database, the clinical information system (CIS) contains the primary data input. An important part of the money of large scale clinical studies is often paid for data creation and maintenance. The objective of this work is to design a decentralized, scalable, reusable database architecture with lower maintenance costs for managing and integrating distributed heterogeneous data required as basis for a large-scale research project. Technical and legal aspects are taken into account based on various use case scenarios. The architecture contains 4 layers: data storage and access are decentralized at their production source, a connector as a proxy between the CIS and the external world, an information mediator as a data access point and the client side. The proposed design will be implemented inside six clinical centers participating in the @neurIST project as part of a larger system on data integration and reuse for aneurism treatment.
-
Osteoporosis therapies: evidence from health-care databases and observational population studies.
Silverman, Stuart L
2010-11-01
Osteoporosis is a well-recognized disease with severe consequences if left untreated. Randomized controlled trials are the most rigorous method for determining the efficacy and safety of therapies. Nevertheless, randomized controlled trials underrepresent the real-world patient population and are costly in both time and money. Modern technology has enabled researchers to use information gathered from large health-care or medical-claims databases to assess the practical utilization of available therapies in appropriate patients. Observational database studies lack randomization but, if carefully designed and successfully completed, can provide valuable information that complements results obtained from randomized controlled trials and extends our knowledge to real-world clinical patients. Randomized controlled trials comparing fracture outcomes among osteoporosis therapies are difficult to perform. In this regard, large observational database studies could be useful in identifying clinically important differences among therapeutic options. Database studies can also provide important information with regard to osteoporosis prevalence, health economics, and compliance and persistence with treatment. This article describes the strengths and limitations of both randomized controlled trials and observational database studies, discusses considerations for observational study design, and reviews a wealth of information generated by database studies in the field of osteoporosis.
-
Large-scale feature searches of collections of medical imagery
NASA Astrophysics Data System (ADS)
Hedgcock, Marcus W.; Karshat, Walter B.; Levitt, Tod S.; Vosky, D. N.
1993-09-01
Large scale feature searches of accumulated collections of medical imagery are required for multiple purposes, including clinical studies, administrative planning, epidemiology, teaching, quality improvement, and research. To perform a feature search of large collections of medical imagery, one can either search text descriptors of the imagery in the collection (usually the interpretation), or (if the imagery is in digital format) the imagery itself. At our institution, text interpretations of medical imagery are all available in our VA Hospital Information System. These are downloaded daily into an off-line computer. The text descriptors of most medical imagery are usually formatted as free text, and so require a user friendly database search tool to make searches quick and easy for any user to design and execute. We are tailoring such a database search tool (Liveview), developed by one of the authors (Karshat). To further facilitate search construction, we are constructing (from our accumulated interpretation data) a dictionary of medical and radiological terms and synonyms. If the imagery database is digital, the imagery which the search discovers is easily retrieved from the computer archive. We describe our database search user interface, with examples, and compare the efficacy of computer assisted imagery searches from a clinical text database with manual searches. Our initial work on direct feature searches of digital medical imagery is outlined.
-
Using Large Diabetes Databases for Research.
Wild, Sarah; Fischbacher, Colin; McKnight, John
2016-09-01
There are an increasing number of clinical, administrative and trial databases that can be used for research. These are particularly valuable if there are opportunities for linkage to other databases. This paper describes examples of the use of large diabetes databases for research. It reviews the advantages and disadvantages of using large diabetes databases for research and suggests solutions for some challenges. Large, high-quality databases offer potential sources of information for research at relatively low cost. Fundamental issues for using databases for research are the completeness of capture of cases within the population and time period of interest and accuracy of the diagnosis of diabetes and outcomes of interest. The extent to which people included in the database are representative should be considered if the database is not population based and there is the intention to extrapolate findings to the wider diabetes population. Information on key variables such as date of diagnosis or duration of diabetes may not be available at all, may be inaccurate or may contain a large amount of missing data. Information on key confounding factors is rarely available for the nondiabetic or general population limiting comparisons with the population of people with diabetes. However comparisons that allow for differences in distribution of important demographic factors may be feasible using data for the whole population or a matched cohort study design. In summary, diabetes databases can be used to address important research questions. Understanding the strengths and limitations of this approach is crucial to interpret the findings appropriately. © 2016 Diabetes Technology Society.
-
van Staa, T-P; Klungel, O; Smeeth, L
2014-06-01
A solid foundation of evidence of the effects of an intervention is a prerequisite of evidence-based medicine. The best source of such evidence is considered to be randomized trials, which are able to avoid confounding. However, they may not always estimate effectiveness in clinical practice. Databases that collate anonymized electronic health records (EHRs) from different clinical centres have been widely used for many years in observational studies. Randomized point-of-care trials have been initiated recently to recruit and follow patients using the data from EHR databases. In this review, we describe how EHR databases can be used for conducting large-scale simple trials and discuss the advantages and disadvantages of their use. © 2014 The Association for the Publication of the Journal of Internal Medicine.
-
Information Model for Reusability in Clinical Trial Documentation
ERIC Educational Resources Information Center
Bahl, Bhanu
2013-01-01
In clinical research, New Drug Application (NDA) to health agencies requires generation of a large number of documents throughout the clinical development life cycle, many of which are also submitted to public databases and external partners. Current processes to assemble the information, author, review and approve the clinical research documents,…
-
DBMap: a TreeMap-based framework for data navigation and visualization of brain research registry
NASA Astrophysics Data System (ADS)
Zhang, Ming; Zhang, Hong; Tjandra, Donny; Wong, Stephen T. C.
2003-05-01
The purpose of this study is to investigate and apply a new, intuitive and space-conscious visualization framework to facilitate efficient data presentation and exploration of large-scale data warehouses. We have implemented the DBMap framework for the UCSF Brain Research Registry. Such a novel utility would facilitate medical specialists and clinical researchers in better exploring and evaluating a number of attributes organized in the brain research registry. The current UCSF Brain Research Registry consists of a federation of disease-oriented database modules, including Epilepsy, Brain Tumor, Intracerebral Hemorrphage, and CJD (Creuzfeld-Jacob disease). These database modules organize large volumes of imaging and non-imaging data to support Web-based clinical research. While the data warehouse supports general information retrieval and analysis, there lacks an effective way to visualize and present the voluminous and complex data stored. This study investigates whether the TreeMap algorithm can be adapted to display and navigate categorical biomedical data warehouse or registry. TreeMap is a space constrained graphical representation of large hierarchical data sets, mapped to a matrix of rectangles, whose size and color represent interested database fields. It allows the display of a large amount of numerical and categorical information in limited real estate of computer screen with an intuitive user interface. The paper will describe, DBMap, the proposed new data visualization framework for large biomedical databases. Built upon XML, Java and JDBC technologies, the prototype system includes a set of software modules that reside in the application server tier and provide interface to backend database tier and front-end Web tier of the brain registry.
-
Wise, Gregory R; Schwartz, Brian P; Dittoe, Nathaniel; Safar, Ammar; Sherman, Steven; Bowdy, Bruce; Hahn, Harvey S
2012-06-01
Percutaneous coronary intervention (PCI) is the most commonly used procedure for coronary revascularization. There are multiple adjuvant anticoagulation strategies available. In this era of cost containment, we performed a comparative effectiveness analysis of clinical outcomes and cost of the major anticoagulant strategies across all types of PCI procedures in a large observational database. A retrospective, comparative effectiveness analysis of the Premier observational database was conducted to determine the impact of anticoagulant treatment on outcomes. Multiple linear regression and logistic regression models were used to assess the association of initial antithrombotic treatment with outcomes while controlling for other factors. A total of 458,448 inpatient PCI procedures with known antithrombotic regimen from 299 hospitals between January 1, 2004 and March 31, 2008 were identified. Compared to patients treated with heparin plus glycoprotein IIb/IIIa inhibitor (GPI), bivalirudin was associated with a 41% relative risk reduction (RRR) for inpatient mortality, a 44% RRR for clinically apparent bleeding, and a 37% RRR for any transfusion. Furthermore, treatment with bivalirudin alone resulted in a cost savings of $976 per case. Similar results were seen between bivalirudin and heparin in all end-points. Combined use of both bivalirudin and GPI substantially attenuated the cost benefits demonstrated with bivalirudin alone. Bivalirudin use was associated with both improved clinical outcomes and decreased hospital costs in this large "real-world" database. To our knowledge, this study is the first to demonstrate the ideal comparative effectiveness end-point of both improved clinical outcomes with decreased costs in PCI. ©2012, Wiley Periodicals, Inc.
-
2004-04-01
To develop a large database on clinical presentation, treatment and prognosis of all clinical diagnosed severe acute respiratory syndrome (SARS) cases in Beijing during the 2003 "crisis", in order to conduct further clinical studies. The database was designed by specialists, under the organization of the Beijing Commanding Center for SARS Treatment and Cure, including 686 data items in six sub-databases: primary medical-care seeking, vital signs, common symptoms and signs, treatment, laboratory and auxiliary test, and cost. All hospitals having received SARS inpatients were involved in the project. Clinical data was transferred and coded by trained doctors and data entry was carried out by trained nurses, according to a uniformed protocol. A series of procedures had been taken before the database was finally established which included programmed logic checking, digit-by-digit check on 5% random sample, data linkage for transferred cases, coding of characterized information, database structure standardization, case reviewe by computer program according to SARS Clinical Diagnosis Criteria issued by the Ministry of Health, and exclusion of unqualified patients. The database involved 2148 probable SARS cases in accordant with the clinical diagnosis criteria, including 1291 with complete records. All cases and record-complete cases showed an almost identical distribution in sex, age, occupation, residence areas and time of onset. The completion rate of data was not significantly different between the two groups except for some items on primary medical-care seeking. Specifically, the data completion rate was 73% - 100% in primary medical-care seeking, 90% in common symptoms and signs, 100% for treatment, 98% for temperature, 90% for pulse, 100% for outcomes and 98% for costs in hospital. The number of cases collected in the Beijing Clinical Database of SARS Patients was fairly complete. Cases with complete records showed that they could serve as excellent representatives of all cases. The completeness of data was quite satisfactory with primary clinical items which allowed for further clinical studies.
-
Analysis of Outcomes After TKA: Do All Databases Produce Similar Findings?
Bedard, Nicholas A; Pugely, Andrew J; McHugh, Michael; Lux, Nathan; Otero, Jesse E; Bozic, Kevin J; Gao, Yubo; Callaghan, John J
2018-01-01
Use of large clinical and administrative databases for orthopaedic research has increased exponentially. Each database represents unique patient populations and varies in their methodology of data acquisition, which makes it possible that similar research questions posed to different databases might result in answers that differ in important ways. (1) What are the differences in reported demographics, comorbidities, and complications for patients undergoing primary TKA among four databases commonly used in orthopaedic research? (2) How does the difference in reported complication rates vary depending on whether only inpatient data or 30-day postoperative data are analyzed? Patients who underwent primary TKA during 2010 to 2012 were identified within the National Surgical Quality Improvement Programs (NSQIP), the Nationwide Inpatient Sample (NIS), the Medicare Standard Analytic Files (MED), and the Humana Administrative Claims database (HAC). NSQIP is a clinical registry that captures both inpatient and outpatient events up to 30 days after surgery using clinical reviewers and strict definitions for each variable. The other databases are administrative claims databases with their comorbidity and adverse event data defined by diagnosis and procedure codes used for reimbursement. NIS is limited to inpatient data only, whereas HAC and MED also have outpatient data. The number of patients undergoing primary TKA from each database was 48,248 in HAC, 783,546 in MED, 393,050 in NIS, and 43,220 in NSQIP. NSQIP definitions for comorbidities and surgical complications were matched to corresponding International Classification of Diseases, 9 Revision/Current Procedural Terminology codes and these coding algorithms were used to query NIS, MED, and HAC. Age, sex, comorbidities, and inpatient versus 30-day postoperative complications were compared across the four databases. Given the large sample sizes, statistical significance was often detected for small, clinically unimportant differences; thus, the focus of comparisons was whether the difference reached an absolute difference of twofold to signify an important clinical difference. Although there was a higher proportion of males in NIS and NSQIP and patients in NIS were younger, the difference was slight and well below our predefined threshold for a clinically important difference. There was variation in the prevalence of comorbidities and rates of postoperative complications among databases. The prevalence of chronic obstructive pulmonary disease (COPD) and coagulopathy in HAC and MED was more than twice that in NIS and NSQIP (relative risk [RR] for COPD: MED versus NIS 3.1, MED versus NSQIP 4.5, HAC versus NIS 3.6, HAC versus NSQIP 5.3; RR for coagulopathy: MED versus NIS 3.9, MED versus NSQIP 3.1, HAC versus NIS 3.3, HAC versus NSQIP 2.7; p < 0.001 for all comparisons). NSQIP had more than twice the obesity as NIS (RR 0.35). Rates of stroke within 30 days of TKA had more than a twofold difference among all databases (p < 0.001). HAC had more than twice the rates of 30-day complications at all endpoints compared with NSQIP and more than twice the 30-day infections as MED. A comparison of inpatient and 30-day complications rates demonstrated more than twice the amount of wound infections and deep vein thromboses is captured when data are analyzed out to 30 days after TKA (p < 0.001 for all comparisons). When evaluating research utilizing large databases, one must pay particular attention to the type of database used (administrative claims, clinical registry, or other kinds of databases), time period included, definitions utilized for specific variables, and the population captured to ensure it is best suited for the specific research question. Furthermore, with the advent of bundled payments, policymakers must meticulously consider the data sources used to ensure the data analytics match historical sources. Level III, therapeutic study.
-
Informatics in neurocritical care: new ideas for Big Data.
Flechet, Marine; Grandas, Fabian Güiza; Meyfroidt, Geert
2016-04-01
Big data is the new hype in business and healthcare. Data storage and processing has become cheap, fast, and easy. Business analysts and scientists are trying to design methods to mine these data for hidden knowledge. Neurocritical care is a field that typically produces large amounts of patient-related data, and these data are increasingly being digitized and stored. This review will try to look beyond the hype, and focus on possible applications in neurointensive care amenable to Big Data research that can potentially improve patient care. The first challenge in Big Data research will be the development of large, multicenter, and high-quality databases. These databases could be used to further investigate recent findings from mathematical models, developed in smaller datasets. Randomized clinical trials and Big Data research are complementary. Big Data research might be used to identify subgroups of patients that could benefit most from a certain intervention, or can be an alternative in areas where randomized clinical trials are not possible. The processing and the analysis of the large amount of patient-related information stored in clinical databases is beyond normal human cognitive ability. Big Data research applications have the potential to discover new medical knowledge, and improve care in the neurointensive care unit.
-
NASA Technical Reports Server (NTRS)
Grams, R. R.
1982-01-01
A system designed to access a large range of available medical textbook information in an online interactive fashion is described. A high level query type database manager, INQUIRE, is used. Operating instructions, system flow diagrams, database descriptions, text generation, and error messages are discussed. User information is provided.
-
Lee, Jong Woo; LaRoche, Suzette; Choi, Hyunmi; Rodriguez Ruiz, Andres A; Fertig, Evan; Politsky, Jeffrey M; Herman, Susan T; Loddenkemper, Tobias; Sansevere, Arnold J; Korb, Pearce J; Abend, Nicholas S; Goldstein, Joshua L; Sinha, Saurabh R; Dombrowski, Keith E; Ritzl, Eva K; Westover, Michael B; Gavvala, Jay R; Gerard, Elizabeth E; Schmitt, Sarah E; Szaflarski, Jerzy P; Ding, Kan; Haas, Kevin F; Buchsbaum, Richard; Hirsch, Lawrence J; Wusthoff, Courtney J; Hopp, Jennifer L; Hahn, Cecil D
2016-04-01
The rapid expansion of the use of continuous critical care electroencephalogram (cEEG) monitoring and resulting multicenter research studies through the Critical Care EEG Monitoring Research Consortium has created the need for a collaborative data sharing mechanism and repository. The authors describe the development of a research database incorporating the American Clinical Neurophysiology Society standardized terminology for critical care EEG monitoring. The database includes flexible report generation tools that allow for daily clinical use. Key clinical and research variables were incorporated into a Microsoft Access database. To assess its utility for multicenter research data collection, the authors performed a 21-center feasibility study in which each center entered data from 12 consecutive intensive care unit monitoring patients. To assess its utility as a clinical report generating tool, three large volume centers used it to generate daily clinical critical care EEG reports. A total of 280 subjects were enrolled in the multicenter feasibility study. The duration of recording (median, 25.5 hours) varied significantly between the centers. The incidence of seizure (17.6%), periodic/rhythmic discharges (35.7%), and interictal epileptiform discharges (11.8%) was similar to previous studies. The database was used as a clinical reporting tool by 3 centers that entered a total of 3,144 unique patients covering 6,665 recording days. The Critical Care EEG Monitoring Research Consortium database has been successfully developed and implemented with a dual role as a collaborative research platform and a clinical reporting tool. It is now available for public download to be used as a clinical data repository and report generating tool.
-
Pseudonymisation of radiology data for research purposes
NASA Astrophysics Data System (ADS)
Noumeir, Rita; Lemay, Alain; Lina, Jean-Marc
2005-04-01
Medical image processing methods and algorithms, developed by researchers, need to be validated and tested. Test data should ideally be real clinical data especially when that clinical data is varied and exists in large volume. In nowadays, clinical data is accessible electronically and has important value for researchers. However, the usage of clinical data for research purposes should respect data confidentiality, patient right to privacy and the patient consent. In fact, clinical data is nominative given that it contains information about the patient such as name, age and identification number. Evidently, clinical data should be de-identified to be exported to research databases. However, the same patient is usually followed during a long period of time. The disease progression and the diagnostic evolution represent extremely valuable information for researchers, as well. Our objective is to build a research database from de-identified clinical data while enabling the database to be easily incremented by exporting new pseudonymous data, acquired over a long period of time. Pseudonymisation is data de-identification such that data belonging to the same individual in the clinical environment bear the same relation to each other in the de-identified research version. In this paper, we propose a software architecture that enables the implementation of a research database that can be incremented in time. We also evaluate its security and discuss its security pitfalls.
-
Batista Rodríguez, Gabriela; Balla, Andrea; Fernández-Ananín, Sonia; Balagué, Carmen; Targarona, Eduard M
2018-05-01
The term big data refers to databases that include large amounts of information used in various areas of knowledge. Currently, there are large databases that allow the evaluation of postoperative evolution, such as the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP), the Healthcare Cost and Utilization Project (HCUP) National Inpatient Sample (NIS), and the National Cancer Database (NCDB). The aim of this review was to evaluate the clinical impact of information obtained from these registries regarding gastroesophageal surgery. A systematic review using the Meta-analysis of Observational Studies in Epidemiology guidelines was performed. The research was carried out using the PubMed database identifying 251 articles. All outcomes related to gastroesophageal surgery were analyzed. A total of 34 articles published between January 2007 and July 2017 were included, for a total of 345 697 patients. Studies were analyzed and divided according to the type of surgery and main theme in (1) esophageal surgery and (2) gastric surgery. The information provided by these databases is an effective way to obtain levels of evidence not obtainable by conventional methods. Furthermore, this information is useful for the external validation of previous studies, to establish benchmarks that allow comparisons between centers and have a positive impact on the quality of care.
-
Turning Access into a web-enabled secure information system for clinical trials.
Dongquan Chen; Chen, Wei-Bang; Soong, Mayhue; Soong, Seng-Jaw; Orthner, Helmuth F
2009-08-01
Organizations that have limited resources need to conduct clinical studies in a cost-effective, but secure way. Clinical data residing in various individual databases need to be easily accessed and secured. Although widely available, digital certification, encryption, and secure web server, have not been implemented as widely, partly due to a lack of understanding of needs and concerns over issues such as cost and difficulty in implementation. The objective of this study was to test the possibility of centralizing various databases and to demonstrate ways of offering an alternative to a large-scale comprehensive and costly commercial product, especially for simple phase I and II trials, with reasonable convenience and security. We report a working procedure to transform and develop a standalone Access database into a secure Web-based secure information system. For data collection and reporting purposes, we centralized several individual databases; developed, and tested a web-based secure server using self-issued digital certificates. The system lacks audit trails. The cost of development and maintenance may hinder its wide application. The clinical trial databases scattered in various departments of an institution could be centralized into a web-enabled secure information system. The limitations such as the lack of a calendar and audit trail can be partially addressed with additional programming. The centralized Web system may provide an alternative to a comprehensive clinical trial management system.
-
A comprehensive global genotype-phenotype database for rare diseases.
Trujillano, Daniel; Oprea, Gabriela-Elena; Schmitz, Yvonne; Bertoli-Avella, Aida M; Abou Jamra, Rami; Rolfs, Arndt
2017-01-01
The ability to discover genetic variants in a patient runs far ahead of the ability to interpret them. Databases with accurate descriptions of the causal relationship between the variants and the phenotype are valuable since these are critical tools in clinical genetic diagnostics. Here, we introduce a comprehensive and global genotype-phenotype database focusing on rare diseases. This database (CentoMD ® ) is a browser-based tool that enables access to a comprehensive, independently curated system utilizing stringent high-quality criteria and a quickly growing repository of genetic and human phenotype ontology (HPO)-based clinical information. Its main goals are to aid the evaluation of genetic variants, to enhance the validity of the genetic analytical workflow, to increase the quality of genetic diagnoses, and to improve evaluation of treatment options for patients with hereditary diseases. The database software correlates clinical information from consented patients and probands of different geographical backgrounds with a large dataset of genetic variants and, when available, biomarker information. An automated follow-up tool is incorporated that informs all users whenever a variant classification has changed. These unique features fully embedded in a CLIA/CAP-accredited quality management system allow appropriate data quality and enhanced patient safety. More than 100,000 genetically screened individuals are documented in the database, resulting in more than 470 million variant detections. Approximately, 57% of the clinically relevant and uncertain variants in the database are novel. Notably, 3% of the genetic variants identified and previously reported in the literature as being associated with a particular rare disease were reclassified, based on internal evidence, as clinically irrelevant. The database offers a comprehensive summary of the clinical validity and causality of detected gene variants with their associated phenotypes, and is a valuable tool for identifying new disease genes through the correlation of novel genetic variants with specific, well-defined phenotypes.
-
Li, Mouduo; Qiao, Cuixia; Qin, Liping; Zhang, Junyong; Ling, Changquan
2012-09-01
To investigate the application of Traditional Chinese Medicine Injections (TCMIs) for treatment of primary liver cancer (PLC). A literature review was conducted using PubMed/Medline, Cochrane Library Controlled Clinical Trials Database, China National Knowledge Infrastructure (CNKI), China Scientific Journal Database (CSJD) and China Biology Medicine (CBM). Online websites including journal websites and databases of ongoing trials, as well as some Traditional Chinese Medicine journals that are not indexed in the electronic databases were also searched. as adjunctive medication for the treatment of PLC could regulate patient immunity, reduce bone marrow suppression, relieve clinical symptoms, and improve quality of life, as well as control disease progression and prolong survival time. Within the limitations of this review, we conclude that application of TCMIs as adjunctive medication may provide benefits for patients with PLC. Further large, high-quality trials are warranted.
-
Quantifying Data Quality for Clinical Trials Using Electronic Data Capture
Nahm, Meredith L.; Pieper, Carl F.; Cunningham, Maureen M.
2008-01-01
Background Historically, only partial assessments of data quality have been performed in clinical trials, for which the most common method of measuring database error rates has been to compare the case report form (CRF) to database entries and count discrepancies. Importantly, errors arising from medical record abstraction and transcription are rarely evaluated as part of such quality assessments. Electronic Data Capture (EDC) technology has had a further impact, as paper CRFs typically leveraged for quality measurement are not used in EDC processes. Methods and Principal Findings The National Institute on Drug Abuse Treatment Clinical Trials Network has developed, implemented, and evaluated methodology for holistically assessing data quality on EDC trials. We characterize the average source-to-database error rate (14.3 errors per 10,000 fields) for the first year of use of the new evaluation method. This error rate was significantly lower than the average of published error rates for source-to-database audits, and was similar to CRF-to-database error rates reported in the published literature. We attribute this largely to an absence of medical record abstraction on the trials we examined, and to an outpatient setting characterized by less acute patient conditions. Conclusions Historically, medical record abstraction is the most significant source of error by an order of magnitude, and should be measured and managed during the course of clinical trials. Source-to-database error rates are highly dependent on the amount of structured data collection in the clinical setting and on the complexity of the medical record, dependencies that should be considered when developing data quality benchmarks. PMID:18725958
-
A Qualitative Study of Resident Learning in Ambulatory Clinic
ERIC Educational Resources Information Center
Smith, C. Scott; Morris, Magdalena; Francovich, Chris; Hill, William; Gieselman, Janet
2004-01-01
Qualitative analysis of a large ethnographic database from observations of a resident teaching clinic revealed three important findings. The first finding was that breakdown, a situation where an "actor" (such as a person or the group) is not achieving expected effectiveness, was the most important category because of its frequency and explanatory…
-
Database systems for knowledge-based discovery.
Jagarlapudi, Sarma A R P; Kishan, K V Radha
2009-01-01
Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery.
-
Variability sensitivity of dynamic texture based recognition in clinical CT data
NASA Astrophysics Data System (ADS)
Kwitt, Roland; Razzaque, Sharif; Lowell, Jeffrey; Aylward, Stephen
2014-03-01
Dynamic texture recognition using a database of template models has recently shown promising results for the task of localizing anatomical structures in Ultrasound video. In order to understand its clinical value, it is imperative to study the sensitivity with respect to inter-patient variability as well as sensitivity to acquisition parameters such as Ultrasound probe angle. Fully addressing patient and acquisition variability issues, however, would require a large database of clinical Ultrasound from many patients, acquired in a multitude of controlled conditions, e.g., using a tracked transducer. Since such data is not readily attainable, we advocate an alternative evaluation strategy using abdominal CT data as a surrogate. In this paper, we describe how to replicate Ultrasound variabilities by extracting subvolumes from CT and interpreting the image material as an ordered sequence of video frames. Utilizing this technique, and based on a database of abdominal CT from 45 patients, we report recognition results on an organ (kidney) recognition task, where we try to discriminate kidney subvolumes/videos from a collection of randomly sampled negative instances. We demonstrate that (1) dynamic texture recognition is relatively insensitive to inter-patient variation while (2) viewing angle variability needs to be accounted for in the template database. Since naively extending the template database to counteract variability issues can lead to impractical database sizes, we propose an alternative strategy based on automated identification of a small set of representative models.
-
The Camden & Islington Research Database: Using electronic mental health records for research.
Werbeloff, Nomi; Osborn, David P J; Patel, Rashmi; Taylor, Matthew; Stewart, Robert; Broadbent, Matthew; Hayes, Joseph F
2018-01-01
Electronic health records (EHRs) are widely used in mental health services. Case registers using EHRs from secondary mental healthcare have the potential to deliver large-scale projects evaluating mental health outcomes in real-world clinical populations. We describe the Camden and Islington NHS Foundation Trust (C&I) Research Database which uses the Clinical Record Interactive Search (CRIS) tool to extract and de-identify routinely collected clinical information from a large UK provider of secondary mental healthcare, and demonstrate its capabilities to answer a clinical research question regarding time to diagnosis and treatment of bipolar disorder. The C&I Research Database contains records from 108,168 mental health patients, of which 23,538 were receiving active care. The characteristics of the patient population are compared to those of the catchment area, of London, and of England as a whole. The median time to diagnosis of bipolar disorder was 76 days (interquartile range: 17-391) and median time to treatment was 37 days (interquartile range: 5-194). Compulsory admission under the UK Mental Health Act was associated with shorter intervals to diagnosis and treatment. Prior diagnoses of other psychiatric disorders were associated with longer intervals to diagnosis, though prior diagnoses of schizophrenia and related disorders were associated with decreased time to treatment. The CRIS tool, developed by the South London and Maudsley NHS Foundation Trust (SLaM) Biomedical Research Centre (BRC), functioned very well at C&I. It is reassuring that data from different organizations deliver similar results, and that applications developed in one Trust can then be successfully deployed in another. The information can be retrieved in a quicker and more efficient fashion than more traditional methods of health research. The findings support the secondary use of EHRs for large-scale mental health research in naturalistic samples and settings investigated across large, diverse geographical areas.
-
Existing data sources for clinical epidemiology: The North Denmark Bacteremia Research Database
Schønheyder, Henrik C; Søgaard, Mette
2010-01-01
Bacteremia is associated with high morbidity and mortality. Improving prevention and treatment requires better knowledge of the disease and its prognosis. However, in order to study the entire spectrum of bacteremia patients, we need valid sources of information, prospective data collection, and complete follow-up. In North Denmark Region, all patients diagnosed with bacteremia have been registered in a population-based database since 1981. The information has been recorded prospectively since 1992 and the main variables are: the patient’s unique civil registration number, date of sampling the first positive blood culture, date of admission, clinical department, date of notification of growth, place of acquisition, focus of infection, microbiological species, antibiogram, and empirical antimicrobial treatment. During the time from 1981 to 2008, information on 22,556 cases of bacteremia has been recorded. The civil registration number makes it possible to link the database to other medical databases and thereby build large cohorts with detailed longitudinal data that include hospital histories since 1977, comorbidity data, and complete follow-up of survival. The database is suited for epidemiological research and, presently, approximately 60 studies have been published. Other Danish departments of clinical microbiology have recently started to record the same information and a population base of 2.3 million will be available for future studies. PMID:20865114
-
2014-10-01
Iowa neuro -ophthalmology clinics. In addition, we can access the University of Iowa Hospital patient database by diagnosis allowing us to obtain an...remains uncut. The caudal incision is just large enough for the transmitter to pass through while the rostral incision is just large enough for the
-
Thompson, Bryony A; Spurdle, Amanda B; Plazzer, John-Paul; Greenblatt, Marc S; Akagi, Kiwamu; Al-Mulla, Fahd; Bapat, Bharati; Bernstein, Inge; Capellá, Gabriel; den Dunnen, Johan T; du Sart, Desiree; Fabre, Aurelie; Farrell, Michael P; Farrington, Susan M; Frayling, Ian M; Frebourg, Thierry; Goldgar, David E; Heinen, Christopher D; Holinski-Feder, Elke; Kohonen-Corish, Maija; Robinson, Kristina Lagerstedt; Leung, Suet Yi; Martins, Alexandra; Moller, Pal; Morak, Monika; Nystrom, Minna; Peltomaki, Paivi; Pineda, Marta; Qi, Ming; Ramesar, Rajkumar; Rasmussen, Lene Juel; Royer-Pokora, Brigitte; Scott, Rodney J; Sijmons, Rolf; Tavtigian, Sean V; Tops, Carli M; Weber, Thomas; Wijnen, Juul; Woods, Michael O; Macrae, Finlay; Genuardi, Maurizio
2014-02-01
The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.
-
Price, Ronald N; Chandrasekhar, Arcot J; Tamirisa, Balaji
1990-01-01
The Department of Medicine at Loyola University Medical Center (LUMC) of Chicago has implemented a local area network (LAN) based Patient Information Management System (PIMS) as part of its integrated departmental database management system. PIMS consists of related database applications encompassing demographic information, current medications, problem lists, clinical data, prior events, and on-line procedure results. Integration into the existing departmental database system permits PIMS to capture and manipulate data in other departmental applications. Standardization of clinical data is accomplished through three data tables that verify diagnosis codes, procedures codes and a standardized set of clinical data elements. The modularity of the system, coupled with standardized data formats, allowed the development of a Patient Information Protocol System (PIPS). PIPS, a userdefinable protocol processor, provides physicians with individualized data entry or review screens customized for their specific research protocols or practice habits. Physician feedback indicates that the PIMS/PIPS combination enhances their ability to collect and review specific patient information by filtering large amount of clinical data.
-
Plazzer, John-Paul; Greenblatt, Marc S.; Akagi, Kiwamu; Al-Mulla, Fahd; Bapat, Bharati; Bernstein, Inge; Capellá, Gabriel; den Dunnen, Johan T.; du Sart, Desiree; Fabre, Aurelie; Farrell, Michael P.; Farrington, Susan M.; Frayling, Ian M.; Frebourg, Thierry; Goldgar, David E.; Heinen, Christopher D.; Holinski-Feder, Elke; Kohonen-Corish, Maija; Robinson, Kristina Lagerstedt; Leung, Suet Yi; Martins, Alexandra; Moller, Pal; Morak, Monika; Nystrom, Minna; Peltomaki, Paivi; Pineda, Marta; Qi, Ming; Ramesar, Rajkumar; Rasmussen, Lene Juel; Royer-Pokora, Brigitte; Scott, Rodney J.; Sijmons, Rolf; Tavtigian, Sean V.; Tops, Carli M.; Weber, Thomas; Wijnen, Juul; Woods, Michael O.; Macrae, Finlay; Genuardi, Maurizio
2015-01-01
Clinical classification of sequence variants identified in hereditary disease genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch Syndrome genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist variant classification, and recognized by microattribution. The scheme was refined by multidisciplinary expert committee review of clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants not obviously protein-truncating from nomenclature. This large-scale endeavor will facilitate consistent management of suspected Lynch Syndrome families, and demonstrates the value of multidisciplinary collaboration for curation and classification of variants in public locus-specific databases. PMID:24362816
-
BRCA Share: A Collection of Clinical BRCA Gene Variants.
Béroud, Christophe; Letovsky, Stanley I; Braastad, Corey D; Caputo, Sandrine M; Beaudoux, Olivia; Bignon, Yves Jean; Bressac-De Paillerets, Brigitte; Bronner, Myriam; Buell, Crystal M; Collod-Béroud, Gwenaëlle; Coulet, Florence; Derive, Nicolas; Divincenzo, Christina; Elzinga, Christopher D; Garrec, Céline; Houdayer, Claude; Karbassi, Izabela; Lizard, Sarab; Love, Angela; Muller, Danièle; Nagan, Narasimhan; Nery, Camille R; Rai, Ghadi; Revillion, Françoise; Salgado, David; Sévenet, Nicolas; Sinilnikova, Olga; Sobol, Hagay; Stoppa-Lyonnet, Dominique; Toulas, Christine; Trautman, Edwin; Vaur, Dominique; Vilquin, Paul; Weymouth, Katelyn S; Willis, Alecia; Eisenberg, Marcia; Strom, Charles M
2016-12-01
As next-generation sequencing increases access to human genetic variation, the challenge of determining clinical significance of variants becomes ever more acute. Germline variants in the BRCA1 and BRCA2 genes can confer substantial lifetime risk of breast and ovarian cancer. Assessment of variant pathogenicity is a vital part of clinical genetic testing for these genes. A database of clinical observations of BRCA variants is a critical resource in that process. This article describes BRCA Share™, a database created by a unique international alliance of academic centers and commercial testing laboratories. By integrating the content of the Universal Mutation Database generated by the French Unicancer Genetic Group with the testing results of two large commercial laboratories, Quest Diagnostics and Laboratory Corporation of America (LabCorp), BRCA Share™ has assembled one of the largest publicly accessible collections of BRCA variants currently available. Although access is available to academic researchers without charge, commercial participants in the project are required to pay a support fee and contribute their data. The fees fund the ongoing curation effort, as well as planned experiments to functionally characterize variants of uncertain significance. BRCA Share™ databases can therefore be considered as models of successful data sharing between private companies and the academic world. © 2016 WILEY PERIODICALS, INC.
-
Corbellini, Carlo; Andreoni, Bruno; Ansaloni, Luca; Sgroi, Giovanni; Martinotti, Mario; Scandroglio, Ildo; Carzaniga, Pierluigi; Longoni, Mauro; Foschi, Diego; Dionigi, Paolo; Morandi, Eugenio; Agnello, Mauro
2018-01-01
Measurement and monitoring of the quality of care using a core set of quality measures are increasing in health service research. Although administrative databases include limited clinical data, they offer an attractive source for quality measurement. The purpose of this study, therefore, was to evaluate the completeness of different administrative data sources compared to a clinical survey in evaluating rectal cancer cases. Between May 2012 and November 2014, a clinical survey was done on 498 Lombardy patients who had rectal cancer and underwent surgical resection. These collected data were compared with the information extracted from administrative sources including Hospital Discharge Dataset, drug database, daycare activity data, fee-exemption database, and regional screening program database. The agreement evaluation was performed using a set of 12 quality indicators. Patient complexity was a difficult indicator to measure for lack of clinical data. Preoperative staging was another suboptimal indicator due to the frequent missing administrative registration of tests performed. The agreement between the 2 data sources regarding chemoradiotherapy treatments was high. Screening detection, minimally invasive techniques, length of stay, and unpreventable readmissions were detected as reliable quality indicators. Postoperative morbidity could be a useful indicator but its agreement was lower, as expected. Healthcare administrative databases are large and real-time collected repositories of data useful in measuring quality in a healthcare system. Our investigation reveals that the reliability of indicators varies between them. Ideally, a combination of data from both sources could be used in order to improve usefulness of less reliable indicators.
-
Moo-Young, Tricia A; Panergo, Jessel; Wang, Chih E; Patel, Subhash; Duh, Hong Yan; Winchester, David J; Prinz, Richard A; Fogelfeld, Leon
2013-11-01
Clinicopathologic variables influence the treatment and prognosis of patients with thyroid cancer. A retrospective analysis of public hospital thyroid cancer database and the Surveillance, Epidemiology and End Results 17 database was conducted. Demographic, clinical, and pathologic data were compared across ethnic groups. Within the public hospital database, Hispanics versus non-Hispanic whites were younger and had more lymph node involvement (34% vs 17%, P < .001). Median tumor size was not statistically different across ethnic groups. Similar findings were demonstrated within the Surveillance, Epidemiology and End Results database. African Americans aged <45 years had the largest tumors but were least likely to have lymph node involvement. Asians had the most stage IV disease despite having no differences in tumor size, lymph node involvement, and capsular invasion. There is considerable variability in the clinical presentation of thyroid cancer across ethnic groups. Such disparities persist within an equal-access health care system. These findings suggest that factors beyond socioeconomics may contribute to such differences. Copyright © 2013 Elsevier Inc. All rights reserved.
-
Batista Rodríguez, Gabriela; Balla, Andrea; Corradetti, Santiago; Martinez, Carmen; Hernández, Pilar; Bollo, Jesús; Targarona, Eduard M
2018-06-01
"Big data" refers to large amount of dataset. Those large databases are useful in many areas, including healthcare. The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) and the National Inpatient Sample (NIS) are big databases that were developed in the USA in order to record surgical outcomes. The aim of the present systematic review is to evaluate the type and clinical impact of the information retrieved through NISQP and NIS big database articles focused on laparoscopic colorectal surgery. A systematic review was conducted using The Meta-Analysis Of Observational Studies in Epidemiology (MOOSE) guidelines. The research was carried out on PubMed database and revealed 350 published papers. Outcomes of articles in which laparoscopic colorectal surgery was the primary aim were analyzed. Fifty-five studies, published between 2007 and February 2017, were included. Articles included were categorized in groups according to the main topic as: outcomes related to surgical technique comparisons, morbidity and perioperatory results, specific disease-related outcomes, sociodemographic disparities, and academic training impact. NSQIP and NIS databases are just the tip of the iceberg for the potential application of Big Data technology and analysis in MIS. Information obtained through big data is useful and could be considered as external validation in those situations where a significant evidence-based medicine exists; also, those databases establish benchmarks to measure the quality of patient care. Data retrieved helps to inform decision-making and improve healthcare delivery.
-
[Developmental status and prospect of musical electroacupuncture].
Wang, Fan; Xu, Chun-Lan; Dong, Gui-Rong; Dong, Hong-Sheng
2014-12-01
Through searching domestic and foreign medical journals in CNKI, Wanfang database, VIP database and Pubmed database from January of 2003 to November of 2013, 39 articles regarding musical electroacupuncture (MEA) were analyzed. The result showed that MEA was clinically used to treat neurological and psychotic disorders; because it was combined with musical therapy and overcame the acupuncture tolerability, and MEA was superior to traditional electroacupuncture. However, problems such as low research efficiency and the mechanism of MEA superiority and the musical specificity not being revealed by research design still exist. In future, large-sample multi-center RCT researches should be performed to clarify MEA clinical efficacy. With modern science and technology and optimized study design, guided by five-element theory of TCM, researches on different musical elements and characteristics of musical pulse current as well as MEA's correlation with meridians and organs should be studied, so as to make a further exploration on MEA mechanisms and broaden the range of its clinical application.
-
Chen, R S; Nadkarni, P; Marenco, L; Levin, F; Erdos, J; Miller, P L
2000-01-01
The entity-attribute-value representation with classes and relationships (EAV/CR) provides a flexible and simple database schema to store heterogeneous biomedical data. In certain circumstances, however, the EAV/CR model is known to retrieve data less efficiently than conventionally based database schemas. To perform a pilot study that systematically quantifies performance differences for database queries directed at real-world microbiology data modeled with EAV/CR and conventional representations, and to explore the relative merits of different EAV/CR query implementation strategies. Clinical microbiology data obtained over a ten-year period were stored using both database models. Query execution times were compared for four clinically oriented attribute-centered and entity-centered queries operating under varying conditions of database size and system memory. The performance characteristics of three different EAV/CR query strategies were also examined. Performance was similar for entity-centered queries in the two database models. Performance in the EAV/CR model was approximately three to five times less efficient than its conventional counterpart for attribute-centered queries. The differences in query efficiency became slightly greater as database size increased, although they were reduced with the addition of system memory. The authors found that EAV/CR queries formulated using multiple, simple SQL statements executed in batch were more efficient than single, large SQL statements. This paper describes a pilot project to explore issues in and compare query performance for EAV/CR and conventional database representations. Although attribute-centered queries were less efficient in the EAV/CR model, these inefficiencies may be addressable, at least in part, by the use of more powerful hardware or more memory, or both.
-
Godown, Justin; Thurm, Cary; Dodd, Debra A; Soslow, Jonathan H; Feingold, Brian; Smith, Andrew H; Mettler, Bret A; Thompson, Bryn; Hall, Matt
2017-12-01
Large clinical, research, and administrative databases are increasingly utilized to facilitate pediatric heart transplant (HTx) research. Linking databases has proven to be a robust strategy across multiple disciplines to expand the possible analyses that can be performed while leveraging the strengths of each dataset. We describe a unique linkage of the Scientific Registry of Transplant Recipients (SRTR) database and the Pediatric Health Information System (PHIS) administrative database to provide a platform to assess resource utilization in pediatric HTx. All pediatric patients (1999-2016) who underwent HTx at a hospital enrolled in the PHIS database were identified. A linkage was performed between the SRTR and PHIS databases in a stepwise approach using indirect identifiers. To determine the feasibility of using these linked data to assess resource utilization, total and post-HTx hospital costs were assessed. A total of 3188 unique transplants were identified as being present in both databases and amenable to linkage. Linkage of SRTR and PHIS data was successful in 3057 (95.9%) patients, of whom 2896 (90.8%) had complete cost data. Median total and post-HTx hospital costs were $518,906 (IQR $324,199-$889,738), and $334,490 (IQR $235,506-$498,803) respectively with significant differences based on patient demographics and clinical characteristics at HTx. Linkage of the SRTR and PHIS databases is feasible and provides an invaluable tool to assess resource utilization. Our analysis provides contemporary cost data for pediatric HTx from the largest US sample reported to date. It also provides a platform for expanded analyses in the pediatric HTx population. Copyright © 2017 Elsevier Inc. All rights reserved.
-
The Danish Testicular Cancer database.
Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel; Mortensen, Mette Saksø; Larsson, Heidi; Søgaard, Mette; Toft, Birgitte Groenkaer; Engvad, Birte; Agerbæk, Mads; Holm, Niels Vilstrup; Lauritsen, Jakob
2016-01-01
The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data collection has been performed from 1984 to 2007 and from 2013 onward, respectively. The retrospective DaTeCa database contains detailed information with more than 300 variables related to histology, stage, treatment, relapses, pathology, tumor markers, kidney function, lung function, etc. A questionnaire related to late effects has been conducted, which includes questions regarding social relationships, life situation, general health status, family background, diseases, symptoms, use of medication, marital status, psychosocial issues, fertility, and sexuality. TC survivors alive on October 2014 were invited to fill in this questionnaire including 160 validated questions. Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database are included. The prospective DMCG DaTeCa database includes variables regarding histology, stage, prognostic group, and treatment. The DMCG DaTeCa database has existed since 2013 and is a young clinical database. It is necessary to extend the data collection in the prospective database in order to answer quality-related questions. Data from the retrospective database will be added to the prospective data. This will result in a large and very comprehensive database for future studies on TC patients.
-
Mancardi, G L; Uccelli, M M; Sonnati, M; Comi, G; Milanese, C; De Vincentiis, A; Battaglia, M A
2000-04-01
The SMile Card was developed as a means for computerising clinical information for the purpose of transferability, accessibility, standardisation and compilation of a national database of demographic and clinical information about multiple sclerosis (MS) patients. In many European countries, centres for MS are organised independently from one another making collaboration, consultation and patient referral complicated. Only the more highly advanced clinical centres, generally located in large urban areas, have had the possibility to utilise technical possibilities for improving the organisation of patient clinical and research information, although independently from other centres. The information system, developed utilising the Visual Basic language for Microsoft Windows 95, stores information via a 'smart card' in a database which is initiated and updated utilising a microprocessor, located at each neurological clinic. The SMile Card, currently being tested in Italy, permits patients to carry with them all relevant medical information without limitations. Neurologists are able to access and update, via the microprocessor, the patient's entire medical history and MS-related information, including the complete neurological examination and laboratory test results. The SMile Card provides MS patients and neurologists with a complete computerised archive of clinical information which is accessible throughout the country. In addition, data from the SMile Card system can be exported to other database programs.
-
Rostami, Reza; Nahm, Meredith; Pieper, Carl F
2009-04-01
Despite a pressing and well-documented need for better sharing of information on clinical trials data quality assurance methods, many research organizations remain reluctant to publish descriptions of and results from their internal auditing and quality assessment methods. We present findings from a review of a decade of internal data quality audits performed at the Duke Clinical Research Institute, a large academic research organization that conducts data management for a diverse array of clinical studies, both academic and industry-sponsored. In so doing, we hope to stimulate discussions that could benefit the wider clinical research enterprise by providing insight into methods of optimizing data collection and cleaning, ultimately helping patients and furthering essential research. We present our audit methodologies, including sampling methods, audit logistics, sample sizes, counting rules used for error rate calculations, and characteristics of audited trials. We also present database error rates as computed according to two analytical methods, which we address in detail, and discuss the advantages and drawbacks of two auditing methods used during this 10-year period. Our review of the DCRI audit program indicates that higher data quality may be achieved from a series of small audits throughout the trial rather than through a single large database audit at database lock. We found that error rates trended upward from year to year in the period characterized by traditional audits performed at database lock (1997-2000), but consistently trended downward after periodic statistical process control type audits were instituted (2001-2006). These increases in data quality were also associated with cost savings in auditing, estimated at 1000 h per year, or the efforts of one-half of a full time equivalent (FTE). Our findings are drawn from retrospective analyses and are not the result of controlled experiments, and may therefore be subject to unanticipated confounding. In addition, the scope and type of audits we examine here are specific to our institution, and our results may not be broadly generalizable. Use of statistical process control methodologies may afford advantages over more traditional auditing methods, and further research will be necessary to confirm the reliability and usability of such techniques. We believe that open and candid discussion of data quality assurance issues among academic and clinical research organizations will ultimately benefit the entire research community in the coming era of increased data sharing and re-use.
-
A data model and database for high-resolution pathology analytical image informatics.
Wang, Fusheng; Kong, Jun; Cooper, Lee; Pan, Tony; Kurc, Tahsin; Chen, Wenjin; Sharma, Ashish; Niedermayr, Cristobal; Oh, Tae W; Brat, Daniel; Farris, Alton B; Foran, David J; Saltz, Joel
2011-01-01
The systematic analysis of imaged pathology specimens often results in a vast amount of morphological information at both the cellular and sub-cellular scales. While microscopy scanners and computerized analysis are capable of capturing and analyzing data rapidly, microscopy image data remain underutilized in research and clinical settings. One major obstacle which tends to reduce wider adoption of these new technologies throughout the clinical and scientific communities is the challenge of managing, querying, and integrating the vast amounts of data resulting from the analysis of large digital pathology datasets. This paper presents a data model, which addresses these challenges, and demonstrates its implementation in a relational database system. This paper describes a data model, referred to as Pathology Analytic Imaging Standards (PAIS), and a database implementation, which are designed to support the data management and query requirements of detailed characterization of micro-anatomic morphology through many interrelated analysis pipelines on whole-slide images and tissue microarrays (TMAs). (1) Development of a data model capable of efficiently representing and storing virtual slide related image, annotation, markup, and feature information. (2) Development of a database, based on the data model, capable of supporting queries for data retrieval based on analysis and image metadata, queries for comparison of results from different analyses, and spatial queries on segmented regions, features, and classified objects. The work described in this paper is motivated by the challenges associated with characterization of micro-scale features for comparative and correlative analyses involving whole-slides tissue images and TMAs. Technologies for digitizing tissues have advanced significantly in the past decade. Slide scanners are capable of producing high-magnification, high-resolution images from whole slides and TMAs within several minutes. Hence, it is becoming increasingly feasible for basic, clinical, and translational research studies to produce thousands of whole-slide images. Systematic analysis of these large datasets requires efficient data management support for representing and indexing results from hundreds of interrelated analyses generating very large volumes of quantifications such as shape and texture and of classifications of the quantified features. We have designed a data model and a database to address the data management requirements of detailed characterization of micro-anatomic morphology through many interrelated analysis pipelines. The data model represents virtual slide related image, annotation, markup and feature information. The database supports a wide range of metadata and spatial queries on images, annotations, markups, and features. We currently have three databases running on a Dell PowerEdge T410 server with CentOS 5.5 Linux operating system. The database server is IBM DB2 Enterprise Edition 9.7.2. The set of databases consists of 1) a TMA database containing image analysis results from 4740 cases of breast cancer, with 641 MB storage size; 2) an algorithm validation database, which stores markups and annotations from two segmentation algorithms and two parameter sets on 18 selected slides, with 66 GB storage size; and 3) an in silico brain tumor study database comprising results from 307 TCGA slides, with 365 GB storage size. The latter two databases also contain human-generated annotations and markups for regions and nuclei. Modeling and managing pathology image analysis results in a database provide immediate benefits on the value and usability of data in a research study. The database provides powerful query capabilities, which are otherwise difficult or cumbersome to support by other approaches such as programming languages. Standardized, semantic annotated data representation and interfaces also make it possible to more efficiently share image data and analysis results.
-
Large-Scale medical image analytics: Recent methodologies, applications and Future directions.
Zhang, Shaoting; Metaxas, Dimitris
2016-10-01
Despite the ever-increasing amount and complexity of annotated medical image data, the development of large-scale medical image analysis algorithms has not kept pace with the need for methods that bridge the semantic gap between images and diagnoses. The goal of this position paper is to discuss and explore innovative and large-scale data science techniques in medical image analytics, which will benefit clinical decision-making and facilitate efficient medical data management. Particularly, we advocate that the scale of image retrieval systems should be significantly increased at which interactive systems can be effective for knowledge discovery in potentially large databases of medical images. For clinical relevance, such systems should return results in real-time, incorporate expert feedback, and be able to cope with the size, quality, and variety of the medical images and their associated metadata for a particular domain. The design, development, and testing of the such framework can significantly impact interactive mining in medical image databases that are growing rapidly in size and complexity and enable novel methods of analysis at much larger scales in an efficient, integrated fashion. Copyright © 2016. Published by Elsevier B.V.
-
Richardson, J; Smith, J E; McCall, G; Richardson, A; Pilkington, K; Kirsch, I
2007-09-01
To systematically review the research evidence on the effectiveness of hypnosis for cancer chemotherapy-induced nausea and vomiting (CINV). A comprehensive search of major biomedical databases including MEDLINE, EMBASE, ClNAHL, PsycINFO and the Cochrane Library was conducted. Specialist complementary and alternative medicine databases were searched and efforts were made to identify unpublished and ongoing research. Citations were included from the databases' inception to March 2005. Randomized controlled trials (RCTs) were appraised and meta-analysis undertaken. Clinical commentaries were obtained. Six RCTs evaluating the effectiveness of hypnosis in CINV were found. In five of these studies the participants were children. Studies report positive results including statistically significant reductions in anticipatory and CINV. Meta-analysis revealed a large effect size of hypnotic treatment when compared with treatment as usual, and the effect was at least as large as that of cognitive-behavioural therapy. Meta-analysis has demonstrated that hypnosis could be a clinically valuable intervention for anticipatory and CINV in children with cancer. Further research into the effectiveness, acceptance and feasibility of hypnosis in CINV, particularly in adults, is suggested. Future studies should assess suggestibility and provide full details of the hypnotic intervention.
-
Open access intrapartum CTG database.
Chudáček, Václav; Spilka, Jiří; Burša, Miroslav; Janků, Petr; Hruban, Lukáš; Huptych, Michal; Lhotská, Lenka
2014-01-13
Cardiotocography (CTG) is a monitoring of fetal heart rate and uterine contractions. Since 1960 it is routinely used by obstetricians to assess fetal well-being. Many attempts to introduce methods of automatic signal processing and evaluation have appeared during the last 20 years, however still no significant progress similar to that in the domain of adult heart rate variability, where open access databases are available (e.g. MIT-BIH), is visible. Based on a thorough review of the relevant publications, presented in this paper, the shortcomings of the current state are obvious. A lack of common ground for clinicians and technicians in the field hinders clinically usable progress. Our open access database of digital intrapartum cardiotocographic recordings aims to change that. The intrapartum CTG database consists in total of 552 intrapartum recordings, which were acquired between April 2010 and August 2012 at the obstetrics ward of the University Hospital in Brno, Czech Republic. All recordings were stored in electronic form in the OB TraceVue®;system. The recordings were selected from 9164 intrapartum recordings with clinical as well as technical considerations in mind. All recordings are at most 90 minutes long and start a maximum of 90 minutes before delivery. The time relation of CTG to delivery is known as well as the length of the second stage of labor which does not exceed 30 minutes. The majority of recordings (all but 46 cesarean sections) is - on purpose - from vaginal deliveries. All recordings have available biochemical markers as well as some more general clinical features. Full description of the database and reasoning behind selection of the parameters is presented in the paper. A new open-access CTG database is introduced which should give the research community common ground for comparison of results on reasonably large database. We anticipate that after reading the paper, the reader will understand the context of the field from clinical and technical perspectives which will enable him/her to use the database and also understand its limitations.
-
Big Data and Total Hip Arthroplasty: How Do Large Databases Compare?
Bedard, Nicholas A; Pugely, Andrew J; McHugh, Michael A; Lux, Nathan R; Bozic, Kevin J; Callaghan, John J
2018-01-01
Use of large databases for orthopedic research has become extremely popular in recent years. Each database varies in the methods used to capture data and the population it represents. The purpose of this study was to evaluate how these databases differed in reported demographics, comorbidities, and postoperative complications for primary total hip arthroplasty (THA) patients. Primary THA patients were identified within National Surgical Quality Improvement Programs (NSQIP), Nationwide Inpatient Sample (NIS), Medicare Standard Analytic Files (MED), and Humana administrative claims database (HAC). NSQIP definitions for comorbidities and complications were matched to corresponding International Classification of Diseases, 9th Revision/Current Procedural Terminology codes to query the other databases. Demographics, comorbidities, and postoperative complications were compared. The number of patients from each database was 22,644 in HAC, 371,715 in MED, 188,779 in NIS, and 27,818 in NSQIP. Age and gender distribution were clinically similar. Overall, there was variation in prevalence of comorbidities and rates of postoperative complications between databases. As an example, NSQIP had more than twice the obesity than NIS. HAC and MED had more than 2 times the diabetics than NSQIP. Rates of deep infection and stroke 30 days after THA had more than 2-fold difference between all databases. Among databases commonly used in orthopedic research, there is considerable variation in complication rates following THA depending upon the database used for analysis. It is important to consider these differences when critically evaluating database research. Additionally, with the advent of bundled payments, these differences must be considered in risk adjustment models. Copyright © 2017 Elsevier Inc. All rights reserved.
-
Kamali, Parisa; Zettervall, Sara L; Wu, Winona; Ibrahim, Ahmed M S; Medin, Caroline; Rakhorst, Hinne A; Schermerhorn, Marc L; Lee, Bernard T; Lin, Samuel J
2017-04-01
Research derived from large-volume databases plays an increasing role in the development of clinical guidelines and health policy. In breast cancer research, the Surveillance, Epidemiology and End Results, National Surgical Quality Improvement Program, and Nationwide Inpatient Sample databases are widely used. This study aims to compare the trends in immediate breast reconstruction and identify the drawbacks and benefits of each database. Patients with invasive breast cancer and ductal carcinoma in situ were identified from each database (2005-2012). Trends of immediate breast reconstruction over time were evaluated. Patient demographics and comorbidities were compared. Subgroup analysis of immediate breast reconstruction use per race was conducted. Within the three databases, 1.2 million patients were studied. Immediate breast reconstruction in invasive breast cancer patients increased significantly over time in all databases. A similar significant upward trend was seen in ductal carcinoma in situ patients. Significant differences in immediate breast reconstruction rates were seen among races; and the disparity differed among the three databases. Rates of comorbidities were similar among the three databases. There has been a significant increase in immediate breast reconstruction; however, the extent of the reporting of overall immediate breast reconstruction rates and of racial disparities differs significantly among databases. The Nationwide Inpatient Sample and the National Surgical Quality Improvement Program report similar findings, with the Surveillance, Epidemiology and End Results database reporting results significantly lower in several categories. These findings suggest that use of the Surveillance, Epidemiology and End Results database may not be universally generalizable to the entire U.S.
-
Development of an Integrated Biospecimen Database among the Regional Biobanks in Korea.
Park, Hyun Sang; Cho, Hune; Kim, Hwa Sun
2016-04-01
This study developed an integrated database for 15 regional biobanks that provides large quantities of high-quality bio-data to researchers to be used for the prevention of disease, for the development of personalized medicines, and in genetics studies. We collected raw data, managed independently by 15 regional biobanks, for database modeling and analyzed and defined the metadata of the items. We also built a three-step (high, middle, and low) classification system for classifying the item concepts based on the metadata. To generate clear meanings of the items, clinical items were defined using the Systematized Nomenclature of Medicine Clinical Terms, and specimen items were defined using the Logical Observation Identifiers Names and Codes. To optimize database performance, we set up a multi-column index based on the classification system and the international standard code. As a result of subdividing 7,197,252 raw data items collected, we refined the metadata into 1,796 clinical items and 1,792 specimen items. The classification system consists of 15 high, 163 middle, and 3,588 low class items. International standard codes were linked to 69.9% of the clinical items and 71.7% of the specimen items. The database consists of 18 tables based on a table from MySQL Server 5.6. As a result of the performance evaluation, the multi-column index shortened query time by as much as nine times. The database developed was based on an international standard terminology system, providing an infrastructure that can integrate the 7,197,252 raw data items managed by the 15 regional biobanks. In particular, it resolved the inevitable interoperability issues in the exchange of information among the biobanks, and provided a solution to the synonym problem, which arises when the same concept is expressed in a variety of ways.
-
Validation of a common data model for active safety surveillance research
Ryan, Patrick B; Reich, Christian G; Hartzema, Abraham G; Stang, Paul E
2011-01-01
Objective Systematic analysis of observational medical databases for active safety surveillance is hindered by the variation in data models and coding systems. Data analysts often find robust clinical data models difficult to understand and ill suited to support their analytic approaches. Further, some models do not facilitate the computations required for systematic analysis across many interventions and outcomes for large datasets. Translating the data from these idiosyncratic data models to a common data model (CDM) could facilitate both the analysts' understanding and the suitability for large-scale systematic analysis. In addition to facilitating analysis, a suitable CDM has to faithfully represent the source observational database. Before beginning to use the Observational Medical Outcomes Partnership (OMOP) CDM and a related dictionary of standardized terminologies for a study of large-scale systematic active safety surveillance, the authors validated the model's suitability for this use by example. Validation by example To validate the OMOP CDM, the model was instantiated into a relational database, data from 10 different observational healthcare databases were loaded into separate instances, a comprehensive array of analytic methods that operate on the data model was created, and these methods were executed against the databases to measure performance. Conclusion There was acceptable representation of the data from 10 observational databases in the OMOP CDM using the standardized terminologies selected, and a range of analytic methods was developed and executed with sufficient performance to be useful for active safety surveillance. PMID:22037893
-
Machine Learning and Decision Support in Critical Care
Johnson, Alistair E. W.; Ghassemi, Mohammad M.; Nemati, Shamim; Niehaus, Katherine E.; Clifton, David A.; Clifford, Gari D.
2016-01-01
Clinical data management systems typically provide caregiver teams with useful information, derived from large, sometimes highly heterogeneous, data sources that are often changing dynamically. Over the last decade there has been a significant surge in interest in using these data sources, from simply re-using the standard clinical databases for event prediction or decision support, to including dynamic and patient-specific information into clinical monitoring and prediction problems. However, in most cases, commercial clinical databases have been designed to document clinical activity for reporting, liability and billing reasons, rather than for developing new algorithms. With increasing excitement surrounding “secondary use of medical records” and “Big Data” analytics, it is important to understand the limitations of current databases and what needs to change in order to enter an era of “precision medicine.” This review article covers many of the issues involved in the collection and preprocessing of critical care data. The three challenges in critical care are considered: compartmentalization, corruption, and complexity. A range of applications addressing these issues are covered, including the modernization of static acuity scoring; on-line patient tracking; personalized prediction and risk assessment; artifact detection; state estimation; and incorporation of multimodal data sources such as genomic and free text data. PMID:27765959
-
Fracture Rates and Lifetime Estimations of CAD/CAM All-ceramic Restorations.
Belli, R; Petschelt, A; Hofner, B; Hajtó, J; Scherrer, S S; Lohbauer, U
2016-01-01
The gathering of clinical data on fractures of dental restorations through prospective clinical trials is a labor- and time-consuming enterprise. Here, we propose an unconventional approach for collecting large datasets, from which clinical information on indirect restorations can be retrospectively analyzed. The authors accessed the database of an industry-scale machining center in Germany and obtained information on 34,911 computer-aided design (CAD)/computer-aided manufacturing (CAM) all-ceramic posterior restorations. The fractures of bridges, crowns, onlays, and inlays fabricated from different all-ceramic systems over a period of 3.5 y were reported by dentists and entered in the database. Survival analyses and estimations of future life revealed differences in performance among ZrO2-based restorations and lithium disilicate and leucite-reinforced glass-ceramics. © International & American Associations for Dental Research 2015.
-
PubMed searches: overview and strategies for clinicians.
Lindsey, Wesley T; Olin, Bernie R
2013-04-01
PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.
-
Designing Reliable Cohorts of Cardiac Patients across MIMIC and eICU
Chronaki, Catherine; Shahin, Abdullah; Mark, Roger
2016-01-01
The design of the patient cohort is an essential and fundamental part of any clinical patient study. Knowledge of the Electronic Health Records, underlying Database Management System, and the relevant clinical workflows are central to an effective cohort design. However, with technical, semantic, and organizational interoperability limitations, the database queries associated with a patient cohort may need to be reconfigured in every participating site. i2b2 and SHRINE advance the notion of patient cohorts as first class objects to be shared, aggregated, and recruited for research purposes across clinical sites. This paper reports on initial efforts to assess the integration of Medical Information Mart for Intensive Care (MIMIC) and Philips eICU, two large-scale anonymized intensive care unit (ICU) databases, using standard terminologies, i.e. LOINC, ICD9-CM and SNOMED-CT. Focus of this work is lab and microbiology observations and key demographics for patients with a primary cardiovascular ICD9-CM diagnosis. Results and discussion reflecting on reference core terminology standards, offer insights on efforts to combine detailed intensive care data from multiple ICUs worldwide. PMID:27774488
-
Image database for digital hand atlas
NASA Astrophysics Data System (ADS)
Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente; Dey, Partha S.; Gertych, Arkadiusz; Pospiech-Kurkowska, Sywia
2003-05-01
Bone age assessment is a procedure frequently performed in pediatric patients to evaluate their growth disorder. A commonly used method is atlas matching by a visual comparison of a hand radiograph with a small reference set of old Greulich-Pyle atlas. We have developed a new digital hand atlas with a large set of clinically normal hand images of diverse ethnic groups. In this paper, we will present our system design and implementation of the digital atlas database to support the computer-aided atlas matching for bone age assessment. The system consists of a hand atlas image database, a computer-aided diagnostic (CAD) software module for image processing and atlas matching, and a Web user interface. Users can use a Web browser to push DICOM images, directly or indirectly from PACS, to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, are then extracted and compared with patterns from the atlas image database to assess the bone age. The digital atlas method built on a large image database and current Internet technology provides an alternative to supplement or replace the traditional one for a quantitative, accurate and cost-effective assessment of bone age.
-
Big data in sleep medicine: prospects and pitfalls in phenotyping
Bianchi, Matt T; Russo, Kathryn; Gabbidon, Harriett; Smith, Tiaundra; Goparaju, Balaji; Westover, M Brandon
2017-01-01
Clinical polysomnography (PSG) databases are a rich resource in the era of “big data” analytics. We explore the uses and potential pitfalls of clinical data mining of PSG using statistical principles and analysis of clinical data from our sleep center. We performed retrospective analysis of self-reported and objective PSG data from adults who underwent overnight PSG (diagnostic tests, n=1835). Self-reported symptoms overlapped markedly between the two most common categories, insomnia and sleep apnea, with the majority reporting symptoms of both disorders. Standard clinical metrics routinely reported on objective data were analyzed for basic properties (missing values, distributions), pairwise correlations, and descriptive phenotyping. Of 41 continuous variables, including clinical and PSG derived, none passed testing for normality. Objective findings of sleep apnea and periodic limb movements were common, with 51% having an apnea–hypopnea index (AHI) >5 per hour and 25% having a leg movement index >15 per hour. Different visualization methods are shown for common variables to explore population distributions. Phenotyping methods based on clinical databases are discussed for sleep architecture, sleep apnea, and insomnia. Inferential pitfalls are discussed using the current dataset and case examples from the literature. The increasing availability of clinical databases for large-scale analytics holds important promise in sleep medicine, especially as it becomes increasingly important to demonstrate the utility of clinical testing methods in management of sleep disorders. Awareness of the strengths, as well as caution regarding the limitations, will maximize the productive use of big data analytics in sleep medicine. PMID:28243157
-
Automatic initialization and quality control of large-scale cardiac MRI segmentations.
Albà, Xènia; Lekadir, Karim; Pereañez, Marco; Medrano-Gracia, Pau; Young, Alistair A; Frangi, Alejandro F
2018-01-01
Continuous advances in imaging technologies enable ever more comprehensive phenotyping of human anatomy and physiology. Concomitant reduction of imaging costs has resulted in widespread use of imaging in large clinical trials and population imaging studies. Magnetic Resonance Imaging (MRI), in particular, offers one-stop-shop multidimensional biomarkers of cardiovascular physiology and pathology. A wide range of analysis methods offer sophisticated cardiac image assessment and quantification for clinical and research studies. However, most methods have only been evaluated on relatively small databases often not accessible for open and fair benchmarking. Consequently, published performance indices are not directly comparable across studies and their translation and scalability to large clinical trials or population imaging cohorts is uncertain. Most existing techniques still rely on considerable manual intervention for the initialization and quality control of the segmentation process, becoming prohibitive when dealing with thousands of images. The contributions of this paper are three-fold. First, we propose a fully automatic method for initializing cardiac MRI segmentation, by using image features and random forests regression to predict an initial position of the heart and key anatomical landmarks in an MRI volume. In processing a full imaging database, the technique predicts the optimal corrective displacements and positions in relation to the initial rough intersections of the long and short axis images. Second, we introduce for the first time a quality control measure capable of identifying incorrect cardiac segmentations with no visual assessment. The method uses statistical, pattern and fractal descriptors in a random forest classifier to detect failures to be corrected or removed from subsequent statistical analysis. Finally, we validate these new techniques within a full pipeline for cardiac segmentation applicable to large-scale cardiac MRI databases. The results obtained based on over 1200 cases from the Cardiac Atlas Project show the promise of fully automatic initialization and quality control for population studies. Copyright © 2017 Elsevier B.V. All rights reserved.
-
Dimensions of clinical nurse specialist work in the UK.
Leary, Alison; Crouch, Heather; Lezard, Anthony; Rawcliffe, Chris; Boden, Louise; Richardson, Alison
To model the work of clinical nurse specialists (CNSs) in the UK. This article examines data mined as part of a national project. The Pandora database was initially collected on a Microsoft Office Access database and subsequently, a Structured Query Language database in several iterations from June 2006 to September 2008. Pandora recorded CNS activity as a series of events with eight dimensions to each event. Data from this were mined to examine the complexity of CNS work. This study represents the work of 463 CNSs over 2,778 days in England, Scotland and Wales. Clinical work, including physical assessment, referral, symptom control and 'rescue' work, accounted for a large part of the CNS's role. Administration was the second highest workload, with about half of these administrative tasks identified as being suitable for secretarial staff to undertake. Research, education and consultation accounted for less time. A significant proportion of the nurses' clinical work is undertaken by telephone. CNSs in this study spent much of their time doing complex clinical work. Payment by Results (Department of Health 2006) should recognise the work undertaken by CNSs, particularly that done on the telephone. Complex clinical work by CNSs takes place in many different contexts using a wide range of interventions. The role of the CNS is complex and diverse, making comparisons of it difficult. More research needs to be done in relation to quality, safety and efficiency.
-
HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.
O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D
2015-04-01
The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples. Copyright © 2015 Elsevier Inc. All rights reserved.
-
Zhao, Lei; Guo, Yi; Wang, Wei; Yan, Li-juan
2011-08-01
To evaluate the effectiveness of acupuncture as a treatment for neurovascular headache and to analyze the current situation related to acupuncture treatment. PubMed database (1966-2010), EMBASE database (1986-2010), Cochrane Library (Issue 1, 2010), Chinese Biomedical Literature Database (1979-2010), China HowNet Knowledge Database (1979-2010), VIP Journals Database (1989-2010), and Wanfang database (1998-2010) were retrieved. Randomized or quasi-randomized controlled studies were included. The priority was given to high-quality randomized, controlled trials. Statistical outcome indicators were measured using RevMan 5.0.20 software. A total of 16 articles and 1 535 cases were included. Meta-analysis showed a significant difference between the acupuncture therapy and Western medicine therapy [combined RR (random efficacy model)=1.46, 95% CI (1.21, 1.75), Z=3.96, P<0.0001], indicating an obvious superior effect of the acupuncture therapy; significant difference also existed between the comprehensive acupuncture therapy and acupuncture therapy alone [combined RR (fixed efficacy model)=3.35, 95% CI (1.92, 5.82), Z=4.28, P<0.0001], indicating that acupuncture combined with other therapies, such as points injection, scalp acupuncture, auricular acupuncture, etc., were superior to the conventional body acupuncture therapy alone. The inclusion of limited clinical studies had verified the efficacy of acupuncture in the treatment of neurovascular headache. Although acupuncture or its combined therapies provides certain advantages, most clinical studies are of small sample sizes. Large sample size, randomized, controlled trials are needed in the future for more definitive results.
-
2012-01-01
Background To establish a common database on particle therapy for the evaluation of clinical studies integrating a large variety of voluminous datasets, different documentation styles, and various information systems, especially in the field of radiation oncology. Methods We developed a web-based documentation system for transnational and multicenter clinical studies in particle therapy. 560 patients have been treated from November 2009 to September 2011. Protons, carbon ions or a combination of both, as well as a combination with photons were applied. To date, 12 studies have been initiated and more are in preparation. Results It is possible to immediately access all patient information and exchange, store, process, and visualize text data, any DICOM images and multimedia data. Accessing the system and submitting clinical data is possible for internal and external users. Integrated into the hospital environment, data is imported both manually and automatically. Security and privacy protection as well as data validation and verification are ensured. Studies can be designed to fit individual needs. Conclusions The described database provides a basis for documentation of large patient groups with specific and specialized questions to be answered. Having recently begun electronic documentation, it has become apparent that the benefits lie in the user-friendly and timely workflow for documentation. The ultimate goal is a simplification of research work, better study analyses quality and eventually, the improvement of treatment concepts by evaluating the effectiveness of particle therapy. PMID:22828013
-
Construction of databases: advances and significance in clinical research.
Long, Erping; Huang, Bingjie; Wang, Liming; Lin, Xiaoyu; Lin, Haotian
2015-12-01
Widely used in clinical research, the database is a new type of data management automation technology and the most efficient tool for data management. In this article, we first explain some basic concepts, such as the definition, classification, and establishment of databases. Afterward, the workflow for establishing databases, inputting data, verifying data, and managing databases is presented. Meanwhile, by discussing the application of databases in clinical research, we illuminate the important role of databases in clinical research practice. Lastly, we introduce the reanalysis of randomized controlled trials (RCTs) and cloud computing techniques, showing the most recent advancements of databases in clinical research.
-
Capkun, Gorana; Lahoz, Raquel; Verdun, Elisabetta; Song, Xue; Chen, Weston; Korn, Jonathan R; Dahlke, Frank; Freitas, Rita; Fraeman, Kathy; Simeone, Jason; Johnson, Barbara H; Nordstrom, Beth
2015-05-01
Administrative claims databases provide a wealth of data for assessing the effect of treatments in clinical practice. Our aim was to propose methodology for real-world studies in multiple sclerosis (MS) using these databases. In three large US administrative claims databases: MarketScan, PharMetrics Plus and Department of Defense (DoD), patients with MS were selected using an algorithm identified in the published literature and refined for accuracy. Algorithms for detecting newly diagnosed ('incident') MS cases were also refined and tested. Methodology based on resource and treatment use was developed to differentiate between relapses with and without hospitalization. When various patient selection criteria were applied to the MarketScan database, an algorithm requiring two MS diagnoses at least 30 days apart was identified as the preferred method of selecting patient cohorts. Attempts to detect incident MS cases were confounded by the limited continuous enrollment of patients in these databases. Relapse detection algorithms identified similar proportions of patients in the MarketScan and PharMetrics Plus databases experiencing relapses with (2% in both databases) and without (15-20%) hospitalization in the 1 year follow-up period, providing findings in the range of those in the published literature. Additional validation of the algorithms proposed here would increase their credibility. The methods suggested in this study offer a good foundation for performing real-world research in MS using administrative claims databases, potentially allowing evidence from different studies to be compared and combined more systematically than in current research practice.
-
Leveraging the power of pooled data for cancer outcomes research.
Hugh-Yeun, Kiara; Cheung, Winson Y
2016-08-02
Clinical trials continue to be the gold standard for determining the efficacy of novel cancer treatments, but they may also expose participants to the potential risks of unpredictable or severe toxicities. The development of validated tools that better inform patients of the benefits and risks associated with clinical trial participation can facilitate the informed consent process. The design and validation of such instruments are strengthened when we leverage the power of pooled data analysis for cancer outcomes research. In a recent study published in the Journal of Clinical Oncology entitled "Determinants of early mortality among 37,568 patients with colon cancer who participated in 25 clinical trials from the adjuvant colon cancer endpoints database," using a large pooled analysis of over 30,000 study participants who were enrolled in clinical trials of adjuvant therapy for early-stage colon cancer, we developed and validated a nomogram depicting the predictors of early cancer mortality. This database of pooled individual-level data allowed for a comprehensive analysis of poor prognostic factors associated with early death; furthermore, it enabled the creation of a nomogram that was able to reliably capture and quantify the benefit-to-risk profile for patients who are considering clinical trial participation. This tool can facilitate treatment decision-making discussions. As China and other Asian countries continue to conduct oncology clinical trials, efforts to collate patient-level information from these studies into a large data repository should be strongly considered since pooled data can increase future capacity for cancer outcomes research, which, in turn, can enhance patient-physician discussions and optimize clinical care.
-
Rostami, Reza; Nahm, Meredith; Pieper, Carl F.
2011-01-01
Background Despite a pressing and well-documented need for better sharing of information on clinical trials data quality assurance methods, many research organizations remain reluctant to publish descriptions of and results from their internal auditing and quality assessment methods. Purpose We present findings from a review of a decade of internal data quality audits performed at the Duke Clinical Research Institute, a large academic research organization that conducts data management for a diverse array of clinical studies, both academic and industry-sponsored. In so doing, we hope to stimulate discussions that could benefit the wider clinical research enterprise by providing insight into methods of optimizing data collection and cleaning, ultimately helping patients and furthering essential research. Methods We present our audit methodologies, including sampling methods, audit logistics, sample sizes, counting rules used for error rate calculations, and characteristics of audited trials. We also present database error rates as computed according to two analytical methods, which we address in detail, and discuss the advantages and drawbacks of two auditing methods used during this ten-year period. Results Our review of the DCRI audit program indicates that higher data quality may be achieved from a series of small audits throughout the trial rather than through a single large database audit at database lock. We found that error rates trended upward from year to year in the period characterized by traditional audits performed at database lock (1997–2000), but consistently trended downward after periodic statistical process control type audits were instituted (2001–2006). These increases in data quality were also associated with cost savings in auditing, estimated at 1000 hours per year, or the efforts of one-half of a full time equivalent (FTE). Limitations Our findings are drawn from retrospective analyses and are not the result of controlled experiments, and may therefore be subject to unanticipated confounding. In addition, the scope and type of audits we examine here are specific to our institution, and our results may not be broadly generalizable. Conclusions Use of statistical process control methodologies may afford advantages over more traditional auditing methods, and further research will be necessary to confirm the reliability and usability of such techniques. We believe that open and candid discussion of data quality assurance issues among academic and clinical research organizations will ultimately benefit the entire research community in the coming era of increased data sharing and re-use. PMID:19342467
-
Integrative neuroscience: the role of a standardized database.
Gordon, E; Cooper, N; Rennie, C; Hermens, D; Williams, L M
2005-04-01
Most brain related databases bring together specialized information, with a growing number that include neuroimaging measures. This article outlines the potential use and insights from the first entirely standardized and centralized database, which integrates information from neuroimaging measures (EEG, event related potential (ERP), structural/functional MRI), arousal (skin conductance responses (SCR)s, heart rate, respiration), neuropsychological and personality tests, genomics and demographics: The Brain Resource International Database. It comprises data from over 2000 "normative" subjects and a growing number of patients with neurological and psychiatric illnesses, acquired from over 50 laboratories (in the U.S.A, United Kingdom, Holland, South Africa, Israel and Australia), all with identical equipment and experimental procedures. Three primary goals of this database are to quantify individual differences in normative brain function, to compare an individual's performance to their database peers, and to provide a robust normative framework for clinical assessment and treatment prediction. We present three example demonstrations in relation to these goals. First, we show how consistent age differences may be quantified when large subject numbers are available, using EEG and ERP data from nearly 2000 stringently screened. normative subjects. Second, the use of a normalization technique provides a means to compare clinical subjects (50 ADHD subjects in this study) to the normative database with the effects of age and gender taken into account. Third, we show how a profile of EEG/ERP and autonomic measures potentially provides a means to predict treatment response in ADHD subjects. The example data consists of EEG under eyes open and eyes closed and ERP data for auditory oddball, working memory and Go-NoGo paradigms. Autonomic measures of skin conductance (tonic skin conductance level, SCL, and phasic skin conductance responses, SCRs) were acquired simultaneously with central EEG/ERP measures. The findings show that the power of large samples, tested using standardized protocols, allows for the quantification of individual differences that can subsequently be used to control such variation and to enhance the sensitivity and specificity of comparisons between normative and clinical groups. In terms of broader significance, the combination of size and multidimensional measures tapping the brain's core cognitive competencies, may provide a normative and evidence-based framework for individually-based assessments in "Personalized Medicine."
-
Abugessaisa, Imad; Gomez-Cabrero, David; Snir, Omri; Lindblad, Staffan; Klareskog, Lars; Malmström, Vivianne; Tegnér, Jesper
2013-04-02
Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical practice generate large amounts of data. This represents an underused data source that has much greater potential in translational research than is currently realized. This research aims at implementing a translational medicine informatics platform to integrate clinical data (disease diagnosis, diseases activity and treatment) of Rheumatoid Arthritis (RA) patients from Karolinska University Hospital and their research database (biobanks, genotype variants and serology) at the Center for Molecular Medicine, Karolinska Institutet. Requirements engineering methods were utilized to identify user requirements. Unified Modeling Language and data modeling methods were used to model the universe of discourse and data sources. Oracle11g were used as the database management system, and the clinical development center (CDC) was used as the application interface. Patient data were anonymized, and we employed authorization and security methods to protect the system. We developed a user requirement matrix, which provided a framework for evaluating three translation informatics systems. The implementation of the CDC successfully integrated biological research database (15172 DNA, serum and synovial samples, 1436 cell samples and 65 SNPs per patient) and clinical database (5652 clinical visit) for the cohort of 379 patients presents three profiles. Basic functionalities provided by the translational medicine platform are research data management, development of bioinformatics workflow and analysis, sub-cohort selection, and re-use of clinical data in research settings. Finally, the system allowed researchers to extract subsets of attributes from cohorts according to specific biological, clinical, or statistical features. Research and clinical database integration is a real challenge and a road-block in translational research. Through this research we addressed the challenges and demonstrated the usefulness of CDC. We adhered to ethical regulations pertaining to patient data, and we determined that the existing software solutions cannot meet the translational research needs at hand. We used RA as a test case since we have ample data on active and longitudinal cohort.
-
2013-01-01
Background Sequencing of the human genome and the subsequent analyses have produced immense volumes of data. The technological advances have opened new windows into genomics beyond the DNA sequence. In parallel, clinical practice generate large amounts of data. This represents an underused data source that has much greater potential in translational research than is currently realized. This research aims at implementing a translational medicine informatics platform to integrate clinical data (disease diagnosis, diseases activity and treatment) of Rheumatoid Arthritis (RA) patients from Karolinska University Hospital and their research database (biobanks, genotype variants and serology) at the Center for Molecular Medicine, Karolinska Institutet. Methods Requirements engineering methods were utilized to identify user requirements. Unified Modeling Language and data modeling methods were used to model the universe of discourse and data sources. Oracle11g were used as the database management system, and the clinical development center (CDC) was used as the application interface. Patient data were anonymized, and we employed authorization and security methods to protect the system. Results We developed a user requirement matrix, which provided a framework for evaluating three translation informatics systems. The implementation of the CDC successfully integrated biological research database (15172 DNA, serum and synovial samples, 1436 cell samples and 65 SNPs per patient) and clinical database (5652 clinical visit) for the cohort of 379 patients presents three profiles. Basic functionalities provided by the translational medicine platform are research data management, development of bioinformatics workflow and analysis, sub-cohort selection, and re-use of clinical data in research settings. Finally, the system allowed researchers to extract subsets of attributes from cohorts according to specific biological, clinical, or statistical features. Conclusions Research and clinical database integration is a real challenge and a road-block in translational research. Through this research we addressed the challenges and demonstrated the usefulness of CDC. We adhered to ethical regulations pertaining to patient data, and we determined that the existing software solutions cannot meet the translational research needs at hand. We used RA as a test case since we have ample data on active and longitudinal cohort. PMID:23548156
-
Cardiac auscultatory recording database: delivering heart sounds through the Internet.
Tuchinda, C.; Thompson, W. R.
2001-01-01
The clinical skill of cardiac auscultation, while known to be sensitive, specific, and inexpensive in screening for cardiac disease among children, has recently been shown to be deficient among residents in training. This decline in clinical skill is partly due to the difficulty in teaching auscultation. Standardization, depth, and breadth of experience has been difficult to reproduce for students due to time constraints and the impracticality of examining large numbers of patients with cardiac pathology. We have developed a web-based multimedia platform that delivers complete heart sound recordings from over 800 different patients seen at the Johns Hopkins Outpatient Pediatric Cardiology Clinic. The database represents more than twenty significant cardiac lesions as well as normal and innocent murmurs. Each patient record is complete with a gold standard echo for diagnostic confirmation and a gold standard auscultatory assessment provided by a pediatric cardiology attending. PMID:11825279
-
Terzian, Arpi; Opoku, Jenevieve; Happ, Lindsey Powers; Younes, Naji; Kharfen, Michael; Greenberg, Alan
2018-01-01
Background Triangulation of data from multiple sources such as clinical cohort and surveillance data can help improve our ability to describe care patterns, service utilization, comorbidities, and ultimately measure and monitor clinical outcomes among persons living with HIV infection. Objectives The objective of this study was to determine whether linkage of clinical cohort data and routinely collected HIV surveillance data would enhance the completeness and accuracy of each database and improve the understanding of care patterns and clinical outcomes. Methods We linked data from the District of Columbia (DC) Cohort, a large HIV observational clinical cohort, with Washington, DC, Department of Health (DOH) surveillance data between January 2011 and June 2015. We determined percent concordance between select variables in the pre- and postlinked databases using kappa test statistics. We compared retention in care (RIC), viral suppression (VS), sexually transmitted diseases (STDs), and non-HIV comorbid conditions (eg, hypertension) and compared HIV clinic visit patterns determined using the prelinked database (DC Cohort) versus the postlinked database (DC Cohort + DOH) using chi-square testing. Additionally, we compared sociodemographic characteristics, RIC, and VS among participants receiving HIV care at ≥3 sites versus <3 sites using chi-square testing. Results Of the 6054 DC Cohort participants, 5521 (91.19%) were included in the postlinked database and enrolled at a single DC Cohort site. The majority of the participants was male, black, and had men who have sex with men (MSM) as their HIV risk factor. In the postlinked database, 619 STD diagnoses previously unknown to the DC Cohort were identified. Additionally, the proportion of participants with RIC was higher compared with the prelinked database (59.83%, 2678/4476 vs 64.95%, 2907/4476; P<.001) and the proportion with VS was lower (87.85%, 2277/2592 vs 85.15%, 2391/2808; P<.001). Almost a quarter of participants (23.06%, 1279/5521) were identified as receiving HIV care at ≥2 sites (postlinked database). The participants using ≥3 care sites were more likely to achieve RIC (80.7%, 234/290 vs 62.61%, 2197/3509) but less likely to achieve VS (72.3%, 154/213 vs 89.51%, 1869/2088). The participants using ≥3 care sites were more likely to have unstable housing (15.1%, 64/424 vs 8.96%, 380/4242), public insurance (86.1%, 365/424 vs 57.57%, 2442/4242), comorbid conditions (eg, hypertension) (37.7%, 160/424 vs 22.98%, 975/4242), and have acquired immunodeficiency syndrome (77.8%, 330/424 vs 61.20%, 2596/4242) (all P<.001). Conclusions Linking surveillance and clinical data resulted in the improved completeness of each database and a larger volume of available data to evaluate HIV outcomes, allowing for refinement of HIV care continuum estimates. The postlinked database also highlighted important differences between participants who sought HIV care at multiple clinical sites. Our findings suggest that combined datasets can enhance evaluation of HIV-related outcomes across an entire metropolitan area. Future research will evaluate how to best utilize this information to improve outcomes in addition to monitoring them. PMID:29549065
-
Big data and ophthalmic research.
Clark, Antony; Ng, Jonathon Q; Morlet, Nigel; Semmens, James B
2016-01-01
Large population-based health administrative databases, clinical registries, and data linkage systems are a rapidly expanding resource for health research. Ophthalmic research has benefited from the use of these databases in expanding the breadth of knowledge in areas such as disease surveillance, disease etiology, health services utilization, and health outcomes. Furthermore, the quantity of data available for research has increased exponentially in recent times, particularly as e-health initiatives come online in health systems across the globe. We review some big data concepts, the databases and data linkage systems used in eye research-including their advantages and limitations, the types of studies previously undertaken, and the future direction for big data in eye research. Copyright © 2016 Elsevier Inc. All rights reserved.
-
A Molecular Framework for Understanding DCIS
2016-10-01
well. Pathologic and Clinical Annotation Database A clinical annotation database titled the Breast Oncology Database has been established to...complement the procured SPORE sample characteristics and annotated pathology data. This Breast Oncology Database is an offsite clinical annotation...database adheres to CSMC Enterprise Information Services (EIS) research database security standards. The Breast Oncology Database consists of: 9 Baseline
-
[A web-based integrated clinical database for laryngeal cancer].
E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu
2014-08-01
To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.
-
Drug development and nonclinical to clinical translational databases: past and current efforts.
Monticello, Thomas M
2015-01-01
The International Consortium for Innovation and Quality (IQ) in Pharmaceutical Development is a science-focused organization of pharmaceutical and biotechnology companies. The mission of the Preclinical Safety Leadership Group (DruSafe) of the IQ is to advance science-based standards for nonclinical development of pharmaceutical products and to promote high-quality and effective nonclinical safety testing that can enable human risk assessment. DruSafe is creating an industry-wide database to determine the accuracy with which the interpretation of nonclinical safety assessments in animal models correctly predicts human risk in the early clinical development of biopharmaceuticals. This initiative aligns with the 2011 Food and Drug Administration strategic plan to advance regulatory science and modernize toxicology to enhance product safety. Although similar in concept to the initial industry-wide concordance data set conducted by International Life Sciences Institute's Health and Environmental Sciences Institute (HESI/ILSI), the DruSafe database will proactively track concordance, include exposure data and large and small molecules, and will continue to expand with longer duration nonclinical and clinical study comparisons. The output from this work will help identify actual human and animal adverse event data to define both the reliability and the potential limitations of nonclinical data and testing paradigms in predicting human safety in phase 1 clinical trials. © 2014 by The Author(s).
-
Wimmer, Helge; Gundacker, Nina C; Griss, Johannes; Haudek, Verena J; Stättner, Stefan; Mohr, Thomas; Zwickl, Hannes; Paulitschke, Verena; Baron, David M; Trittner, Wolfgang; Kubicek, Markus; Bayer, Editha; Slany, Astrid; Gerner, Christopher
2009-06-01
Interpretation of proteome data with a focus on biomarker discovery largely relies on comparative proteome analyses. Here, we introduce a database-assisted interpretation strategy based on proteome profiles of primary cells. Both 2-D-PAGE and shotgun proteomics are applied. We obtain high data concordance with these two different techniques. When applying mass analysis of tryptic spot digests from 2-D gels of cytoplasmic fractions, we typically identify several hundred proteins. Using the same protein fractions, we usually identify more than thousand proteins by shotgun proteomics. The data consistency obtained when comparing these independent data sets exceeds 99% of the proteins identified in the 2-D gels. Many characteristic differences in protein expression of different cells can thus be independently confirmed. Our self-designed SQL database (CPL/MUW - database of the Clinical Proteomics Laboratories at the Medical University of Vienna accessible via www.meduniwien.ac.at/proteomics/database) facilitates (i) quality management of protein identification data, which are based on MS, (ii) the detection of cell type-specific proteins and (iii) of molecular signatures of specific functional cell states. Here, we demonstrate, how the interpretation of proteome profiles obtained from human liver tissue and hepatocellular carcinoma tissue is assisted by the Clinical Proteomics Laboratories at the Medical University of Vienna-database. Therefore, we suggest that the use of reference experiments supported by a tailored database may substantially facilitate data interpretation of proteome profiling experiments.
-
Assessment of COPD-related outcomes via a national electronic medical record database.
Asche, Carl; Said, Quayyim; Joish, Vijay; Hall, Charles Oaxaca; Brixner, Diana
2008-01-01
The technology and sophistication of healthcare utilization databases have expanded over the last decade to include results of lab tests, vital signs, and other clinical information. This review provides an assessment of the methodological and analytical challenges of conducting chronic obstructive pulmonary disease (COPD) outcomes research in a national electronic medical records (EMR) dataset and its potential application towards the assessment of national health policy issues, as well as a description of the challenges or limitations. An EMR database and its application to measuring outcomes for COPD are described. The ability to measure adherence to the COPD evidence-based practice guidelines, generated by the NIH and HEDIS quality indicators, in this database was examined. Case studies, before and after their publication, were used to assess the adherence to guidelines and gauge the conformity to quality indicators. EMR was the only source of information for pulmonary function tests, but low frequency in ordering by primary care was an issue. The EMR data can be used to explore impact of variation in healthcare provision on clinical outcomes. The EMR database permits access to specific lab data and biometric information. The richness and depth of information on "real world" use of health services for large population-based analytical studies at relatively low cost render such databases an attractive resource for outcomes research. Various sources of information exist to perform outcomes research. It is important to understand the desired endpoints of such research and choose the appropriate database source.
-
WebCIS: large scale deployment of a Web-based clinical information system.
Hripcsak, G; Cimino, J J; Sengupta, S
1999-01-01
WebCIS is a Web-based clinical information system. It sits atop the existing Columbia University clinical information system architecture, which includes a clinical repository, the Medical Entities Dictionary, an HL7 interface engine, and an Arden Syntax based clinical event monitor. WebCIS security features include authentication with secure tokens, authorization maintained in an LDAP server, SSL encryption, permanent audit logs, and application time outs. WebCIS is currently used by 810 physicians at the Columbia-Presbyterian center of New York Presbyterian Healthcare to review and enter data into the electronic medical record. Current deployment challenges include maintaining adequate database performance despite complex queries, replacing large numbers of computers that cannot run modern Web browsers, and training users that have never logged onto the Web. Although the raised expectations and higher goals have increased deployment costs, the end result is a far more functional, far more available system.
-
Open-access MIMIC-II database for intensive care research.
Lee, Joon; Scott, Daniel J; Villarroel, Mauricio; Clifford, Gari D; Saeed, Mohammed; Mark, Roger G
2011-01-01
The critical state of intensive care unit (ICU) patients demands close monitoring, and as a result a large volume of multi-parameter data is collected continuously. This represents a unique opportunity for researchers interested in clinical data mining. We sought to foster a more transparent and efficient intensive care research community by building a publicly available ICU database, namely Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II). The data harnessed in MIMIC-II were collected from the ICUs of Beth Israel Deaconess Medical Center from 2001 to 2008 and represent 26,870 adult hospital admissions (version 2.6). MIMIC-II consists of two major components: clinical data and physiological waveforms. The clinical data, which include patient demographics, intravenous medication drip rates, and laboratory test results, were organized into a relational database. The physiological waveforms, including 125 Hz signals recorded at bedside and corresponding vital signs, were stored in an open-source format. MIMIC-II data were also deidentified in order to remove protected health information. Any interested researcher can gain access to MIMIC-II free of charge after signing a data use agreement and completing human subjects training. MIMIC-II can support a wide variety of research studies, ranging from the development of clinical decision support algorithms to retrospective clinical studies. We anticipate that MIMIC-II will be an invaluable resource for intensive care research by stimulating fair comparisons among different studies.
-
Database on veterinary clinical research in homeopathy.
Clausen, Jürgen; Albrecht, Henning
2010-07-01
The aim of the present report is to provide an overview of the first database on clinical research in veterinary homeopathy. Detailed searches in the database 'Veterinary Clinical Research-Database in Homeopathy' (http://www.carstens-stiftung.de/clinresvet/index.php). The database contains about 200 entries of randomised clinical trials, non-randomised clinical trials, observational studies, drug provings, case reports and case series. Twenty-two clinical fields are covered and eight different groups of species are included. The database is free of charge and open to all interested veterinarians and researchers. The database enables researchers and veterinarians, sceptics and supporters to get a quick overview of the status of veterinary clinical research in homeopathy and alleviates the preparation of systematical reviews or may stimulate reproductions or even new studies. 2010 Elsevier Ltd. All rights reserved.
-
Sharma, Vishal K; Fraulin, Frankie Og; Harrop, A Robertson; McPhalen, Donald F
2011-01-01
Databases are useful tools in clinical settings. The authors review the benefits and challenges associated with the development and implementation of an efficient electronic database for the multidisciplinary Vascular Birthmark Clinic at the Alberta Children's Hospital, Calgary, Alberta. The content and structure of the database were designed using the technical expertise of a data analyst from the Calgary Health Region. Relevant clinical and demographic data fields were included with the goal of documenting ongoing care of individual patients, and facilitating future epidemiological studies of this patient population. After completion of this database, 10 challenges encountered during development were retrospectively identified. Practical solutions for these challenges are presented. THE CHALLENGES IDENTIFIED DURING THE DATABASE DEVELOPMENT PROCESS INCLUDED: identification of relevant data fields; balancing simplicity and user-friendliness with complexity and comprehensive data storage; database expertise versus clinical expertise; software platform selection; linkage of data from the previous spreadsheet to a new data management system; ethics approval for the development of the database and its utilization for research studies; ensuring privacy and limited access to the database; integration of digital photographs into the database; adoption of the database by support staff in the clinic; and maintaining up-to-date entries in the database. There are several challenges involved in the development of a useful and efficient clinical database. Awareness of these potential obstacles, in advance, may simplify the development of clinical databases by others in various surgical settings.
-
The prevalence and clinical characteristics of punding in Parkinson's disease.
Spencer, Ashley H; Rickards, Hugh; Fasano, Alfonso; Cavanna, Andrea E
2011-03-01
Punding (the display of stereotyped, repetitive behaviors) is a relatively recently discovered feature of Parkinson's disease (PD). Little is known about the prevalence and clinical characteristics of punding in PD. In this review, four large scientific databases were comprehensively searched for literature in relation to punding prevalence and clinical correlates in the context of PD. Prevalence was found to vary greatly (between 0.34 to 14%), although there were large disparities in study populations, assessment methods, and criteria. We observed an association between punding, dopaminergic medications, and impulse control disorder. Other characteristics, which may be more common among punders, include a higher severity of dyskinesia, younger age of disease onset, longer disease duration, and male gender. More research in large clinical datasets is required in many areas before conclusions are drawn. The pathophysiology behind the punding phenomenon is also poorly understood at present, rendering it difficult to develop targeted therapy. The current mainstay of treatment is the reduction in the dose of dopaminergic medications, the evidence for other suggested therapies being purely empirical.
-
Development and implementation of a psychotherapy tracking database in primary care.
Craner, Julia R; Sawchuk, Craig N; Mack, John D; LeRoy, Michelle A
2017-06-01
Although there is a rapid increase in the integration of behavioral health services in primary care, few studies have evaluated the effectiveness of these services in real-world clinical settings, in part due to the difficulty of translating traditional mental health research designs to this setting. Accordingly, innovative approaches are needed to fit the unique challenges of conducting research in primary care. The development and implementation of one such approach is described in this article. A continuously populating database for psychotherapy services was implemented across 5 primary care clinics in a large health system to assess several levels of patient care, including service utilization, symptomatic outcomes, and session-by-session use of psychotherapy principles by providers. Each phase of implementation revealed challenges, including clinician time, dissemination to clinics with different resources, and fidelity of data collection strategy across providers, as well as benefits, including the generation of useful data to inform clinical care, program development, and empirical research. The feasible and sustainable implementation of data collection for routine clinical practice in primary care has the potential to fuel the evidence base around integrated care. The current project describes the development of an innovative approach that, with further empirical study and refinement, could enable health care professionals and systems to understand their population and clinical process in a way that addresses essential gaps in the integrated care literature. (PsycINFO Database Record (c) 2017 APA, all rights reserved).
-
Lee, Ken Ka-Yin; Tang, Wai-Choi; Choi, Kup-Sze
2013-04-01
Clinical data are dynamic in nature, often arranged hierarchically and stored as free text and numbers. Effective management of clinical data and the transformation of the data into structured format for data analysis are therefore challenging issues in electronic health records development. Despite the popularity of relational databases, the scalability of the NoSQL database model and the document-centric data structure of XML databases appear to be promising features for effective clinical data management. In this paper, three database approaches--NoSQL, XML-enabled and native XML--are investigated to evaluate their suitability for structured clinical data. The database query performance is reported, together with our experience in the databases development. The results show that NoSQL database is the best choice for query speed, whereas XML databases are advantageous in terms of scalability, flexibility and extensibility, which are essential to cope with the characteristics of clinical data. While NoSQL and XML technologies are relatively new compared to the conventional relational database, both of them demonstrate potential to become a key database technology for clinical data management as the technology further advances. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
-
Value of shared preclinical safety studies - The eTOX database.
Briggs, Katharine; Barber, Chris; Cases, Montserrat; Marc, Philippe; Steger-Hartmann, Thomas
2015-01-01
A first analysis of a database of shared preclinical safety data for 1214 small molecule drugs and drug candidates extracted from 3970 reports donated by thirteen pharmaceutical companies for the eTOX project (www.etoxproject.eu) is presented. Species, duration of exposure and administration route data were analysed to assess if large enough subsets of homogenous data are available for building in silico predictive models. Prevalence of treatment related effects for the different types of findings recorded were analysed. The eTOX ontology was used to determine the most common treatment-related clinical chemistry and histopathology findings reported in the database. The data were then mined to evaluate sensitivity of established in vivo biomarkers for liver toxicity risk assessment. The value of the database to inform other drug development projects during early drug development is illustrated by a case study.
-
ECG-ViEW II, a freely accessible electrocardiogram database
Park, Man Young; Lee, Sukhoon; Jeon, Min Seok; Yoon, Dukyong; Park, Rae Woong
2017-01-01
The Electrocardiogram Vigilance with Electronic data Warehouse II (ECG-ViEW II) is a large, single-center database comprising numeric parameter data of the surface electrocardiograms of all patients who underwent testing from 1 June 1994 to 31 July 2013. The electrocardiographic data include the test date, clinical department, RR interval, PR interval, QRS duration, QT interval, QTc interval, P axis, QRS axis, and T axis. These data are connected with patient age, sex, ethnicity, comorbidities, age-adjusted Charlson comorbidity index, prescribed drugs, and electrolyte levels. This longitudinal observational database contains 979,273 electrocardiograms from 461,178 patients over a 19-year study period. This database can provide an opportunity to study electrocardiographic changes caused by medications, disease, or other demographic variables. ECG-ViEW II is freely available at http://www.ecgview.org. PMID:28437484
-
Should we search Chinese biomedical databases when performing systematic reviews?
Cohen, Jérémie F; Korevaar, Daniël A; Wang, Junfeng; Spijker, René; Bossuyt, Patrick M
2015-03-06
Chinese biomedical databases contain a large number of publications available to systematic reviewers, but it is unclear whether they are used for synthesizing the available evidence. We report a case of two systematic reviews on the accuracy of anti-cyclic citrullinated peptide for diagnosing rheumatoid arthritis. In one of these, the authors did not search Chinese databases; in the other, they did. We additionally assessed the extent to which Cochrane reviewers have searched Chinese databases in a systematic overview of the Cochrane Library (inception to 2014). The two diagnostic reviews included a total of 269 unique studies, but only 4 studies were included in both reviews. The first review included five studies published in the Chinese language (out of 151) while the second included 114 (out of 118). The summary accuracy estimates from the two reviews were comparable. Only 243 of the published 8,680 Cochrane reviews (less than 3%) searched one or more of the five major Chinese databases. These Chinese databases index about 2,500 journals, of which less than 6% are also indexed in MEDLINE. All 243 Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation; 118 (49%) addressed a topic in complementary or alternative medicine. Although searching Chinese databases may lead to the identification of a large amount of additional clinical evidence, Cochrane reviewers have rarely included them in their search strategy. We encourage future initiatives to evaluate more systematically the relevance of searching Chinese databases, as well as collaborative efforts to allow better incorporation of Chinese resources in systematic reviews.
-
Zampieri, Fernando Godinho; Soares, Márcio; Borges, Lunna Perdigão; Salluh, Jorge Ibrain Figueira; Ranzani, Otávio Tavares
2017-01-01
To describe the Epimed Monitor Database®, a Brazilian intensive care unit quality improvement database. We described the Epimed Monitor® Database, including its structure and core data. We presented aggregated informative data from intensive care unit admissions from 2010 to 2016 using descriptive statistics. We also described the expansion and growth of the database along with the geographical distribution of participating units in Brazil. The core data from the database includes demographic, administrative and physiological parameters, as well as specific report forms used to gather detailed data regarding the use of intensive care unit resources, infectious episodes, adverse events and checklists for adherence to best clinical practices. As of the end of 2016, 598 adult intensive care units in 318 hospitals totaling 8,160 intensive care unit beds were participating in the database. Most units were located at private hospitals in the southeastern region of the country. The number of yearly admissions rose during this period and included a predominance of medical admissions. The proportion of admissions due to cardiovascular disease declined, while admissions due to sepsis or infections became more common. Illness severity (Simplified Acute Physiology Score - SAPS 3 - 62 points), patient age (mean = 62 years) and hospital mortality (approximately 17%) remained reasonably stable during this time period. A large private database of critically ill patients is feasible and may provide relevant nationwide epidemiological data for quality improvement and benchmarking purposes among the participating intensive care units. This database is useful not only for administrative reasons but also for the improvement of daily care by facilitating the adoption of best practices and use for clinical research.
-
Miyoshi, Newton Shydeo Brandão; Pinheiro, Daniel Guariz; Silva, Wilson Araújo; Felipe, Joaquim Cezar
2013-06-06
The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. We have implemented an extension of Chado - the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different "omics" technologies with patient's clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans.
-
Amelogenin test: From forensics to quality control in clinical and biochemical genomics.
Francès, F; Portolés, O; González, J I; Coltell, O; Verdú, F; Castelló, A; Corella, D
2007-01-01
The increasing number of samples from the biomedical genetic studies and the number of centers participating in the same involves increasing risk of mistakes in the different sample handling stages. We have evaluated the usefulness of the amelogenin test for quality control in sample identification. Amelogenin test (frequently used in forensics) was undertaken on 1224 individuals participating in a biomedical study. Concordance between referred sex in the database and amelogenin test was estimated. Additional sex-error genetic detecting systems were developed. The overall concordance rate was 99.84% (1222/1224). Two samples showed a female amelogenin test outcome, being codified as males in the database. The first, after checking sex-specific biochemical and clinical profile data was found to be due to a codification error in the database. In the second, after checking the database, no apparent error was discovered because a correct male profile was found. False negatives in amelogenin male sex determination were discarded by additional tests, and feminine sex was confirmed. A sample labeling error was revealed after a new DNA extraction. The amelogenin test is a useful quality control tool for detecting sex-identification errors in large genomic studies, and can contribute to increase its validity.
-
Zhang, Zhongheng; Chen, Kun; Ni, Hongying
2015-01-01
Observational studies have linked hypocalcemia with adverse clinical outcome in critically ill patients. However, calcium supplementation has never been formally investigated for its beneficial effect in critically ill patients. To investigate whether calcium supplementation can improve 28-day survival in adult critically ill patients. Secondary analysis of a large clinical database consisting over 30,000 critical ill patients was performed. Multivariable analysis was performed to examine the independent association of calcium supplementation and 28-day morality. Furthermore, propensity score matching technique was employed to investigate the role of calcium supplementation in improving survival. none. Primary outcome was the 28-day mortality. 90-day mortality was used as secondary outcome. A total of 32,551 adult patients, including 28,062 survivors and 4489 non-survivors (28-day mortality rate: 13.8 %) were included. Calcium supplementation was independently associated with improved 28-day mortality after adjusting for confounding variables (hazard ratio: 0.51; 95 % CI 0.47-0.56). Propensity score matching was performed and the after-matching cohort showed well balanced covariates. The results showed that calcium supplementation was associated with improved 28- and 90-day mortality (p < 0.05 for both Log-rank test). In adult critically ill patients, calcium supplementation during their ICU stay improved 28-day survival. This finding supports the use of calcium supplementation in critically ill patients.
-
Nichols, A W
2008-11-01
To identify sports medicine-related clinical trial research articles in the PubMed MEDLINE database published between 1996 and 2005 and conduct a review and analysis of topics of research, experimental designs, journals of publication and the internationality of authorships. Sports medicine research is international in scope with improving study methodology and an evolution of topics. Structured review of articles identified in a search of a large electronic medical database. PubMed MEDLINE database. Sports medicine-related clinical research trials published between 1996 and 2005. Review and analysis of articles that meet inclusion criteria. Articles were examined for study topics, research methods, experimental subject characteristics, journal of publication, lead authors and journal countries of origin and language of publication. The search retrieved 414 articles, of which 379 (345 English language and 34 non-English language) met the inclusion criteria. The number of publications increased steadily during the study period. Randomised clinical trials were the most common study type and the "diagnosis, management and treatment of sports-related injuries and conditions" was the most popular study topic. The knee, ankle/foot and shoulder were the most frequent anatomical sites of study. Soccer players and runners were the favourite study subjects. The American Journal of Sports Medicine had the highest number of publications and shared the greatest international diversity of authorships with the British Journal of Sports Medicine. The USA, Australia, Germany and the UK produced a good number of the lead authorships. In all, 91% of articles and 88% of journals were published in English. Sports medicine-related research is internationally diverse, clinical trial publications are increasing and the sophistication of research design may be improving.
-
DEXTER: Disease-Expression Relation Extraction from Text.
Gupta, Samir; Dingerdissen, Hayley; Ross, Karen E; Hu, Yu; Wu, Cathy H; Mazumder, Raja; Vijay-Shanker, K
2018-01-01
Gene expression levels affect biological processes and play a key role in many diseases. Characterizing expression profiles is useful for clinical research, and diagnostics and prognostics of diseases. There are currently several high-quality databases that capture gene expression information, obtained mostly from large-scale studies, such as microarray and next-generation sequencing technologies, in the context of disease. The scientific literature is another rich source of information on gene expression-disease relationships that not only have been captured from large-scale studies but have also been observed in thousands of small-scale studies. Expression information obtained from literature through manual curation can extend expression databases. While many of the existing databases include information from literature, they are limited by the time-consuming nature of manual curation and have difficulty keeping up with the explosion of publications in the biomedical field. In this work, we describe an automated text-mining tool, Disease-Expression Relation Extraction from Text (DEXTER) to extract information from literature on gene and microRNA expression in the context of disease. One of the motivations in developing DEXTER was to extend the BioXpress database, a cancer-focused gene expression database that includes data derived from large-scale experiments and manual curation of publications. The literature-based portion of BioXpress lags behind significantly compared to expression information obtained from large-scale studies and can benefit from our text-mined results. We have conducted two different evaluations to measure the accuracy of our text-mining tool and achieved average F-scores of 88.51 and 81.81% for the two evaluations, respectively. Also, to demonstrate the ability to extract rich expression information in different disease-related scenarios, we used DEXTER to extract information on differential expression information for 2024 genes in lung cancer, 115 glycosyltransferases in 62 cancers and 826 microRNA in 171 cancers. All extractions using DEXTER are integrated in the literature-based portion of BioXpress.Database URL: http://biotm.cis.udel.edu/DEXTER.
-
Promise and Limitations of Big Data Research in Plastic Surgery.
Zhu, Victor Zhang; Tuggle, Charles Thompson; Au, Alexander Francis
2016-04-01
The use of "Big Data" in plastic surgery outcomes research has increased dramatically in the last 5 years. This article addresses some of the benefits and limitations of such research. This is a narrative review of large database studies in plastic surgery. There are several benefits to database research as compared with traditional forms of research, such as randomized controlled studies and cohort studies. These include the ease in patient recruitment, reduction in selection bias, and increased generalizability. As such, the types of outcomes research that are particularly suited for database studies include determination of geographic variations in practice, volume outcome analysis, evaluation of how sociodemographic factors affect access to health care, and trend analyses over time. The limitations of database research include data which are limited only to what was captured in the database, high power which can cause clinically insignificant differences to achieve statistical significance, and fishing which can lead to increased type I errors. The National Surgical Quality Improvement Project is an important general surgery database that may be useful for plastic surgeons because it is validated and has a large number of patients after over a decade of collecting data. The Tracking Operations and Outcomes for Plastic Surgeons Program is a newer database specific to plastic surgery. Databases are a powerful tool for plastic surgery outcomes research. It is critically important to understand their benefits and limitations when designing research projects or interpreting studies whose data have been drawn from them. For plastic surgeons, National Surgical Quality Improvement Project has a greater number of publications, but Tracking Operations and Outcomes for Plastic Surgeons Program is the most applicable database for plastic surgery research.
-
Fonseca, Carissa G; Backhaus, Michael; Bluemke, David A; Britten, Randall D; Chung, Jae Do; Cowan, Brett R; Dinov, Ivo D; Finn, J Paul; Hunter, Peter J; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Medrano-Gracia, Pau; Shivkumar, Kalyanam; Suinesiaputra, Avan; Tao, Wenchao; Young, Alistair A
2011-08-15
Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape and wall motion and characterize cardiac function among and within population groups. Three main open-source software components were developed: (i) a database with web-interface; (ii) a modeling client for 3D + time visualization and parametric description of shape and motion; and (iii) open data formats for semantic characterization of models and annotations. The database was implemented using a three-tier architecture utilizing MySQL, JBoss and Dcm4chee, in compliance with the DICOM standard to provide compatibility with existing clinical networks and devices. Parts of Dcm4chee were extended to access image specific attributes as search parameters. To date, approximately 3000 de-identified cardiac imaging examinations are available in the database. All software components developed by the CAP are open source and are freely available under the Mozilla Public License Version 1.1 (http://www.mozilla.org/MPL/MPL-1.1.txt). http://www.cardiacatlas.org a.young@auckland.ac.nz Supplementary data are available at Bioinformatics online.
-
Background: Electronic health records (EHRs) are now a ubiquitous component of the US healthcare system and are attractive for secondary data analysis as they contain detailed and longitudinal clinical records on potentially millions of individuals. However, due to their relative...
-
Administrative Databases in Orthopaedic Research: Pearls and Pitfalls of Big Data.
Patel, Alpesh A; Singh, Kern; Nunley, Ryan M; Minhas, Shobhit V
2016-03-01
The drive for evidence-based decision-making has highlighted the shortcomings of traditional orthopaedic literature. Although high-quality, prospective, randomized studies in surgery are the benchmark in orthopaedic literature, they are often limited by size, scope, cost, time, and ethical concerns and may not be generalizable to larger populations. Given these restrictions, there is a growing trend toward the use of large administrative databases to investigate orthopaedic outcomes. These datasets afford the opportunity to identify a large numbers of patients across a broad spectrum of comorbidities, providing information regarding disparities in care and outcomes, preoperative risk stratification parameters for perioperative morbidity and mortality, and national epidemiologic rates and trends. Although there is power in these databases in terms of their impact, potential problems include administrative data that are at risk of clerical inaccuracies, recording bias secondary to financial incentives, temporal changes in billing codes, a lack of numerous clinically relevant variables and orthopaedic-specific outcomes, and the absolute requirement of an experienced epidemiologist and/or statistician when evaluating results and controlling for confounders. Despite these drawbacks, administrative database studies are fundamental and powerful tools in assessing outcomes on a national scale and will likely be of substantial assistance in the future of orthopaedic research.
-
Clinical Databases for Chest Physicians.
Courtwright, Andrew M; Gabriel, Peter E
2018-04-01
A clinical database is a repository of patient medical and sociodemographic information focused on one or more specific health condition or exposure. Although clinical databases may be used for research purposes, their primary goal is to collect and track patient data for quality improvement, quality assurance, and/or actual clinical management. This article aims to provide an introduction and practical advice on the development of small-scale clinical databases for chest physicians and practice groups. Through example projects, we discuss the pros and cons of available technical platforms, including Microsoft Excel and Access, relational database management systems such as Oracle and PostgreSQL, and Research Electronic Data Capture. We consider approaches to deciding the base unit of data collection, creating consensus around variable definitions, and structuring routine clinical care to complement database aims. We conclude with an overview of regulatory and security considerations for clinical databases. Copyright © 2018 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.
-
Robinson, William P
2017-12-01
Ruptured abdominal aortic aneurysm is one of the most difficult clinical problems in surgical practice, with extraordinarily high morbidity and mortality. During the past 23 years, the literature has become replete with reports regarding ruptured endovascular aneurysm repair. A variety of study designs and databases have been utilized to compare ruptured endovascular aneurysm repair and open surgical repair for ruptured abdominal aortic aneurysm and studies of various designs from different databases have yielded vastly different conclusions. It therefore remains controversial whether ruptured endovascular aneurysm repair improves outcomes after ruptured abdominal aortic aneurysm in comparison to open surgical repair. The purpose of this article is to review the best available evidence comparing ruptured endovascular aneurysm repair and open surgical repair of ruptured abdominal aortic aneurysm, including single institution and multi-institutional retrospective observational studies, large national population-based studies, large national registries of prospectively collected data, and randomized controlled clinical trials. This article will analyze the study designs and databases utilized with their attendant strengths and weaknesses to understand the sometimes vastly different conclusions the studies have reached. This article will attempt to integrate the data to distill some of the lessons that have been learned regarding ruptured endovascular aneurysm repair and identify ongoing needs in this field. Copyright © 2017 Elsevier Inc. All rights reserved.
-
2013-01-01
Background Large-scale pharmaco-epidemiological studies of Chinese herbal medicine (CHM) for treatment of urticaria are few, even though clinical trials showed some CHM are effective. The purpose of this study was to explore the frequencies and patterns of CHM prescriptions for urticaria by analysing the population-based CHM database in Taiwan. Methods This study was linked to and processed through the complete traditional CHM database of the National Health Insurance Research Database in Taiwan during 2009. We calculated the frequencies and patterns of CHM prescriptions used for treatment of urticaria, of which the diagnosis was defined as the single ICD-9 Code of 708. Frequent itemset mining, as applied to data mining, was used to analyse co-prescription of CHM for patients with urticaria. Results There were 37,386 subjects who visited traditional Chinese Medicine clinics for urticaria in Taiwan during 2009 and received a total of 95,765 CHM prescriptions. Subjects between 18 and 35 years of age comprised the largest number of those treated (32.76%). In addition, women used CHM for urticaria more frequently than men (female:male = 1.94:1). There was an average of 5.54 items prescribed in the form of either individual Chinese herbs or a formula in a single CHM prescription for urticaria. Bai-Xian-Pi (Dictamnus dasycarpus Turcz) was the most commonly prescribed single Chinese herb while Xiao-Feng San was the most commonly prescribed Chinese herbal formula. The most commonly prescribed CHM drug combination was Xiao-Feng San plus Bai-Xian-Pi while the most commonly prescribed triple drug combination was Xiao-Feng San, Bai-Xian-Pi, and Di-Fu Zi (Kochia scoparia). Conclusions In view of the popularity of CHM such as Xiao-Feng San prescribed for the wind-heat pattern of urticaria in this study, a large-scale, randomized clinical trial is warranted to research their efficacy and safety. PMID:23947955
-
Chien, Pei-Shan; Tseng, Yu-Fang; Hsu, Yao-Chin; Lai, Yu-Kai; Weng, Shih-Feng
2013-08-15
Large-scale pharmaco-epidemiological studies of Chinese herbal medicine (CHM) for treatment of urticaria are few, even though clinical trials showed some CHM are effective. The purpose of this study was to explore the frequencies and patterns of CHM prescriptions for urticaria by analysing the population-based CHM database in Taiwan. This study was linked to and processed through the complete traditional CHM database of the National Health Insurance Research Database in Taiwan during 2009. We calculated the frequencies and patterns of CHM prescriptions used for treatment of urticaria, of which the diagnosis was defined as the single ICD-9 Code of 708. Frequent itemset mining, as applied to data mining, was used to analyse co-prescription of CHM for patients with urticaria. There were 37,386 subjects who visited traditional Chinese Medicine clinics for urticaria in Taiwan during 2009 and received a total of 95,765 CHM prescriptions. Subjects between 18 and 35 years of age comprised the largest number of those treated (32.76%). In addition, women used CHM for urticaria more frequently than men (female:male = 1.94:1). There was an average of 5.54 items prescribed in the form of either individual Chinese herbs or a formula in a single CHM prescription for urticaria. Bai-Xian-Pi (Dictamnus dasycarpus Turcz) was the most commonly prescribed single Chinese herb while Xiao-Feng San was the most commonly prescribed Chinese herbal formula. The most commonly prescribed CHM drug combination was Xiao-Feng San plus Bai-Xian-Pi while the most commonly prescribed triple drug combination was Xiao-Feng San, Bai-Xian-Pi, and Di-Fu Zi (Kochia scoparia). In view of the popularity of CHM such as Xiao-Feng San prescribed for the wind-heat pattern of urticaria in this study, a large-scale, randomized clinical trial is warranted to research their efficacy and safety.
-
Standards for Clinical Grade Genomic Databases.
Yohe, Sophia L; Carter, Alexis B; Pfeifer, John D; Crawford, James M; Cushman-Vokoun, Allison; Caughron, Samuel; Leonard, Debra G B
2015-11-01
Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.
-
2013-01-01
Background A large-scale, highly accurate, machine-understandable drug-disease treatment relationship knowledge base is important for computational approaches to drug repurposing. The large body of published biomedical research articles and clinical case reports available on MEDLINE is a rich source of FDA-approved drug-disease indication as well as drug-repurposing knowledge that is crucial for applying FDA-approved drugs for new diseases. However, much of this information is buried in free text and not captured in any existing databases. The goal of this study is to extract a large number of accurate drug-disease treatment pairs from published literature. Results In this study, we developed a simple but highly accurate pattern-learning approach to extract treatment-specific drug-disease pairs from 20 million biomedical abstracts available on MEDLINE. We extracted a total of 34,305 unique drug-disease treatment pairs, the majority of which are not included in existing structured databases. Our algorithm achieved a precision of 0.904 and a recall of 0.131 in extracting all pairs, and a precision of 0.904 and a recall of 0.842 in extracting frequent pairs. In addition, we have shown that the extracted pairs strongly correlate with both drug target genes and therapeutic classes, therefore may have high potential in drug discovery. Conclusions We demonstrated that our simple pattern-learning relationship extraction algorithm is able to accurately extract many drug-disease pairs from the free text of biomedical literature that are not captured in structured databases. The large-scale, accurate, machine-understandable drug-disease treatment knowledge base that is resultant of our study, in combination with pairs from structured databases, will have high potential in computational drug repurposing tasks. PMID:23742147
-
WE-F-BRB-01: The Power of Ontologies and Standardized Terminologies for Capturing Clinical Knowledge
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gabriel, P.
2015-06-15
Advancements in informatics in radiotherapy are opening up opportunities to improve our ability to assess treatment plans. Models on individualizing patient dose constraints from prior patient data and shape relationships have been extensively researched and are now making their way into commercial products. New developments in knowledge based treatment planning involve understanding the impact of the radiation dosimetry on the patient. Akin to radiobiology models that have driven intensity modulated radiotherapy optimization, toxicity and outcome predictions based on treatment plans and prior patient experiences may be the next step in knowledge based planning. In order to realize these predictions, itmore » is necessary to understand how the clinical information can be captured, structured and organized with ontologies and databases designed for recall. Large databases containing radiation dosimetry and outcomes present the opportunity to evaluate treatment plans against predictions of toxicity and disease response. Such evaluations can be based on dose volume histogram or even the full 3-dimensional dose distribution and its relation to the critical anatomy. This session will provide an understanding of ontologies and standard terminologies used to capture clinical knowledge into structured databases; How data can be organized and accessed to utilize the knowledge in planning; and examples of research and clinical efforts to incorporate that clinical knowledge into planning for improved care for our patients. Learning Objectives: Understand the role of standard terminologies, ontologies and data organization in oncology Understand methods to capture clinical toxicity and outcomes in a clinical setting Understand opportunities to learn from clinical data and its application to treatment planning Todd McNutt receives funding from Philips, Elekta and Toshiba for some of the work presented.« less
-
de Carvalho, Elias César Araujo; Batilana, Adelia Portero; Simkins, Julie; Martins, Henrique; Shah, Jatin; Rajgor, Dimple; Shah, Anand; Rockart, Scott; Pietrobon, Ricardo
2010-02-19
Sharing of epidemiological and clinical data sets among researchers is poor at best, in detriment of science and community at large. The purpose of this paper is therefore to (1) describe a novel Web application designed to share information on study data sets focusing on epidemiological clinical research in a collaborative environment and (2) create a policy model placing this collaborative environment into the current scientific social context. The Database of Databases application was developed based on feedback from epidemiologists and clinical researchers requiring a Web-based platform that would allow for sharing of information about epidemiological and clinical study data sets in a collaborative environment. This platform should ensure that researchers can modify the information. A Model-based predictions of number of publications and funding resulting from combinations of different policy implementation strategies (for metadata and data sharing) were generated using System Dynamics modeling. The application allows researchers to easily upload information about clinical study data sets, which is searchable and modifiable by other users in a wiki environment. All modifications are filtered by the database principal investigator in order to maintain quality control. The application has been extensively tested and currently contains 130 clinical study data sets from the United States, Australia, China and Singapore. Model results indicated that any policy implementation would be better than the current strategy, that metadata sharing is better than data-sharing, and that combined policies achieve the best results in terms of publications. Based on our empirical observations and resulting model, the social network environment surrounding the application can assist epidemiologists and clinical researchers contribute and search for metadata in a collaborative environment, thus potentially facilitating collaboration efforts among research communities distributed around the globe.
-
De-identifying an EHR database - anonymity, correctness and readability of the medical record.
Pantazos, Kostas; Lauesen, Soren; Lippert, Soren
2011-01-01
Electronic health records (EHR) contain a large amount of structured data and free text. Exploring and sharing clinical data can improve healthcare and facilitate the development of medical software. However, revealing confidential information is against ethical principles and laws. We de-identified a Danish EHR database with 437,164 patients. The goal was to generate a version with real medical records, but related to artificial persons. We developed a de-identification algorithm that uses lists of named entities, simple language analysis, and special rules. Our algorithm consists of 3 steps: collect lists of identifiers from the database and external resources, define a replacement for each identifier, and replace identifiers in structured data and free text. Some patient records could not be safely de-identified, so the de-identified database has 323,122 patient records with an acceptable degree of anonymity, readability and correctness (F-measure of 95%). The algorithm has to be adjusted for each culture, language and database.
-
Challenges in evaluating cancer as a clinical outcome in postapproval studies of drug safety
Pinheiro, Simone P.; Rivera, Donna R.; Graham, David J.; Freedman, Andrew N.; Major, Jacqueline M.; Penberthy, Lynne; Levenson, Mark; Bradley, Marie C.; Wong, Hui-Lee; Ouellet-Hellstrom, Rita
2017-01-01
Pharmaceuticals approved in the United States are largely not known human carcinogens. However, cancer signals associated with pharmaceuticals may be hypothesized or arise after product approval. There are many study designs that can be used to evaluate cancer as an outcome in the postapproval setting. Because prospective systematic collection of cancer outcomes from a large number of individuals may be lengthy, expensive, and challenging, leveraging data from large existing databases are an integral approach. Such studies have the capability to evaluate the clinical experience of a large number of individuals, yet there are unique methodological challenges involved in their use to evaluate cancer outcomes. To discuss methodological challenges and potential solutions, the Food and Drug Administration and the National Cancer Institute convened a two-day public meeting in 2014. This commentary summarizes the most salient issues discussed at the meeting. PMID:27663208
-
Challenges in evaluating cancer as a clinical outcome in postapproval studies of drug safety.
Pinheiro, Simone P; Rivera, Donna R; Graham, David J; Freedman, Andrew N; Major, Jacqueline M; Penberthy, Lynne; Levenson, Mark; Bradley, Marie C; Wong, Hui-Lee; Ouellet-Hellstrom, Rita
2016-11-01
Pharmaceuticals approved in the United States are largely not known human carcinogens. However, cancer signals associated with pharmaceuticals may be hypothesized or arise after product approval. There are many study designs that can be used to evaluate cancer as an outcome in the postapproval setting. Because prospective systematic collection of cancer outcomes from a large number of individuals may be lengthy, expensive, and challenging, leveraging data from large existing databases are an integral approach. Such studies have the capability to evaluate the clinical experience of a large number of individuals, yet there are unique methodological challenges involved in their use to evaluate cancer outcomes. To discuss methodological challenges and potential solutions, the Food and Drug Administration and the National Cancer Institute convened a two-day public meeting in 2014. This commentary summarizes the most salient issues discussed at the meeting. Published by Elsevier Inc.
-
[The future of clinical laboratory database management system].
Kambe, M; Imidy, D; Matsubara, A; Sugimoto, Y
1999-09-01
To assess the present status of the clinical laboratory database management system, the difference between the Clinical Laboratory Information System and Clinical Laboratory System was explained in this study. Although three kinds of database management systems (DBMS) were shown including the relational model, tree model and network model, the relational model was found to be the best DBMS for the clinical laboratory database based on our experience and developments of some clinical laboratory expert systems. As a future clinical laboratory database management system, the IC card system connected to an automatic chemical analyzer was proposed for personal health data management and a microscope/video system was proposed for dynamic data management of leukocytes or bacteria.
-
Endrikat, J; Schwenke, C; Prince, M R
2015-07-01
To assess the safety of gadobutrol administration in elderly patients (≥65 years) by comparing the incidence of adverse drug reactions (ADRs) following gadobutrol-enhanced magnetic resonance imaging (MRI) procedures in elderly patients with that in adults aged 18-64 years. Safety data on gadobutrol administration from clinical trials, post-marketing surveillance (PMS) studies, and pharmacovigilance reports were collected in three databases. In each dataset, absolute and relative frequencies of ADRs between age groups were analysed, along with odds ratios and 95% confidence intervals. Logistic regression was used to identify significant influencing factors on ADRs in the PMS and pharmacovigilance data. Rates of reported ADRs were lower in elderly patients versus adults aged <65 years due to a reduced incidence of non-serious ADRs; this was statistically significant for the clinical trials and pharmacovigilance populations, with a trend in the PMS database. Serious ADRs occurred infrequently in the clinical trials and PMS populations (too low for statistical comparison), and pharmacovigilance data demonstrated a low incidence (<0.005%) in both age groups. This evaluation involving three large databases demonstrated no greater incidence of ADRs following gadobutrol-enhanced MRI in elderly patients (≥65 years) compared with younger adults, with gadobutrol having a favourable safety profile in both age groups. Copyright © 2015 The Royal College of Radiologists. All rights reserved.
-
Programmed database system at the Chang Gung Craniofacial Center: part II--digitizing photographs.
Chuang, Shiow-Shuh; Hung, Kai-Fong; de Villa, Glenda H; Chen, Philip K T; Lo, Lun-Jou; Chang, Sophia C N; Yu, Chung-Chih; Chen, Yu-Ray
2003-07-01
The archival tools used for digital images in advertising are not to fulfill the clinic requisition and are just beginning to develop. The storage of a large amount of conventional photographic slides needs a lot of space and special conditions. In spite of special precautions, degradation of the slides still occurs. The most common degradation is the appearance of fungus flecks. With the recent advances in digital technology, it is now possible to store voluminous numbers of photographs on a computer hard drive and keep them for a long time. A self-programmed interface has been developed to integrate database and image browser system that can build and locate needed files archive in a matter of seconds with the click of a button. This system requires hardware and software were market provided. There are 25,200 patients recorded in the database that involve 24,331 procedures. In the image files, there are 6,384 patients with 88,366 digital pictures files. From 1999 through 2002, NT400,000 dollars have been saved using the new system. Photographs can be managed with the integrating Database and Browse software for database archiving. This allows labeling of the individual photographs with demographic information and browsing. Digitized images are not only more efficient and economical than the conventional slide images, but they also facilitate clinical studies.
-
Kamitsuji, Shigeo; Matsuda, Takashi; Nishimura, Koichi; Endo, Seiko; Wada, Chisa; Watanabe, Kenji; Hasegawa, Koichi; Hishigaki, Haretsugu; Masuda, Masatoshi; Kuwahara, Yusuke; Tsuritani, Katsuki; Sugiura, Kenkichi; Kubota, Tomoko; Miyoshi, Shinji; Okada, Kinya; Nakazono, Kazuyuki; Sugaya, Yuki; Yang, Woosung; Sawamoto, Taiji; Uchida, Wataru; Shinagawa, Akira; Fujiwara, Tsutomu; Yamada, Hisaharu; Suematsu, Koji; Tsutsui, Naohisa; Kamatani, Naoyuki; Liou, Shyh-Yuh
2015-06-01
Japan Pharmacogenomics Data Science Consortium (JPDSC) has assembled a database for conducting pharmacogenomics (PGx) studies in Japanese subjects. The database contains the genotypes of 2.5 million single-nucleotide polymorphisms (SNPs) and 5 human leukocyte antigen loci from 2994 Japanese healthy volunteers, as well as 121 kinds of clinical information, including self-reports, physiological data, hematological data and biochemical data. In this article, the reliability of our data was evaluated by principal component analysis (PCA) and association analysis for hematological and biochemical traits by using genome-wide SNP data. PCA of the SNPs showed that all the samples were collected from the Japanese population and that the samples were separated into two major clusters by birthplace, Okinawa and other than Okinawa, as had been previously reported. Among 87 SNPs that have been reported to be associated with 18 hematological and biochemical traits in genome-wide association studies (GWAS), the associations of 56 SNPs were replicated using our data base. Statistical power simulations showed that the sample size of the JPDSC control database is large enough to detect genetic markers having a relatively strong association even when the case sample size is small. The JPDSC database will be useful as control data for conducting PGx studies to explore genetic markers to improve the safety and efficacy of drugs either during clinical development or in post-marketing.
-
Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials
Federer, Callie; Yoo, Minjae
2016-01-01
Abstract Drug adverse events (AEs) are a major health threat to patients seeking medical treatment and a significant barrier in drug discovery and development. AEs are now required to be submitted during clinical trials and can be extracted from ClinicalTrials.gov (https://clinicaltrials.gov/), a database of clinical studies around the world. By extracting drug and AE information from ClinicalTrials.gov and structuring it into a database, drug-AEs could be established for future drug development and repositioning. To our knowledge, current AE databases contain mainly U.S. Food and Drug Administration (FDA)-approved drugs. However, our database contains both FDA-approved and experimental compounds extracted from ClinicalTrials.gov. Our database contains 8,161 clinical trials of 3,102,675 patients and 713,103 reported AEs. We extracted the information from ClinicalTrials.gov using a set of python scripts, and then used regular expressions and a drug dictionary to process and structure relevant information into a relational database. We performed data mining and pattern analysis of drug-AEs in our database. Our database can serve as a tool to assist researchers to discover drug-AE relationships for developing, repositioning, and repurposing drugs. PMID:27631620
-
Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials.
Federer, Callie; Yoo, Minjae; Tan, Aik Choon
2016-12-01
Drug adverse events (AEs) are a major health threat to patients seeking medical treatment and a significant barrier in drug discovery and development. AEs are now required to be submitted during clinical trials and can be extracted from ClinicalTrials.gov ( https://clinicaltrials.gov/ ), a database of clinical studies around the world. By extracting drug and AE information from ClinicalTrials.gov and structuring it into a database, drug-AEs could be established for future drug development and repositioning. To our knowledge, current AE databases contain mainly U.S. Food and Drug Administration (FDA)-approved drugs. However, our database contains both FDA-approved and experimental compounds extracted from ClinicalTrials.gov . Our database contains 8,161 clinical trials of 3,102,675 patients and 713,103 reported AEs. We extracted the information from ClinicalTrials.gov using a set of python scripts, and then used regular expressions and a drug dictionary to process and structure relevant information into a relational database. We performed data mining and pattern analysis of drug-AEs in our database. Our database can serve as a tool to assist researchers to discover drug-AE relationships for developing, repositioning, and repurposing drugs.
-
[Advances in the research of application of artificial intelligence in burn field].
Li, H H; Bao, Z X; Liu, X B; Zhu, S H
2018-04-20
Artificial intelligence has been able to automatically learn and judge large-scale data to some extent. Based on database of a large amount of burn data and in-depth learning, artificial intelligence can assist burn surgeons to evaluate burn surface, diagnose burn depth, guide fluid supply during shock stage, and predict prognosis, with high accuracy. With the development of technology, artificial intelligence can provide more accurate information for burn surgeons to make clinical diagnosis and treatment strategies.
-
Prototype Packaged Databases and Software in Health
Gardenier, Turkan K.
1980-01-01
This paper describes the recent demand for packaged databases and software for health applications in light of developments in mini-and micro-computer technology. Specific features for defining prospective user groups are discussed; criticisms generated for large-scale epidemiological data use as a means of replacing clinical trials and associated controls are posed to the reader. The available collaborative efforts for access and analysis of jointly structured health data are stressed, with recommendations for new analytical techniques specifically geared to monitoring data such as the CTSS (Cumulative Transitional State Score) generated for tacking ongoing patient status over time in clinical trials. Examples of graphic display are given from the Domestic Information Display System (DIDS) which is a collaborative multi-agency effort to computerize and make accessible user-specified U.S. and local maps relating to health, environment, socio-economic and energy data.
-
Model-based query language for analyzing clinical processes.
Barzdins, Janis; Barzdins, Juris; Rencis, Edgars; Sostaks, Agris
2013-01-01
Nowadays large databases of clinical process data exist in hospitals. However, these data are rarely used in full scope. In order to perform queries on hospital processes, one must either choose from the predefined queries or develop queries using MS Excel-type software system, which is not always a trivial task. In this paper we propose a new query language for analyzing clinical processes that is easily perceptible also by non-IT professionals. We develop this language based on a process modeling language which is also described in this paper. Prototypes of both languages have already been verified using real examples from hospitals.
-
Federal Register 2010, 2011, 2012, 2013, 2014
2010-01-29
...; Comment Request Clinical Trials Reporting Program (CTRP) Database (NCI) Summary: Under the provisions of... Collection: Title: Clinical Trials Reporting Program (CTRP) Database. Type of Information Collection Request... Program (CTRP) Database, to serve as a single, definitive source of information about all NCI-supported...
-
Electronic data collection for clinical trials using tablet and handheld PCs
NASA Astrophysics Data System (ADS)
Alaoui, Adil; Vo, Minh; Patel, Nikunj; McCall, Keith; Lindisch, David; Watson, Vance; Cleary, Kevin
2005-04-01
This paper describes a system that uses electronic forms to collect patient and procedure data for clinical trials. During clinical trials, patients are typically required to provide background information such as demographics and medical history, as well as review and complete any consent forms. Physicians or their assistants then usually have additional forms for recording technical data from the procedure and for gathering follow-up information from patients after completion of the procedure. This approach can lead to substantial amounts of paperwork to collect and manage over the course of a clinical trial with a large patient base. By using e-forms instead, data can be transmitted to a single, centralized database, reducing the problem of managing paper forms. Additionally, the system can provide a means for relaying information from the database to the physician on his/her portable wireless device, such as to alert the physician when a patient has completed the pre-procedure forms and is ready to begin the procedure. This feature could improve the workflow in busy clinical practices. In the future, the system could be expanded so physicians could use their portable wireless device to pull up entire hospital records and view other pre-procedure data and patient images.
-
Dietzel, Matthias; Baltzer, Pascal A T; Dietzel, Andreas; Zoubi, Ramy; Gröschel, Tobias; Burmeister, Hartmut P; Bogdan, Martin; Kaiser, Werner A
2012-07-01
Differential diagnosis of lesions in MR-Mammography (MRM) remains a complex task. The aim of this MRM study was to design and to test robustness of Artificial Neural Network architectures to predict malignancy using a large clinical database. For this IRB-approved investigation standardized protocols and study design were applied (T1w-FLASH; 0.1 mmol/kgBW Gd-DTPA; T2w-TSE; histological verification after MRM). All lesions were evaluated by two experienced (>500 MRM) radiologists in consensus. In every lesion, 18 previously published descriptors were assessed and documented in the database. An Artificial Neural Network (ANN) was developed to process this database (The-MathWorks/Inc., feed-forward-architecture/resilient back-propagation-algorithm). All 18 descriptors were set as input variables, whereas histological results (malignant vs. benign) was defined as classification variable. Initially, the ANN was optimized in terms of "Training Epochs" (TE), "Hidden Layers" (HL), "Learning Rate" (LR) and "Neurons" (N). Robustness of the ANN was addressed by repeated evaluation cycles (n: 9) with receiver operating characteristics (ROC) analysis of the results applying 4-fold Cross Validation. The best network architecture was identified comparing the corresponding Area under the ROC curve (AUC). Histopathology revealed 436 benign and 648 malignant lesions. Enhancing the level of complexity could not increase diagnostic accuracy of the network (P: n.s.). The optimized ANN architecture (TE: 20, HL: 1, N: 5, LR: 1.2) was accurate (mean-AUC 0.888; P: <0.001) and robust (CI: 0.885-0.892; range: 0.880-0.898). The optimized neural network showed robust performance and high diagnostic accuracy for prediction of malignancy on unknown data. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.
-
Accuracy of administrative data for identification of patients with infective endocarditis.
Tan, Charlie; Hansen, Mark; Cohen, Gideon; Boyle, Karl; Daneman, Nick; Adhikari, Neill K J
2016-12-01
Infective endocarditis is associated with high morbidity and mortality rates that have plateaued over recent decades. Research to improve outcomes for these patients is limited by the rarity of this condition. Therefore, we sought to validate administrative database codes for the diagnosis of infective endocarditis. We conducted a retrospective validation study of International Classification of Diseases (ICD-10-CM) codes for infective endocarditis against clinical Duke criteria (definite and probable) at a large acute care hospital between October 1, 2013 and June 30, 2015. To identify potential cases missed by ICD-10-CM codes, we also screened the hospital's valvular heart surgery database and the microbiology laboratory database (the latter for patients with bacteremia due to organisms commonly causing endocarditis). Using definite Duke criteria or probable criteria with clinical suspicion as the reference standard, the ICD-10-CM codes had a sensitivity (SN) of 0.90 (95% confidence interval (CI), 0.81-0.95), specificity (SP) of 1 (95% CI, 1-1), positive predictive value (PPV) of 0.78 (95% CI, 0.68-0.85) and negative predictive value (NPV) of 1 (95% CI, 1-1). Restricting the case definition to definite Duke criteria resulted in an increase in SN to 0.95 (95% CI, 0.86-0.99) and a decrease in PPV to 0.6 (95% CI, 0.49-0.69), with no change in specificity. ICD-10-CM codes can accurately identify patients with infective endocarditis, and so administrative databases offer a potential means to study this infection over large jurisdictions, and thereby improve the prediction, diagnosis, treatment and prevention of this rare but serious infection. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
-
WE-F-BRB-00: New Developments in Knowledge-Based Treatment Planning and Automation
DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
2015-06-15
Advancements in informatics in radiotherapy are opening up opportunities to improve our ability to assess treatment plans. Models on individualizing patient dose constraints from prior patient data and shape relationships have been extensively researched and are now making their way into commercial products. New developments in knowledge based treatment planning involve understanding the impact of the radiation dosimetry on the patient. Akin to radiobiology models that have driven intensity modulated radiotherapy optimization, toxicity and outcome predictions based on treatment plans and prior patient experiences may be the next step in knowledge based planning. In order to realize these predictions, itmore » is necessary to understand how the clinical information can be captured, structured and organized with ontologies and databases designed for recall. Large databases containing radiation dosimetry and outcomes present the opportunity to evaluate treatment plans against predictions of toxicity and disease response. Such evaluations can be based on dose volume histogram or even the full 3-dimensional dose distribution and its relation to the critical anatomy. This session will provide an understanding of ontologies and standard terminologies used to capture clinical knowledge into structured databases; How data can be organized and accessed to utilize the knowledge in planning; and examples of research and clinical efforts to incorporate that clinical knowledge into planning for improved care for our patients. Learning Objectives: Understand the role of standard terminologies, ontologies and data organization in oncology Understand methods to capture clinical toxicity and outcomes in a clinical setting Understand opportunities to learn from clinical data and its application to treatment planning Todd McNutt receives funding from Philips, Elekta and Toshiba for some of the work presented.« less
-
WE-F-BRB-02: Setting the Stage for Incorporation of Toxicity Measures in Treatment Plan Assessments
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mayo, C.
2015-06-15
Advancements in informatics in radiotherapy are opening up opportunities to improve our ability to assess treatment plans. Models on individualizing patient dose constraints from prior patient data and shape relationships have been extensively researched and are now making their way into commercial products. New developments in knowledge based treatment planning involve understanding the impact of the radiation dosimetry on the patient. Akin to radiobiology models that have driven intensity modulated radiotherapy optimization, toxicity and outcome predictions based on treatment plans and prior patient experiences may be the next step in knowledge based planning. In order to realize these predictions, itmore » is necessary to understand how the clinical information can be captured, structured and organized with ontologies and databases designed for recall. Large databases containing radiation dosimetry and outcomes present the opportunity to evaluate treatment plans against predictions of toxicity and disease response. Such evaluations can be based on dose volume histogram or even the full 3-dimensional dose distribution and its relation to the critical anatomy. This session will provide an understanding of ontologies and standard terminologies used to capture clinical knowledge into structured databases; How data can be organized and accessed to utilize the knowledge in planning; and examples of research and clinical efforts to incorporate that clinical knowledge into planning for improved care for our patients. Learning Objectives: Understand the role of standard terminologies, ontologies and data organization in oncology Understand methods to capture clinical toxicity and outcomes in a clinical setting Understand opportunities to learn from clinical data and its application to treatment planning Todd McNutt receives funding from Philips, Elekta and Toshiba for some of the work presented.« less
-
DOE Office of Scientific and Technical Information (OSTI.GOV)
McNutt, T.
Advancements in informatics in radiotherapy are opening up opportunities to improve our ability to assess treatment plans. Models on individualizing patient dose constraints from prior patient data and shape relationships have been extensively researched and are now making their way into commercial products. New developments in knowledge based treatment planning involve understanding the impact of the radiation dosimetry on the patient. Akin to radiobiology models that have driven intensity modulated radiotherapy optimization, toxicity and outcome predictions based on treatment plans and prior patient experiences may be the next step in knowledge based planning. In order to realize these predictions, itmore » is necessary to understand how the clinical information can be captured, structured and organized with ontologies and databases designed for recall. Large databases containing radiation dosimetry and outcomes present the opportunity to evaluate treatment plans against predictions of toxicity and disease response. Such evaluations can be based on dose volume histogram or even the full 3-dimensional dose distribution and its relation to the critical anatomy. This session will provide an understanding of ontologies and standard terminologies used to capture clinical knowledge into structured databases; How data can be organized and accessed to utilize the knowledge in planning; and examples of research and clinical efforts to incorporate that clinical knowledge into planning for improved care for our patients. Learning Objectives: Understand the role of standard terminologies, ontologies and data organization in oncology Understand methods to capture clinical toxicity and outcomes in a clinical setting Understand opportunities to learn from clinical data and its application to treatment planning Todd McNutt receives funding from Philips, Elekta and Toshiba for some of the work presented.« less
-
Farrell, L J; Lo, R; Wanford, J J; Jenkins, A; Maxwell, A; Piddock, L J V
2018-06-11
The current state of antibiotic discovery, research and development is insufficient to respond to the need for new treatments for drug-resistant bacterial infections. The process has changed over the last decade, with most new agents that are in Phases 1-3, or recently approved, having been discovered in small- and medium-sized enterprises or academia. These agents have then been licensed or sold to large companies for further development with the goal of taking them to market. However, early drug discovery and development, including the possibility of developing previously discontinued agents, would benefit from a database of antibacterial compounds for scrutiny by the developers. This article describes the first free, open-access searchable database of antibacterial compounds, including discontinued agents, drugs under pre-clinical development and those in clinical trials: AntibioticDB (AntibioticDB.com). Data were obtained from publicly available sources. This article summarizes the compounds and drugs in AntibioticDB, including their drug class, mode of action, development status and propensity to select drug-resistant bacteria. AntibioticDB includes compounds currently in pre-clinical development and 834 that have been discontinued and that reached varying stages of development. These may serve as starting points for future research and development.
-
CYP21A2 mutation update: Comprehensive analysis of databases and published genetic variants.
Simonetti, Leandro; Bruque, Carlos D; Fernández, Cecilia S; Benavides-Mori, Belén; Delea, Marisol; Kolomenski, Jorge E; Espeche, Lucía D; Buzzalino, Noemí D; Nadra, Alejandro D; Dain, Liliana
2018-01-01
Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders of adrenal steroidogenesis. Disorders in steroid 21-hydroxylation account for over 95% of patients with CAH. Clinically, the 21-hydroxylase deficiency has been classified in a broad spectrum of clinical forms, ranging from severe or classical, to mild late onset or non-classical. Known allelic variants in the disease causing CYP21A2 gene are spread among different sources. Until recently, most variants reported have been identified in the clinical setting, which presumably bias described variants to pathogenic ones, as those found in the CYPAlleles database. Nevertheless, a large number of variants are being described in massive genome projects, many of which are found in dbSNP, but lack functional implications and/or their phenotypic effect. In this work, we gathered a total of 1,340 GVs in the CYP21A2 gene, from which 899 variants were unique and 230 have an effect on human health, and compiled all this information in an integrated database. We also connected CYP21A2 sequence information to phenotypic effects for all available mutations, including double mutants in cis. Data compiled in the present work could help physicians in the genetic counseling of families affected with 21-hydroxylase deficiency. © 2017 Wiley Periodicals, Inc.
-
Schweizer, Anja; Dejager, Sylvie; Foley, James E; Kothny, Wolfgang
2011-01-01
Aim: Analyzing safety aspects of a drug from individual studies can lead to difficult-to-interpret results. The aim of this paper is therefore to assess the general safety and tolerability, including incidences of the most common adverse events (AEs), of vildagliptin based on a large pooled database of Phase II and III clinical trials. Methods: Safety data were pooled from 38 studies of ≥12 to ≥104 weeks’ duration. AE profiles of vildagliptin (50 mg bid; N = 6116) were evaluated relative to a pool of comparators (placebo and active comparators; N = 6210). Absolute incidence rates were calculated for all AEs, serious AEs (SAEs), discontinuations due to AEs, and deaths. Results: Overall AEs, SAEs, discontinuations due to AEs, and deaths were all reported with a similar frequency in patients receiving vildagliptin (69.1%, 8.9%, 5.7%, and 0.4%, respectively) and patients receiving comparators (69.0%, 9.0%, 6.4%, and 0.4%, respectively), whereas drug-related AEs were seen with a lower frequency in vildagliptin-treated patients (15.7% vs 21.7% with comparators). The incidences of the most commonly reported specific AEs were also similar between vildagliptin and comparators, except for increased incidences of hypoglycemia, tremor, and hyperhidrosis in the comparator group related to the use of sulfonylureas. Conclusions: The present pooled analysis shows that vildagliptin was overall well tolerated in clinical trials of up to >2 years in duration. The data further emphasize the value of a pooled analysis from a large safety database versus assessing safety and tolerability from individual studies. PMID:21415917
-
Edgren, Gustaf; Hjalgrim, Henrik
2010-11-01
At current safety levels, with adverse events from transfusions being relatively rare, further progress in risk reductions will require large-scale investigations. Thus, truly prospective studies may prove unfeasible and other alternatives deserve consideration. In this review, we will try to give an overview of recent and historical developments in the use of blood donation and transfusion databases in research. In addition, we will go over important methodological issues. There are at least three nationwide or near-nationwide donation/transfusion databases with the possibility for long-term follow-up of donors and recipients. During the past few years, a large number of reports have been published utilizing such data sources to investigate transfusion-associated risks. In addition, numerous clinics systematically collect and use such data on a smaller scale. Combining systematically recorded donation and transfusion data with long-term health follow-up opens up exciting opportunities for transfusion medicine research. However, the correct analysis of such data requires close attention to methodological issues, especially including the indication for transfusion and reverse causality.
-
Lee, Howard; Chapiro, Julius; Schernthaner, Rüdiger; Duran, Rafael; Wang, Zhijun; Gorodetski, Boris; Geschwind, Jean-François; Lin, MingDe
2015-04-01
The objective of this study was to demonstrate that an intra-arterial liver therapy clinical research database system is a more workflow efficient and robust tool for clinical research than a spreadsheet storage system. The database system could be used to generate clinical research study populations easily with custom search and retrieval criteria. A questionnaire was designed and distributed to 21 board-certified radiologists to assess current data storage problems and clinician reception to a database management system. Based on the questionnaire findings, a customized database and user interface system were created to perform automatic calculations of clinical scores including staging systems such as the Child-Pugh and Barcelona Clinic Liver Cancer, and facilitates data input and output. Questionnaire participants were favorable to a database system. The interface retrieved study-relevant data accurately and effectively. The database effectively produced easy-to-read study-specific patient populations with custom-defined inclusion/exclusion criteria. The database management system is workflow efficient and robust in retrieving, storing, and analyzing data. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.
-
[Quality management and participation into clinical database].
Okubo, Suguru; Miyata, Hiroaki; Tomotaki, Ai; Motomura, Noboru; Murakami, Arata; Ono, Minoru; Iwanaka, Tadashi
2013-07-01
Quality management is necessary for establishing useful clinical database in cooperation with healthcare professionals and facilities. The ways of management are 1) progress management of data entry, 2) liaison with database participants (healthcare professionals), and 3) modification of data collection form. In addition, healthcare facilities are supposed to consider ethical issues and information security for joining clinical databases. Database participants should check ethical review boards and consultation service for patients.
-
Crawford, E D; Batuello, J T; Snow, P; Gamito, E J; McLeod, D G; Partin, A W; Stone, N; Montie, J; Stock, R; Lynch, J; Brandt, J
2000-05-01
The current study assesses artificial intelligence methods to identify prostate carcinoma patients at low risk for lymph node spread. If patients can be assigned accurately to a low risk group, unnecessary lymph node dissections can be avoided, thereby reducing morbidity and costs. A rule-derivation technology for simple decision-tree analysis was trained and validated using patient data from a large database (4,133 patients) to derive low risk cutoff values for Gleason sum and prostate specific antigen (PSA) level. An empiric analysis was used to derive a low risk cutoff value for clinical TNM stage. These cutoff values then were applied to 2 additional, smaller databases (227 and 330 patients, respectively) from separate institutions. The decision-tree protocol derived cutoff values of < or = 6 for Gleason sum and < or = 10.6 ng/mL for PSA. The empiric analysis yielded a clinical TNM stage low risk cutoff value of < or = T2a. When these cutoff values were applied to the larger database, 44% of patients were classified as being at low risk for lymph node metastases (0.8% false-negative rate). When the same cutoff values were applied to the smaller databases, between 11 and 43% of patients were classified as low risk with a false-negative rate of between 0.0 and 0.7%. The results of the current study indicate that a population of prostate carcinoma patients at low risk for lymph node metastases can be identified accurately using a simple decision algorithm that considers preoperative PSA, Gleason sum, and clinical TNM stage. The risk of lymph node metastases in these patients is < or = 1%; therefore, pelvic lymph node dissection may be avoided safely. The implications of these findings in surgical and nonsurgical treatment are significant.
-
Amadoz, Alicia; González-Candelas, Fernando
2007-04-20
Most research scientists working in the fields of molecular epidemiology, population and evolutionary genetics are confronted with the management of large volumes of data. Moreover, the data used in studies of infectious diseases are complex and usually derive from different institutions such as hospitals or laboratories. Since no public database scheme incorporating clinical and epidemiological information about patients and molecular information about pathogens is currently available, we have developed an information system, composed by a main database and a web-based interface, which integrates both types of data and satisfies requirements of good organization, simple accessibility, data security and multi-user support. From the moment a patient arrives to a hospital or health centre until the processing and analysis of molecular sequences obtained from infectious pathogens in the laboratory, lots of information is collected from different sources. We have divided the most relevant data into 12 conceptual modules around which we have organized the database schema. Our schema is very complete and it covers many aspects of sample sources, samples, laboratory processes, molecular sequences, phylogenetics results, clinical tests and results, clinical information, treatments, pathogens, transmissions, outbreaks and bibliographic information. Communication between end-users and the selected Relational Database Management System (RDMS) is carried out by default through a command-line window or through a user-friendly, web-based interface which provides access and management tools for the data. epiPATH is an information system for managing clinical and molecular information from infectious diseases. It facilitates daily work related to infectious pathogens and sequences obtained from them. This software is intended for local installation in order to safeguard private data and provides advanced SQL-users the flexibility to adapt it to their needs. The database schema, tool scripts and web-based interface are free software but data stored in our database server are not publicly available. epiPATH is distributed under the terms of GNU General Public License. More details about epiPATH can be found at http://genevo.uv.es/epipath.
-
Clauson, Kevin A; Polen, Hyla H; Marsh, Wallace A
2007-12-01
To evaluate personal digital assistant (PDA) drug information databases used to support clinical decision-making, and to compare the performance of PDA databases with their online versions. Prospective evaluation with descriptive analysis. Five drug information databases available for PDAs and online were evaluated according to their scope (inclusion of correct answers), completeness (on a 3-point scale), and ease of use; 158 question-answer pairs across 15 weighted categories of drug information essential to health care professionals were used to evaluate these databases. An overall composite score integrating these three measures was then calculated. Scores for the PDA databases and for each PDA-online pair were compared. Among the PDA databases, composite rankings, from highest to lowest, were as follows: Lexi-Drugs, Clinical Pharmacology OnHand, Epocrates Rx Pro, mobileMicromedex (now called Thomson Clinical Xpert), and Epocrates Rx free version. When we compared database pairs, online databases that had greater scope than their PDA counterparts were Clinical Pharmacology (137 vs 100 answers, p<0.001), Micromedex (132 vs 96 answers, p<0.001), Lexi-Comp Online (131 vs 119 answers, p<0.001), and Epocrates Online Premium (103 vs 98 answers, p=0.001). Only Micromedex online was more complete than its PDA version (p=0.008). Regarding ease of use, the Lexi-Drugs PDA database was superior to Lexi-Comp Online (p<0.001); however, Epocrates Online Premium, Epocrates Online Free, and Micromedex online were easier to use than their PDA counterparts (p<0.001). In terms of composite scores, only the online versions of Clinical Pharmacology and Micromedex demonstrated superiority over their PDA versions (p>0.01). Online and PDA drug information databases assist practitioners in improving their clinical decision-making. Lexi-Drugs performed significantly better than all of the other PDA databases evaluated. No PDA database demonstrated superiority to its online counterpart; however, the online versions of Clinical Pharmacology and Micromedex were superior to their PDA versions in answering questions.
-
Large Dosage of Chishao in Formulae for Cholestatic Hepatitis: A Systematic Review and Meta-Analysis
Ma, Xiao; Wang, Ji; He, Xuan; Zhao, Yanling; Wang, Jiabo; Zhang, Ping; Zhu, Yun; Zhong, Lin; Zheng, Quanfu; Xiao, Xiaohe
2014-01-01
Objective. To evaluate the efficacy and safety of large dosage of Chishao in formulae for treatment of cholestatic hepatitis. Methods. The major databases (PubMed, Embase, Cochrane Library, Chinese Biomedical Database Wanfang, VIP medicine information system, and China National Knowledge Infrastructure) were searched until January 2014. Randomized controlled trials (RCTs) of large dosage of Chishao in formulae that reported on publications in treatment of cholestatic hepatitis with total efficacy rate, together with the biochemical indices including alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), and direct bilirubin (DBIL), were extracted by two reviewers. The Cochrane tool was used for the assessment of risk of bias included trials. Data were analyzed with RevMan 5.2.7 software. Results. 11 RCTs involving 1275 subjects with cholestatic hepatitis were included. Compared with essential therapy, large dosage of Chishao in formulae demonstrated more efficiently with down regulation of serum ALT, AST, TBIL, DBIL. Meanwhile, there were no obvious adverse events. Conclusion. As a promising novel treatment approach, widely using large dosage of Chishao in formulae may enhance the curative efficacy for cholestatic hepatitis. Considering being accepted by more and more practitioners, further rigorously designed clinical studies are required. PMID:24987427
-
A systematic review of administrative and clinical databases of infants admitted to neonatal units.
Statnikov, Yevgeniy; Ibrahim, Buthaina; Modi, Neena
2017-05-01
High quality information, increasingly captured in clinical databases, is a useful resource for evaluating and improving newborn care. We conducted a systematic review to identify neonatal databases, and define their characteristics. We followed a preregistered protocol using MesH terms to search MEDLINE, EMBASE, CINAHL, Web of Science and OVID Maternity and Infant Care Databases for articles identifying patient level databases covering more than one neonatal unit. Full-text articles were reviewed and information extracted on geographical coverage, criteria for inclusion, data source, and maternal and infant characteristics. We identified 82 databases from 2037 publications. Of the country-specific databases there were 39 regional and 39 national. Sixty databases restricted entries to neonatal unit admissions by birth characteristic or insurance cover; 22 had no restrictions. Data were captured specifically for 53 databases; 21 administrative sources; 8 clinical sources. Two clinical databases hold the largest range of data on patient characteristics, USA's Pediatrix BabySteps Clinical Data Warehouse and UK's National Neonatal Research Database. A number of neonatal databases exist that have potential to contribute to evaluating neonatal care. The majority is created by entering data specifically for the database, duplicating information likely already captured in other administrative and clinical patient records. This repetitive data entry represents an unnecessary burden in an environment where electronic patient records are increasingly used. Standardisation of data items is necessary to facilitate linkage within and between countries. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.
-
Uncovering Capgras delusion using a large-scale medical records database
Marshall, Caryl; Kanji, Zara; Wilkinson, Sam; Halligan, Peter; Deeley, Quinton
2017-01-01
Background Capgras delusion is scientifically important but most commonly reported as single case studies. Studies analysing large clinical records databases focus on common disorders but none have investigated rare syndromes. Aims Identify cases of Capgras delusion and associated psychopathology, demographics, cognitive function and neuropathology in light of existing models. Method Combined computational data extraction and qualitative classification using 250 000 case records from South London and Maudsley Clinical Record Interactive Search (CRIS) database. Results We identified 84 individuals and extracted diagnosis-matched comparison groups. Capgras was not ‘monothematic’ in the majority of cases. Most cases involved misidentified family members or close partners but others were misidentified in 25% of cases, contrary to dual-route face recognition models. Neuroimaging provided no evidence for predominantly right hemisphere damage. Individuals were ethnically diverse with a range of psychosis spectrum diagnoses. Conclusions Capgras is more diverse than current models assume. Identification of rare syndromes complements existing ‘big data’ approaches in psychiatry. Declaration of interests V.B. is supported by a Wellcome Trust Seed Award in Science (200589/Z/16/Z) and the UCLH NIHR Biomedical Research Centre. S.W. is supported by a Wellcome Trust Strategic Award (WT098455MA). Q.D. has received a grant from King’s Health Partners. Copyright and usage © The Royal College of Psychiatrists 2017. This is an open access article distributed under the terms of the Creative Commons Non-Commercial, No Derivatives (CC BY-NC-ND) license. PMID:28794897
-
Rendic, Slobodan P; Guengerich, Frederick P
2018-01-01
The present work describes development of offline and web-searchable metabolism databases for drugs, other chemicals, and physiological compounds using human and model species, prompted by the large amount of data published after year 1990. The intent was to provide a rapid and accurate approach to published data to be applied both in science and to assist therapy. Searches for the data were done using the Pub Med database, accessing the Medline database of references and abstracts. In addition, data presented at scientific conferences (e.g., ISSX conferences) are included covering the publishing period beginning with the year 1976. Application of the data is illustrated by the properties of benzo[a]pyrene (B[a]P) and its metabolites. Analysis show higher activity of P450 1A1 for activation of the (-)- isomer of trans-B[a]P-7,8-diol, while P4501B1 exerts higher activity for the (+)- isomer. P450 1A2 showed equally low activity in the metabolic activation of both isomers. The information collected in the databases is applicable in prediction of metabolic drug-drug and/or drug-chemical interactions in clinical and environmental studies. The data on the metabolism of searched compound (exemplified by benzo[a]pyrene and its metabolites) also indicate toxicological properties of the products of specific reactions. The offline and web-searchable databases had wide range of applications (e.g. computer assisted drug design and development, optimization of clinical therapy, toxicological applications) and adjustment in everyday life styles. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
-
A dynamic clinical dental relational database.
Taylor, D; Naguib, R N G; Boulton, S
2004-09-01
The traditional approach to relational database design is based on the logical organization of data into a number of related normalized tables. One assumption is that the nature and structure of the data is known at the design stage. In the case of designing a relational database to store historical dental epidemiological data from individual clinical surveys, the structure of the data is not known until the data is presented for inclusion into the database. This paper addresses the issues concerned with the theoretical design of a clinical dynamic database capable of adapting the internal table structure to accommodate clinical survey data, and presents a prototype database application capable of processing, displaying, and querying the dental data.
-
Psychopathology in a Large Cohort of Sexually Abused Children Followed up to 43 Years
ERIC Educational Resources Information Center
Cutajar, Margaret C.; Mullen, Paul E.; Ogloff, James R. P.; Thomas, Stuart D.; Wells, David L.; Spataro, Josie
2010-01-01
Objective: To determine the rate and risk of clinical and personality disorders diagnosed in childhood and adulthood in those known to have been sexually abused during childhood. Methods: Forensic medical records of 2,759 sexually abused children assessed between 1964 and 1995 were linked with a public psychiatric database between 12 and 43 years…
-
ERIC Educational Resources Information Center
Fleming, Steven T.
1992-01-01
The concept of risk-adjusted measures of quality is discussed, and a methodology is proposed for risk-adjusting and integrating multiple adverse outcomes of anesthesia services into measures for quality assurance and quality improvement programs. Although designed for a new anesthesiology database, the methods should apply to other health…
-
Comparative effectiveness research in hand surgery.
Johnson, Shepard P; Chung, Kevin C
2014-08-01
Comparative effectiveness research (CER) is a concept initiated by the Institute of Medicine and financially supported by the federal government. The primary objective of CER is to improve decision making in medicine. This research is intended to evaluate the effectiveness, benefits, and harmful effects of alternative interventions. CER studies are commonly large, simple, observational, and conducted using electronic databases. To date, there is little comparative effectiveness evidence within hand surgery to guide therapeutic decisions. To draw conclusions on effectiveness through electronic health records, databases must contain clinical information and outcomes relevant to hand surgery interventions, such as patient-related outcomes. Copyright © 2014 Elsevier Inc. All rights reserved.
-
Medication safety research by observational study design.
Lao, Kim S J; Chui, Celine S L; Man, Kenneth K C; Lau, Wallis C Y; Chan, Esther W; Wong, Ian C K
2016-06-01
Observational studies have been recognised to be essential for investigating the safety profile of medications. Numerous observational studies have been conducted on the platform of large population databases, which provide adequate sample size and follow-up length to detect infrequent and/or delayed clinical outcomes. Cohort and case-control are well-accepted traditional methodologies for hypothesis testing, while within-individual study designs are developing and evolving, addressing previous known methodological limitations to reduce confounding and bias. Respective examples of observational studies of different study designs using medical databases are shown. Methodology characteristics, study assumptions, strengths and weaknesses of each method are discussed in this review.
-
Multicenter neonatal databases: Trends in research uses.
Creel, Liza M; Gregory, Sean; McNeal, Catherine J; Beeram, Madhava R; Krauss, David R
2017-01-13
In the US, approximately 12.7% of all live births are preterm, 8.2% of live births were low birth weight (LBW), and 1.5% are very low birth weight (VLBW). Although technological advances have improved mortality rates among preterm and LBW infants, improving overall rates of prematurity and LBW remains a national priority. Monitoring short- and long-term outcomes is critical for advancing medical treatment and minimizing morbidities associated with prematurity or LBW; however, studying these infants can be challenging. Several large, multi-center neonatal databases have been developed to improve research and quality improvement of treatments for and outcomes of premature and LBW infants. The purpose of this systematic review was to describe three multi-center neonatal databases. We conducted a literature search using PubMed and Google Scholar over the period 1990 to August 2014. Studies were included in our review if one of the databases was used as a primary source of data or comparison. Included studies were categorized by year of publication; study design employed, and research focus. A total of 343 studies published between 1991 and 2014 were included. Studies of premature and LBW infants using these databases have increased over time, and provide evidence for both neonatology and community-based pediatric practice. Research into treatment and outcomes of premature and LBW infants is expanding, partially due to the availability of large, multicenter databases. The consistency of clinical conditions and neonatal outcomes studied since 1990 demonstrates that there are dedicated research agendas and resources that allow for long-term, and potentially replicable, studies within this population.
-
Public variant databases: liability?
Thorogood, Adrian; Cook-Deegan, Robert; Knoppers, Bartha Maria
2017-07-01
Public variant databases support the curation, clinical interpretation, and sharing of genomic data, thus reducing harmful errors or delays in diagnosis. As variant databases are increasingly relied on in the clinical context, there is concern that negligent variant interpretation will harm patients and attract liability. This article explores the evolving legal duties of laboratories, public variant databases, and physicians in clinical genomics and recommends a governance framework for databases to promote responsible data sharing.Genet Med advance online publication 15 December 2016.
-
Kawazoe, Yoshimasa; Imai, Takeshi; Ohe, Kazuhiko
2016-04-05
Health level seven version 2.5 (HL7 v2.5) is a widespread messaging standard for information exchange between clinical information systems. By applying Semantic Web technologies for handling HL7 v2.5 messages, it is possible to integrate large-scale clinical data with life science knowledge resources. Showing feasibility of a querying method over large-scale resource description framework (RDF)-ized HL7 v2.5 messages using publicly available drug databases. We developed a method to convert HL7 v2.5 messages into the RDF. We also converted five kinds of drug databases into RDF and provided explicit links between the corresponding items among them. With those linked drug data, we then developed a method for query expansion to search the clinical data using semantic information on drug classes along with four types of temporal patterns. For evaluation purpose, medication orders and laboratory test results for a 3-year period at the University of Tokyo Hospital were used, and the query execution times were measured. Approximately 650 million RDF triples for medication orders and 790 million RDF triples for laboratory test results were converted. Taking three types of query in use cases for detecting adverse events of drugs as an example, we confirmed these queries were represented in SPARQL Protocol and RDF Query Language (SPARQL) using our methods and comparison with conventional query expressions were performed. The measurement results confirm that the query time is feasible and increases logarithmically or linearly with the amount of data and without diverging. The proposed methods enabled query expressions that separate knowledge resources and clinical data, thereby suggesting the feasibility for improving the usability of clinical data by enhancing the knowledge resources. We also demonstrate that when HL7 v2.5 messages are automatically converted into RDF, searches are still possible through SPARQL without modifying the structure. As such, the proposed method benefits not only our hospitals, but also numerous hospitals that handle HL7 v2.5 messages. Our approach highlights a potential of large-scale data federation techniques to retrieve clinical information, which could be applied as applications of clinical intelligence to improve clinical practices, such as adverse drug event monitoring and cohort selection for a clinical study as well as discovering new knowledge from clinical information.
-
Perioperative medicine and Taiwan National Health Insurance Research Database.
Chang, C C; Liao, C C; Chen, T L
2016-09-01
"Big data", characterized by 'volume', 'velocity', 'variety', and 'veracity', being routinely collected in huge amounts of clinical and administrative healthcare-related data are becoming common and generating promising viewpoints for a better understanding of the complexity for medical situations. Taiwan National Health Insurance Research Database (NHIRD), one of large and comprehensive nationwide population reimbursement databases in the world, provides the strength of sample size avoiding selection and participation bias. Abundant with the demographics, clinical diagnoses, and capable of linking diverse laboratory and imaging information allowing for integrated analysis, NHIRD studies could inform us of the incidence, prevalence, managements, correlations and associations of clinical outcomes and diseases, under the universal coverage of healthcare used. Perioperative medicine has emerged as an important clinical research field over the past decade, moving the categorization of the specialty of "Anesthesiology and Perioperative Medicine". Many studies concerning perioperative medicine based on retrospective cohort analyses have been published in the top-ranked journal, but studies utilizing Taiwan NHIRD were still not fully visualized. As the prominent growth curve of NHIRD studies, we have contributed the studies covering surgical adverse outcomes, trauma, stroke, diabetes, and healthcare inequality, etc., to this ever growing field for the past five years. It will definitely become a trend of research using Taiwan NHIRD and contributing to the progress of perioperative medicine with the recruitment of devotion from more research groups and become a famous doctrine. Copyright © 2016. Published by Elsevier B.V.
-
Folks, Russell D; Savir-Baruch, Bital; Garcia, Ernest V; Verdes, Liudmila; Taylor, Andrew T
2012-12-01
Our objective was to design and implement a clinical history database capable of linking to our database of quantitative results from (99m)Tc-mercaptoacetyltriglycine (MAG3) renal scans and export a data summary for physicians or our software decision support system. For database development, we used a commercial program. Additional software was developed in Interactive Data Language. MAG3 studies were processed using an in-house enhancement of a commercial program. The relational database has 3 parts: a list of all renal scans (the RENAL database), a set of patients with quantitative processing results (the Q2 database), and a subset of patients from Q2 containing clinical data manually transcribed from the hospital information system (the CLINICAL database). To test interobserver variability, a second physician transcriber reviewed 50 randomly selected patients in the hospital information system and tabulated 2 clinical data items: hydronephrosis and presence of a current stent. The CLINICAL database was developed in stages and contains 342 fields comprising demographic information, clinical history, and findings from up to 11 radiologic procedures. A scripted algorithm is used to reliably match records present in both Q2 and CLINICAL. An Interactive Data Language program then combines data from the 2 databases into an XML (extensible markup language) file for use by the decision support system. A text file is constructed and saved for review by physicians. RENAL contains 2,222 records, Q2 contains 456 records, and CLINICAL contains 152 records. The interobserver variability testing found a 95% match between the 2 observers for presence or absence of ureteral stent (κ = 0.52), a 75% match for hydronephrosis based on narrative summaries of hospitalizations and clinical visits (κ = 0.41), and a 92% match for hydronephrosis based on the imaging report (κ = 0.84). We have developed a relational database system to integrate the quantitative results of MAG3 image processing with clinical records obtained from the hospital information system. We also have developed a methodology for formatting clinical history for review by physicians and export to a decision support system. We identified several pitfalls, including the fact that important textual information extracted from the hospital information system by knowledgeable transcribers can show substantial interobserver variation, particularly when record retrieval is based on the narrative clinical records.
-
NASA Technical Reports Server (NTRS)
Saeed, M.; Lieu, C.; Raber, G.; Mark, R. G.
2002-01-01
Development and evaluation of Intensive Care Unit (ICU) decision-support systems would be greatly facilitated by the availability of a large-scale ICU patient database. Following our previous efforts with the MIMIC (Multi-parameter Intelligent Monitoring for Intensive Care) Database, we have leveraged advances in networking and storage technologies to develop a far more massive temporal database, MIMIC II. MIMIC II is an ongoing effort: data is continuously and prospectively archived from all ICU patients in our hospital. MIMIC II now consists of over 800 ICU patient records including over 120 gigabytes of data and is growing. A customized archiving system was used to store continuously up to four waveforms and 30 different parameters from ICU patient monitors. An integrated user-friendly relational database was developed for browsing of patients' clinical information (lab results, fluid balance, medications, nurses' progress notes). Based upon its unprecedented size and scope, MIMIC II will prove to be an important resource for intelligent patient monitoring research, and will support efforts in medical data mining and knowledge-discovery.
-
Public variant databases: liability?
Thorogood, Adrian; Cook-Deegan, Robert; Knoppers, Bartha Maria
2017-01-01
Public variant databases support the curation, clinical interpretation, and sharing of genomic data, thus reducing harmful errors or delays in diagnosis. As variant databases are increasingly relied on in the clinical context, there is concern that negligent variant interpretation will harm patients and attract liability. This article explores the evolving legal duties of laboratories, public variant databases, and physicians in clinical genomics and recommends a governance framework for databases to promote responsible data sharing. Genet Med advance online publication 15 December 2016 PMID:27977006
-
Ono, Yosuke; Ono, Sachiko; Yasunaga, Hideo; Matsui, Hiroki; Fushimi, Kiyohide; Tanaka, Yuji
2017-03-01
Myxedema coma is a life-threatening and emergency presentation of hypothyroidism. However, the clinical features and outcomes of this condition have been poorly defined because of its rarity. We conducted a retrospective observational study of patients diagnosed with myxedema coma from July 2010 through March 2013 using a national inpatient database in Japan. We investigated characteristics, comorbidities, treatments, and in-hospital mortality of patients with myxedema coma. We identified 149 patients diagnosed with myxedema coma out of approximately 19 million inpatients in the database. The mean (standard deviation) age was 77 (12) years, and two-thirds of the patients were female. The overall proportion of in-hospital mortality among cases was 29.5%. The number of patients was highest in the winter season. Patients treated with steroids, catecholamines, or mechanical ventilation showed higher in-hospital mortality than those without. Variations in type and dosage of thyroid hormone replacement were not associated with in-hospital mortality. The most common comorbidity was cardiovascular diseases (40.3%). The estimated incidence of myxedema coma was 1.08 per million people per year in Japan. Multivariable logistic regression analysis revealed that higher age and use of catecholamines (with or without steroids) were significantly associated with higher in-hospital mortality. The present study identified the clinical characteristics and outcomes of patients with myxedema coma using a large-scale database. Myxedema coma mortality was independently associated with age and severe conditions requiring treatment with catecholamines. Copyright © 2016 The Authors. Production and hosting by Elsevier B.V. All rights reserved.
-
Nørgaard, M; Johnsen, S P
2016-02-01
In Denmark, the need for monitoring of clinical quality and patient safety with feedback to the clinical, administrative and political systems has resulted in the establishment of a network of more than 60 publicly financed nationwide clinical quality databases. Although primarily devoted to monitoring and improving quality of care, the potential of these databases as data sources in clinical research is increasingly being recognized. In this review, we describe these databases focusing on their use as data sources for clinical research, including their strengths and weaknesses as well as future concerns and opportunities. The research potential of the clinical quality databases is substantial but has so far only been explored to a limited extent. Efforts related to technical, legal and financial challenges are needed in order to take full advantage of this potential. © 2016 The Association for the Publication of the Journal of Internal Medicine.
-
Hartung, Daniel M; Zarin, Deborah A; Guise, Jeanne-Marie; McDonagh, Marian; Paynter, Robin; Helfand, Mark
2014-04-01
ClinicalTrials.gov requires reporting of result summaries for many drug and device trials. To evaluate the consistency of reporting of trials that are registered in the ClinicalTrials.gov results database and published in the literature. ClinicalTrials.gov results database and matched publications identified through ClinicalTrials.gov and a manual search of 2 electronic databases. 10% random sample of phase 3 or 4 trials with results in the ClinicalTrials.gov results database, completed before 1 January 2009, with 2 or more groups. One reviewer extracted data about trial design and results from the results database and matching publications. A subsample was independently verified. Of 110 trials with results, most were industry-sponsored, parallel-design drug studies. The most common inconsistency was the number of secondary outcome measures reported (80%). Sixteen trials (15%) reported the primary outcome description inconsistently, and 22 (20%) reported the primary outcome value inconsistently. Thirty-eight trials inconsistently reported the number of individuals with a serious adverse event (SAE); of these, 33 (87%) reported more SAEs in ClinicalTrials.gov. Among the 84 trials that reported SAEs in ClinicalTrials.gov, 11 publications did not mention SAEs, 5 reported them as zero or not occurring, and 21 reported a different number of SAEs. Among 29 trials that reported deaths in ClinicalTrials.gov, 28% differed from the matched publication. Small sample that included earliest results posted to the database. Reporting discrepancies between the ClinicalTrials.gov results database and matching publications are common. Which source contains the more accurate account of results is unclear, although ClinicalTrials.gov may provide a more comprehensive description of adverse events than the publication. Agency for Healthcare Research and Quality.
-
... Terms and Conditions Disclaimer ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted ... world. ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of ...
-
DOE Office of Scientific and Technical Information (OSTI.GOV)
Robertson, SP; Quon, H; Kiess, AP
Purpose: To develop a framework for automatic extraction of clinically meaningful dosimetric-outcome relationships from an in-house, analytic oncology database. Methods: Dose-volume histograms (DVH) and clinical outcome-related structured data elements have been routinely stored to our database for 513 HN cancer patients treated from 2007 to 2014. SQL queries were developed to extract outcomes that had been assessed for at least 100 patients, as well as DVH curves for organs-at-risk (OAR) that were contoured for at least 100 patients. DVH curves for paired OAR (e.g., left and right parotids) were automatically combined and included as additional structures for analysis. For eachmore » OAR-outcome combination, DVH dose points, D(V{sub t}), at a series of normalized volume thresholds, V{sub t}=[0.01,0.99], were stratified into two groups based on outcomes after treatment completion. The probability, P[D(V{sub t})], of an outcome was modeled at each V{sub t} by logistic regression. Notable combinations, defined as having P[D(V{sub t})] increase by at least 5% per Gy (p<0.05), were further evaluated for clinical relevance using a custom graphical interface. Results: A total of 57 individual and combined structures and 115 outcomes were queried, resulting in over 6,500 combinations for analysis. Of these, 528 combinations met the 5%/Gy requirement, with further manual inspection revealing a number of reasonable models based on either reported literature or proximity between neighboring OAR. The data mining algorithm confirmed the following well-known toxicity/outcome relationships: dysphagia/larynx, voice changes/larynx, esophagitis/esophagus, xerostomia/combined parotids, and mucositis/oral mucosa. Other notable relationships included dysphagia/pharyngeal constrictors, nausea/brainstem, nausea/spinal cord, weight-loss/mandible, and weight-loss/combined parotids. Conclusion: Our database platform has enabled large-scale analysis of dose-outcome relationships. The current data-mining framework revealed both known and novel dosimetric and clinical relationships, underscoring the potential utility of this analytic approach. Multivariate models may be necessary to further evaluate the complex relationship between neighboring OARs and observed outcomes. This research was supported through collaborations with Elekta, Philips, and Toshiba.« less
-
Image-guided decision support system for pulmonary nodule classification in 3D thoracic CT images
NASA Astrophysics Data System (ADS)
Kawata, Yoshiki; Niki, Noboru; Ohmatsu, Hironobu; Kusumoto, Masahiro; Kakinuma, Ryutaro; Mori, Kiyoshi; Yamada, Kozo; Nishiyama, Hiroyuki; Eguchi, Kenji; Kaneko, Masahiro; Moriyama, Noriyuki
2004-05-01
The purpose of this study is to develop an image-guided decision support system that assists decision-making in clinical differential diagnosis of pulmonary nodules. This approach retrieves and displays nodules that exhibit morphological and internal profiles consistent to the nodule in question. It uses a three-dimensional (3-D) CT image database of pulmonary nodules for which diagnosis is known. In order to build the system, there are following issues that should be solved: 1) to categorize the nodule database with respect to morphological and internal features, 2) to quickly search nodule images similar to an indeterminate nodule from a large database, and 3) to reveal malignancy likelihood computed by using similar nodule images. Especially, the first problem influences the design of other issues. The successful categorization of nodule pattern might lead physicians to find important cues that characterize benign and malignant nodules. This paper focuses on an approach to categorize the nodule database with respect to nodule shape and CT density patterns inside nodule.
-
Pharmacoepidemiology resources in Ireland-an introduction to pharmacy claims data.
Sinnott, Sarah-Jo; Bennett, Kathleen; Cahir, Caitriona
2017-11-01
Administrative health data, such as pharmacy claims data, present a valuable resource for conducting pharmacoepidemiological and health services research. Often, data are available for whole populations allowing population level analyses. Moreover, their routine collection ensures that the data reflect health care utilisation in the real-world setting compared to data collected in clinical trials. The Irish Health Service Executive-Primary Care Reimbursement Service (HSE-PCRS) community pharmacy claims database is described. The availability of demographic variables and drug-related information is discussed. The strengths and limitations associated using this database for conducting research are presented, in particular, internal and external validity. Examples of recently conducted research using the HSE-PCRS pharmacy claims database are used to illustrate the breadth of its use. The HSE-PCRS national pharmacy claims database is a large, high-quality, valid and accurate data source for measuring drug exposure in specific populations in Ireland. The main limitation is the lack of generalisability for those aged <70 years and the lack of information on indication or outcome.
-
Low Cost Comprehensive Microcomputer-Based Medical History Database Acquisition
Buchan, Robert R. C.
1980-01-01
A carefully detailed, comprehensive medical history database is the fundamental essence of patient-physician interaction. Computer generated medical history acquisition has repeatedly been shown to be highly acceptable to both patient and physician while consistantly providing a superior product. Cost justification of machine derived problem and history databases, however, has in the past been marginal, at best. Routine use of the technology has therefore been limited to large clinics, university hospitals and federal installations where feasible volume applications are supported by endowment, research funds or taxes. This paper summarizes the use of a unique low cost device which marries advanced microprocessor technology with random access, variable-frame film projection techniques to acquire a detailed comprehensive medical history database. Preliminary data are presented which compare patient, physician, and machine generated histories for content, discovery, compliance and acceptability. Results compare favorably with the findings in similar studies by a variety of authors. ImagesFigure 1Figure 2Figure 3Figure 4
-
Search Filter Precision Can Be Improved By NOTing Out Irrelevant Content
Wilczynski, Nancy L.; McKibbon, K. Ann; Haynes, R. Brian
2011-01-01
Background: Most methodologic search filters developed for use in large electronic databases such as MEDLINE have low precision. One method that has been proposed but not tested for improving precision is NOTing out irrelevant content. Objective: To determine if search filter precision can be improved by NOTing out the text words and index terms assigned to those articles that are retrieved but are off-target. Design: Analytic survey. Methods: NOTing out unique terms in off-target articles and testing search filter performance in the Clinical Hedges Database. Main Outcome Measures: Sensitivity, specificity, precision and number needed to read (NNR). Results: For all purpose categories (diagnosis, prognosis and etiology) except treatment and for all databases (MEDLINE, EMBASE, CINAHL and PsycINFO), constructing search filters that NOTed out irrelevant content resulted in substantive improvements in NNR (over four-fold for some purpose categories and databases). Conclusion: Search filter precision can be improved by NOTing out irrelevant content. PMID:22195215
-
The FREGAT biobank: a clinico-biological database dedicated to esophageal and gastric cancers.
Mariette, Christophe; Renaud, Florence; Piessen, Guillaume; Gele, Patrick; Copin, Marie-Christine; Leteurtre, Emmanuelle; Delaeter, Christine; Dib, Malek; Clisant, Stéphanie; Harter, Valentin; Bonnetain, Franck; Duhamel, Alain; Christophe, Véronique; Adenis, Antoine
2018-02-06
While the incidence of esophageal and gastric cancers is increasing, the prognosis of these cancers remains bleak. Endoscopy and surgery are the standard treatments for localized tumors, but multimodal treatments, associated chemotherapy, targeted therapies, immunotherapy, radiotherapy, and surgery are needed for the vast majority of patients who present with locally advanced or metastatic disease at diagnosis. Although survival has improved, most patients still present with advanced disease at diagnosis. In addition, most patients exhibit a poor or incomplete response to treatment, experience early recurrence and have an impaired quality of life. Compared with several other cancers, the therapeutic approach is not personalized, and research is much less developed. It is, therefore, urgent to hasten the development of research protocols, and consequently, develop a large, ambitious and innovative tool through which future scientific questions may be answered. This research must be patient-related so that rapid feedback to the bedside is achieved and should aim to identify clinical-, biological- and tumor-related factors that are associated with treatment resistance. Finally, this research should also seek to explain epidemiological and social facets of disease behavior. The prospective FREGAT database, established by the French National Cancer Institute, is focused on adult patients with carcinomas of the esophagus and stomach and on whatever might be the tumor stage or therapeutic strategy. The database includes epidemiological, clinical, and tumor characteristics data as well as follow-up, human and social sciences quality of life data, along with a tumor and serum bank. This innovative method of research will allow for the banking of millions of data for the development of excellent basic, translational and clinical research programs for esophageal and gastric cancer. This will ultimately improve general knowledge of these diseases, therapeutic strategies and patient survival. This database was initially developed in France on a nationwide basis, but currently, the database is available for worldwide contributions with respect to the input of patient data or the request for data for scientific projects. The FREGAT database has a dedicated website ( www.fregat-database.org ) and is registered on the Clinicaltrials.gov site, number NCT 02526095 , since August 8, 2015.
-
Pasquini, Marcelo C; Logan, Brent; Jones, Richard J; Alousi, Amin M; Appelbaum, Frederick R; Bolaños-Meade, Javier; Flowers, Mary E D; Giralt, Sergio; Horowitz, Mary M; Jacobsohn, David; Koreth, John; Levine, John E; Luznik, Leo; Maziarz, Richard; Mendizabal, Adam; Pavletic, Steven; Perales, Miguel-Angel; Porter, David; Reshef, Ran; Weisdorf, Daniel; Antin, Joseph H
2018-06-01
Graft-versus-host disease (GVHD) is a common complication after hematopoietic cell transplantation (HCT) and associated with significant morbidity and mortality. Preventing GVHD without chronic therapy or increasing relapse is a desired goal. Here we report a benchmark analysis to evaluate the performance of 6 GVHD prevention strategies tested at single institutions compared with a large multicenter outcomes database as a control. Each intervention was compared with the control for the incidence of acute and chronic GVHD and overall survival and against novel composite endpoints: acute and chronic GVHD, relapse-free survival (GRFS), and chronic GVHD, relapse-free survival (CRFS). Modeling GRFS and CRFS using the benchmark analysis further informed the design of 2 clinical trials testing GVHD prophylaxis interventions. This study demonstrates the potential benefit of using an outcomes database to select promising interventions for multicenter clinical trials and proposes novel composite endpoints for use in GVHD prevention trials. Copyright © 2018 The American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.
-
Clinical Effects of Prebiotics in Pediatric Population.
Orel, Rok; Reberšak, Lea Vodušek
2016-12-15
Prebiotics are non-digestible components of food that in a selective manner trigger the expansion of microbes in the gut with valuable effects for the health of the host. In our document, current literature pertaining to the clinical effects of the use of prebiotics for the treatment and prevention of some common pediatric pathology such as infantile colic, constipation, absorption of minerals, weight gain, diarrhea, respiratory infections, and eczema is reviewed. Data was collected through search of the MEDLINE, PubMed, UpToDate, Cochrane Database of Systemic Reviews, and the Cochrane Controlled Trials Register database as well as through references from relevant articles, all until September 2015. However, only the results of publications with adequate methodological quality were included. Prebiotics seem to be very appealing in treatment of many clinical conditions, explicitly in the fight against constipation, poor weight gain in preterm infants, and eczema in atopic children. In contrast to probiotics, the evidence of true clinical efficacy of prebiotics, supported with exact type and dose information are rather sparse, and there are a limited number of randomized controlled trials concerning prebiotics in children, especially beyond the age of infancy. Large well-designed, controlled, confirmatory clinical trials are required, using commercially available products, to help healthcare providers in making an appropriate decision concerning the appropriate use of prebiotics in different conditions.
-
Pediatric post-marketing safety systems in North America: assessment of the current status.
McMahon, Ann W; Wharton, Gerold T; Bonnel, Renan; DeCelle, Mary; Swank, Kimberley; Testoni, Daniela; Cope, Judith U; Smith, Phillip Brian; Wu, Eileen; Murphy, Mary Dianne
2015-08-01
It is critical to have pediatric post-marketing safety systems that contain enough clinical and epidemiological detail to draw regulatory, public health, and clinical conclusions. The pediatric safety surveillance workshop (PSSW), coordinated by the Food and Drug Administration (FDA), identified these pediatric systems as of 2010. This manuscript aims to update the information from the PSSW and look critically at the systems currently in use. We reviewed North American pediatric post-marketing safety systems such as databases, networks, and research consortiums found in peer-reviewed journals and other online sources. We detail clinical examples from three systems that FDA used to assess pediatric medical product safety. Of the 59 systems reviewed for pediatric content, only nine were pediatric-focused and met the inclusion criteria. Brief descriptions are provided for these nine. The strengths and weaknesses of three systems (two of the nine pediatric-focused and one including both children and adults) are illustrated with clinical examples. Systems reviewed in this manuscript have strengths such as clinical detail, a large enough sample size to capture rare adverse events, and/or a patient denominator internal to the database. Few systems include all of these attributes. Pediatric drug safety would be better informed by utilizing multiple systems to take advantage of their individual characteristics. Copyright © 2015 John Wiley & Sons, Ltd.
-
Bergamino, Maurizio; Hamilton, David J; Castelletti, Lara; Barletta, Laura; Castellan, Lucio
2015-03-01
In this study, we describe the development and utilization of a relational database designed to manage the clinical and radiological data of patients with brain tumors. The Brain Tumor Database was implemented using MySQL v.5.0, while the graphical user interface was created using PHP and HTML, thus making it easily accessible through a web browser. This web-based approach allows for multiple institutions to potentially access the database. The BT Database can record brain tumor patient information (e.g. clinical features, anatomical attributes, and radiological characteristics) and be used for clinical and research purposes. Analytic tools to automatically generate statistics and different plots are provided. The BT Database is a free and powerful user-friendly tool with a wide range of possible clinical and research applications in neurology and neurosurgery. The BT Database graphical user interface source code and manual are freely available at http://tumorsdatabase.altervista.org. © The Author(s) 2013.
-
Virk, Sohrab S; Phillips, Frank M; Khan, Safdar N
2018-03-01
OBJECTIVE Cervical spondylotic myelopathy (CSM) is a progressive spinal condition that often requires surgery. Studies have shown the clinical equivalency of anterior versus posterior approaches for CSM surgery. The purpose of this study was to determine the amount and type of resources used for anterior and posterior surgical treatment of CSM by using large national databases of clinical and financial information from patients. METHODS This study consists of 2 large cohorts of patients who underwent either an anterior or posterior approach for treatment of CSM. These patients were selected from the Medicare 5% National Sample Administrative Database (SAF5) and the Humana orthopedic database (HORTHO), which is a database of patients with private payer health insurance. The outcome measures were the cost of a 90-day episode of care, as well as a breakdown of the cost components for each surgical procedure between 2005 and 2014. RESULTS A total of 16,444 patients were included in this analysis. In HORTHO, there were 10,332 and 1556 patients treated with an anterior or posterior approach for CSM, respectively. In SAF5, there were 3851 and 705 patients who were treated by an anterior or posterior approach for CSM, respectively. The mean ± SD reimbursements for anterior and posterior approaches in the HORTHO database were $20,863 ± $2014 and $23,813 ± $4258, respectively (p = 0.048). The mean ± SD reimbursements for anterior and posterior approaches in the SAF5 database were $18,219 ± $1053 and $25,598 ± $1686, respectively (p < 0.0001). There were also significantly higher reimbursements for a rehabilitation/skilled nursing facility and hospital/inpatient care for patients who underwent a posterior approach in both the private payer and Medicare databases. In all cohorts in this study, the hospital-related reimbursement was more than double the surgeon-related reimbursement. CONCLUSIONS This study provides resource utilization information for a 90-day episode of care for both anterior and posterior approaches for CSM surgery. There is a statistically significant higher resource utilization for patients undergoing the posterior approach for CSM, which is consistent with the literature. Understanding the reimbursement patterns for anterior versus posterior approaches for CSM will help providers design a bundled payment for patients requiring surgery for CSM, and this study suggests that a subset of patients who require the posterior approach for treatment also require greater resources. The data also suggest that hospital-related reimbursement is the major driver of payments.
-
Li, Yuanfang; Zhou, Zhiwei
2016-02-01
Precision medicine is a new medical concept and medical model, which is based on personalized medicine, rapid progress of genome sequencing technology and cross application of biological information and big data science. Precision medicine improves the diagnosis and treatment of gastric cancer to provide more convenience through more profound analyses of characteristics, pathogenesis and other core issues in gastric cancer. Cancer clinical database is important to promote the development of precision medicine. Therefore, it is necessary to pay close attention to the construction and management of the database. The clinical database of Sun Yat-sen University Cancer Center is composed of medical record database, blood specimen bank, tissue bank and medical imaging database. In order to ensure the good quality of the database, the design and management of the database should follow the strict standard operation procedure(SOP) model. Data sharing is an important way to improve medical research in the era of medical big data. The construction and management of clinical database must also be strengthened and innovated.
-
2010-01-01
Background A plant-based diet protects against chronic oxidative stress-related diseases. Dietary plants contain variable chemical families and amounts of antioxidants. It has been hypothesized that plant antioxidants may contribute to the beneficial health effects of dietary plants. Our objective was to develop a comprehensive food database consisting of the total antioxidant content of typical foods as well as other dietary items such as traditional medicine plants, herbs and spices and dietary supplements. This database is intended for use in a wide range of nutritional research, from in vitro and cell and animal studies, to clinical trials and nutritional epidemiological studies. Methods We procured samples from countries worldwide and assayed the samples for their total antioxidant content using a modified version of the FRAP assay. Results and sample information (such as country of origin, product and/or brand name) were registered for each individual food sample and constitute the Antioxidant Food Table. Results The results demonstrate that there are several thousand-fold differences in antioxidant content of foods. Spices, herbs and supplements include the most antioxidant rich products in our study, some exceptionally high. Berries, fruits, nuts, chocolate, vegetables and products thereof constitute common foods and beverages with high antioxidant values. Conclusions This database is to our best knowledge the most comprehensive Antioxidant Food Database published and it shows that plant-based foods introduce significantly more antioxidants into human diet than non-plant foods. Because of the large variations observed between otherwise comparable food samples the study emphasizes the importance of using a comprehensive database combined with a detailed system for food registration in clinical and epidemiological studies. The present antioxidant database is therefore an essential research tool to further elucidate the potential health effects of phytochemical antioxidants in diet. PMID:20096093
-
Yang, Wei; Xie, Yanming; Zhuang, Yan
2011-10-01
There are many kinds of Chinese traditional patent medicine used in clinical practice and many adverse events have been reported by clinical professionals. Chinese patent medicine's safety problems are the most concerned by patients and physicians. At present, many researchers have studied re-evaluation methods about post marketing Chinese medicine safety inside and outside China. However, it is rare that using data from hospital information system (HIS) to re-evaluating post marketing Chinese traditional patent medicine safety problems. HIS database in real world is a good resource with rich information to research medicine safety. This study planed to analyze HIS data selected from ten top general hospitals in Beijing, formed a large HIS database in real world with a capacity of 1 000 000 cases in total after a series of data cleaning and integrating procedures. This study could be a new project that using information to evaluate traditional Chinese medicine safety based on HIS database. A clear protocol has been completed as for the first step for the whole study. The protocol is as follows. First of all, separate each of the Chinese traditional patent medicines existing in the total HIS database as a single database. Secondly, select some related laboratory tests indexes as the safety evaluating outcomes, such as routine blood, routine urine, feces routine, conventional coagulation, liver function, kidney function and other tests. Thirdly, use the data mining method to analyze those selected safety outcomes which had abnormal change before and after using Chinese patent medicines. Finally, judge the relationship between those abnormal changing and Chinese patent medicine. We hope this method could imply useful information to Chinese medicine researchers interested in safety evaluation of traditional Chinese medicine.
-
Uses and limitations of registry and academic databases.
Williams, William G
2010-01-01
A database is simply a structured collection of information. A clinical database may be a Registry (a limited amount of data for every patient undergoing heart surgery) or Academic (an organized and extensive dataset of an inception cohort of carefully selected subset of patients). A registry and an academic database have different purposes and cost. The data to be collected for a database is defined by its purpose and the output reports required for achieving that purpose. A Registry's purpose is to ensure quality care, an Academic Database, to discover new knowledge through research. A database is only as good as the data it contains. Database personnel must be exceptionally committed and supported by clinical faculty. A system to routinely validate and verify data integrity is essential to ensure database utility. Frequent use of the database improves its accuracy. For congenital heart surgeons, routine use of a Registry Database is an essential component of clinical practice. Copyright (c) 2010 Elsevier Inc. All rights reserved.
-
Immunoinformatics: an integrated scenario
Tomar, Namrata; De, Rajat K
2010-01-01
Genome sequencing of humans and other organisms has led to the accumulation of huge amounts of data, which include immunologically relevant data. A large volume of clinical data has been deposited in several immunological databases and as a result immunoinformatics has emerged as an important field which acts as an intersection between experimental immunology and computational approaches. It not only helps in dealing with the huge amount of data but also plays a role in defining new hypotheses related to immune responses. This article reviews classical immunology, different databases and prediction tools. It also describes applications of immunoinformatics in designing in silico vaccination and immune system modelling. All these efforts save time and reduce cost. PMID:20722763
-
Burton, Tanya; Le Nestour, Elisabeth; Neary, Maureen; Ludlam, William H
2016-04-01
This study aimed to develop an algorithm to identify patients with CD, and quantify the clinical and economic burden that patients with CD face compared to CD-free controls. A retrospective cohort study of CD patients was conducted in a large US commercial health plan database between 1/1/2007 and 12/31/2011. A control group with no evidence of CD during the same time was matched 1:3 based on demographics. Comorbidity rates were compared using Poisson and health care costs were compared using robust variance estimation. A case-finding algorithm identified 877 CD patients, who were matched to 2631 CD-free controls. The age and sex distribution of the selected population matched the known epidemiology of CD. CD patients were found to have comorbidity rates that were two to five times higher and health care costs that were four to seven times higher than CD-free controls. An algorithm based on eight pituitary conditions and procedures appeared to identify CD patients in a claims database without a unique diagnosis code. Young CD patients had high rates of comorbidities that are more commonly observed in an older population (e.g., diabetes, hypertension, and cardiovascular disease). Observed health care costs were also high for CD patients compared to CD-free controls, but may have been even higher if the sample had included healthier controls with no health care use as well. Earlier diagnosis, improved surgery success rates, and better treatments may all help to reduce the chronic comorbidity and high health care costs associated with CD.
-
Franch Nadal, Josep; Mata Cases, Manel; Mauricio Puente, Dídac
2016-11-01
Type 2 diabetes mellitus is currently the most frequent chronic metabolic disease. In spain, according to the di@bet.es study, its prevalence is 13.8% in the adult population (although it is undiagnosed in 6%). The main risk factor for type 2 diabetes mellitus is obesity. The severity of type 2 diabetes mellitus is determined not only by the presence of hyperglycaemia, but also by the coexistence of other risk factors such as hypertension or dyslipidaemia, which are often associated with the disease. Its impact on the presence of chronic diabetic complications varies. While hyperglycaemia mainly influences the presence of microvascular complications, hypertension, dyslipidaemia and smoking play a greater role in macrovascular atherosclerotic disease. One of the most powerful ways to study the epidemiology of the disease is through the use of large databases that analyse the situation in the routine clinical management of huge numbers of patients. Recently, the data provided by the e-Management Project, based on the SIDIAP database, have allowed updating of many data on the health care of diabetic persons in Catalonia. This not only allows determination of the epidemiology of the disease but is also a magnificent starting point for the design of future studies that will provide answers to more questions. However, the use of large databases is not free of certain problems, especially those concerning the reliability of registries. This article analyses some of the data obtained by the e-Management study and other spanish epidemiological studies of equal importance. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.
-
Suija, Kadri; Kivisto, Katrin; Sarria-Santamera, Antonio; Kokko, Simo; Liseckiene, Ida; Bredehorst, Maren; Jaruseviciene, Lina; Papp, Renata; Oona, Marje; Kalda, Ruth
2015-02-01
The purpose of the study was to measure clinical quality by doing an audit of clinical records and to compare the performance based on clinical quality indicators (CQI) for hypertension and type 2 diabetes across seven European countries: Estonia, Finland, Germany, Hungary, Italy, Lithuania and Spain. Two common chronic conditions in primary care (PC), hypertension and type 2 diabetes, were selected for audit. The assessment of CQI started with a literature review of different databases: Organization for Economic Co-operation and Development, World Health Organization, European Commission European Community Health Indicators, US National Library of Medicine. Data were collected from clinical records. Although it was agreed to obtain the clinical indicators in a similar way from each country, the specific data collection process in every country varied greatly, due to different traditions in collecting and keeping the patients' data, as well as differences in regulation regarding access to clinical information. Also, there was a huge variability across countries in the level of compliance with the indicators. Measurement of clinical performance in PC by audit is methodologically challenging: different databases provide different information, indicators of quality of care have insufficient scientific proof and there are country-specific regulations. There are large differences not only in quality of health care across Europe but also in how it is measured. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
-
Jeong, Sohyun; Han, Nayoung; Choi, Boyoon; Sohn, Minji; Song, Yun-Kyoung; Chung, Myeon-Woo; Na, Han-Sung; Ji, Eunhee; Kim, Hyunah; Rhew, Ki Yon; Kim, Therasa; Kim, In-Wha; Oh, Jung Mi
2016-06-01
To construct a database of published clinical drug trials suitable for use 1) as a research tool in accessing clinical trial information and 2) in evidence-based decision-making by regulatory professionals, clinical research investigators, and medical practitioners. Comprehensive information obtained from a search of design elements and results of clinical trials in peer reviewed journals using PubMed (http://www.ncbi.nlm.ih.gov/pubmed). The methodology to develop a structured database was devised by a panel composed of experts in medical, pharmaceutical, information technology, and members of Ministry of Food and Drug Safety (MFDS) using a step by step approach. A double-sided system consisting of user mode and manager mode served as the framework for the database; elements of interest from each trial were entered via secure manager mode enabling the input information to be accessed in a user-friendly manner (user mode). Information regarding methodology used and results of drug treatment were extracted as detail elements of each data set and then inputted into the web-based database system. Comprehensive information comprising 2,326 clinical trial records, 90 disease states, and 939 drugs entities and concerning study objectives, background, methods used, results, and conclusion could be extracted from published information on phase II/III drug intervention clinical trials appearing in SCI journals within the last 10 years. The extracted data was successfully assembled into a clinical drug trial database with easy access suitable for use as a research tool. The clinically most important therapeutic categories, i.e., cancer, cardiovascular, respiratory, neurological, metabolic, urogenital, gastrointestinal, psychological, and infectious diseases were covered by the database. Names of test and control drugs, details on primary and secondary outcomes and indexed keywords could also be retrieved and built into the database. The construction used in the database enables the user to sort and download targeted information as a Microsoft Excel spreadsheet. Because of the comprehensive and standardized nature of the clinical drug trial database and its ease of access it should serve as valuable information repository and research tool for accessing clinical trial information and making evidence-based decisions by regulatory professionals, clinical research investigators, and medical practitioners.
-
Savige, Judy; Dagher, Hayat; Povey, Sue
2014-07-01
This study examined whether gene-specific DNA variant databases for inherited diseases of the kidney fulfilled the Human Variome Project recommendations of being complete, accurate, clinically relevant and freely available. A recent review identified 60 inherited renal diseases caused by mutations in 132 genes. The disease name, MIM number, gene name, together with "mutation" or "database," were used to identify web-based databases. Fifty-nine diseases (98%) due to mutations in 128 genes had a variant database. Altogether there were 349 databases (a median of 3 per gene, range 0-6), but no gene had two databases with the same number of variants, and 165 (50%) databases included fewer than 10 variants. About half the databases (180, 54%) had been updated in the previous year. Few (77, 23%) were curated by "experts" but these included nine of the 11 with the most variants. Even fewer databases (41, 12%) included clinical features apart from the name of the associated disease. Most (223, 67%) could be accessed without charge, including those for 50 genes (40%) with the maximum number of variants. Future efforts should focus on encouraging experts to collaborate on a single database for each gene affected in inherited renal disease, including both unpublished variants, and clinical phenotypes. © 2014 WILEY PERIODICALS, INC.
-
From randomized controlled trials to observational studies.
Silverman, Stuart L
2009-02-01
Randomized controlled trials are considered the gold standard in the hierarchy of research designs for evaluating the efficacy and safety of a treatment intervention. However, their results can have limited applicability to patients in clinical settings. Observational studies using large health care databases can complement findings from randomized controlled trials by assessing treatment effectiveness in patients encountered in day-to-day clinical practice. Results from these designs can expand upon outcomes of randomized controlled trials because of the use of larger and more diverse patient populations with common comorbidities and longer follow-up periods. Furthermore, well-designed observational studies can identify clinically important differences among therapeutic options and provide data on long-term drug effectiveness and safety.
-
Scott, Frank I; McConnell, Ryan A; Lewis, Matthew E; Lewis, James D
2012-04-01
Significant advances have been made in clinical and epidemiologic research methods over the past 30 years. We sought to demonstrate the impact of these advances on published gastroenterology research from 1980 to 2010. Twenty original clinical articles were randomly selected from each of three journals from 1980, 1990, 2000, and 2010. Each article was assessed for topic, whether the outcome was clinical or physiologic, study design, sample size, number of authors and centers collaborating, reporting of various statistical methods, and external funding. From 1980 to 2010, there was a significant increase in analytic studies, clinical outcomes, number of authors per article, multicenter collaboration, sample size, and external funding. There was increased reporting of P values, confidence intervals, and power calculations, and increased use of large multicenter databases, multivariate analyses, and bioinformatics. The complexity of clinical gastroenterology and hepatology research has increased dramatically, highlighting the need for advanced training of clinical investigators.
-
Song, Peipei; He, Jiangjiang; Li, Fen; Jin, Chunlin
2017-02-01
China is facing the great challenge of treating the world's largest rare disease population, an estimated 16 million patients with rare diseases. One effort offering promise has been a pilot national project that was launched in 2013 and that focused on 20 representative rare diseases. Another government-supported special research program on rare diseases - the "Rare Diseases Clinical Cohort Study" - was launched in December 2016. According to the plan for this research project, the unified National Rare Diseases Registry System of China will be established as of 2020, and a large-scale cohort study will be conducted from 2016 to 2020. The project plans to develop 109 technical standards, to establish and improve 2 national databases of rare diseases - a multi-center clinical database and a biological sample library, and to conduct studies on more than 50,000 registered cases of 50 different rare diseases. More importantly, this study will be combined with the concept of precision medicine. Chinese population-specific basic information on rare diseases, clinical information, and genomic information will be integrated to create a comprehensive predictive model with a follow-up database system and a model to evaluate prognosis. This will provide the evidence for accurate classification, diagnosis, treatment, and estimation of prognosis for rare diseases in China. Numerous challenges including data standardization, protecting patient privacy, big data processing, and interpretation of genetic information still need to be overcome, but research prospects offer great promise.
-
ERIC Educational Resources Information Center
Brett, Denise; Warnell, Frances; McConachie, Helen; Parr, Jeremy R.
2016-01-01
Clinical initiatives have aimed to reduce the age at ASD diagnosis in the UK. This study investigated whether the median age at diagnosis in childhood has reduced in recent years, and identified the factors associated with earlier diagnosis in the UK. Data on 2,134 children with ASD came from two large family databases. Results showed that the age…
-
Yilmaz, T; Cordero-Coma, M; Gallagher, M J
2012-01-01
To assess the effectiveness of ketorolac vs control for prevention of acute pseudophakic cystoid macular edema (CME). The following databases were searched: Medline (1950–June 11, 2011), The Cochrane Library (Issue 2, 2011), and the TRIP Database (up to 11 June 2011), using no language or other limits. Randomized controlled clinical trials (RCTs) were included that consisted of patients with acute pseudophakic cystoid macular edema, those comparing ketorolac with control, and those having at least a minimum follow-up of 28 days. In the four RCTs evaluating ketorolac vs control, treatment with ketorolac significantly reduced the risk of CME development at the end of treatment (∼4 weeks) compared to control (P=0.008; 95% confidence interval (0.03–0.58)). When analyzed individually, each individual study was statistically nonsignificant in its findings with the exception of one study. When the pooled relative risk was calculated, the large sample size of this systematic review led to overall statistical significance, which is attributable to the review's large sample size and not to the individual studies themselves. In this systematic review of four RCTs, two of which compared ketorolac with no treatment and two of which evaluated ketorolac vs placebo drops, treatment with ketorolac significantly reduced the risk of developing CME at the end of ∼4 weeks of treatment compared with controls. These results, however, should be interpreted with caution considering the paucity of large randomized clinical trials in the literature. PMID:22094296
-
Goldacre, Ben; Gray, Jonathan
2016-04-08
OpenTrials is a collaborative and open database for all available structured data and documents on all clinical trials, threaded together by individual trial. With a versatile and expandable data schema, it is initially designed to host and match the following documents and data for each trial: registry entries; links, abstracts, or texts of academic journal papers; portions of regulatory documents describing individual trials; structured data on methods and results extracted by systematic reviewers or other researchers; clinical study reports; and additional documents such as blank consent forms, blank case report forms, and protocols. The intention is to create an open, freely re-usable index of all such information and to increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data and drive up standards around open data in evidence-based medicine. The project has phase I funding. This will allow us to create a practical data schema and populate the database initially through web-scraping, basic record linkage techniques, crowd-sourced curation around selected drug areas, and import of existing sources of structured and documents. It will also allow us to create user-friendly web interfaces onto the data and conduct user engagement workshops to optimise the database and interface designs. Where other projects have set out to manually and perfectly curate a narrow range of information on a smaller number of trials, we aim to use a broader range of techniques and attempt to match a very large quantity of information on all trials. We are currently seeking feedback and additional sources of structured data.
-
LOINC, a universal standard for identifying laboratory observations: a 5-year update.
McDonald, Clement J; Huff, Stanley M; Suico, Jeffrey G; Hill, Gilbert; Leavelle, Dennis; Aller, Raymond; Forrey, Arden; Mercer, Kathy; DeMoor, Georges; Hook, John; Williams, Warren; Case, James; Maloney, Pat
2003-04-01
The Logical Observation Identifier Names and Codes (LOINC) database provides a universal code system for reporting laboratory and other clinical observations. Its purpose is to identify observations in electronic messages such as Health Level Seven (HL7) observation messages, so that when hospitals, health maintenance organizations, pharmaceutical manufacturers, researchers, and public health departments receive such messages from multiple sources, they can automatically file the results in the right slots of their medical records, research, and/or public health systems. For each observation, the database includes a code (of which 25 000 are laboratory test observations), a long formal name, a "short" 30-character name, and synonyms. The database comes with a mapping program called Regenstrief LOINC Mapping Assistant (RELMA(TM)) to assist the mapping of local test codes to LOINC codes and to facilitate browsing of the LOINC results. Both LOINC and RELMA are available at no cost from http://www.regenstrief.org/loinc/. The LOINC medical database carries records for >30 000 different observations. LOINC codes are being used by large reference laboratories and federal agencies, e.g., the CDC and the Department of Veterans Affairs, and are part of the Health Insurance Portability and Accountability Act (HIPAA) attachment proposal. Internationally, they have been adopted in Switzerland, Hong Kong, Australia, and Canada, and by the German national standards organization, the Deutsches Instituts für Normung. Laboratories should include LOINC codes in their outbound HL7 messages so that clinical and research clients can easily integrate these results into their clinical and research repositories. Laboratories should also encourage instrument vendors to deliver LOINC codes in their instrument outputs and demand LOINC codes in HL7 messages they get from reference laboratories to avoid the need to lump so many referral tests under the "send out lab" code.
-
Arbefeville, S; Harris, A; Ferrieri, P
2017-09-01
Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data. 85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases. The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank. Our results indicated that the MicroSEQ® D2 LSU rDNA Fungal Identification Kit was equivalent to the in-house developed ITS regions assay to identify fungi at the genus level. The MycoBank database gave a better curated database and thus allowed a better genus and species identification for both D2 region of the LSU rRNA gene and ITS regions. Copyright © 2017 Elsevier B.V. All rights reserved.
-
Schiodt, Morten; Larsson Wexell, Cecilia; Herlofson, Bente Brokstad; Giltvedt, Karen Marie; Norholt, Sven Erik; Ehrenstein, Vera
2015-01-01
Osteonecrosis of the jaw (ONJ) is a severe side effect associated with antiresorptive treatment. Monitoring of ONJ using routine databases in Scandinavian countries is a challenge owing to lack of valid algorithms and to heterogeneous referral practices. The aim of this paper is to describe the process of establishing a Scandinavian ONJ Cohort enrolling all ONJ cases related to antiresorptive treatment arising in Denmark, Norway, and Sweden between 2011 and 2019. The initial purpose of the cohort is to support an ongoing pharmacovigilance study of denosumab and zoledronic acid in Denmark, Norway, and Sweden. The three countries, with their 199 clinics, departments, and units of oral and maxillofacial surgery, both hospital-based and freestanding, differ somewhat in referral practices of the ONJ patients. By directly contacting all providers of care to ONJ patients in the three countries, we established a network for reporting incident cases to each country’s research database directly or through a member of the Scandinavian ONJ task force as a liaison. The task force includes a Scandinavian coordinator and three national coordinators collaborating directly with the clinics. A uniform ONJ registration form has been developed, and the relevant medical community has been informed either directly or through presentations at professional meetings. A website with study information is published in each country, and data entry is ongoing. This large-scale systematic uniform registration of ONJ cases in Denmark, Norway, and Sweden, with an underlying total population of more than 20 million people, merged into the Scandinavian ONJ Cohort, will contribute to better knowledge and understanding of this challenging group of patients, and ultimately, help improve patient care. The Scandinavian ONJ Cohort as a whole and its component national ONJ research databases may offer the potential for large-scale multinational intervention and safety studies in the future. PMID:25657594
-
Nwaru, Bright I; Soyiri, Ireneous N; Simpson, Colin R; Griffiths, Chris; Sheikh, Aziz
2016-05-26
Randomised clinical trials are the 'gold standard' for evaluating the effectiveness of healthcare interventions. However, successful recruitment of participants remains a key challenge for many trialists. In this paper, we present a conceptual framework for creating a digital, population-based database for the recruitment of asthma patients into future asthma trials in the UK. Having set up the database, the goal is to then make it available to support investigators planning asthma clinical trials. The UK Database of Asthma Research Volunteers will comprise a web-based front-end that interactively allows participant registration, and a back-end that houses the database containing participants' key relevant data. The database will be hosted and maintained at a secure server at the Asthma UK Centre for Applied Research based at The University of Edinburgh. Using a range of invitation strategies, key demographic and clinical data will be collected from those pre-consenting to consider participation in clinical trials. These data will, with consent, in due course, be linkable to other healthcare, social, economic, and genetic datasets. To use the database, asthma investigators will send their eligibility criteria for participant recruitment; eligible participants will then be informed about the new trial and asked if they wish to participate. A steering committee will oversee the running of the database, including approval of usage access. Novel communication strategies will be utilised to engage participants who are recruited into the database in order to avoid attrition as a result of waiting time to participation in a suitable trial, and to minimise the risk of their being approached when already enrolled in a trial. The value of this database will be whether it proves useful and usable to researchers in facilitating recruitment into clinical trials on asthma and whether patient privacy and data security are protected in meeting this aim. Successful recruitment is fundamental to the success of a clinical trial. The UK Database of Asthma Research Volunteers, the first of its kind in the context of asthma, presents a novel approach to overcoming recruitment barriers and will facilitate the catalysing of important clinical trials on asthma in the UK.
-
Swetha, Rayapadi G; Kala Sekar, Dinesh Kumar; Ramaiah, Sudha; Anbarasu, Anand; Sekar, Kanagaraj
2014-12-01
Haemophilus influenzae (H. Influenzae) is the causative agent of pneumonia, bacteraemia and meningitis. The organism is responsible for large number of deaths in both developed and developing countries. Even-though the first bacterial genome to be sequenced was that of H. Influenzae, there is no exclusive database dedicated for H. Influenzae. This prompted us to develop the Haemophilus influenzae Genome Database (HIGDB). All data of HIGDB are stored and managed in MySQL database. The HIGDB is hosted on Solaris server and developed using PERL modules. Ajax and JavaScript are used for the interface development. The HIGDB contains detailed information on 42,741 proteins, 18,077 genes including 10 whole genome sequences and also 284 three dimensional structures of proteins of H. influenzae. In addition, the database provides "Motif search" and "GBrowse". The HIGDB is freely accessible through the URL: http://bioserver1.physics.iisc.ernet.in/HIGDB/. The HIGDB will be a single point access for bacteriological, clinical, genomic and proteomic information of H. influenzae. The database can also be used to identify DNA motifs within H. influenzae genomes and to compare gene or protein sequences of a particular strain with other strains of H. influenzae. Copyright © 2014 Elsevier Ltd. All rights reserved.
-
Vail, Paris J; Morris, Brian; van Kan, Aric; Burdett, Brianna C; Moyes, Kelsey; Theisen, Aaron; Kerr, Iain D; Wenstrup, Richard J; Eggington, Julie M
2015-10-01
Genetic variants of uncertain clinical significance (VUSs) are a common outcome of clinical genetic testing. Locus-specific variant databases (LSDBs) have been established for numerous disease-associated genes as a research tool for the interpretation of genetic sequence variants to facilitate variant interpretation via aggregated data. If LSDBs are to be used for clinical practice, consistent and transparent criteria regarding the deposition and interpretation of variants are vital, as variant classifications are often used to make important and irreversible clinical decisions. In this study, we performed a retrospective analysis of 2017 consecutive BRCA1 and BRCA2 genetic variants identified from 24,650 consecutive patient samples referred to our laboratory to establish an unbiased dataset representative of the types of variants seen in the US patient population, submitted by clinicians and researchers for BRCA1 and BRCA2 testing. We compared the clinical classifications of these variants among five publicly accessible BRCA1 and BRCA2 variant databases: BIC, ClinVar, HGMD (paid version), LOVD, and the UMD databases. Our results show substantial disparity of variant classifications among publicly accessible databases. Furthermore, it appears that discrepant classifications are not the result of a single outlier but widespread disagreement among databases. This study also shows that databases sometimes favor a clinical classification when current best practice guidelines (ACMG/AMP/CAP) would suggest an uncertain classification. Although LSDBs have been well established for research applications, our results suggest several challenges preclude their wider use in clinical practice.
-
The use of intelligent database systems in acute pancreatitis--a systematic review.
van den Heever, Marc; Mittal, Anubhav; Haydock, Matthew; Windsor, John
2014-01-01
Acute pancreatitis (AP) is a complex disease with multiple aetiological factors, wide ranging severity, and multiple challenges to effective triage and management. Databases, data mining and machine learning algorithms (MLAs), including artificial neural networks (ANNs), may assist by storing and interpreting data from multiple sources, potentially improving clinical decision-making. 1) Identify database technologies used to store AP data, 2) collate and categorise variables stored in AP databases, 3) identify the MLA technologies, including ANNs, used to analyse AP data, and 4) identify clinical and non-clinical benefits and obstacles in establishing a national or international AP database. Comprehensive systematic search of online reference databases. The predetermined inclusion criteria were all papers discussing 1) databases, 2) data mining or 3) MLAs, pertaining to AP, independently assessed by two reviewers with conflicts resolved by a third author. Forty-three papers were included. Three data mining technologies and five ANN methodologies were reported in the literature. There were 187 collected variables identified. ANNs increase accuracy of severity prediction, one study showed ANNs had a sensitivity of 0.89 and specificity of 0.96 six hours after admission--compare APACHE II (cutoff score ≥8) with 0.80 and 0.85 respectively. Problems with databases were incomplete data, lack of clinical data, diagnostic reliability and missing clinical data. This is the first systematic review examining the use of databases, MLAs and ANNs in the management of AP. The clinical benefits these technologies have over current systems and other advantages to adopting them are identified. Copyright © 2013 IAP and EPC. Published by Elsevier B.V. All rights reserved.
-
Application of Genetic/Genomic Approaches to Allergic Disorders
Baye, Tesfaye M.; Martin, Lisa J.; Khurana Hershey, Gurjit K.
2010-01-01
Completion of the human genome project and rapid progress in genetics and bioinformatics have enabled the development of large public databases, which include genetic and genomic data linked to clinical health data. With the massive amount of information available, clinicians and researchers have the unique opportunity to complement and integrate their daily practice with the existing resources to clarify the underlying etiology of complex phenotypes such as allergic diseases. The genome itself is now often utilized as a starting point for many studies and multiple innovative approaches have emerged applying genetic/genomic strategies to key questions in the field of allergy and immunology. There have been several successes, which have uncovered new insights into the biologic underpinnings of allergic disorders. Herein, we will provide an in depth review of genomic approaches to identifying genes and biologic networks involved in allergic diseases. We will discuss genetic and phenotypic variation, statistical approaches for gene discovery, public databases, functional genomics, clinical implications, and the challenges that remain. PMID:20638111
-
Yang, Wei; Yi, Dan-Hui; Xie, Yan-Ming; Yang, Wei; Dai, Yi; Zhi, Ying-Jie; Zhuang, Yan; Yang, Hu
2013-09-01
To estimate treatment effects of Shuxuetong injection on abnormal changes on ALT index, that is, to explore whether the Shuxuetong injection harms liver function in clinical settings and to provide clinical guidance for its safe application. Clinical information of traditional Chinese medicine (TCM) injections is gathered from hospital information system (HIS) of eighteen general hospitals. This is a retrospective cohort study, using abnormal changes in ALT index as an outcome. A large number of confounding biases are taken into account through the generalized boosted models (GBM) and multiple logistic regression model (MLRM) to estimate the treatment effects of Shuxuetong injections on abnormal changes in ALT index and to explore possible influencing factors. The advantages and process of application of GBM has been demonstrated with examples which eliminate the biases from most confounding variables between groups. This serves to modify the estimation of treatment effects of Shuxuetong injection on ALT index making the results more reliable. Based on large scale clinical observational data from HIS database, significant effects of Shuxuetong injection on abnormal changes in ALT have not been found.
-
Willemsen, Marjolein H; de Leeuw, Nicole; de Brouwer, Arjan P M; Pfundt, Rolph; Hehir-Kwa, Jayne Y; Yntema, Helger G; Nillesen, Willy M; de Vries, Bert B A; van Bokhoven, Hans; Kleefstra, Tjitske
2012-11-01
Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex. This study provides an overview of the X-Chromosome copy number variations that we have identified by genome-wide array analysis in a large cohort of 4407 male and female patients. We have made an interpretation of the clinical relevance of each of these copy number variations based on well-defined criteria and previous reports in literature and databases. The prevalence of X-chromosome copy number variations in this cohort was 57/4407 (∼1.3%), of which 15 (0.3%) were interpreted as (likely) pathogenic. Copyright © 2012 Elsevier Masson SAS. All rights reserved.
-
Large scale validation of the M5L lung CAD on heterogeneous CT datasets.
Torres, E Lopez; Fiorina, E; Pennazio, F; Peroni, C; Saletta, M; Camarlinghi, N; Fantacci, M E; Cerello, P
2015-04-01
M5L, a fully automated computer-aided detection (CAD) system for the detection and segmentation of lung nodules in thoracic computed tomography (CT), is presented and validated on several image datasets. M5L is the combination of two independent subsystems, based on the Channeler Ant Model as a segmentation tool [lung channeler ant model (lungCAM)] and on the voxel-based neural approach. The lungCAM was upgraded with a scan equalization module and a new procedure to recover the nodules connected to other lung structures; its classification module, which makes use of a feed-forward neural network, is based of a small number of features (13), so as to minimize the risk of lacking generalization, which could be possible given the large difference between the size of the training and testing datasets, which contain 94 and 1019 CTs, respectively. The lungCAM (standalone) and M5L (combined) performance was extensively tested on 1043 CT scans from three independent datasets, including a detailed analysis of the full Lung Image Database Consortium/Image Database Resource Initiative database, which is not yet found in literature. The lungCAM and M5L performance is consistent across the databases, with a sensitivity of about 70% and 80%, respectively, at eight false positive findings per scan, despite the variable annotation criteria and acquisition and reconstruction conditions. A reduced sensitivity is found for subtle nodules and ground glass opacities (GGO) structures. A comparison with other CAD systems is also presented. The M5L performance on a large and heterogeneous dataset is stable and satisfactory, although the development of a dedicated module for GGOs detection could further improve it, as well as an iterative optimization of the training procedure. The main aim of the present study was accomplished: M5L results do not deteriorate when increasing the dataset size, making it a candidate for supporting radiologists on large scale screenings and clinical programs.
-
Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database
Keator, David B.; Wei, Dingying; Fennema-Notestine, Christine; Pease, Karen R.; Bockholt, Jeremy; Grethe, Jeffrey S.
2010-01-01
Managing vast datasets collected throughout multiple clinical imaging communities has become critical with the ever increasing and diverse nature of datasets. Development of data management infrastructure is further complicated by technical and experimental advances that drive modifications to existing protocols and acquisition of new types of research data to be incorporated into existing data management systems. In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit. The database schema is constructed to support the storage of new data types without changes to the underlying schema. The complex infrastructure allows management of experiment data, such as image protocol and behavioral task parameters, as well as subject-specific data, including demographics, clinical assessments, and behavioral task performance metrics. Of significant interest, embedded clinical data entry and management tools enhance both consistency of data reporting and automatic entry of data into the database. The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic clinical assessment management engine (GAME). Importantly, the system is designed to operate in a distributed environment, serving both human users and client applications in a service-oriented manner. Querying capabilities use a built-in multi-database parallel query builder/result combiner, allowing web-accessible queries within and across multiple federated databases. The system along with its documentation is open-source and available from the Neuroimaging Informatics Tools and Resource Clearinghouse (NITRC) site. PMID:20567938
-
Federated web-accessible clinical data management within an extensible neuroimaging database.
Ozyurt, I Burak; Keator, David B; Wei, Dingying; Fennema-Notestine, Christine; Pease, Karen R; Bockholt, Jeremy; Grethe, Jeffrey S
2010-12-01
Managing vast datasets collected throughout multiple clinical imaging communities has become critical with the ever increasing and diverse nature of datasets. Development of data management infrastructure is further complicated by technical and experimental advances that drive modifications to existing protocols and acquisition of new types of research data to be incorporated into existing data management systems. In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit. The database schema is constructed to support the storage of new data types without changes to the underlying schema. The complex infrastructure allows management of experiment data, such as image protocol and behavioral task parameters, as well as subject-specific data, including demographics, clinical assessments, and behavioral task performance metrics. Of significant interest, embedded clinical data entry and management tools enhance both consistency of data reporting and automatic entry of data into the database. The Clinical Assessment Layout Manager (CALM) allows users to create on-line data entry forms for use within and across sites, through which data is pulled into the underlying database via the generic clinical assessment management engine (GAME). Importantly, the system is designed to operate in a distributed environment, serving both human users and client applications in a service-oriented manner. Querying capabilities use a built-in multi-database parallel query builder/result combiner, allowing web-accessible queries within and across multiple federated databases. The system along with its documentation is open-source and available from the Neuroimaging Informatics Tools and Resource Clearinghouse (NITRC) site.
-
Assessment of quality guidelines implementation using a continuous quality improvement programme.
Richards, Nick; Ayala, Juan Antonio; Cesare, Salvatore; Chazot, Charles; Di Benedetto, Attilio; Gassia, Jean-Paul; Merello, Jose-Ignacio; Rentero, Ramon; Scatizzi, Laura; Marcelli, Daniele
2007-01-01
Data from the Dialysis Outcomes and Practice Patterns Study (DOPPS) study suggest that the level of implementation of the European Best Practice Guidelines (EBPG) is at best partial. The main aim of this study is to describe the level of implementation of the EBPG in the European Fresenius Medical Care (FME) clinic network. Data presented in this investigation were gained through the FME database EuCliD (European Clinical Database). Patient data from 4 countries (Great Britain, France, Italy, Spain) were selected from the EuCliD database. The parameters chosen were haemodialysis adequacy, biocompatibility, anaemia control and serum phosphate control, which are surrogate indicators for quality of care. They were compared, by country, between the first quarter (Q1) 2002 and the fourth quarter (Q4) 2005. During Q1 2002 and Q4 2005, respectively, a total of 7,067 and 9,232 patients were treated in FME clinics located in France, Italy, Spain and the UK. This study confirms variations in haemodialysis practices between countries as already described by the DOPPS study. A large proportion of patients in each country achieved the targets recommended by the EBPG in Q4 2005 and this represented a significant improvement over the results achieved in Q1 2002. Differences in practices between countries still exist. The FME CQI programme allows some of these differences to be overcome leading to an improvement in the quality of the treatment delivered. Copyright 2007 S. Karger AG, Basel.
-
Comparing features sets for content-based image retrieval in a medical-case database
NASA Astrophysics Data System (ADS)
Muller, Henning; Rosset, Antoine; Vallee, Jean-Paul; Geissbuhler, Antoine
2004-04-01
Content-based image retrieval systems (CBIRSs) have frequently been proposed for the use in medical image databases and PACS. Still, only few systems were developed and used in a real clinical environment. It rather seems that medical professionals define their needs and computer scientists develop systems based on data sets they receive with little or no interaction between the two groups. A first study on the diagnostic use of medical image retrieval also shows an improvement in diagnostics when using CBIRSs which underlines the potential importance of this technique. This article explains the use of an open source image retrieval system (GIFT - GNU Image Finding Tool) for the retrieval of medical images in the medical case database system CasImage that is used in daily, clinical routine in the university hospitals of Geneva. Although the base system of GIFT shows an unsatisfactory performance, already little changes in the feature space show to significantly improve the retrieval results. The performance of variations in feature space with respect to color (gray level) quantizations and changes in texture analysis (Gabor filters) is compared. Whereas stock photography relies mainly on colors for retrieval, medical images need a large number of gray levels for successful retrieval, especially when executing feedback queries. The results also show that a too fine granularity in the gray levels lowers the retrieval quality, especially with single-image queries. For the evaluation of the retrieval peformance, a subset of the entire case database of more than 40,000 images is taken with a total of 3752 images. Ground truth was generated by a user who defined the expected query result of a perfect system by selecting images relevant to a given query image. The results show that a smaller number of gray levels (32 - 64) leads to a better retrieval performance, especially when using relevance feedback. The use of more scales and directions for the Gabor filters in the texture analysis also leads to improved results but response time is going up equally due to the larger feature space. CBIRSs can be of great use in managing large medical image databases. They allow to find images that might otherwise be lost for research and publications. They also give students students the possibility to navigate within large image repositories. In the future, CBIR might also become more important in case-based reasoning and evidence-based medicine to support the diagnostics because first studies show good results.
-
Digital hand atlas for web-based bone age assessment: system design and implementation
NASA Astrophysics Data System (ADS)
Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente
2000-04-01
A frequently used assessment method of skeletal age is atlas matching by a radiological examination of a hand image against a small set of Greulich-Pyle patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas based on middle upper class white populations in the 1950s, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. The system consists of a hand atlas database, a CAD module and a Java-based Web user interface. The atlas database is based on a large set of clinically normal hand images of diverse ethnic groups. The Java-based Web user interface allows users to interact with the hand image database form browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, is then extracted and compared with patterns from the atlas database to assess the bone age.
-
Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates.
Heunis, Tiaan; Dippenaar, Anzaan; Warren, Robin M; van Helden, Paul D; van der Merwe, Ruben G; Gey van Pittius, Nicolaas C; Pain, Arnab; Sampson, Samantha L; Tabb, David L
2017-10-06
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of the utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study, we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M. tuberculosis Latin American-Mediterranean isolates. Using this approach, we identified 59 peptides containing single amino acid variants, which covered ∼9% of all coding nonsynonymous single nucleotide variants detected by whole-genome sequencing. Furthermore, we identified 29 distinct peptides that mapped to a hypothetical protein not present in the M. tuberculosis H37Rv reference proteome. Here, we provide evidence for the expression of this protein in the clinical M. tuberculosis SAWC3651 isolate. The strain-specific databases enabled confirmation of genomic differences (i.e., large genomic regions of difference and nonsynonymous single nucleotide variants) in these two clinical M. tuberculosis isolates and allowed strain differentiation at the proteome level. Our results contribute to the growing field of clinical microbial proteogenomics and can improve our understanding of phenotypic variation in clinical M. tuberculosis isolates.
-
Roffi, Alice; Krishnakumar, Gopal Shankar; Gostynska, Natalia; Kon, Elizaveta; Candrian, Christian; Filardo, Giuseppe
2017-01-01
Long bone defects represent a clinical challenge. Bone tissue engineering (BTE) has been developed to overcome problems associated with conventional methods. The aim of this study was to assess the BTE strategies available in preclinical and clinical settings and the current evidence supporting this approach. A systematic literature screening was performed on PubMed database, searching for both preclinical (only on large animals) and clinical studies. The following string was used: "(Scaffold OR Implant) AND (Long bone defect OR segmental bone defect OR large bone defect OR bone loss defect)." The search retrieved a total of 1573 articles: 51 preclinical and 4 clinical studies were included. The great amount of preclinical papers published over the past few years showed promising findings in terms of radiological and histological evidence. Unfortunately, this in vivo situation is not reflected by a corresponding clinical impact, with few published papers, highly heterogeneous and with small patient populations. Several aspects should be further investigated to translate positive preclinical findings into clinical protocols: the identification of the best biomaterial, with both biological and biomechanical suitable properties, and the selection of the best choice between cells, GFs, or their combination through standardized models to be validated by randomized trials.
-
Rigoard, P; Slavin, K
2015-03-01
In the context of failed back surgery syndrome (FBSS) treatment, the current practice in neurostimulation varies from center-to-center and most clinical decisions are based on an individual diagnosis. Neurostimulation evaluation tools and pain relief assessment are of major concern, as they now constitute one of the main biases of clinical trials. Moreover, the proliferation of technological devices, in a fertile and unsatisfied market, fosters and only furthers the confusion. There are three options available to apply scientific debates to our daily neurostimulation practice: intentional ignorance, standardized evidence-based practice or alternative data mining approach. In view of the impossibility of conducting multiple randomized clinical trials comparing various devices, one by one, the proposed concept would be to redefine the indications and the respective roles of the various spinal cord and peripheral nerve stimulation devices with large-scale computational modeling/data mining approach, by conducting a multicenter prospective database registry, supported by a clinician's global network called "PROBACK". We chose to specifically analyze 6 parameters: device coverage performance/coverage selectivity/persistence of the long-term electrical response (technical criteria) and comparative mapping of patient pain relief/persistence of the long-term clinical response/safety and complications occurrence (clinical criteria). Two types of analysis will be performed: immediate analysis (including cost analysis) and computational analysis, i.e. demonstration of the robustness of certain correlations of variables, in order to extract response predictors. By creating an international prospective database, the purpose of the PROBACK project was to set up a process of extraction and comparative analysis of data derived from the selection, implantation and follow-up of FBSS patients candidates for implanted neurostimulation. This evaluation strategy should help to change the opinions of each implanter and each health system towards a more rational decision-making approach subtended by mathematical reality. Copyright © 2014 Elsevier Masson SAS. All rights reserved.
-
Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Erturan, Zayre; Ener, Beyza; Akdagli, Sevtap Arikan; Muslumanoglu, Hamza; Cetinkaya, Zafer
2015-10-01
Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis. © 2015 Blackwell Verlag GmbH.
-
Prevalence rates for depression by industry: a claims database analysis
Alterman, Toni; Bushnell, P. Timothy; Li, Jia; Shen, Rui
2015-01-01
Purpose To estimate and interpret differences in depression prevalence rates among industries, using a large, group medical claims database. Methods Depression cases were identified by ICD-9 diagnosis code in a population of 214,413 individuals employed during 2002–2005 by employers based in western Pennsylvania. Data were provided by Highmark, Inc. (Pittsburgh and Camp Hill, PA). Rates were adjusted for age, gender, and employee share of health care costs. National industry measures of psychological distress, work stress, and physical activity at work were also compiled from other data sources. Results Rates for clinical depression in 55 industries ranged from 6.9 to 16.2 %, (population rate = 10.45 %). Industries with the highest rates tended to be those which, on the national level, require frequent or difficult interactions with the public or clients, and have high levels of stress and low levels of physical activity. Conclusions Additional research is needed to help identify industries with relatively high rates of depression in other regions and on the national level, and to determine whether these differences are due in part to specific work stress exposures and physical inactivity at work. Clinical significance Claims database analyses may provide a cost-effective way to identify priorities for depression treatment and prevention in the workplace. PMID:24907896
-
Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease*
Good, David M.; Zürbig, Petra; Argilés, Àngel; Bauer, Hartwig W.; Behrens, Georg; Coon, Joshua J.; Dakna, Mohammed; Decramer, Stéphane; Delles, Christian; Dominiczak, Anna F.; Ehrich, Jochen H. H.; Eitner, Frank; Fliser, Danilo; Frommberger, Moritz; Ganser, Arnold; Girolami, Mark A.; Golovko, Igor; Gwinner, Wilfried; Haubitz, Marion; Herget-Rosenthal, Stefan; Jankowski, Joachim; Jahn, Holger; Jerums, George; Julian, Bruce A.; Kellmann, Markus; Kliem, Volker; Kolch, Walter; Krolewski, Andrzej S.; Luppi, Mario; Massy, Ziad; Melter, Michael; Neusüss, Christian; Novak, Jan; Peter, Karlheinz; Rossing, Kasper; Rupprecht, Harald; Schanstra, Joost P.; Schiffer, Eric; Stolzenburg, Jens-Uwe; Tarnow, Lise; Theodorescu, Dan; Thongboonkerd, Visith; Vanholder, Raymond; Weissinger, Eva M.; Mischak, Harald; Schmitt-Kopplin, Philippe
2010-01-01
Because of its availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics. However, the lack of comparable data sets from large cohorts has greatly hindered the development of clinical proteomics. Here, we report the establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS. All processed data were deposited in an Structured Query Language (SQL) database. This database currently contains 5,010 relevant unique urinary peptides that serve as a pool of potential classifiers for diagnosis and monitoring of various diseases. As an example, by using this source of information, we were able to define urinary peptide biomarkers for chronic kidney diseases, allowing diagnosis of these diseases with high accuracy. Application of the chronic kidney disease-specific biomarker set to an independent test cohort in the subsequent replication phase resulted in 85.5% sensitivity and 100% specificity. These results indicate the potential usefulness of capillary electrophoresis coupled to MS for clinical applications in the analysis of naturally occurring urinary peptides. PMID:20616184
-
Application of cloud database in the management of clinical data of patients with skin diseases.
Mao, Xiao-fei; Liu, Rui; DU, Wei; Fan, Xue; Chen, Dian; Zuo, Ya-gang; Sun, Qiu-ning
2015-04-01
To evaluate the needs and applications of using cloud database in the daily practice of dermatology department. The cloud database was established for systemic scleroderma and localized scleroderma. Paper forms were used to record the original data including personal information, pictures, specimens, blood biochemical indicators, skin lesions,and scores of self-rating scales. The results were input into the cloud database. The applications of the cloud database in the dermatology department were summarized and analyzed. The personal and clinical information of 215 systemic scleroderma patients and 522 localized scleroderma patients were included and analyzed using the cloud database. The disease status,quality of life, and prognosis were obtained by statistical calculations. The cloud database can efficiently and rapidly store and manage the data of patients with skin diseases. As a simple, prompt, safe, and convenient tool, it can be used in patients information management, clinical decision-making, and scientific research.
-
Radiology and Enterprise Medical Imaging Extensions (REMIX).
Erdal, Barbaros S; Prevedello, Luciano M; Qian, Songyue; Demirer, Mutlu; Little, Kevin; Ryu, John; O'Donnell, Thomas; White, Richard D
2018-02-01
Radiology and Enterprise Medical Imaging Extensions (REMIX) is a platform originally designed to both support the medical imaging-driven clinical and clinical research operational needs of Department of Radiology of The Ohio State University Wexner Medical Center. REMIX accommodates the storage and handling of "big imaging data," as needed for large multi-disciplinary cancer-focused programs. The evolving REMIX platform contains an array of integrated tools/software packages for the following: (1) server and storage management; (2) image reconstruction; (3) digital pathology; (4) de-identification; (5) business intelligence; (6) texture analysis; and (7) artificial intelligence. These capabilities, along with documentation and guidance, explaining how to interact with a commercial system (e.g., PACS, EHR, commercial database) that currently exists in clinical environments, are to be made freely available.
-
Semantic Technologies for Re-Use of Clinical Routine Data.
Kreuzthaler, Markus; Martínez-Costa, Catalina; Kaiser, Peter; Schulz, Stefan
2017-01-01
Routine patient data in electronic patient records are only partly structured, and an even smaller segment is coded, mainly for administrative purposes. Large parts are only available as free text. Transforming this content into a structured and semantically explicit form is a prerequisite for querying and information extraction. The core of the system architecture presented in this paper is based on SAP HANA in-memory database technology using the SAP Connected Health platform for data integration as well as for clinical data warehousing. A natural language processing pipeline analyses unstructured content and maps it to a standardized vocabulary within a well-defined information model. The resulting semantically standardized patient profiles are used for a broad range of clinical and research application scenarios.
-
MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.
Grimes, Susan M; Ji, Hanlee P
2014-08-27
Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.
-
Visual Systems for Interactive Exploration and Mining of Large-Scale Neuroimaging Data Archives
Bowman, Ian; Joshi, Shantanu H.; Van Horn, John D.
2012-01-01
While technological advancements in neuroimaging scanner engineering have improved the efficiency of data acquisition, electronic data capture methods will likewise significantly expedite the populating of large-scale neuroimaging databases. As they do and these archives grow in size, a particular challenge lies in examining and interacting with the information that these resources contain through the development of compelling, user-driven approaches for data exploration and mining. In this article, we introduce the informatics visualization for neuroimaging (INVIZIAN) framework for the graphical rendering of, and dynamic interaction with the contents of large-scale neuroimaging data sets. We describe the rationale behind INVIZIAN, detail its development, and demonstrate its usage in examining a collection of over 900 T1-anatomical magnetic resonance imaging (MRI) image volumes from across a diverse set of clinical neuroimaging studies drawn from a leading neuroimaging database. Using a collection of cortical surface metrics and means for examining brain similarity, INVIZIAN graphically displays brain surfaces as points in a coordinate space and enables classification of clusters of neuroanatomically similar MRI images and data mining. As an initial step toward addressing the need for such user-friendly tools, INVIZIAN provides a highly unique means to interact with large quantities of electronic brain imaging archives in ways suitable for hypothesis generation and data mining. PMID:22536181
-
Baxter, Roger; Hansen, John; Timbol, Julius; Pool, Vitali; Greenberg, David P; Johnson, David R; Decker, Michael D
2016-11-01
An observational post-licensure (Phase IV) retrospective large-database safety study was conducted at Kaiser Permanente, a US integrated medical care organization, to assess the safety of Tetanus Toxoid, Reduced Diphtheria Toxoid and 5-Component Acellular Pertussis Vaccine (Tdap5) administered as part of routine healthcare among adolescents and adults. We evaluated incidence rates of various clinical events resulting in outpatient clinic, emergency department (ED), and hospital visits during various time intervals (windows) following Tdap5 vaccination using 2 pharmacoepidemiological methods (risk interval and historic cohort) and several screening thresholds. Plausible outcomes of interest with elevated incidence rate ratios (IRRs) were further evaluated by reviewing individual patient records to confirm the diagnosis, timing (temporal relationship), alternative etiology, and other health record details to discern possible relatedness of the health events to vaccination. Overall, 124,139 people received Tdap5 vaccine from September 2005 through mid-October 2006, and 203,154 in the comparison cohort received a tetanus and diphtheria toxoid adsorbed vaccine (and no live virus vaccine) during the year prior to initiation of this study. In the outpatient, ED and hospital databases, respectively, we identified 11/26, 179/700 and 187/700 unique health outcomes with IRRs significantly >1.0. Among the same unique health outcomes in the outpatient, ED, and hospital databases, 9, 146, and 385, respectively, had IRRs significantly <1.0. Further scrutiny of the outcomes with elevated IRRs did not reveal unexpected signals of adverse outcomes related to vaccination. In conclusion, Tdap5 vaccine was found to be safe among this large population of adolescents and adults.
-
Fujino, Yuri; Asaoka, Ryo; Murata, Hiroshi; Miki, Atsuya; Tanito, Masaki; Mizoue, Shiro; Mori, Kazuhiko; Suzuki, Katsuyoshi; Yamashita, Takehiro; Kashiwagi, Kenji; Shoji, Nobuyuki
2016-04-01
To develop a large-scale real clinical database of glaucoma (Japanese Archive of Multicentral Databases in Glaucoma: JAMDIG) and to investigate the effect of treatment. The study included a total of 1348 eyes of 805 primary open-angle glaucoma patients with 10 visual fields (VFs) measured with 24-2 or 30-2 Humphrey Field Analyzer (HFA) and intraocular pressure (IOP) records in 10 institutes in Japan. Those with 10 reliable VFs were further identified (638 eyes of 417 patients). Mean total deviation (mTD) of the 52 test points in the 24-2 HFA VF was calculated, and the relationship between mTD progression rate and seven variables (age, mTD of baseline VF, average IOP, standard deviation (SD) of IOP, previous argon/selective laser trabeculoplasties (ALT/SLT), previous trabeculectomy, and previous trabeculotomy) was analyzed. The mTD in the initial VF was -6.9 ± 6.2 dB and the mTD progression rate was -0.26 ± 0.46 dB/year. Mean IOP during the follow-up period was 13.5 ± 2.2 mm Hg. Age and SD of IOP were related to mTD progression rate. However, in eyes with average IOP below 15 and also 13 mm Hg, only age and baseline VF mTD were related to mTD progression rate. Age and the degree of VF damage were related to future progression. Average IOP was not related to the progression rate; however, fluctuation of IOP was associated with faster progression, although this was not the case when average IOP was below 15 mm Hg.
-
Baxter, Roger; Hansen, John; Timbol, Julius; Pool, Vitali; Greenberg, David P.; Johnson, David R.; Decker, Michael D.
2016-01-01
ABSTRACT An observational post-licensure (Phase IV) retrospective large-database safety study was conducted at Kaiser Permanente, a US integrated medical care organization, to assess the safety of Tetanus Toxoid, Reduced Diphtheria Toxoid and 5-Component Acellular Pertussis Vaccine (Tdap5) administered as part of routine healthcare among adolescents and adults. We evaluated incidence rates of various clinical events resulting in outpatient clinic, emergency department (ED), and hospital visits during various time intervals (windows) following Tdap5 vaccination using 2 pharmacoepidemiological methods (risk interval and historic cohort) and several screening thresholds. Plausible outcomes of interest with elevated incidence rate ratios (IRRs) were further evaluated by reviewing individual patient records to confirm the diagnosis, timing (temporal relationship), alternative etiology, and other health record details to discern possible relatedness of the health events to vaccination. Overall, 124,139 people received Tdap5 vaccine from September 2005 through mid-October 2006, and 203,154 in the comparison cohort received a tetanus and diphtheria toxoid adsorbed vaccine (and no live virus vaccine) during the year prior to initiation of this study. In the outpatient, ED and hospital databases, respectively, we identified 11/26, 179/700 and 187/700 unique health outcomes with IRRs significantly >1.0. Among the same unique health outcomes in the outpatient, ED, and hospital databases, 9, 146, and 385, respectively, had IRRs significantly <1.0. Further scrutiny of the outcomes with elevated IRRs did not reveal unexpected signals of adverse outcomes related to vaccination. In conclusion, Tdap5 vaccine was found to be safe among this large population of adolescents and adults. PMID:27388557
-
Mapel, D; Pearson, M
2002-08-01
Healthcare payers make decisions on funding for treatments for diseases, such as chronic obstructive pulmonary disease (COPD), on a population level, so require evidence of treatment success in appropriate populations, using usual routine care as the comparison for alternative management approaches. Such health outcomes evidence can be obtained from a number of sources. The 'gold standard' method for obtaining evidence of treatment success is usually taken as the randomized controlled prospective clinical trial. Yet the value of such studies in providing evidence for decision-makers can be questioned due to the restricted entry criteria limiting the ability to generalize to real life populations, narrow focus on individual parameters, use of placebo for comparison rather than usual therapy and unrealistic intense monitoring of patients. Evidence obtained from retrospective and observational studies can supplement that from randomized clinical trials, providing that care is taken to guard against bias and confounders. However, very large numbers of patients must be investigated if small differences between drugs and treatment approaches are to be detected. Administrative databases from healthcare systems provide an opportunity to obtain observational data on large numbers of patients. Such databases have shown that high healthcare costs in patients with COPD are associated with co-morbid conditions and current smoking status. Analysis of an administrative database has also shown that elderly patients with COPD who received inhaled corticosteroids within 90 days of discharge from hospital had 24% fewer repeat hospitalizations for COPD and were 29% less likely to die during the 1-year follow-up period. In conclusion, there are a number of sources of meaningful evidence of the health outcomes arising from different therapeutic approaches that should be of value to healthcare payers making decisions on resource allocation.
-
Kessel, K A; Habermehl, D; Bohn, C; Jäger, A; Floca, R O; Zhang, L; Bougatf, N; Bendl, R; Debus, J; Combs, S E
2012-12-01
Especially in the field of radiation oncology, handling a large variety of voluminous datasets from various information systems in different documentation styles efficiently is crucial for patient care and research. To date, conducting retrospective clinical analyses is rather difficult and time consuming. With the example of patients with pancreatic cancer treated with radio-chemotherapy, we performed a therapy evaluation by using an analysis system connected with a documentation system. A total number of 783 patients have been documented into a professional, database-based documentation system. Information about radiation therapy, diagnostic images and dose distributions have been imported into the web-based system. For 36 patients with disease progression after neoadjuvant chemoradiation, we designed and established an analysis workflow. After an automatic registration of the radiation plans with the follow-up images, the recurrence volumes are segmented manually. Based on these volumes the DVH (dose volume histogram) statistic is calculated, followed by the determination of the dose applied to the region of recurrence. All results are saved in the database and included in statistical calculations. The main goal of using an automatic analysis tool is to reduce time and effort conducting clinical analyses, especially with large patient groups. We showed a first approach and use of some existing tools, however manual interaction is still necessary. Further steps need to be taken to enhance automation. Already, it has become apparent that the benefits of digital data management and analysis lie in the central storage of data and reusability of the results. Therefore, we intend to adapt the analysis system to other types of tumors in radiation oncology.
-
Zhang, Chi; Cai, You-Zhi; Lin, Xiang-Jin
2016-05-01
A literature review of the first-, second- and third-generation autologous chondrocyte implantation (ACI) technique for the treatment of large-sized (>4 cm(2)) and full-thickness knee cartilage defects in young adults was conducted, examining the current literature on features, clinical scores, complications, magnetic resonance image (MRI) and histological outcomes, rehabilitation and cost-effectiveness. A literature review was carried out in the main medical databases to evaluate the several studies concerning ACI treatment of large-sized and full-thickness knee cartilage defects in young adults. ACI technique has been shown to relieve symptoms and improve functional assessment in large-sized (>4 cm(2)) and full-thickness knee articular cartilage defect of young adults in short- and medium-term follow-up. Besides, low level of evidence demonstrated its efficiency and durability at long-term follow-up after implantation. Furthermore, MRI and histological evaluations provided the evidence that graft can return back to the previous nearly normal cartilage via ACI techniques. Clinical outcomes tend to be similar in different ACI techniques, but with simplified procedure, low complication rate and better graft quality in the third-generation ACI technique. ACI based on the experience of cell-based therapy, with the high potential to regenerate hyaline-like tissue, represents clinical development in treatment of large-sized and full-thickness knee cartilage defects. IV.
-
Impact of database quality in knowledge-based treatment planning for prostate cancer.
Wall, Phillip D H; Carver, Robert L; Fontenot, Jonas D
2018-03-13
This article investigates dose-volume prediction improvements in a common knowledge-based planning (KBP) method using a Pareto plan database compared with using a conventional, clinical plan database. Two plan databases were created using retrospective, anonymized data of 124 volumetric modulated arc therapy (VMAT) prostate cancer patients. The clinical plan database (CPD) contained planning data from each patient's clinically treated VMAT plan, which were manually optimized by various planners. The multicriteria optimization database (MCOD) contained Pareto-optimal plan data from VMAT plans created using a standardized multicriteria optimization protocol. Overlap volume histograms, incorporating fractional organ at risk volumes only within the treatment fields, were computed for each patient and used to match new patient anatomy to similar database patients. For each database patient, CPD and MCOD KBP predictions were generated for D 10 , D 30 , D 50 , D 65 , and D 80 of the bladder and rectum in a leave-one-out manner. Prediction achievability was evaluated through a replanning study on a subset of 31 randomly selected database patients using the best KBP predictions, regardless of plan database origin, as planning goals. MCOD predictions were significantly lower than CPD predictions for all 5 bladder dose-volumes and rectum D 50 (P = .004) and D 65 (P < .001), whereas CPD predictions for rectum D 10 (P = .005) and D 30 (P < .001) were significantly less than MCOD predictions. KBP predictions were statistically achievable in the replans for all predicted dose-volumes, excluding D 10 of bladder (P = .03) and rectum (P = .04). Compared with clinical plans, replans showed significant average reductions in D mean for bladder (7.8 Gy; P < .001) and rectum (9.4 Gy; P < .001), while maintaining statistically similar planning target volume, femoral head, and penile bulb dose. KBP dose-volume predictions derived from Pareto plans were more optimal overall than those resulting from manually optimized clinical plans, which significantly improved KBP-assisted plan quality. This work investigates how the plan quality of knowledge databases affects the performance and achievability of dose-volume predictions from a common knowledge-based planning approach for prostate cancer. Bladder and rectum dose-volume predictions derived from a database of standardized Pareto-optimal plans were compared with those derived from clinical plans manually designed by various planners. Dose-volume predictions from the Pareto plan database were significantly lower overall than those from the clinical plan database, without compromising achievability. Copyright © 2018 Elsevier Inc. All rights reserved.
-
The STEP (Safety and Toxicity of Excipients for Paediatrics) database: part 2 - the pilot version.
Salunke, Smita; Brandys, Barbara; Giacoia, George; Tuleu, Catherine
2013-11-30
The screening and careful selection of excipients is a critical step in paediatric formulation development as certain excipients acceptable in adult formulations, may not be appropriate for paediatric use. While there is extensive toxicity data that could help in better understanding and highlighting the gaps in toxicity studies, the data are often scattered around the information sources and saddled with incompatible data types and formats. This paper is the second in a series that presents the update on the Safety and Toxicity of Excipients for Paediatrics ("STEP") database being developed by Eu-US PFIs, and describes the architecture data fields and functions of the database. The STEP database is a user designed resource that compiles the safety and toxicity data of excipients that is scattered over various sources and presents it in one freely accessible source. Currently, in the pilot database data from over 2000 references/10 excipients presenting preclinical, clinical, regulatory information and toxicological reviews, with references and source links. The STEP database allows searching "FOR" excipients and "BY" excipients. This dual nature of the STEP database, in which toxicity and safety information can be searched in both directions, makes it unique from existing sources. If the pilot is successful, the aim is to increase the number of excipients in the existing database so that a database large enough to be of practical research use will be available. It is anticipated that this source will prove to be a useful platform for data management and data exchange of excipient safety information. Copyright © 2013 Elsevier B.V. All rights reserved.
-
Bonfill, Xavier; Osorio, Dimelza; Solà, Ivan; Pijoan, Jose Ignacio; Balasso, Valentina; Quintana, Maria Jesús; Puig, Teresa; Bolibar, Ignasi; Urrútia, Gerard; Zamora, Javier; Emparanza, José Ignacio; Gómez de la Cámara, Agustín; Ferreira-González, Ignacio
2016-01-01
To describe the development of a novel on-line database aimed to serve as a source of information concerning healthcare interventions appraised for their clinical value and appropriateness by several initiatives worldwide, and to present a retrospective analysis of the appraisals already included in the database. Database development and a retrospective analysis. The database DianaHealth.com is already on-line and it is regularly updated, independent, open access and available in English and Spanish. Initiatives are identified in medical news, in article references, and by contacting experts in the field. We include appraisals in the form of clinical recommendations, expert analyses, conclusions from systematic reviews, and original research that label any health care intervention as low-value or inappropriate. We obtain the information necessary to classify the appraisals according to type of intervention, specialties involved, publication year, authoring initiative, and key words. The database is accessible through a search engine which retrieves a list of appraisals and a link to the website where they were published. DianaHealth.com also provides a brief description of the initiatives and a section where users can report new appraisals or suggest new initiatives. From January 2014 to July 2015, the on-line database included 2940 appraisals from 22 initiatives: eleven campaigns gathering clinical recommendations from scientific societies, five sets of conclusions from literature review, three sets of recommendations from guidelines, two collections of articles on low clinical value in medical journals, and an initiative of our own. We have developed an open access on-line database of appraisals about healthcare interventions considered of low clinical value or inappropriate. DianaHealth.com could help physicians and other stakeholders make better decisions concerning patient care and healthcare systems sustainability. Future efforts should be focused on assessing the impact of these appraisals in the clinical practice.
-
Bonfill, Xavier; Osorio, Dimelza; Solà, Ivan; Pijoan, Jose Ignacio; Balasso, Valentina; Quintana, Maria Jesús; Puig, Teresa; Bolibar, Ignasi; Urrútia, Gerard; Zamora, Javier; Emparanza, José Ignacio; Gómez de la Cámara, Agustín; Ferreira-González, Ignacio
2016-01-01
Objective To describe the development of a novel on-line database aimed to serve as a source of information concerning healthcare interventions appraised for their clinical value and appropriateness by several initiatives worldwide, and to present a retrospective analysis of the appraisals already included in the database. Methods and Findings Database development and a retrospective analysis. The database DianaHealth.com is already on-line and it is regularly updated, independent, open access and available in English and Spanish. Initiatives are identified in medical news, in article references, and by contacting experts in the field. We include appraisals in the form of clinical recommendations, expert analyses, conclusions from systematic reviews, and original research that label any health care intervention as low-value or inappropriate. We obtain the information necessary to classify the appraisals according to type of intervention, specialties involved, publication year, authoring initiative, and key words. The database is accessible through a search engine which retrieves a list of appraisals and a link to the website where they were published. DianaHealth.com also provides a brief description of the initiatives and a section where users can report new appraisals or suggest new initiatives. From January 2014 to July 2015, the on-line database included 2940 appraisals from 22 initiatives: eleven campaigns gathering clinical recommendations from scientific societies, five sets of conclusions from literature review, three sets of recommendations from guidelines, two collections of articles on low clinical value in medical journals, and an initiative of our own. Conclusions We have developed an open access on-line database of appraisals about healthcare interventions considered of low clinical value or inappropriate. DianaHealth.com could help physicians and other stakeholders make better decisions concerning patient care and healthcare systems sustainability. Future efforts should be focused on assessing the impact of these appraisals in the clinical practice. PMID:26840451
-
Pearson, Sallie-Anne; Schaffer, Andrea
2014-01-01
Introduction After medicines have been subsidised in Australia we know little about their use in routine clinical practice, impact on resource utilisation, effectiveness or safety. Routinely collected administrative health data are available to address these issues in large population-based pharmacoepidemiological studies. By bringing together cross-jurisdictional data collections that link drug exposure to real-world outcomes, this research programme aims to evaluate the use and impact of cancer medicines in a subset of elderly Australians in the real-world clinical setting. Methods and analysis This ongoing research programme involves a series of retrospective cohort studies of Australian Government Department of Veterans’ Affairs (DVA) clients. The study population includes 104 635 veterans who reside in New South Wales, Australia, and were aged 65 years and over as of 1 July 2004. We will investigate trends in cancer medicines use according to cancer type and other sociodemographic characteristics as well as predictors of the initiation of cancer medicines and other treatment modalities, survival and adverse outcomes among patients with cancer. The programme is underpinned by the linkage of eight health administrative databases under the custodianship of the DVA and the New South Wales Ministry of Health, including cancer notifications, medicines dispensing data, hospitalisation data and health services data. The cancer notifications database is available from 1994 with all other databases available from 2005 onwards. Ethics and dissemination Ethics approval has been granted by the DVA and New South Wales Population and Health Service Research Ethics Committees. Results Results will be reported in peer-reviewed publications, conference presentations and policy forums. The programme has high translational potential, providing invaluable evidence about cancer medicines in an elderly population who are under-represented in clinical trials. PMID:24793244
-
The Clinical Research Landscape in Rhode Island.
Mao, George; Ramratnam, Bharat
2017-01-06
To present an overview of clinical research activity and the state of medical research funding in Rhode Island. We utilized clinicaltrials.gov registry to profile clinical studies between 2011 to 2016. NIH RePORT and other federal databases were used to extract information on levels of federal funding. Previously published hospital financial reports were reviewed for data on hospital-specific total external research funding. During 2011-2016, 1651 clinical studies were registered in clinicaltrials.gov. Nearly a third of all clinical studies were in oncology (21%) and cardiovascular diseases (10%). Alzheimer's dementia, breast cancer, HIV, and hepatitis C accounted for nearly 17% of all clinical trials. Seventy-five percent (75%) of clinical trials in RI were conducted in hospitals affiliated with Lifespan or Care New England. Financial support for clinical trials largely came from industry (60%) with 23% being supported by the National Institutes of Health (NIH). The rest are funded by nonprofit organizations, charitable foundations, educational institutions, and unlisted concerns. [Full article available at http://rimed.org/rimedicaljournal-2017-01.asp].
-
NASA Astrophysics Data System (ADS)
Yin, Lucy; Andrews, Jennifer; Heaton, Thomas
2018-05-01
Earthquake parameter estimations using nearest neighbor searching among a large database of observations can lead to reliable prediction results. However, in the real-time application of Earthquake Early Warning (EEW) systems, the accurate prediction using a large database is penalized by a significant delay in the processing time. We propose to use a multidimensional binary search tree (KD tree) data structure to organize large seismic databases to reduce the processing time in nearest neighbor search for predictions. We evaluated the performance of KD tree on the Gutenberg Algorithm, a database-searching algorithm for EEW. We constructed an offline test to predict peak ground motions using a database with feature sets of waveform filter-bank characteristics, and compare the results with the observed seismic parameters. We concluded that large database provides more accurate predictions of the ground motion information, such as peak ground acceleration, velocity, and displacement (PGA, PGV, PGD), than source parameters, such as hypocenter distance. Application of the KD tree search to organize the database reduced the average searching process by 85% time cost of the exhaustive method, allowing the method to be feasible for real-time implementation. The algorithm is straightforward and the results will reduce the overall time of warning delivery for EEW.
-
Application of kernel functions for accurate similarity search in large chemical databases.
Wang, Xiaohong; Huan, Jun; Smalter, Aaron; Lushington, Gerald H
2010-04-29
Similarity search in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that structure based methods provide an efficient way to do the query. Recently various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models, graph kernel functions can not be applied to large chemical compound database due to the high computational complexity and the difficulties in indexing similarity search for large databases. To bridge graph kernel function and similarity search in chemical databases, we applied a novel kernel-based similarity measurement, developed in our team, to measure similarity of graph represented chemicals. In our method, we utilize a hash table to support new graph kernel function definition, efficient storage and fast search. We have applied our method, named G-hash, to large chemical databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Moreover, the similarity measurement and the index structure is scalable to large chemical databases with smaller indexing size, and faster query processing time as compared to state-of-the-art indexing methods such as Daylight fingerprints, C-tree and GraphGrep. Efficient similarity query processing method for large chemical databases is challenging since we need to balance running time efficiency and similarity search accuracy. Our previous similarity search method, G-hash, provides a new way to perform similarity search in chemical databases. Experimental study validates the utility of G-hash in chemical databases.
-
Predicting adverse hemodynamic events in critically ill patients.
Yoon, Joo H; Pinsky, Michael R
2018-06-01
The art of predicting future hemodynamic instability in the critically ill has rapidly become a science with the advent of advanced analytical processed based on computer-driven machine learning techniques. How these methods have progressed beyond severity scoring systems to interface with decision-support is summarized. Data mining of large multidimensional clinical time-series databases using a variety of machine learning tools has led to our ability to identify alert artifact and filter it from bedside alarms, display real-time risk stratification at the bedside to aid in clinical decision-making and predict the subsequent development of cardiorespiratory insufficiency hours before these events occur. This fast evolving filed is primarily limited by linkage of high-quality granular to physiologic rationale across heterogeneous clinical care domains. Using advanced analytic tools to glean knowledge from clinical data streams is rapidly becoming a reality whose clinical impact potential is great.
-
Generation of Natural-Language Textual Summaries from Longitudinal Clinical Records.
Goldstein, Ayelet; Shahar, Yuval
2015-01-01
Physicians are required to interpret, abstract and present in free-text large amounts of clinical data in their daily tasks. This is especially true for chronic-disease domains, but holds also in other clinical domains. We have recently developed a prototype system, CliniText, which, given a time-oriented clinical database, and appropriate formal abstraction and summarization knowledge, combines the computational mechanisms of knowledge-based temporal data abstraction, textual summarization, abduction, and natural-language generation techniques, to generate an intelligent textual summary of longitudinal clinical data. We demonstrate our methodology, and the feasibility of providing a free-text summary of longitudinal electronic patient records, by generating summaries in two very different domains - Diabetes Management and Cardiothoracic surgery. In particular, we explain the process of generating a discharge summary of a patient who had undergone a Coronary Artery Bypass Graft operation, and a brief summary of the treatment of a diabetes patient for five years.
-
Identifying type 1 and type 2 diabetic cases using administrative data: a tree-structured model.
Lo-Ciganic, Weihsuan; Zgibor, Janice C; Ruppert, Kristine; Arena, Vincent C; Stone, Roslyn A
2011-05-01
To date, few administrative diabetes mellitus (DM) registries have distinguished type 1 diabetes mellitus (T1DM) from type 2 diabetes mellitus (T2DM). Using a classification tree model, a prediction rule was developed to distinguish T1DM from T2DM in a large administrative database. The Medical Archival Retrieval System at the University of Pittsburgh Medical Center included administrative and clinical data from January 1, 2000, through September 30, 2009, for 209,647 DM patients aged ≥18 years. Probable cases (8,173 T1DM and 125,111 T2DM) were identified by applying clinical criteria to administrative data. Nonparametric classification tree models were fit using TIBCO Spotfire S+ 8.1 (TIBCO Software), with model size based on 10-fold cross validation. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of T1DM were estimated. The main predictors that distinguished T1DM from T2DM are age <40 years; International Classification of Disease, 9th revision, codes of T1DM or T2DM diagnosis; inpatient oral hypoglycemic agent use; inpatient insulin use; and episode(s) of diabetic ketoacidosis diagnosis. Compared with a complex clinical algorithm, the tree-structured model to predict T1DM had 92.8% sensitivity, 99.3% specificity, 89.5% PPV, and 99.5% NPV. The preliminary predictive rule appears to be promising. Being able to distinguish between DM subtypes in administrative databases will allow large-scale subtype-specific analyses of medical care costs, morbidity, and mortality. © 2011 Diabetes Technology Society.
-
Ruling out Legionella in community-acquired pneumonia.
Haubitz, Sebastian; Hitz, Fabienne; Graedel, Lena; Batschwaroff, Marcus; Wiemken, Timothy Lee; Peyrani, Paula; Ramirez, Julio A; Fux, Christoph Andreas; Mueller, Beat; Schuetz, Philipp
2014-10-01
Assessing the likelihood for Legionella sp. in community-acquired pneumonia is important because of differences in treatment regimens. Currently used antigen tests and culture have limited sensitivity with important time delays, making empirical broad-spectrum coverage necessary. Therefore, a score with 6 variables recently has been proposed. We sought to validate these parameters in an independent cohort. We analyzed adult patients with community-acquired pneumonia from a large multinational database (Community Acquired Pneumonia Organization) who were treated between 2001 and 2012 with more than 4 of the 6 prespecified clinical variables available. Association and discrimination were assessed using logistic regression analysis and area under the curve (AUC). Of 1939 included patients, the infectious cause was known in 594 (28.9%), including Streptococcus pneumoniae in 264 (13.6%) and Legionella sp. in 37 (1.9%). The proposed clinical predictors fever, cough, hyponatremia, lactate dehydrogenase, C-reactive protein, and platelet count were all associated or tended to be associated with Legionella cause. A logistic regression analysis including all these predictors showed excellent discrimination with an AUC of 0.91 (95% confidence interval, 0.87-0.94). The original dichotomized score showed good discrimination (AUC, 0.73; 95% confidence interval, 0.65-0.81) and a high negative predictive value of 99% for patients with less than 2 parameters present. With the use of a large independent patient sample from an international database, this analysis validates previously proposed clinical variables to accurately rule out Legionella sp., which may help to optimize initial empiric therapy. Copyright © 2014 Elsevier Inc. All rights reserved.
-
Cohort profile: the Western Australian Sleep Health Study.
Mukherjee, Sutapa; Hillman, David; Lee, Jessica; Fedson, Annette; Simpson, Laila; Ward, Kim; Love, Gregory; Edwards, Cass; Szegner, Bernadett; Palmer, Lyle John
2012-03-01
Epidemiologic and genetic studies of obstructive sleep apnoea (OSA) are limited by a lack of large-scale, well-characterized OSA cohorts. These studies require large sample size to provide adequate power to detect differences between groups. This study describes the development of such a cohort (The Western Australian Sleep Health Study) in OSA patients of Caucasian-European origin attending the only public sleep clinic in Western Australia (WA). The main aim of the study is to phenotype 4,000 OSA patients in order to define the genetics of OSA and its co-morbidities. Almost all underwent laboratory-based attended polysomnography (PSG). Currently complete data (questionnaire, biochemistry, DNA, and PSG) has been obtained on over 3,000 individuals and will reach the target of 4,000 individuals by the end of 2010. In a separate but related study, we have developed a sleep study database containing data from all patients who have undergone PSG at the sleep laboratory since its inception in 1988 until the present day (over 30,000 PSG studies representing data from approximately 20,000 individuals). In addition, data from both cohorts have been linked prospectively to statutory health data collected by the WA Department of Health. This study will be the largest sleep clinic cohort database internationally with access to genetic and epidemiological data. It is unique among sleep clinic cohorts because of its size, the breadth of data collected and the ability to link prospectively to statutory health data. It will be a major tool to comprehensively assess genetic and epidemiologic factors determining OSA and its co-morbidities.
-
A comprehensive clinical research database based on CDISC ODM and i2b2.
Meineke, Frank A; Stäubert, Sebastian; Löbe, Matthias; Winter, Alfred
2014-01-01
We present a working approach for a clinical research database as part of an archival information system. The CDISC ODM standard is target for clinical study and research relevant routine data, thus decoupling the data ingest process from the access layer. The presented research database is comprehensive as it covers annotating, mapping and curation of poorly annotated source data. Besides a conventional relational database the medical data warehouse i2b2 serves as main frontend for end-users. The system we developed is suitable to support patient recruitment, cohort identification and quality assurance in daily routine.
-
Risks associated with clinical databases.
Eleazar, P Y
1991-11-01
Providers will succeed who are evaluating themselves, and who are continuously striving to examine who they are and where they are going. Conscientious providers know that countless other agencies have them under the microscope and that they have to work to stay ahead in assessing their actions through their clinical database. "Medical care value purchasing" is what every employer and payor is looking for, and providers need to find ways to illustrate cost in relation to quality. The basics of data security and protection should be in place in order to concentrate on the bigger picture. The knowledge of the risk associated with individual hospital databases as well as the risk associated with comparative databases is critical. The hospital-level clinical database is the hub of the wheel. If the risk there can be minimized, the data headed for various investigative sites will have less inherent risk. When it is really recognized and accepted that all financial decisions are made based upon the clinical data generated at the site of care, then data integrity will become a strategic advantage for the industry. Clinical database goals will, over time, cause minimization of risk at all levels. As this occurs, variation in treatment will be explained artfully.
-
Potential use of routine databases in health technology assessment.
Raftery, J; Roderick, P; Stevens, A
2005-05-01
To develop criteria for classifying databases in relation to their potential use in health technology (HT) assessment and to apply them to a list of databases of relevance in the UK. To explore the extent to which prioritized databases could pick up those HTs being assessed by the National Coordinating Centre for Health Technology Assessment (NCCHTA) and the extent to which these databases have been used in HT assessment. To explore the validation of the databases and their cost. Electronic databases. Key literature sources. Experienced users of routine databases. A 'first principles' examination of the data necessary for each type of HT assessment was carried out, supplemented by literature searches and a historical review. The principal investigators applied the criteria to the databases. Comments of the 'keepers' of the prioritized databases were incorporated. Details of 161 topics funded by the NHS R&D Health Technology Assessment (HTA) programme were reviewed iteratively by the principal investigators. Uses of databases in HTAs were identified by literature searches, which included the title of each prioritized database as a keyword. Annual reports of databases were examined and 'keepers' queried. The validity of each database was assessed using criteria based on a literature search and involvement by the authors in a national academic network. The costs of databases were established from annual reports, enquiries to 'keepers' of databases and 'guesstimates' based on cost per record. For assessing effectiveness, equity and diffusion, routine databases were classified into three broad groups: (1) group I databases, identifying both HTs and health states, (2) group II databases, identifying the HTs, but not a health state, and (3) group III databases, identifying health states, but not an HT. Group I datasets were disaggregated into clinical registries, clinical administrative databases and population-oriented databases. Group III were disaggregated into adverse event reporting, confidential enquiries, disease-only registers and health surveys. Databases in group I can be used not only to assess effectiveness but also to assess diffusion and equity. Databases in group II can only assess diffusion. Group III has restricted scope for assessing HTs, except for analysis of adverse events. For use in costing, databases need to include unit costs or prices. Some databases included unit cost as well as a specific HT. A list of around 270 databases was identified at the level of UK, England and Wales or England (over 1000 including Scotland, Wales and Northern Ireland). Allocation of these to the above groups identified around 60 databases with some potential for HT assessment, roughly half to group I. Eighteen clinical registers were identified as having the greatest potential although the clinical administrative datasets had potential mainly owing to their inclusion of a wide range of technologies. Only two databases were identified that could directly be used in costing. The review of the potential capture of HTs prioritized by the UK's NHS R&D HTA programme showed that only 10% would be captured in these databases, mainly drugs prescribed in primary care. The review of the use of routine databases in any form of HT assessment indicated that clinical registers were mainly used for national comparative audit. Some databases have only been used in annual reports, usually time trend analysis. A few peer-reviewed papers used a clinical register to assess the effectiveness of a technology. Accessibility is suggested as a barrier to using most databases. Clinical administrative databases (group Ib) have mainly been used to build population needs indices and performance indicators. A review of the validity of used databases showed that although internal consistency checks were common, relatively few had any form of external audit. Some comparative audit databases have data scrutinised by participating units. Issues around coverage and coding have, in general, received little attention. NHS funding of databases has been mainly for 'Central Returns' for management purposes, which excludes those databases with the greatest potential for HT assessment. Funding for databases was various, but some are unfunded, relying on goodwill. The estimated total cost of databases in group I plus selected databases from groups II and III has been estimated at pound 50 million or around 0.1% of annual NHS spend. A few databases with limited potential for HT assessment account for the bulk of spending. Suggestions for policy include clarification of responsibility for the strategic development of databases, improved resourcing, and issues around coding, confidentiality, ownership and access, maintenance of clinical support, optimal use of information technology, filling gaps and remedying deficiencies. Recommendations for researchers include closer policy links between routine data and R&D, and selective investment in the more promising databases. Recommended research topics include optimal capture and coding of the range of HTs, international comparisons of the role, funding and use of routine data in healthcare systems and use of routine database in trials and in modelling. Independent evaluations are recommended for information strategies (such as those around the National Service Frameworks and various collaborations) and for electronic patient and health records.
-
The relational clinical database: a possible solution to the star wars in registry systems.
Michels, D K; Zamieroski, M
1990-12-01
In summary, having data from other service areas available in a relational clinical database could resolve many of the problems existing in today's registry systems. Uniting sophisticated information systems into a centralized database system could definitely be a corporate asset in managing the bottom line.
-
Treatment of transverse patellar fractures: a comparison between metallic and non-metallic implants.
Heusinkveld, Maarten H G; den Hamer, Anniek; Traa, Willeke A; Oomen, Pim J A; Maffulli, Nicola
2013-01-01
Several methods of transverse patellar fixation have been described. This study compares the clinical outcome and the occurrence of complications of various fixation methods. The databases PubMed, Web of Science, Science Direct, Google Scholar and Google were searched. A direct comparison between fixation techniques using mixed or non-metallic implants and metallic K-wire and tension band fixation shows no significant difference in clinical outcome between both groups. Additionally, studies reporting novel operation techniques show good clinical results. Studies describing the treatment of patients using non-metallic or mixed implants are fewer compared with those using metallic fixation. A large variety of clinical scoring systems were used for assessing the results of treatment, which makes direct comparison difficult. More data of fracture treatment using non-metallic or mixed implants is needed to achieve a more balanced comparison.
-
B cells gone rogue: the intersection of diffuse large B cell lymphoma and autoimmune disease.
Koff, Jean L; Flowers, Christopher R
2016-06-01
Diffuse large B cell lymphoma (DLBCL) is characterized by genetic, genomic and clinical heterogeneity. Autoimmune diseases (AIDs) have recently been shown to represent significant risk factors for development of DLBCL. Studies that examined the relationships between AIDs and lymphoma in terms of pathogenesis, genetic lesions, and treatment were identified in the MEDLINE database using combinations of medical subject heading (MeSH) terms. Co-authors independently performed study selection for inclusion based on appropriateness of the study question and nature of the study design and sample size. Expert commentary: Identification of AID as a substantial risk factor for DLBCL raises new questions regarding how autoimmunity influences lymphomagenesis and disease behavior. It will be important to identify whether DLBCL cases arising in the setting of AID harbor inferior prognoses, and, if so, whether they also exhibit certain molecular abnormalities that may be targeted to overcome such a gap in clinical outcomes.
-
Lesho, Emil; Lin, Xiaoxu; Clifford, Robert; Snesrud, Erik; Onmus-Leone, Fatma; Appalla, Lakshmi; Ong, Ana; Maybank, Rosslyn; Nielsen, Lindsey; Kwak, Yoon; Hinkle, Mary; Turco, John; Marin, Juan A; Hooks, Sally; Matthews, Stacy; Hyland, Stephen; Little, Jered; Waterman, Paige; McGann, Patrick
2016-07-01
Awareness, responsiveness, and throughput characterize an approach for enhancing the clinical impact of whole genome sequencing for austere environments and for large geographically dispersed health systems. This Department of Defense approach is informing interagency efforts linking antibiograms of multidrug-resistant organisms to their genome sequences in a public database. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.
-
Cutaneous Infections in Wrestlers
Wilson, Eugene K.; deWeber, Kevin; Berry, James W.; Wilckens, John H.
2013-01-01
Context: Cutaneous infections are common in wrestlers. Although many are simply a nuisance in the everyday population, they can be problematic to wrestlers because such infections may result in disqualification from practice or competition. Prompt diagnosis and treatment are therefore important. Evidence Acquisition: Medline and PubMed databases, the Cochrane Database of Systematic Reviews, and UpToDate were searched through 2012 with the following keywords in various combinations: skin infections, cutaneous infections, wrestlers, athletes, methicillin-resistant Staphylococcus aureus, skin and soft tissue infections, tinea corporis, tinea capitis, herpes simplex, varicella zoster, molluscum contagiosum, verruca vulgaris, warts, scabies, and pediculosis. Relevant articles found in the primary search, and selected references from those articles were reviewed for pertinent clinical information. Results: The most commonly reported cutaneous infections in wrestlers are herpes simplex virus infections (herpes gladiatorum), bacterial skin and soft tissue infections, and dermatophyte infections (tinea gladiatorum). The clinical appearance of these infections can be different in wrestlers than in the community at large. Conclusion: For most cutaneous infections, diagnosis and management options in wrestlers are similar to those in the community at large. With atypical presentations, testing methods are recommended to confirm the diagnosis of herpes gladiatorum and tinea gladiatorum. There is evidence to support the use of prophylactic medications to prevent recurrence of herpes simplex virus and reduce the incidence of dermatophyte infections in wrestlers. PMID:24427413
-
Large-scale exploration and analysis of drug combinations.
Li, Peng; Huang, Chao; Fu, Yingxue; Wang, Jinan; Wu, Ziyin; Ru, Jinlong; Zheng, Chunli; Guo, Zihu; Chen, Xuetong; Zhou, Wei; Zhang, Wenjuan; Li, Yan; Chen, Jianxin; Lu, Aiping; Wang, Yonghua
2015-06-15
Drug combinations are a promising strategy for combating complex diseases by improving the efficacy and reducing corresponding side effects. Currently, a widely studied problem in pharmacology is to predict effective drug combinations, either through empirically screening in clinic or pure experimental trials. However, the large-scale prediction of drug combination by a systems method is rarely considered. We report a systems pharmacology framework to predict drug combinations (PreDCs) on a computational model, termed probability ensemble approach (PEA), for analysis of both the efficacy and adverse effects of drug combinations. First, a Bayesian network integrating with a similarity algorithm is developed to model the combinations from drug molecular and pharmacological phenotypes, and the predictions are then assessed with both clinical efficacy and adverse effects. It is illustrated that PEA can predict the combination efficacy of drugs spanning different therapeutic classes with high specificity and sensitivity (AUC = 0.90), which was further validated by independent data or new experimental assays. PEA also evaluates the adverse effects (AUC = 0.95) quantitatively and detects the therapeutic indications for drug combinations. Finally, the PreDC database includes 1571 known and 3269 predicted optimal combinations as well as their potential side effects and therapeutic indications. The PreDC database is available at http://sm.nwsuaf.edu.cn/lsp/predc.php. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
-
Management of pancreatic pseudocysts—A retrospective analysis
Nötzel, Bärbel; Phillip, Veit; Lahmer, Tobias; Schmid, Roland M.; Algül, Hana
2017-01-01
Background Pancreatic pseudocysts arise mostly in patients with alcohol induced chronic pancreatitis causing various symptoms and complications. However, data on the optimal management are rare. To address this problem, we analysed patients with pancreatic pseudocysts treated at our clinic retrospectively. Methods We searched our clinical database for the diagnosis pancreatitis from 2004 till 2014, selected patients with pseudocysts larger than 10 mm and entered all relevant information in a database for statistical analysis. Results In total, 129 patients with pancreatic pseudocysts were treated at our institution during the study period. Most patients suffered from alcohol induced chronic pancreatitis (43.4%; 56/129). Pseudocysts were more frequent in female than in male (2:1) and were mainly located in the pancreatic head (47.3%; 61/129). Local complications like obstructive jaundice were associated with the diameter of the cysts (AUC 0.697 in ROC-curve analysis). However, even cysts up to a diameter of 160 mm can regress spontaneously. Besides a lower re-intervention rate in surgically treated patients, endoscopic, percutaneous and surgical drainage are equally effective. Most treatment related complications occur in large pseudocysts located in the pancreatic head. Conclusion Conservative management of large pseudocysts is successful in many patients. Therefore, indication for treatment should be made carefully considering the presence and risk of local complications. Endoscopic and surgical drainage are equally effective. PMID:28877270
-
Monitoring product safety in the postmarketing environment.
Sharrar, Robert G; Dieck, Gretchen S
2013-10-01
The safety profile of a medicinal product may change in the postmarketing environment. Safety issues not identified in clinical development may be seen and need to be evaluated. Methods of evaluating spontaneous adverse experience reports and identifying new safety risks include a review of individual reports, a review of a frequency distribution of a list of the adverse experiences, the development and analysis of a case series, and various ways of examining the database for signals of disproportionality, which may suggest a possible association. Regulatory agencies monitor product safety through a variety of mechanisms including signal detection of the adverse experience safety reports in databases and by requiring and monitoring risk management plans, periodic safety update reports and postauthorization safety studies. The United States Food and Drug Administration is working with public, academic and private entities to develop methods for using large electronic databases to actively monitor product safety. Important identified risks will have to be evaluated through observational studies and registries.
-
Bluetooth wireless database for scoliosis clinics.
Lou, E; Fedorak, M V; Hill, D L; Raso, J V; Moreau, M J; Mahood, J K
2003-05-01
A database system with Bluetooth wireless connectivity has been developed so that scoliosis clinics can be run more efficiently and data can be mined for research studies without significant increases in equipment cost. The wireless database system consists of a Bluetooth-enabled laptop or PC and a Bluetooth-enabled handheld personal data assistant (PDA). Each patient has a profile in the database, which has all of his or her clinical history. Immediately prior to the examination, the orthopaedic surgeon selects a patient's profile from the database and uploads that data to the PDA over a Bluetooth wireless connection. The surgeon can view the entire clinical history of the patient while in the examination room and, at the same time, enter in any new measurements and comments from the current examination. After seeing the patient, the surgeon synchronises the newly entered information with the database wirelessly and prints a record for the chart. This combination of the database and the PDA both improves efficiency and accuracy and can save significant time, as there is less duplication of work, and no dictation is required. The equipment required to implement this solution is a Bluetooth-enabled PDA and a Bluetooth wireless transceiver for the PC or laptop.
-
The TREAT-NMD DMD Global Database: Analysis of More than 7,000 Duchenne Muscular Dystrophy Mutations
Bladen, Catherine L; Salgado, David; Monges, Soledad; Foncuberta, Maria E; Kekou, Kyriaki; Kosma, Konstantina; Dawkins, Hugh; Lamont, Leanne; Roy, Anna J; Chamova, Teodora; Guergueltcheva, Velina; Chan, Sophelia; Korngut, Lawrence; Campbell, Craig; Dai, Yi; Wang, Jen; Barišić, Nina; Brabec, Petr; Lahdetie, Jaana; Walter, Maggie C; Schreiber-Katz, Olivia; Karcagi, Veronika; Garami, Marta; Viswanathan, Venkatarman; Bayat, Farhad; Buccella, Filippo; Kimura, En; Koeks, Zaïda; van den Bergen, Janneke C; Rodrigues, Miriam; Roxburgh, Richard; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Zimowski, Janusz; Santos, Rosário; Neagu, Elena; Artemieva, Svetlana; Rasic, Vedrana Milic; Vojinovic, Dina; Posada, Manuel; Bloetzer, Clemens; Jeannet, Pierre-Yves; Joncourt, Franziska; Díaz-Manera, Jordi; Gallardo, Eduard; Karaduman, A Ayşe; Topaloğlu, Haluk; El Sherif, Rasha; Stringer, Angela; Shatillo, Andriy V; Martin, Ann S; Peay, Holly L; Bellgard, Matthew I; Kirschner, Jan; Flanigan, Kevin M; Straub, Volker; Bushby, Kate; Verschuuren, Jan; Aartsma-Rus, Annemieke; Béroud, Christophe; Lochmüller, Hanns
2015-01-01
Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations). PMID:25604253
-
Torgerson, Carinna M; Quinn, Catherine; Dinov, Ivo; Liu, Zhizhong; Petrosyan, Petros; Pelphrey, Kevin; Haselgrove, Christian; Kennedy, David N; Toga, Arthur W; Van Horn, John Darrell
2015-03-01
Under the umbrella of the National Database for Clinical Trials (NDCT) related to mental illnesses, the National Database for Autism Research (NDAR) seeks to gather, curate, and make openly available neuroimaging data from NIH-funded studies of autism spectrum disorder (ASD). NDAR has recently made its database accessible through the LONI Pipeline workflow design and execution environment to enable large-scale analyses of cortical architecture and function via local, cluster, or "cloud"-based computing resources. This presents a unique opportunity to overcome many of the customary limitations to fostering biomedical neuroimaging as a science of discovery. Providing open access to primary neuroimaging data, workflow methods, and high-performance computing will increase uniformity in data collection protocols, encourage greater reliability of published data, results replication, and broaden the range of researchers now able to perform larger studies than ever before. To illustrate the use of NDAR and LONI Pipeline for performing several commonly performed neuroimaging processing steps and analyses, this paper presents example workflows useful for ASD neuroimaging researchers seeking to begin using this valuable combination of online data and computational resources. We discuss the utility of such database and workflow processing interactivity as a motivation for the sharing of additional primary data in ASD research and elsewhere.
-
Biermann, Martin
2014-04-01
Clinical trials aiming for regulatory approval of a therapeutic agent must be conducted according to Good Clinical Practice (GCP). Clinical Data Management Systems (CDMS) are specialized software solutions geared toward GCP-trials. They are however less suited for data management in small non-GCP research projects. For use in researcher-initiated non-GCP studies, we developed a client-server database application based on the public domain CakePHP framework. The underlying MySQL database uses a simple data model based on only five data tables. The graphical user interface can be run in any web browser inside the hospital network. Data are validated upon entry. Data contained in external database systems can be imported interactively. Data are automatically anonymized on import, and the key lists identifying the subjects being logged to a restricted part of the database. Data analysis is performed by separate statistics and analysis software connecting to the database via a generic Open Database Connectivity (ODBC) interface. Since its first pilot implementation in 2011, the solution has been applied to seven different clinical research projects covering different clinical problems in different organ systems such as cancer of the thyroid and the prostate glands. This paper shows how the adoption of a generic web application framework is a feasible, flexible, low-cost, and user-friendly way of managing multidimensional research data in researcher-initiated non-GCP clinical projects. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.
-
Viennas, Emmanouil; Komianou, Angeliki; Mizzi, Clint; Stojiljkovic, Maja; Mitropoulou, Christina; Muilu, Juha; Vihinen, Mauno; Grypioti, Panagiota; Papadaki, Styliani; Pavlidis, Cristiana; Zukic, Branka; Katsila, Theodora; van der Spek, Peter J.; Pavlovic, Sonja; Tzimas, Giannis; Patrinos, George P.
2017-01-01
FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications. PMID:27924022
-
Decision support methods for the detection of adverse events in post-marketing data.
Hauben, M; Bate, A
2009-04-01
Spontaneous reporting is a crucial component of post-marketing drug safety surveillance despite its significant limitations. The size and complexity of some spontaneous reporting system databases represent a challenge for drug safety professionals who traditionally have relied heavily on the scientific and clinical acumen of the prepared mind. Computer algorithms that calculate statistical measures of reporting frequency for huge numbers of drug-event combinations are increasingly used to support pharamcovigilance analysts screening large spontaneous reporting system databases. After an overview of pharmacovigilance and spontaneous reporting systems, we discuss the theory and application of contemporary computer algorithms in regular use, those under development, and the practical considerations involved in the implementation of computer algorithms within a comprehensive and holistic drug safety signal detection program.
-
Au, Lewis; Turner, Natalie; Wong, Hui-Li; Field, Kathryn; Lee, Belinda; Boadle, David; Cooray, Prasad; Karikios, Deme; Kosmider, Suzanne; Lipton, Lara; Nott, Louise; Parente, Phillip; Tie, Jeanne; Tran, Ben; Wong, Rachel; Yip, Desmond; Shapiro, Jeremy; Gibbs, Peter
2018-04-01
Current efforts to understand patient management in clinical practice are largely based on clinician surveys with uncertain reliability. The TRACC (Treatment of Recurrent and Advanced Colorectal Cancer) database is a multisite registry collecting comprehensive treatment and outcome data on consecutive metastatic colorectal cancer (mCRC) patients at multiple sites across Australia. This study aims to determine the accuracy of oncologists' impressions of real-word practice by comparing clinicians' estimates to data captured by TRACC. Nineteen medical oncologists from nine hospitals contributing data to TRACC completed a 34-question survey regarding their impression of the management and outcomes of mCRC at their own practice and other hospitals contributing to the database. Responses were then compared with TRACC data to determine how closely their impressions reflected actual practice. Data on 1300 patients with mCRC were available. Median clinician estimated frequency of KRAS testing within 6 months of diagnosis was 80% (range: 20-100%); the TRACC documented rate was 43%. Clinicians generally overestimated the rates of first-line treatment, particularly in patients over 75 years. Estimate for bevacizumab in first line was 60% (35-80%) versus 49% in TRACC. Estimated rate for liver resection varied substantially (5-35%), and the estimated median (27%) was inconsistent with the TRACC rate (12%). Oncologists generally felt their practice was similar to other hospitals. Oncologists' estimates of current clinical practice varied and were discordant with the TRACC database, often with a tendency to overestimate interventions. Clinician surveys alone do not reliably capture contemporary clinical practices in mCRC. © 2017 John Wiley & Sons Australia, Ltd.
-
Krischer, Jeffrey P; Gopal-Srivastava, Rashmi; Groft, Stephen C; Eckstein, David J
2014-08-01
Established in 2003 by the Office of Rare Diseases Research (ORDR), in collaboration with several National Institutes of Health (NIH) Institutes/Centers, the Rare Diseases Clinical Research Network (RDCRN) consists of multiple clinical consortia conducting research in more than 200 rare diseases. The RDCRN supports longitudinal or natural history, pilot, Phase I, II, and III, case-control, cross-sectional, chart review, physician survey, bio-repository, and RDCRN Contact Registry (CR) studies. To date, there have been 24,684 participants enrolled on 120 studies from 446 sites worldwide. An additional 11,533 individuals participate in the CR. Through a central data management and coordinating center (DMCC), the RDCRN's platform for the conduct of observational research encompasses electronic case report forms, federated databases, and an online CR for epidemiological and survey research. An ORDR-governed data repository (through dbGaP, a database for genotype and phenotype information from the National Library of Medicine) has been created. DMCC coordinates with ORDR to register and upload study data to dbGaP for data sharing with the scientific community. The platform provided by the RDCRN DMCC has supported 128 studies, six of which were successfully conducted through the online CR, with 2,352 individuals accrued and a median enrollment time of just 2 months. The RDCRN has built a powerful suite of web-based tools that provide for integration of federated and online database support that can accommodate a large number of rare diseases on a global scale. RDCRN studies have made important advances in the diagnosis and treatment of rare diseases.
-
Cross-checking of Large Evaluated and Experimental Nuclear Reaction Databases
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zeydina, O.; Koning, A.J.; Soppera, N.
2014-06-15
Automated methods are presented for the verification of large experimental and evaluated nuclear reaction databases (e.g. EXFOR, JEFF, TENDL). These methods allow an assessment of the overall consistency of the data and detect aberrant values in both evaluated and experimental databases.
-
Mackey, Aaron J; Pearson, William R
2004-10-01
Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.
-
Shibata, Natsumi; Kimura, Shinya; Hoshino, Takahiro; Takeuchi, Masato; Urushihara, Hisashi
2018-05-11
To date, few large-scale comparative effectiveness studies of influenza vaccination have been conducted in Japan, since marketing authorization for influenza vaccines in Japan has been granted based only on the results of seroconversion and safety in small-sized populations in clinical trial phases not on the vaccine effectiveness. We evaluated the clinical effectiveness of influenza vaccination for children aged 1-15 years in Japan throughout four influenza seasons from 2010 to 2014 in the real world setting. We conducted a cohort study using a large-scale claims database for employee health care insurance plans covering more than 3 million people, including enrollees and their dependents. Vaccination status was identified using plan records for the influenza vaccination subsidies. The effectiveness of influenza vaccination in preventing influenza and its complications was evaluated. To control confounding related to influenza vaccination, odds ratios (OR) were calculated by applying a doubly robust method using the propensity score for vaccination. Total study population throughout the four consecutive influenza seasons was over 116,000. Vaccination rate was higher in younger children and in the recent influenza seasons. Throughout the four seasons, the estimated ORs for influenza onset were statistically significant and ranged from 0.797 to 0.894 after doubly robust adjustment. On age stratification, significant ORs were observed in younger children. Additionally, ORs for influenza complication outcomes, such as pneumonia, hospitalization with influenza and respiratory tract diseases, were significantly reduced, except for hospitalization with influenza in the 2010/2011 and 2012/2013 seasons. We confirmed the clinical effectiveness of influenza vaccination in children aged 1-15 years from the 2010/2011 to 2013/2014 influenza seasons. Influenza vaccine significantly prevented the onset of influenza and was effective in reducing its secondary complications. Copyright © 2018 Elsevier Ltd. All rights reserved.
-
HMDB 4.0: the human metabolome database for 2018
Feunang, Yannick Djoumbou; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vázquez-Fresno, Rosa; Sajed, Tanvir; Johnson, Daniel; Li, Carin; Karu, Naama; Sayeeda, Zinat; Lo, Elvis; Assempour, Nazanin; Berjanskii, Mark; Singhal, Sandeep; Arndt, David; Liang, Yonjie; Badran, Hasan; Grant, Jason; Serra-Cayuela, Arnau; Liu, Yifeng; Mandal, Rupa; Neveu, Vanessa; Pon, Allison; Knox, Craig; Wilson, Michael; Manach, Claudine; Scalbert, Augustin
2018-01-01
Abstract The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB’s chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC–MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science. PMID:29140435
-
Surgical research using national databases
Leland, Hyuma; Heckmann, Nathanael
2016-01-01
Recent changes in healthcare and advances in technology have increased the use of large-volume national databases in surgical research. These databases have been used to develop perioperative risk stratification tools, assess postoperative complications, calculate costs, and investigate numerous other topics across multiple surgical specialties. The results of these studies contain variable information but are subject to unique limitations. The use of large-volume national databases is increasing in popularity, and thorough understanding of these databases will allow for a more sophisticated and better educated interpretation of studies that utilize such databases. This review will highlight the composition, strengths, and weaknesses of commonly used national databases in surgical research. PMID:27867945
-
Surgical research using national databases.
Alluri, Ram K; Leland, Hyuma; Heckmann, Nathanael
2016-10-01
Recent changes in healthcare and advances in technology have increased the use of large-volume national databases in surgical research. These databases have been used to develop perioperative risk stratification tools, assess postoperative complications, calculate costs, and investigate numerous other topics across multiple surgical specialties. The results of these studies contain variable information but are subject to unique limitations. The use of large-volume national databases is increasing in popularity, and thorough understanding of these databases will allow for a more sophisticated and better educated interpretation of studies that utilize such databases. This review will highlight the composition, strengths, and weaknesses of commonly used national databases in surgical research.
-
Hays, Harlen; Castel, Amanda D; Subramanian, Thilakavathy; Happ, Lindsey Powers; Jaurretche, Maria; Binkley, Jeff; Kalmin, Mariah M; Wood, Kathy; Hart, Rachel
2016-01-01
Objective Electronic medical records (EMRs) are being increasingly utilized to conduct clinical and epidemiologic research in numerous fields. To monitor and improve care of HIV-infected patients in Washington, DC, one of the most severely affected urban areas in the United States, we developed a city-wide database across 13 clinical sites using electronic data abstraction and manual data entry from EMRs. Materials and Methods To develop this unique longitudinal cohort, a web-based electronic data capture system (Discovere®) was used. An Agile software development methodology was implemented across multiple EMR platforms. Clinical informatics staff worked with information technology specialists from each site to abstract data electronically from each respective site’s EMR through an extract, transform, and load process. Results Since enrollment began in 2011, more than 7000 patients have been enrolled, with longitudinal clinical data available on all patients. Data sets are produced for scientific analyses on a quarterly basis, and benchmarking reports are generated semi-annually enabling each site to compare their participants’ clinical status, treatments, and outcomes to the aggregated summaries from all other sites. Discussion Numerous technical challenges were identified and innovative solutions developed to ensure the successful implementation of the DC Cohort. Central to the success of this project was the broad collaboration established between government, academia, clinics, community, information technology staff, and the patients themselves. Conclusions Our experiences may have practical implications for researchers who seek to merge data from diverse clinical databases, and are applicable to the study of health-related issues beyond HIV. PMID:26721732
-
Degli Esposti, Luca; Saragoni, Stefania; Buda, Stefano; Sturani, Alessandra; Degli Esposti, Ezio
2013-01-01
Diabetes is one of the most prevalent chronic diseases, and its prevalence is predicted to increase in the next two decades. Diabetes imposes a staggering financial burden on the health care system, so information about the costs and experiences of collecting and reporting quality measures of data is vital for practices deciding whether to adopt quality improvements or monitor existing initiatives. The aim of this study was to quantify the association between health care costs and level of glycemic control in patients with type 2 diabetes using clinical and administrative databases. A retrospective analysis using a large administrative database and a clinical registry containing laboratory results was performed. Patients were subdivided according to their glycated hemoglobin level. Multivariate analyses were used to control for differences in potential confounding factors, including age, gender, Charlson comorbidity index, presence of dyslipidemia, hypertension, or cardiovascular disease, and degree of adherence with antidiabetic drugs among the study groups. Of the total population of 700,000 subjects, 31,022 were identified as being diabetic (4.4% of the entire population). Of these, 21,586 met the study inclusion criteria. In total, 31.5% of patients had very poor glycemic control and 25.7% had excellent control. Over 2 years, the mean diabetes-related cost per person was: €1291.56 in patients with excellent control; €1545.99 in those with good control; €1584.07 in those with fair control; €1839.42 in those with poor control; and €1894.80 in those with very poor control. After adjustment, compared with the group having excellent control, the estimated excess cost per person associated with the groups with good control, fair control, poor control, and very poor control was €219.28, €264.65, €513.18, and €564.79, respectively. Many patients showed suboptimal glycemic control. Lower levels of glycated hemoglobin were associated with lower diabetes-related health care costs. Integration of administrative databases and a laboratory database appears to be suitable for showing that appropriate management of diabetes can help to achieve better resource allocation.
-
Some Reliability Issues in Very Large Databases.
ERIC Educational Resources Information Center
Lynch, Clifford A.
1988-01-01
Describes the unique reliability problems of very large databases that necessitate specialized techniques for hardware problem management. The discussion covers the use of controlled partial redundancy to improve reliability, issues in operating systems and database management systems design, and the impact of disk technology on very large…
-
Managing Attribute—Value Clinical Trials Data Using the ACT/DB Client—Server Database System
Nadkarni, Prakash M.; Brandt, Cynthia; Frawley, Sandra; Sayward, Frederick G.; Einbinder, Robin; Zelterman, Daniel; Schacter, Lee; Miller, Perry L.
1998-01-01
ACT/DB is a client—server database application for storing clinical trials and outcomes data, which is currently undergoing initial pilot use. It stores most of its data in entity—attribute—value form. Such data are segregated according to data type to allow indexing by value when possible, and binary large object data are managed in the same way as other data. ACT/DB lets an investigator design a study rapidly by defining the parameters (or attributes) that are to be gathered, as well as their logical grouping for purposes of display and data entry. ACT/DB generates customizable data entry. The data can be viewed through several standard reports as well as exported as text to external analysis programs. ACT/DB is designed to encourage reuse of parameters across multiple studies and has facilities for dictionary search and maintenance. It uses a Microsoft Access client running on Windows 95 machines, which communicates with an Oracle server running on a UNIX platform. ACT/DB is being used to manage the data for seven studies in its initial deployment. PMID:9524347
-
[Artificial intelligence applied to radiation oncology].
Bibault, J-E; Burgun, A; Giraud, P
2017-05-01
Performing randomised comparative clinical trials in radiation oncology remains a challenge when new treatment modalities become available. One of the most recent examples is the lack of phase III trials demonstrating the superiority of intensity-modulated radiation therapy in most of its current indications. A new paradigm is developing that consists in the mining of large databases to answer clinical or translational issues. Beyond national databases (such as SEER or NCDB), that often lack the necessary level of details on the population studied or the treatments performed, electronic health records can be used to create detailed phenotypic profiles of any patients. In parallel, the Record-and-Verify Systems used in radiation oncology precisely document the planned and performed treatments. Artificial Intelligence and machine learning algorithms can be used to incrementally analyse these data in order to generate hypothesis to better personalize treatments. This review discusses how these methods have already been used in previous studies. Copyright © 2017 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.
-
Roudier, B; Davit, B; Schütz, H; Cardot, J-M
2015-01-01
The in vitro-in vivo correlation (IVIVC) (Food and Drug Administration 1997) aims to predict performances in vivo of a pharmaceutical formulation based on its in vitro characteristics. It is a complex process that (i) incorporates in a gradual and incremental way a large amount of information and (ii) requires information from different properties (formulation, analytical, clinical) and associated dedicated treatments (statistics, modeling, simulation). These results in many studies that are initiated and integrated into the specifications (quality target product profile, QTPP). This latter defines the appropriate experimental designs (quality by design, QbD) (Food and Drug Administration 2011, 2012) whose main objectives are determination (i) of key factors of development and manufacturing (critical process parameters, CPPs) and (ii) of critical points of physicochemical nature relating to active ingredients (API) and critical quality attribute (CQA) which may have implications in terms of efficiency, safety, and inoffensiveness for the patient, due to their non-inclusion. These processes generate a very large amount of data that is necessary to structure. In this context, the storage of information in a database (DB) and the management of this database (database management system, DBMS) become an important issue for the management of projects and IVIVC and more generally for development of new pharmaceutical forms. This article describes the implementation of a prototype object-oriented database (OODB) considered as a tool, which is helpful for decision taking, responding in a structured and consistent way to the issues of project management of IVIVC (including bioequivalence and bioavailability) (Food and Drug Administration 2003) necessary for the implementation of QTPP.
-
Chow, Wing; Miyasato, Gavin; Kokkotos, Fotios K; Bailey, Robert A; Buysman, Erin K; Henk, Henry J
2016-09-01
Randomized controlled trials have found that treatment of type 2 diabetes mellitus with canagliflozin, a sodium glucose co-transporter 2 inhibitor, is associated with significant reductions in glycosylated hemoglobin (HbA1c) levels. However, very few studies have evaluated the effectiveness of sodium glucose co-transporter 2 inhibitors in a real-world context. This data synthesis aims to examine the demographic characteristics and glycemic control among patients treated with canagliflozin in clinical practice, using results obtained from 2 US-specific retrospective administrative claims databases. Data included in the synthesis were derived from 2 large claims databases (the Optum Research Database and the Inovalon MORE(2) Registry, Research Edition) and were obtained from 3 recently published retrospective observational studies of adult patients with type 2 diabetes mellitus who were treated with canagliflozin. Two of the studies used the Optum database (3-month and 6-month follow-up) and 1 study used the Inovalon database (mean follow-up of 4 months). Patient demographic characteristics, clinical characteristics, treatment utilization, and achievement of glycemic goals at baseline and after canagliflozin treatment were evaluated across the 3 studies. Results were assessed using univariate descriptive statistics. Baseline demographic characteristics were generally similar between the Optum and Inovalon cohorts. Mean baseline HbA1c was 8.7% in the Optum and 8.3% in the Inovalon cohort. Seventy-five percent of the Optum (3-month study) cohort and 74% of the Inovalon cohort used 2 or more antihyperglycemic agents. During follow-up, in both cohorts, the proportion of patients who achieved tight glycemic control (HbA1c <7.0%) more than doubled, while the proportion who had poor control (HbA1c ≥9.0%) decreased by approximately 50%. Among patients who had baseline HbA1c ≥7.0%, 21% of the Optum cohort and 24% of the Inovalon cohort achieved tight glycemic control (HbA1c <7.0%), and the proportion of patients achieving HbA1c <8.0% more than doubled in both cohorts (from 30% to 61% in the Optum cohort, and from 33% to 69% in the Inovalon cohort). This synthesis of real-world data from 2 large patient databases suggests that treatment of type 2 diabetes mellitus with canagliflozin is associated with significant and consistent improvements in glycemic control. Patients with varying HbA1c control and multiple antihyperglycemic agent use were able to lower their HbA1c levels with canagliflozin treatment. Additional studies with longer follow-up would be beneficial to evaluate the durability of the real-world effectiveness of canagliflozin. Copyright © 2016 Elsevier HS Journals, Inc. All rights reserved.
-
National Administrative Databases in Adult Spinal Deformity Surgery: A Cautionary Tale.
Buckland, Aaron J; Poorman, Gregory; Freitag, Robert; Jalai, Cyrus; Klineberg, Eric O; Kelly, Michael; Passias, Peter G
2017-08-15
Comparison between national administrative databases and a prospective multicenter physician managed database. This study aims to assess the applicability of National Administrative Databases (NADs) in adult spinal deformity (ASD). Our hypothesis is that NADs do not include comparable patients as in a physician-managed database (PMD) for surgical outcomes in adult spinal deformity. NADs such as National Inpatient Sample (NIS) and National Surgical Quality Improvement Program (NSQIP) provide large numbers of publications owing to ease of data access and lack of IRB approval requirement. These databases utilize billing codes, not clinical inclusion criteria, and have not been validated against PMDs in ASD surgery. The NIS was searched for years 2002 to 2012 and NSQIP for years 2006 to 2013 using validated spinal deformity diagnostic codes. Procedural codes (ICD-9 and CPT) were then applied to each database. A multicenter PMD including years 2008 to 2015 was used for comparison. Databases were assessed for levels fused, osteotomies, decompressed levels, and invasiveness. Database comparisons for surgical details were made in all patients, and also for patients with ≥ 5 level spinal fusions. Approximately, 37,368 NIS, 1291 NSQIP, and 737 PMD patients were identified. NADs showed an increased use of deformity billing codes over the study period (NIS doubled, 68x NSQIP, P < 0.001), but ASD remained stable in the PMD.Surgical invasiveness, levels fused and use of 3-column osteotomy (3-CO) were significantly lower for all patients in the NIS (11.4-13.7) and NSQIP databases (6.4-12.7) compared with PMD (27.5-32.3). When limited to patients with ≥5 levels, invasiveness, levels fused, and use of 3-CO remained significantly higher in the PMD compared with NADs (P < 0.001). National databases NIS and NSQIP do not capture the same patient population as is captured in PMDs in ASD. Physicians should remain cautious in interpreting conclusions drawn from these databases. 4.
-
An algorithm of discovering signatures from DNA databases on a computer cluster.
Lee, Hsiao Ping; Sheu, Tzu-Fang
2014-10-05
Signatures are short sequences that are unique and not similar to any other sequence in a database that can be used as the basis to identify different species. Even though several signature discovery algorithms have been proposed in the past, these algorithms require the entirety of databases to be loaded in the memory, thus restricting the amount of data that they can process. It makes those algorithms unable to process databases with large amounts of data. Also, those algorithms use sequential models and have slower discovery speeds, meaning that the efficiency can be improved. In this research, we are debuting the utilization of a divide-and-conquer strategy in signature discovery and have proposed a parallel signature discovery algorithm on a computer cluster. The algorithm applies the divide-and-conquer strategy to solve the problem posed to the existing algorithms where they are unable to process large databases and uses a parallel computing mechanism to effectively improve the efficiency of signature discovery. Even when run with just the memory of regular personal computers, the algorithm can still process large databases such as the human whole-genome EST database which were previously unable to be processed by the existing algorithms. The algorithm proposed in this research is not limited by the amount of usable memory and can rapidly find signatures in large databases, making it useful in applications such as Next Generation Sequencing and other large database analysis and processing. The implementation of the proposed algorithm is available at http://www.cs.pu.edu.tw/~fang/DDCSDPrograms/DDCSD.htm.
-
Koeks, Zaïda; Bladen, Catherine L.; Salgado, David; van Zwet, Erik; Pogoryelova, Oksana; McMacken, Grace; Monges, Soledad; Foncuberta, Maria E.; Kekou, Kyriaki; Kosma, Konstantina; Dawkins, Hugh; Lamont, Leanne; Bellgard, Matthew I.; Roy, Anna J.; Chamova, Teodora; Guergueltcheva, Velina; Chan, Sophelia; Korngut, Lawrence; Campbell, Craig; Dai, Yi; Wang, Jen; Barišić, Nina; Brabec, Petr; Lähdetie, Jaana; Walter, Maggie C.; Schreiber-Katz, Olivia; Karcagi, Veronika; Garami, Marta; Herczegfalvi, Agnes; Viswanathan, Venkatarman; Bayat, Farhad; Buccella, Filippo; Ferlini, Alessandra; Kimura, En; van den Bergen, Janneke C.; Rodrigues, Miriam; Roxburgh, Richard; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Santos, Rosário; Neagu, Elena; Artemieva, Svetlana; Rasic, Vedrana Milic; Vojinovic, Dina; Posada, Manuel; Bloetzer, Clemens; Klein, Andrea; Díaz-Manera, Jordi; Gallardo, Eduard; Karaduman, A. Ayşe; Oznur, Tunca; Topaloğlu, Haluk; El Sherif, Rasha; Stringer, Angela; Shatillo, Andriy V.; Martin, Ann S.; Peay, Holly L.; Kirschner, Jan; Flanigan, Kevin M.; Straub, Volker; Bushby, Kate; Béroud, Christophe; Verschuuren, Jan J.; Lochmüller, Hanns
2017-01-01
Background: Recent short-term clinical trials in patients with Duchenne Muscular Dystrophy (DMD) have indicated greater disease variability in terms of progression than expected. In addition, as average life-expectancy increases, reliable data is required on clinical progression in the older DMD population. Objective: To determine the effects of corticosteroids on major clinical outcomes of DMD in a large multinational cohort of genetically confirmed DMD patients. Methods: In this cross-sectional study we analysed clinical data from 5345 genetically confirmed DMD patients from 31 countries held within the TREAT-NMD global DMD database. For analysis patients were categorised by corticosteroid background and further stratified by age. Results: Loss of ambulation in non-steroid treated patients was 10 years and in corticosteroid treated patients 13 years old (p = 0.0001). Corticosteroid treated patients were less likely to need scoliosis surgery (p < 0.001) or ventilatory support (p < 0.001) and there was a mild cardioprotective effect of corticosteroids in the patient population aged 20 years and older (p = 0.0035). Patients with a single deletion of exon 45 showed an increased survival in contrast to other single exon deletions. Conclusions: This study provides data on clinical outcomes of DMD across many healthcare settings and including a sizeable cohort of older patients. Our data confirm the benefits of corticosteroid treatment on ambulation, need for scoliosis surgery, ventilation and, to a lesser extent, cardiomyopathy. This study underlines the importance of data collection via patient registries and the critical role of multi-centre collaboration in the rare disease field. PMID:29125504
-
2010-01-01
Background Our Thyroid-Multidisciplinary Clinic is a large referral site for thyroid diseases. Thyroid biopsies are mainly performed for thyroid cancer screening. Yet, Hashimoto thyroiditis (HT) is being too frequently diagnosed. The prevalence of HT is reported as 0.3-1.2% or twice the prevalence of type 1 diabetes. However, the prevalence of HT confirmed by cytology is still uncertain. To evaluate different aspects of thyroid physiopathology including prevalence of Hashimoto's, a database of clinical features, ultrasound images and cytology results of patients referred for FNA of thyroid nodules was prospectively developed. Methods We retrospectively studied 811 consecutive patients for whom ultrasound guided thyroid FNA biopsies were performed at our clinic over 2.5 year period (Mar/2006-Sep/2008). Results The analysis of our database revealed that from 761 patients, 102 (13.4%) had HT, from whom 56 (7.4%) were euthyroid or had sub-clinical (non-hypothyroid) disease, and 46 (6%) were clinically hypothyroid. Conclusions This is the first study to show such a high prevalence of HT diagnosed by ultrasound-guided FNA. More strikingly, the prevalence of euthyroid HT, appears to be >5% similar to that of type 2 diabetes. Based on our results, there might be a need to follow up on cytological Hashimoto's to monitor for thyroid failure, especially in high risk states, like pregnancy. The potential risk for thyroid cancer in patients with biopsy-proven inflammation of thyroid epithelium remains to be established prospectively. However, it may explain the increased risk for thyroid cancer observed in patients with elevated but within normal TSH. PMID:21172028
-
Koeks, Zaïda; Bladen, Catherine L; Salgado, David; van Zwet, Erik; Pogoryelova, Oksana; McMacken, Grace; Monges, Soledad; Foncuberta, Maria E; Kekou, Kyriaki; Kosma, Konstantina; Dawkins, Hugh; Lamont, Leanne; Bellgard, Matthew I; Roy, Anna J; Chamova, Teodora; Guergueltcheva, Velina; Chan, Sophelia; Korngut, Lawrence; Campbell, Craig; Dai, Yi; Wang, Jen; Barišić, Nina; Brabec, Petr; Lähdetie, Jaana; Walter, Maggie C; Schreiber-Katz, Olivia; Karcagi, Veronika; Garami, Marta; Herczegfalvi, Agnes; Viswanathan, Venkatarman; Bayat, Farhad; Buccella, Filippo; Ferlini, Alessandra; Kimura, En; van den Bergen, Janneke C; Rodrigues, Miriam; Roxburgh, Richard; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Santos, Rosário; Neagu, Elena; Artemieva, Svetlana; Rasic, Vedrana Milic; Vojinovic, Dina; Posada, Manuel; Bloetzer, Clemens; Klein, Andrea; Díaz-Manera, Jordi; Gallardo, Eduard; Karaduman, A Ayşe; Oznur, Tunca; Topaloğlu, Haluk; El Sherif, Rasha; Stringer, Angela; Shatillo, Andriy V; Martin, Ann S; Peay, Holly L; Kirschner, Jan; Flanigan, Kevin M; Straub, Volker; Bushby, Kate; Béroud, Christophe; Verschuuren, Jan J; Lochmüller, Hanns
2017-01-01
Recent short-term clinical trials in patients with Duchenne Muscular Dystrophy (DMD) have indicated greater disease variability in terms of progression than expected. In addition, as average life-expectancy increases, reliable data is required on clinical progression in the older DMD population. To determine the effects of corticosteroids on major clinical outcomes of DMD in a large multinational cohort of genetically confirmed DMD patients. In this cross-sectional study we analysed clinical data from 5345 genetically confirmed DMD patients from 31 countries held within the TREAT-NMD global DMD database. For analysis patients were categorised by corticosteroid background and further stratified by age. Loss of ambulation in non-steroid treated patients was 10 years and in corticosteroid treated patients 13 years old (p = 0.0001). Corticosteroid treated patients were less likely to need scoliosis surgery (p < 0.001) or ventilatory support (p < 0.001) and there was a mild cardioprotective effect of corticosteroids in the patient population aged 20 years and older (p = 0.0035). Patients with a single deletion of exon 45 showed an increased survival in contrast to other single exon deletions. This study provides data on clinical outcomes of DMD across many healthcare settings and including a sizeable cohort of older patients. Our data confirm the benefits of corticosteroid treatment on ambulation, need for scoliosis surgery, ventilation and, to a lesser extent, cardiomyopathy. This study underlines the importance of data collection via patient registries and the critical role of multi-centre collaboration in the rare disease field.
-
Xu, Jie; Liu, Yi; Tao, Yongli; Xie, Xuewei; Gu, Hongqiu; Pan, Yuesong; Zhao, Xingquan; Wang, Yongjun; Yan, Aoshuang; Wang, Yilong
2016-01-01
The relationship between poststroke blood pressure (BP) and clinical outcomes in ischemic stroke (IS) is still controversial. However, there is no large BP database for IS or transient ischemic attack (TIA) in China. This study aims to describe the rationale, study design, and baseline characteristics of a nationwide BP database in IS or TIA patients in China. The BOSS (blood pressure and clinical outcome in TIA or ischemic stroke) study was a hospital-based, prospective cohort study aiming to assess BP parameters and clinical outcome in IS/TIA patients. BP parameters were based on office BP, ambulatory BP, and home BP. Clinical outcomes included stroke recurrence, combined vascular events, and disability. Electronic case-report forms were used to record baseline and follow-up data. The patients were followed up for clinical outcomes at 3 months through face-to-face interview and at 12 months by telephone. Between October 2012 and February 2014, the BOSS registry recruited 2,608 patients from 61 hospitals, with a mean age of 62.5 years, 32.4% of whom were female, 88.9% with an entry diagnosis of IS, and 86% diagnosed with hypertension. The rates of patients lost-to-follow-up were 3.1% at 3 months and 5.1% at 1 year; 93% of patients completed ambulatory BP monitoring during hospitalization and 94.7% finished a 3-month BP diary. The BOSS registry will provide important evidence about BP management in the acute phase and secondary prevention for IS/TIA patients.
-
Pollack, C D; Diers, D
1996-01-01
Hospital information systems have been collecting patient-related data systematically for years. This article describes a course developed at the Yale University School of Nursing that uses hospital data as "textbook" to teach graduate nursing students to navigate a large hospital data set, enabling a multitude of nursing questions to be addressed. The approach used in this course is easily transferrable to the practice setting as demonstrated by the authors. Through understanding patient-level data, their aggregate patterns, and overall database construction, nurses can expand their contributions to clinical practice and management.
-
Leary, Alison; Cook, Rob; Jones, Sarahjane; Smith, Judith; Gough, Malcolm; Maxwell, Elaine; Punshon, Geoffrey; Radford, Mark
2016-12-16
Nursing is a safety critical activity but not easily quantified. This makes the building of predictive staffing models a challenge. The aim of this study was to determine if relationships between registered and non-registered nurse staffing levels and clinical outcomes could be discovered through the mining of routinely collected clinical data. The secondary aim was to examine the feasibility and develop the use of 'big data' techniques commonly used in industry for this area of healthcare and examine future uses. The data were obtained from 1 large acute National Health Service hospital trust in England. Routinely collected physiological, signs and symptom data from a clinical database were extracted, imported and mined alongside a bespoke staffing and outcomes database using Mathmatica V.10. The physiological data consisted of 120 million patient entries over 6 years, the bespoke database consisted of 9 years of daily data on staffing levels and safety factors such as falls. To discover patterns in these data or non-linear relationships that would contribute to modelling. To examine feasibility of this technique in this field. After mining, 40 correlations (p<0.00005) emerged between safety factors, physiological data (such as the presence or absence of nausea) and staffing factors. Several inter-related factors demonstrated step changes where registered nurse availability appeared to relate to physiological parameters or outcomes such as falls and the management of symptoms. Data extraction proved challenging as some commercial databases were not built for extraction of the massive data sets they contain. The relationship between staffing and outcomes appears to exist. It appears to be non-linear but calculable and a data-driven model appears possible. These findings could be used to build an initial mathematical model for acute staffing which could be further tested. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.
-
Zhou, Quan; Tao, Jing; Song, Huamei; Chen, Aihua; Yang, Huaijie; Zuo, Manzhen; Li, Hairong
2016-12-01
Kuntai capsule has been widely used for the treatment of menopausal syndrome in China for long time. We conducted this review to assess efficacy and safety of Kuntai capsule for the treatment of menopausal syndrome. We searched studies in PubMed, ClinicalTrials, the Cochrane Library, China National Knowledge Infrastructure Database(CNKI), China Science and Technology Journal Database (VIP), Wan fang Database and Chinese Biomedical Literature Database(CBM) until November 20, 2014. Randomized trials on Kuntai capsule for menopausal syndrome, compared with placebo or hormone replacement therapy (HRT) were included. Two reviewers independently retrieved the randomized controlled trials (RCTs) and extracted the information. The Cochrane risk of bias method was used to assess the quality of the included studies, and a Meta-analysis was conducted with Review Manager 5.2 software. A total of 17 RCTs (1455 participants) were included. The studies were of low methodological quality. Meta-analysis indicated that there was no statistical difference in the Kupperman index (KI) [WMD=0.51, 95% CI (-0.04, 1.06)], the effective rate of KI [OR=1.21, 95% CI (0.72, 2.04)], E2 level [WMD=-15.18, 95% CI (-33.93, 3.56)], and FSH level [WMD=-3.46, 95% CI (-7.2, 0.28)] after treatment between Kuntai versus HRT group (P>0.05). However, Compared with HRT, Kuntai capsule could significantly reduce the total incidence of adverse events [OR=0.28, 95% CI (0.17, 0.45)]. Kuntai capsule may be effective for treating menopausal syndrome and lower risk of side effects. The studies we analyzed were of low methodological quality. Therefore, more strictly designed large-scale randomized clinical trials are needed to evaluate the efficacy of Kuntai capsule in menopausal syndrome. Copyright © 2016 Elsevier Ltd. All rights reserved.
-
From Pharmacovigilance to Clinical Care Optimization.
Celi, Leo Anthony; Moseley, Edward; Moses, Christopher; Ryan, Padhraig; Somai, Melek; Stone, David; Tang, Kai-Ou
2014-09-01
In order to ensure the continued, safe administration of pharmaceuticals, particularly those agents that have been recently introduced into the market, there is a need for improved surveillance after product release. This is particularly so because drugs are used by a variety of patients whose particular characteristics may not have been fully captured in the original market approval studies. Even well-conducted, randomized controlled trials are likely to have excluded a large proportion of individuals because of any number of issues. The digitization of medical care, which yields rich and accessible drug data amenable to analytic techniques, provides an opportunity to capture the required information via observational studies. We propose the development of an open, accessible database containing properly de-identified data, to provide the substrate for the required improvement in pharmacovigilance. A range of stakeholders could use this to identify delayed and low-frequency adverse events. Moreover, its power as a research tool could extend to the detection of complex interactions, potential novel uses, and subtle subpopulation effects. This far-reaching potential is demonstrated by our experience with the open Multi-parameter Intelligent Monitoring in Intensive Care (MIMIC) intensive care unit database. The new database could also inform the development of objective, robust clinical practice guidelines. Careful systematization and deliberate standardization of a fully digitized pharmacovigilance process is likely to save both time and resources for healthcare in general.
-
A Naive Bayes machine learning approach to risk prediction using censored, time-to-event data.
Wolfson, Julian; Bandyopadhyay, Sunayan; Elidrisi, Mohamed; Vazquez-Benitez, Gabriela; Vock, David M; Musgrove, Donald; Adomavicius, Gediminas; Johnson, Paul E; O'Connor, Patrick J
2015-09-20
Predicting an individual's risk of experiencing a future clinical outcome is a statistical task with important consequences for both practicing clinicians and public health experts. Modern observational databases such as electronic health records provide an alternative to the longitudinal cohort studies traditionally used to construct risk models, bringing with them both opportunities and challenges. Large sample sizes and detailed covariate histories enable the use of sophisticated machine learning techniques to uncover complex associations and interactions, but observational databases are often 'messy', with high levels of missing data and incomplete patient follow-up. In this paper, we propose an adaptation of the well-known Naive Bayes machine learning approach to time-to-event outcomes subject to censoring. We compare the predictive performance of our method with the Cox proportional hazards model which is commonly used for risk prediction in healthcare populations, and illustrate its application to prediction of cardiovascular risk using an electronic health record dataset from a large Midwest integrated healthcare system. Copyright © 2015 John Wiley & Sons, Ltd.
-
Similarity-based modeling in large-scale prediction of drug-drug interactions.
Vilar, Santiago; Uriarte, Eugenio; Santana, Lourdes; Lorberbaum, Tal; Hripcsak, George; Friedman, Carol; Tatonetti, Nicholas P
2014-09-01
Drug-drug interactions (DDIs) are a major cause of adverse drug effects and a public health concern, as they increase hospital care expenses and reduce patients' quality of life. DDI detection is, therefore, an important objective in patient safety, one whose pursuit affects drug development and pharmacovigilance. In this article, we describe a protocol applicable on a large scale to predict novel DDIs based on similarity of drug interaction candidates to drugs involved in established DDIs. The method integrates a reference standard database of known DDIs with drug similarity information extracted from different sources, such as 2D and 3D molecular structure, interaction profile, target and side-effect similarities. The method is interpretable in that it generates drug interaction candidates that are traceable to pharmacological or clinical effects. We describe a protocol with applications in patient safety and preclinical toxicity screening. The time frame to implement this protocol is 5-7 h, with additional time potentially necessary, depending on the complexity of the reference standard DDI database and the similarity measures implemented.
-
The development of health care data warehouses to support data mining.
Lyman, Jason A; Scully, Kenneth; Harrison, James H
2008-03-01
Clinical data warehouses offer tremendous benefits as a foundation for data mining. By serving as a source for comprehensive clinical and demographic information on large patient populations, they streamline knowledge discovery efforts by providing standard and efficient mechanisms to replace time-consuming and expensive original data collection, organization, and processing. Building effective data warehouses requires knowledge of and attention to key issues in database design, data acquisition and processing, and data access and security. In this article, the authors provide an operational and technical definition of data warehouses, present examples of data mining projects enabled by existing data warehouses, and describe key issues and challenges related to warehouse development and implementation.
-
Willison, Hugh J; Jacobs, Bart C; van Doorn, Pieter A
2016-08-13
Guillain-Barré syndrome is the most common and most severe acute paralytic neuropathy, with about 100,000 people developing the disorder every year worldwide. Under the umbrella term of Guillain-Barré syndrome are several recognisable variants with distinct clinical and pathological features. The severe, generalised manifestation of Guillain-Barré syndrome with respiratory failure affects 20-30% of cases. Treatment with intravenous immunoglobulin or plasma exchange is the optimal management approach, alongside supportive care. Understanding of the infectious triggers and immunological and pathological mechanisms has advanced substantially in the past 10 years, and is guiding clinical trials investigating new treatments. Investigators of large, worldwide, collaborative studies of the spectrum of Guillain-Barré syndrome are accruing data for clinical and biological databases to inform the development of outcome predictors and disease biomarkers. Such studies are transforming the clinical and scientific landscape of acute autoimmune neuropathies. Copyright © 2016 Elsevier Ltd. All rights reserved.
-
Large image microscope array for the compilation of multimodality whole organ image databases.
Namati, Eman; De Ryk, Jessica; Thiesse, Jacqueline; Towfic, Zaid; Hoffman, Eric; Mclennan, Geoffrey
2007-11-01
Three-dimensional, structural and functional digital image databases have many applications in education, research, and clinical medicine. However, to date, apart from cryosectioning, there have been no reliable means to obtain whole-organ, spatially conserving histology. Our aim was to generate a system capable of acquiring high-resolution images, featuring microscopic detail that could still be spatially correlated to the whole organ. To fulfill these objectives required the construction of a system physically capable of creating very fine whole-organ sections and collecting high-magnification and resolution digital images. We therefore designed a large image microscope array (LIMA) to serially section and image entire unembedded organs while maintaining the structural integrity of the tissue. The LIMA consists of several integrated components: a novel large-blade vibrating microtome, a 1.3 megapixel peltier cooled charge-coupled device camera, a high-magnification microscope, and a three axis gantry above the microtome. A custom control program was developed to automate the entire sectioning and automated raster-scan imaging sequence. The system is capable of sectioning unembedded soft tissue down to a thickness of 40 microm at specimen dimensions of 200 x 300 mm to a total depth of 350 mm. The LIMA system has been tested on fixed lung from sheep and mice, resulting in large high-quality image data sets, with minimal distinguishable disturbance in the delicate alveolar structures. Copyright 2007 Wiley-Liss, Inc.
-
Rosato, Stefano; D'Errigo, Paola; Badoni, Gabriella; Fusco, Danilo; Perucci, Carlo A; Seccareccia, Fulvia
2008-08-01
The availability of two contemporary sources of information about coronary artery bypass graft (CABG) interventions, allowed 1) to verify the feasibility of performing outcome evaluation studies using administrative data sources, and 2) to compare hospital performance obtainable using the CABG Project clinical database with hospital performance derived from the use of current administrative data. Interventions recorded in the CABG Project were linked to the hospital discharge record (HDR) administrative database. Only the linked records were considered for subsequent analyses (46% of the total CABG Project). A new selected population "clinical card-HDR" was then defined. Two independent risk-adjustment models were applied, each of them using information derived from one of the two different sources. Then, HDR information was supplemented with some patient preoperative conditions from the CABG clinical database. The two models were compared in terms of their adaptability to data. Hospital performances identified by the two different models and significantly different from the mean was compared. In only 4 of the 13 hospitals considered for analysis, the results obtained using the HDR model did not completely overlap with those obtained by the CABG model. When comparing statistical parameters of the HDR model and the HDR model + patient preoperative conditions, the latter showed the best adaptability to data. In this "clinical card-HDR" population, hospital performance assessment obtained using information from the clinical database is similar to that derived from the use of current administrative data. However, when risk-adjustment models built on administrative databases are supplemented with a few clinical variables, their statistical parameters improve and hospital performance assessment becomes more accurate.
-
Does filler database size influence identification accuracy?
Bergold, Amanda N; Heaton, Paul
2018-06-01
Police departments increasingly use large photo databases to select lineup fillers using facial recognition software, but this technological shift's implications have been largely unexplored in eyewitness research. Database use, particularly if coupled with facial matching software, could enable lineup constructors to increase filler-suspect similarity and thus enhance eyewitness accuracy (Fitzgerald, Oriet, Price, & Charman, 2013). However, with a large pool of potential fillers, such technologies might theoretically produce lineup fillers too similar to the suspect (Fitzgerald, Oriet, & Price, 2015; Luus & Wells, 1991; Wells, Rydell, & Seelau, 1993). This research proposes a new factor-filler database size-as a lineup feature affecting eyewitness accuracy. In a facial recognition experiment, we select lineup fillers in a legally realistic manner using facial matching software applied to filler databases of 5,000, 25,000, and 125,000 photos, and find that larger databases are associated with a higher objective similarity rating between suspects and fillers and lower overall identification accuracy. In target present lineups, witnesses viewing lineups created from the larger databases were less likely to make correct identifications and more likely to select known innocent fillers. When the target was absent, database size was associated with a lower rate of correct rejections and a higher rate of filler identifications. Higher algorithmic similarity ratings were also associated with decreases in eyewitness identification accuracy. The results suggest that using facial matching software to select fillers from large photograph databases may reduce identification accuracy, and provides support for filler database size as a meaningful system variable. (PsycINFO Database Record (c) 2018 APA, all rights reserved).
-
Lovell, Karina; Bee, Penny
2011-12-01
Obsessive-compulsive disorder (OCD) is a chronic and disabling mental health problem. Only a minority of people receive evidence-based psychological treatments, and this deficit has prompted an increasing focus on delivering cognitive behaviour therapy (CBT) in new and innovative ways. To conduct a scoping review of the published evidence base for CBT-based interventions incorporating a health technology in the treatment of OCD. The questions posed by the review were (a) are technology-assisted treatments clinically effective, (b) are patient outcomes durable and (c) are more innovative services deemed acceptable by those individuals who engage in them? Scoping review of published studies using any study design examining CBT interventions incorporating a health technology for OCD. Electronic databases searched included MEDLINE (1966-2010), PsycInfo (1967-2010), EMBASE (1980-2010) and CINAHL databases (1982-2010). Thirteen studies were identified, of these, five used bibliotherapy, five examined computerised CBT (cCBT), two investigated telephone delivered CBT and one evaluated video conferencing. Overall studies were small and methodologically flawed, which precludes definitive conclusions of clinical effectiveness, durability or stakeholder satisfaction. To date the evidence base for technology-enhanced OCD treatments has undergone limited development. Future research should seek to overcome the methodological shortcomings of published work by conducting large-scale trials that incorporate clinical, cost and acceptability outcomes.
-
Clinical nursing and midwifery research in Latin American and Caribbean countries: A scoping review.
Iribarren, Sarah; Stonbraker, Samantha; Larsen, Brandon; Santos, Islane; Faria, Renata; Góes, Fernanda S N; Binfa, Lorena; Larson, Elaine
2018-04-01
To identify and describe published, nursing-led and midwifery-led, clinical research that has been conducted in Latin America and the Caribbean. Peer-reviewed published research may correspond to and elucidate country's realities, priorities, and needs. A 6-stage scoping review methodology was used to search scientific databases using an applied search strategy. Five databases were searched for articles published in English, Spanish, or Portuguese conducted in a Latin American or Caribbean country between January 1, 2006 and June 14, 2016. Articles were independently considered for inclusion by 2 researchers, data extracted, and study characteristics described. Of 6922 articles identified, 404 were included. The majority were conducted in Brazil (90.6%) followed by Chile (2.5%). Most were nurse-led (95.8%) and were implemented in hospitals (48.6%). Studies frequently explored patient knowledge or characterized patient populations (61.3%) and commonly assessed chronic disease (19.3%) or maternity/child health outcomes (15.9%). Findings revealed a large number of publications but an uneven geographical distribution of nurse-led clinical research and an evident gap of midwifery-related research in Latin America and the Caribbean. Results may be used to build research agendas to promote nursing and midwifery research capacity and further establish evidence-based practice. © 2018 John Wiley & Sons Australia, Ltd.
-
Aromatherapy as an adjuvant treatment in cancer care--a descriptive systematic review.
Boehm, Katja; Büssing, Arndt; Ostermann, Thomas
2012-01-01
Claims of benefits of aromatherapy for cancer patients include reduced anxiety levels and relief of emotional stress, pain, muscular tension and fatigue. The objective of this paper is to provide an updated descriptive, systematic review of evidence from pre-clinical and clinical trials assessing the benefits and safety of aromatherapy for cancer patients. Literature databases such as Medline (via Ovid), the Cochrane database of systematic reviews, Cochrane Central were searched from their inception until October 2010. Only studies on cancer cells or cancer patients were included. There is no long lasting effect of aromatherapy massage, while short term improvements were reported for general well being, anxiety and depression up to 8 weeks after treatment. The reviewed studies indicate short-term effects of aromatherapy on depression, anxiety and overall wellbeing. Specifically, some clinical trials found an increase in patient-identified symptom relief, psychological wellbeing and improved sleep. Furthermore, some found a short-term improvement (up to 2 weeks after treatment) in anxiety and depression scores and better pain control. Although essential oils have generally shown minimal adverse effects, potential risks include ingesting large amounts (intentional misuse); local skin irritation, especially with prolonged skin contact; allergic contact dermatitis; and phototoxicity from reaction to sunlight (some oils). Repeated topical administration of lavender and tea tree oil was associated with reversible prepubertal gynecomastia.
-
Hwang, Thomas J; Kesselheim, Aaron S
2016-02-01
Many serious diseases lack safe and effective vaccines. Using a large commercial database, we examined trends in global vaccine research and development and found that the proportion of new vaccine candidates entering all stages of clinical development increased by 3-5 percentage points over the past two decades. Small and medium-size companies accounted for nearly twice as many new Phase I vaccine trials compared to large companies, but late-stage (Phase III) vaccine trials were dominated by large companies. There were no significant differences between vaccines and drugs in the probability of success in clinical trials or in profitability. Small and medium-size companies, including spin-outs from academic research centers, play an important role in innovative research and discovery. Our findings suggest that policy making targeted at smaller companies, such as prizes or opportunities for public-private partnerships, could support the development of new vaccines, particularly those targeting unmet medical needs and emerging public health threats. Project HOPE—The People-to-People Health Foundation, Inc.
-
Towards building high performance medical image management system for clinical trials
NASA Astrophysics Data System (ADS)
Wang, Fusheng; Lee, Rubao; Zhang, Xiaodong; Saltz, Joel
2011-03-01
Medical image based biomarkers are being established for therapeutic cancer clinical trials, where image assessment is among the essential tasks. Large scale image assessment is often performed by a large group of experts by retrieving images from a centralized image repository to workstations to markup and annotate images. In such environment, it is critical to provide a high performance image management system that supports efficient concurrent image retrievals in a distributed environment. There are several major challenges: high throughput of large scale image data over the Internet from the server for multiple concurrent client users, efficient communication protocols for transporting data, and effective management of versioning of data for audit trails. We study the major bottlenecks for such a system, propose and evaluate a solution by using a hybrid image storage with solid state drives and hard disk drives, RESTfulWeb Services based protocols for exchanging image data, and a database based versioning scheme for efficient archive of image revision history. Our experiments show promising results of our methods, and our work provides a guideline for building enterprise level high performance medical image management systems.
-
Federal Register 2010, 2011, 2012, 2013, 2014
2013-02-01
... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Proposed Collection; Comment Request (60-Day FRN); The Clinical Trials Reporting Program (CTRP) Database (NCI) SUMMARY: In compliance... publication. Proposed Collection: The Clinical Trials Reporting Program (CTRP) Database, 0925-0600, Expiration...
-
Sex differences in mortality following acute coronary syndromes.
Berger, Jeffrey S; Elliott, Laine; Gallup, Dianne; Roe, Matthew; Granger, Christopher B; Armstrong, Paul W; Simes, R John; White, Harvey D; Van de Werf, Frans; Topol, Eric J; Hochman, Judith S; Newby, L Kristin; Harrington, Robert A; Califf, Robert M; Becker, Richard C; Douglas, Pamela S
2009-08-26
Conflicting information exists about whether sex differences modulate short-term mortality following acute coronary syndromes (ACS). To investigate the relationship between sex and 30-day mortality in ACS, and to determine whether this relationship was modified by clinical syndrome or coronary anatomy using a large database across the spectrum of ACS and adjusting for potentially confounding clinical covariates. A convenience sample of patients pooled from 11 independent, international, randomized ACS clinical trials between 1993 and 2006 whose databases are maintained at the Duke Clinical Research Institute, Durham, North Carolina. Of 136 247 patients, 38 048 (28%) were women; 102 004 (26% women) with ST-segment elevation myocardial infarction (STEMI), 14 466 (29% women) with non-STEMI (NSTEMI), and 19 777 (40% women) with unstable angina. Thirty-day mortality following ACS. Thirty-day mortality was 9.6% in women and 5.3% in men (odds ratio [OR], 1.91; 95% confidence interval [CI], 1.83-2.00). After multivariable adjustment, mortality was not significantly different between women and men (adjusted OR, 1.06; 95% CI, 0.99-1.15). A significant sex by type of ACS interaction was demonstrated (P < .001). In STEMI, 30-day mortality was higher among women (adjusted OR, 1.15; 95% CI, 1.06-1.24), whereas in NSTEMI (adjusted OR, 0.77; 95% CI, 0.63-0.95) and unstable angina, mortality was lower among women (adjusted OR, 0.55; 95% CI, 0.43-0.70). In a cohort of 35 128 patients with angiographic data, women more often had nonobstructive (15% vs 8%) and less often had 2-vessel (25% vs 28%) and 3-vessel (23% vs 26%) coronary disease, regardless of ACS type. After additional adjustment for angiographic disease severity, 30-day mortality among women was not significantly different than men, regardless of ACS type. The relationship between sex and 30-day mortality was similar across the levels of angiographic disease severity (P for interaction = .70). Sex-based differences existed in 30-day mortality among patients with ACS and vary depending on clinical presentation. However, these differences appear to be largely explained by clinical differences at presentation and severity of angiographically documented disease.
-
Narayana, D B Anantha; Durg, Sharanbasappa; Manohar, P Ram; Mahapatra, Anita; Aramya, A R
2017-02-02
Chyawanprash (CP), a traditional immune booster recipe, has a long history of ethnic origin, development, household preparation and usage. There are even mythological stories about the origin of this recipe including its nomenclature. In the last six decades, CP, because of entrepreneurial actions of some research Vaidyas (traditional doctors) has grown to industrial production and marketing in packed forms to a large number of consumers/patients like any food or health care product. Currently, CP has acquired a large accepted user base in India and in a few countries out-side India. Authoritative texts, recognized by the Drugs and Cosmetics Act of India, describe CP as an immunity enhancer and strength giver meant for improving lung functions in diseases with compromised immunity. This review focuses on published clinical efficacy and safety studies of CP for correlation with health benefits as documented in the authoritative texts, and also briefs on its recipes and processes. Authoritative texts were searched for recipes, processes, and other technical details of CP. Labels of marketing CP products (Indian) were studied for the health claims. Electronic search for studies of CP on efficacy and safety data were performed in PubMed/MEDLINE and DHARA (Digital Helpline for Ayurveda Research Articles), and Ayurvedic books were also searched for clinical studies. The documented clinical studies from electronic databases and Ayurvedic books evidenced that individuals who consume CP regularly for a definite period of time showed improvement in overall health status and immunity. However, most of the clinical studies in this review are of smaller sample size and short duration. Further, limitation to access and review significant data on traditional products like CP in electronic databases was noted. Randomized controlled trials of high quality with larger sample size and longer follow-up are needed to have significant evidence on the clinical use of CP as immunity booster. Additional studies involving measurement of current biomarkers of immunity pre- and post-consumption of the product as well as benefits accruing with the use of CP as an adjuvant are suggested. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
-
Su, Xiaoquan; Xu, Jian; Ning, Kang
2012-10-01
It has long been intriguing scientists to effectively compare different microbial communities (also referred as 'metagenomic samples' here) in a large scale: given a set of unknown samples, find similar metagenomic samples from a large repository and examine how similar these samples are. With the current metagenomic samples accumulated, it is possible to build a database of metagenomic samples of interests. Any metagenomic samples could then be searched against this database to find the most similar metagenomic sample(s). However, on one hand, current databases with a large number of metagenomic samples mostly serve as data repositories that offer few functionalities for analysis; and on the other hand, methods to measure the similarity of metagenomic data work well only for small set of samples by pairwise comparison. It is not yet clear, how to efficiently search for metagenomic samples against a large metagenomic database. In this study, we have proposed a novel method, Meta-Storms, that could systematically and efficiently organize and search metagenomic data. It includes the following components: (i) creating a database of metagenomic samples based on their taxonomical annotations, (ii) efficient indexing of samples in the database based on a hierarchical taxonomy indexing strategy, (iii) searching for a metagenomic sample against the database by a fast scoring function based on quantitative phylogeny and (iv) managing database by index export, index import, data insertion, data deletion and database merging. We have collected more than 1300 metagenomic data from the public domain and in-house facilities, and tested the Meta-Storms method on these datasets. Our experimental results show that Meta-Storms is capable of database creation and effective searching for a large number of metagenomic samples, and it could achieve similar accuracies compared with the current popular significance testing-based methods. Meta-Storms method would serve as a suitable database management and search system to quickly identify similar metagenomic samples from a large pool of samples. ningkang@qibebt.ac.cn Supplementary data are available at Bioinformatics online.
-
Huang, Taoying; Shenoy, Pareen J.; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W.; Flowers, Christopher R.
2009-01-01
Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid™ (caBIG™) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system™ (LEAD™), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute’s Center for Bioinformatics to establish the LEAD™ platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD™ could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG™ can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG™ to the management of clinical and biological data. PMID:19492074
-
Development of the Lymphoma Enterprise Architecture Database: a caBIG Silver level compliant system.
Huang, Taoying; Shenoy, Pareen J; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W; Flowers, Christopher R
2009-04-03
Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid (caBIG) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system (LEAD), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute's Center for Bioinformatics to establish the LEAD platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG to the management of clinical and biological data.
-
Online database for documenting clinical pathology resident education.
Hoofnagle, Andrew N; Chou, David; Astion, Michael L
2007-01-01
Training of clinical pathologists is evolving and must now address the 6 core competencies described by the Accreditation Council for Graduate Medical Education (ACGME), which include patient care. A substantial portion of the patient care performed by the clinical pathology resident takes place while the resident is on call for the laboratory, a practice that provides the resident with clinical experience and assists the laboratory in providing quality service to clinicians in the hospital and surrounding community. Documenting the educational value of these on-call experiences and providing evidence of competence is difficult for residency directors. An online database of these calls, entered by residents and reviewed by faculty, would provide a mechanism for documenting and improving the education of clinical pathology residents. With Microsoft Access we developed an online database that uses active server pages and secure sockets layer encryption to document calls to the clinical pathology resident. Using the data collected, we evaluated the efficacy of 3 interventions aimed at improving resident education. The database facilitated the documentation of more than 4 700 calls in the first 21 months it was online, provided archived resident-generated data to assist in serving clients, and demonstrated that 2 interventions aimed at improving resident education were successful. We have developed a secure online database, accessible from any computer with Internet access, that can be used to easily document clinical pathology resident education and competency.
-
[Design of computerised database for clinical and basic management of uveal melanoma].
Bande Rodríguez, M F; Santiago Varela, M; Blanco Teijeiro, M J; Mera Yañez, P; Pardo Perez, M; Capeans Tome, C; Piñeiro Ces, A
2012-09-01
The uveal melanoma is the most common primary intraocular tumour in adults. The objective of this work is to show how a computerised database has been formed with specific applications, for clinical and research use, to an extensive group of patients diagnosed with uveal melanoma. For the design of the database a selection of categories, attributes and values was created based on the classifications and parameters given by various authors of articles which have had great relevance in the field of uveal melanoma in recent years. The database has over 250 patient entries with specific information on their clinical history, diagnosis, treatment and progress. It enables us to search any parameter of the entry and make quick and simple statistical studies of them. The database models have been transformed into a basic tool for clinical practice, as they are an efficient way of storing, compiling and selective searching of information. When creating a database it is very important to define a common strategy and the use of a standard language. Copyright © 2011 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.
-
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lopez Torres, E., E-mail: Ernesto.Lopez.Torres@cern.ch, E-mail: cerello@to.infn.it; Fiorina, E.; Pennazio, F.
Purpose: M5L, a fully automated computer-aided detection (CAD) system for the detection and segmentation of lung nodules in thoracic computed tomography (CT), is presented and validated on several image datasets. Methods: M5L is the combination of two independent subsystems, based on the Channeler Ant Model as a segmentation tool [lung channeler ant model (lungCAM)] and on the voxel-based neural approach. The lungCAM was upgraded with a scan equalization module and a new procedure to recover the nodules connected to other lung structures; its classification module, which makes use of a feed-forward neural network, is based of a small number ofmore » features (13), so as to minimize the risk of lacking generalization, which could be possible given the large difference between the size of the training and testing datasets, which contain 94 and 1019 CTs, respectively. The lungCAM (standalone) and M5L (combined) performance was extensively tested on 1043 CT scans from three independent datasets, including a detailed analysis of the full Lung Image Database Consortium/Image Database Resource Initiative database, which is not yet found in literature. Results: The lungCAM and M5L performance is consistent across the databases, with a sensitivity of about 70% and 80%, respectively, at eight false positive findings per scan, despite the variable annotation criteria and acquisition and reconstruction conditions. A reduced sensitivity is found for subtle nodules and ground glass opacities (GGO) structures. A comparison with other CAD systems is also presented. Conclusions: The M5L performance on a large and heterogeneous dataset is stable and satisfactory, although the development of a dedicated module for GGOs detection could further improve it, as well as an iterative optimization of the training procedure. The main aim of the present study was accomplished: M5L results do not deteriorate when increasing the dataset size, making it a candidate for supporting radiologists on large scale screenings and clinical programs.« less
-
Using SQL Databases for Sequence Similarity Searching and Analysis.
Pearson, William R; Mackey, Aaron J
2017-09-13
Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.
-
Integrated care in rural health: Seeking sustainability.
Peterson, Mary; Turgesen, Jeri; Fisk, Laura; McCarthy, Seamus
2017-06-01
The increased awareness of the financial impact associated with social determinants of health coincides with expectations of the Affordable Care Act (HR 3590) to improve care while reducing costs. The integration of behavioral health providers (BHPs) into primary care has demonstrated improved clinical outcomes. This study was designed with 2 aims, including the evaluation of the financial viability of an integrated care model in a rural setting and the demonstration of incorporating practice-based research into clinical work. A rural health plan caring for 22,000 members funded a pilot project placing BHPs in 3 clinics to provide integrated care. Patient utilization of medical services for 6 months following BHP services was compared with baseline utilization. The BHPs treated 256 unique patients, with a total of 459 consultations. The percentage of patients receiving BHP services varied between clinics (Clinic A = 1.4%, Clinic B = 2.7%, and Clinic C = 3.9%). A between-clinic analysis showed differences in medical claims data between baseline and post-BH services. The overall effect sizes for reduced medical utilization for patients at clinics B and C were very large, Hedge's g = -2.31 and -4.79, respectively. Utilization of 4 of the services (emergency, lab, outpatient, and primary care) showed the large reductions in their costs. In contrast, the data for Clinic A showed no change. Patients receiving behavioral health services within the integrated care model may decrease utilization of medical services following treatment, resulting in cost offset. Potential reasons for variability between clinics are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).
-
An image database management system for conducting CAD research
NASA Astrophysics Data System (ADS)
Gruszauskas, Nicholas; Drukker, Karen; Giger, Maryellen L.
2007-03-01
The development of image databases for CAD research is not a trivial task. The collection and management of images and their related metadata from multiple sources is a time-consuming but necessary process. By standardizing and centralizing the methods in which these data are maintained, one can generate subsets of a larger database that match the specific criteria needed for a particular research project in a quick and efficient manner. A research-oriented management system of this type is highly desirable in a multi-modality CAD research environment. An online, webbased database system for the storage and management of research-specific medical image metadata was designed for use with four modalities of breast imaging: screen-film mammography, full-field digital mammography, breast ultrasound and breast MRI. The system was designed to consolidate data from multiple clinical sources and provide the user with the ability to anonymize the data. Input concerning the type of data to be stored as well as desired searchable parameters was solicited from researchers in each modality. The backbone of the database was created using MySQL. A robust and easy-to-use interface for entering, removing, modifying and searching information in the database was created using HTML and PHP. This standardized system can be accessed using any modern web-browsing software and is fundamental for our various research projects on computer-aided detection, diagnosis, cancer risk assessment, multimodality lesion assessment, and prognosis. Our CAD database system stores large amounts of research-related metadata and successfully generates subsets of cases that match the user's desired search criteria.
-
Mayo, Charles; Conners, Steve; Warren, Christopher; Miller, Robert; Court, Laurence; Popple, Richard
2013-01-01
Purpose: With emergence of clinical outcomes databases as tools utilized routinely within institutions, comes need for software tools to support automated statistical analysis of these large data sets and intrainstitutional exchange from independent federated databases to support data pooling. In this paper, the authors present a design approach and analysis methodology that addresses both issues. Methods: A software application was constructed to automate analysis of patient outcomes data using a wide range of statistical metrics, by combining use of C#.Net and R code. The accuracy and speed of the code was evaluated using benchmark data sets. Results: The approach provides data needed to evaluate combinations of statistical measurements for ability to identify patterns of interest in the data. Through application of the tools to a benchmark data set for dose-response threshold and to SBRT lung data sets, an algorithm was developed that uses receiver operator characteristic curves to identify a threshold value and combines use of contingency tables, Fisher exact tests, Welch t-tests, and Kolmogorov-Smirnov tests to filter the large data set to identify values demonstrating dose-response. Kullback-Leibler divergences were used to provide additional confirmation. Conclusions: The work demonstrates the viability of the design approach and the software tool for analysis of large data sets. PMID:24320426
-
Mayo, Charles; Conners, Steve; Warren, Christopher; Miller, Robert; Court, Laurence; Popple, Richard
2013-11-01
With emergence of clinical outcomes databases as tools utilized routinely within institutions, comes need for software tools to support automated statistical analysis of these large data sets and intrainstitutional exchange from independent federated databases to support data pooling. In this paper, the authors present a design approach and analysis methodology that addresses both issues. A software application was constructed to automate analysis of patient outcomes data using a wide range of statistical metrics, by combining use of C#.Net and R code. The accuracy and speed of the code was evaluated using benchmark data sets. The approach provides data needed to evaluate combinations of statistical measurements for ability to identify patterns of interest in the data. Through application of the tools to a benchmark data set for dose-response threshold and to SBRT lung data sets, an algorithm was developed that uses receiver operator characteristic curves to identify a threshold value and combines use of contingency tables, Fisher exact tests, Welch t-tests, and Kolmogorov-Smirnov tests to filter the large data set to identify values demonstrating dose-response. Kullback-Leibler divergences were used to provide additional confirmation. The work demonstrates the viability of the design approach and the software tool for analysis of large data sets.
-
Evaluation of consumer drug information databases.
Choi, J A; Sullivan, J; Pankaskie, M; Brufsky, J
1999-01-01
To evaluate prescription drug information contained in six consumer drug information databases available on CD-ROM, and to make health care professionals aware of the information provided, so that they may appropriately recommend these databases for use by their patients. Observational study of six consumer drug information databases: The Corner Drug Store, Home Medical Advisor, Mayo Clinic Family Pharmacist, Medical Drug Reference, Mosby's Medical Encyclopedia, and PharmAssist. Not applicable. Not applicable. Information on 20 frequently prescribed drugs was evaluated in each database. The databases were ranked using a point-scale system based on primary and secondary assessment criteria. For the primary assessment, 20 categories of information based on those included in the 1998 edition of the USP DI Volume II, Advice for the Patient: Drug Information in Lay Language were evaluated for each of the 20 drugs, and each database could earn up to 400 points (for example, 1 point was awarded if the database mentioned a drug's mechanism of action). For the secondary assessment, the inclusion of 8 additional features that could enhance the utility of the databases was evaluated (for example, 1 point was awarded if the database contained a picture of the drug), and each database could earn up to 8 points. The results of the primary and secondary assessments, listed in order of highest to lowest number of points earned, are as follows: Primary assessment--Mayo Clinic Family Pharmacist (379), Medical Drug Reference (251), PharmAssist (176), Home Medical Advisor (113.5), The Corner Drug Store (98), and Mosby's Medical Encyclopedia (18.5); secondary assessment--The Mayo Clinic Family Pharmacist (8), The Corner Drug Store (5), Mosby's Medical Encyclopedia (5), Home Medical Advisor (4), Medical Drug Reference (4), and PharmAssist (3). The Mayo Clinic Family Pharmacist was the most accurate and complete source of prescription drug information based on the USP DI Volume II and would be an appropriate database for health care professionals to recommend to patients.
-
Dodd, Lori E; Wagner, Robert F; Armato, Samuel G; McNitt-Gray, Michael F; Beiden, Sergey; Chan, Heang-Ping; Gur, David; McLennan, Geoffrey; Metz, Charles E; Petrick, Nicholas; Sahiner, Berkman; Sayre, Jim
2004-04-01
Cancer of the lung and bronchus is the leading fatal malignancy in the United States. Five-year survival is low, but treatment of early stage disease considerably improves chances of survival. Advances in multidetector-row computed tomography technology provide detection of smaller lung nodules and offer a potentially effective screening tool. The large number of images per exam, however, requires considerable radiologist time for interpretation and is an impediment to clinical throughput. Thus, computer-aided diagnosis (CAD) methods are needed to assist radiologists with their decision making. To promote the development of CAD methods, the National Cancer Institute formed the Lung Image Database Consortium (LIDC). The LIDC is charged with developing the consensus and standards necessary to create an image database of multidetector-row computed tomography lung images as a resource for CAD researchers. To develop such a prospective database, its potential uses must be anticipated. The ultimate applications will influence the information that must be included along with the images, the relevant measures of algorithm performance, and the number of required images. In this article we outline assessment methodologies and statistical issues as they relate to several potential uses of the LIDC database. We review methods for performance assessment and discuss issues of defining "truth" as well as the complications that arise when truth information is not available. We also discuss issues about sizing and populating a database.
-
[National Database of Genotypes--ethical and legal issues].
Franková, Vera; Tesínová, Jolana; Brdicka, Radim
2011-01-01
National Database of Genotypes--ethical and legal issues The aim of the project National Database of Genotypes is to outline structure and rules for the database operation collecting information about genotypes of individual persons. The database should be used entirely for health care. Its purpose is to enable physicians to gain quick and easy access to the information about persons requiring specialized care due to their genetic constitution. In the future, another introduction of new genetic tests into the clinical practice can be expected thus the database of genotypes facilitates substantial financial savings by exclusion of duplicates of the expensive genetic testing. Ethical questions connected with the creating and functioning of such database concern mainly privacy protection, confidentiality of personal sensitive data, protection of database from misuse, consent with participation and public interests. Due to necessity of correct interpretation by qualified professional (= clinical geneticist), particular categorization of genetic data within the database is discussed. The function of proposed database has to be governed in concordance with the Czech legislation together with solving ethical problems.
-
The utility of an automated electronic system to monitor and audit transfusion practice.
Grey, D E; Smith, V; Villanueva, G; Richards, B; Augustson, B; Erber, W N
2006-05-01
Transfusion laboratories with transfusion committees have a responsibility to monitor transfusion practice and generate improvements in clinical decision-making and red cell usage. However, this can be problematic and expensive because data cannot be readily extracted from most laboratory information systems. To overcome this problem, we developed and introduced a system to electronically extract and collate extensive amounts of data from two laboratory information systems and to link it with ICD10 clinical codes in a new database using standard information technology. Three data files were generated from two laboratory information systems, ULTRA (version 3.2) and TM, using standard information technology scripts. These were patient pre- and post-transfusion haemoglobin, blood group and antibody screen, and cross match and transfusion data. These data together with ICD10 codes for surgical cases were imported into an MS ACCESS database and linked by means of a unique laboratory number. Queries were then run to extract the relevant information and processed in Microsoft Excel for graphical presentation. We assessed the utility of this data extraction system to audit transfusion practice in a 600-bed adult tertiary hospital over an 18-month period. A total of 52 MB of data were extracted from the two laboratory information systems for the 18-month period and together with 2.0 MB theatre ICD10 data enabled case-specific transfusion information to be generated. The audit evaluated 15,992 blood group and antibody screens, 25,344 cross-matched red cell units and 15,455 transfused red cell units. Data evaluated included cross-matched to transfusion ratios and pre- and post-transfusion haemoglobin levels for a range of clinical diagnoses. Data showed significant differences between clinical units and by ICD10 code. This method to electronically extract large amounts of data and linkage with clinical databases has provided a powerful and sustainable tool for monitoring transfusion practice. It has been successfully used to identify areas requiring education, training and clinical guidance and allows for comparison with national haemoglobin-based transfusion guidelines.
-
Pelliccia, Francesco; Tanzilli, Gaetano; Schiariti, Michele; Viceconte, Nicola; Greco, Cesare; Gaudio, Carlo
2016-12-01
Anticoagulant therapy has been used with great effect for decades for the prevention of stroke among patients with atrial fibrillation. In recent years, the therapeutic armamentarium has been strengthened considerably, with the addition of anticoagulants acting through novel pathways. The currently available novel agents are apixaban, rivaroxaban and dabigatran. These novel oral anticoagulants (NOACs) were approved for use on the basis of major clinical trials clearly demonstrating improved risk reductions compared to warfarin for stroke and/or major bleeding events. In these studies, apixaban and dabigatran 150 mg each significantly reduced the risk of stroke, while apixaban and dabigatran 110 mg reduced the risk of major bleeding compared to warfarin. Extrapolating the results of the randomized clinical trials on NOACs to all patients is not possible, as the strict design of clinical trials yields information that is directly applicable to a relatively narrow spectrum of patients. To control for confounding variables, randomized studies restrict enrolment to a prespecified set of criteria that do not necessarily reflect the profiles of all those who could potentially benefit from these agents. Research continues using the trial databases, in an attempt to better identify patient subgroups who do or do not benefit from each of the agents. At the European Society of Cardiology (ESC) annual meetings in London in 2015 and in Rome in 2016, there were several presentations and posters providing this type of evidence. Perhaps more important, as real-world experience with these agents grows, we are beginning to obtain meaningful new information about the NOACs in everyday use. This has involved the study of large databases including patients receiving these medications in clinical situations less stringently defined than in the randomized clinical trials. These include purpose-built registries, observational studies, and analyses of healthcare administrative databases. At both ESC meetings in 2015 and 2016, a wealth of information was presented using these types of sources. In many cases, these new data reinforce the key learnings from the randomized clinical trials. The following report provides highlights of registry and other post-marketing data presented at both ESC meetings in 2015 and 2016.
-
Hierarchical data security in a Query-By-Example interface for a shared database.
Taylor, Merwyn
2002-06-01
Whenever a shared database resource, containing critical patient data, is created, protecting the contents of the database is a high priority goal. This goal can be achieved by developing a Query-By-Example (QBE) interface, designed to access a shared database, and embedding within the QBE a hierarchical security module that limits access to the data. The security module ensures that researchers working in one clinic do not get access to data from another clinic. The security can be based on a flexible taxonomy structure that allows ordinary users to access data from individual clinics and super users to access data from all clinics. All researchers submit queries through the same interface and the security module processes the taxonomy and user identifiers to limit access. Using this system, two different users with different access rights can submit the same query and get different results thus reducing the need to create different interfaces for different clinics and access rights.
-
Gastric cancer in India: epidemiology and standard of treatment.
Servarayan Murugesan, Chandramohan; Manickavasagam, Kanagavel; Chandramohan, Apsara; Jebaraj, Abishai; Jameel, Abdul Rehman Abdul; Jain, Mayank Shikar; Venkataraman, Jayanthi
2018-04-02
India has a low incidence of gastric cancer. It ranks among the top five most common cancers. Regional diversity of incidence is of importance. It is the second most common cause of cancer related deaths among Indian men and women in the age between 15 and 44. Helicobacter pylori carcinogenesis is low in India. Advanced stage at presentation is a cause of concern. Basic and clinical research in India reveals a globally comparable standard of care and outcome. The large population, sociodemographic profile and challenges in health expenditure, however, remain a major challenge for health care policy managers. The newer formation of National Cancer Grid, integration of national databases and the creation of social identification database Aadhaar by The Unique Identification Authority of India are set to enhance the health care provision and optimal outcome.
-
Di Chiara, Antonio; Zonzin, Pietro; Pavoni, Daisy; Fioretti, Paolo Maria
2003-06-01
In the era of evidence-based medicine, the monitoring of the adherence to the guidelines is fundamental, in order to verify the diagnostic and therapeutic processes. Informatic paperless databases allow a higher data quality, lower costs and timely analysis with overall advantages over the traditional surveys. The RUTA project (acronym of Triveneto Registry of ANMCO CCUs) was designed in 1999, aiming at creating an informatic network among the coronary care units of a large Italian region, for a permanent survey of patients admitted for acute myocardial infarction. Information ranges from the pre-hospital phase to discharge, including all relevant clinical and management variables. The database uses DBMS Personal Oracle and Power-Builder as user interface, on Windows platform. Anonymous data are sent to a central server.
-
Prevention of Posttraumatic Contractures with Ketotifen (PERK)
2016-10-01
the Peer Reviewed Orthopaedic Research Program (PRORP) Clinical Trial Award (CTA), W81XWH-16-PRORP-CTA, was submitted. Database development and Pre...and Safety Months Identify database and partner – Clinical Research Unit 1-2 Completed Develop Case Report Forms, consent forms 6-12 Case...report forms completed, consent forms pending – 80% completed Develop database and multicenter submission process 12-18 In progress, 30% completed
-
CORE-Hom: a powerful and exhaustive database of clinical trials in homeopathy.
Clausen, Jürgen; Moss, Sian; Tournier, Alexander; Lüdtke, Rainer; Albrecht, Henning
2014-10-01
The CORE-Hom database was created to answer the need for a reliable and publicly available source of information in the field of clinical research in homeopathy. As of May 2014 it held 1048 entries of clinical trials, observational studies and surveys in the field of homeopathy, including second publications and re-analyses. 352 of the trials referenced in the database were published in peer reviewed journals, 198 of which were randomised controlled trials. The most often used remedies were Arnica montana (n = 103) and Traumeel(®) (n = 40). The most studied medical conditions were respiratory tract infections (n = 126) and traumatic injuries (n = 110). The aim of this article is to introduce the database to the public, describing and explaining the interface, features and content of the CORE-Hom database. Copyright © 2014 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.
-
Viral genome analysis and knowledge management.
Kuiken, Carla; Yoon, Hyejin; Abfalterer, Werner; Gaschen, Brian; Lo, Chienchi; Korber, Bette
2013-01-01
One of the challenges of genetic data analysis is to combine information from sources that are distributed around the world and accessible through a wide array of different methods and interfaces. The HIV database and its footsteps, the hepatitis C virus (HCV) and hemorrhagic fever virus (HFV) databases, have made it their mission to make different data types easily available to their users. This involves a large amount of behind-the-scenes processing, including quality control and analysis of the sequences and their annotation. Gene and protein sequences are distilled from the sequences that are stored in GenBank; to this end, both submitter annotation and script-generated sequences are used. Alignments of both nucleotide and amino acid sequences are generated, manually curated, distilled into an alignment model, and regenerated in an iterative cycle that results in ever better new alignments. Annotation of epidemiological and clinical information is parsed, checked, and added to the database. User interfaces are updated, and new interfaces are added based upon user requests. Vital for its success, the database staff are heavy users of the system, which enables them to fix bugs and find opportunities for improvement. In this chapter we describe some of the infrastructure that keeps these heavily used analysis platforms alive and vital after nearly 25 years of use. The database/analysis platforms described in this chapter can be accessed at http://hiv.lanl.gov http://hcv.lanl.gov http://hfv.lanl.gov.
-
Development of imaging biomarkers and generation of big data.
Alberich-Bayarri, Ángel; Hernández-Navarro, Rafael; Ruiz-Martínez, Enrique; García-Castro, Fabio; García-Juan, David; Martí-Bonmatí, Luis
2017-06-01
Several image processing algorithms have emerged to cover unmet clinical needs but their application to radiological routine with a clear clinical impact is still not straightforward. Moving from local to big infrastructures, such as Medical Imaging Biobanks (millions of studies), or even more, Federations of Medical Imaging Biobanks (in some cases totaling to hundreds of millions of studies) require the integration of automated pipelines for fast analysis of pooled data to extract clinically relevant conclusions, not uniquely linked to medical imaging, but in combination to other information such as genetic profiling. A general strategy for the development of imaging biomarkers and their integration in the cloud for the quantitative management and exploitation in large databases is herein presented. The proposed platform has been successfully launched and is being validated nowadays among the early adopters' community of radiologists, clinicians, and medical imaging researchers.
-
Incorporating Semantics into Data Driven Workflows for Content Based Analysis
NASA Astrophysics Data System (ADS)
Argüello, M.; Fernandez-Prieto, M. J.
Finding meaningful associations between text elements and knowledge structures within clinical narratives in a highly verbal domain, such as psychiatry, is a challenging goal. The research presented here uses a small corpus of case histories and brings into play pre-existing knowledge, and therefore, complements other approaches that use large corpus (millions of words) and no pre-existing knowledge. The paper describes a variety of experiments for content-based analysis: Linguistic Analysis using NLP-oriented approaches, Sentiment Analysis, and Semantically Meaningful Analysis. Although it is not standard practice, the paper advocates providing automatic support to annotate the functionality as well as the data for each experiment by performing semantic annotation that uses OWL and OWL-S. Lessons learnt can be transmitted to legacy clinical databases facing the conversion of clinical narratives according to prominent Electronic Health Records standards.
-
Using a fingerprint recognition system in a vaccine trial to avoid misclassification
2007-01-01
Abstract Problem The potential for misidentification of trial participants, leading to misclassification, is a threat to the integrity of randomized controlled trials. The correct identification of study subjects in large trials over prolonged periods is of vital importance to those conducting clinical trials. Currently used means of identifying study participants, such as identity cards and records of name, address, name of household head and demographic characteristics, require large numbers of well-trained personnel, and still leave room for uncertainty. Approach We used fingerprint recognition technology for the identification of trial participants. This technology is already widely used in security and commercial contexts but not so far in clinical trials. Local setting A phase 2 cholera vaccine trial in SonLa, Viet Nam. Relevant changes An optical sensor was used to scan fingerprints. The fingerprint template of each participant was used to verify his or her identity during each of eight follow-up visits. Lessons learned A system consisting of a laptop computer and sensor is small in size, requires minimal training and on average six seconds for scanning and recognition. All participants’ identities were verified in the trial. Fingerprint recognition should become the standard technology for identification of participants in field trials. Fears exist, however, regarding the potential for invasion of privacy. It will therefore be necessary to convince not only trial participants but also investigators that templates of fingerprints stored in databases are less likely to be subject to abuse than currently used information databases. PMID:17242760
-
Siregar, S; Pouw, M E; Moons, K G M; Versteegh, M I M; Bots, M L; van der Graaf, Y; Kalkman, C J; van Herwerden, L A; Groenwold, R H H
2014-01-01
Objective To compare the accuracy of data from hospital administration databases and a national clinical cardiac surgery database and to compare the performance of the Dutch hospital standardised mortality ratio (HSMR) method and the logistic European System for Cardiac Operative Risk Evaluation, for the purpose of benchmarking of mortality across hospitals. Methods Information on all patients undergoing cardiac surgery between 1 January 2007 and 31 December 2010 in 10 centres was extracted from The Netherlands Association for Cardio-Thoracic Surgery database and the Hospital Discharge Registry. The number of cardiac surgery interventions was compared between both databases. The European System for Cardiac Operative Risk Evaluation and hospital standardised mortality ratio models were updated in the study population and compared using the C-statistic, calibration plots and the Brier-score. Results The number of cardiac surgery interventions performed could not be assessed using the administrative database as the intervention code was incorrect in 1.4–26.3%, depending on the type of intervention. In 7.3% no intervention code was registered. The updated administrative model was inferior to the updated clinical model with respect to discrimination (c-statistic of 0.77 vs 0.85, p<0.001) and calibration (Brier Score of 2.8% vs 2.6%, p<0.001, maximum score 3.0%). Two average performing hospitals according to the clinical model became outliers when benchmarking was performed using the administrative model. Conclusions In cardiac surgery, administrative data are less suitable than clinical data for the purpose of benchmarking. The use of either administrative or clinical risk-adjustment models can affect the outlier status of hospitals. Risk-adjustment models including procedure-specific clinical risk factors are recommended. PMID:24334377
-
Holland, A; Whittington, J; Cohen, O; Curfs, L; Delahaye, F; Dudley, O; Horsthemke, B; Lindgren, A-C; Nourissier, C; Sharma, N; Vogels, A
2009-06-01
Prader-Willi Syndrome (PWS) is a rare genetically determined neurodevelopmental disorder with a complex phenotype that changes with age. The rarity of the syndrome and the need to control for different variables such as genetic sub-type, age and gender limits clinical studies of sufficient size in any one country. A clinical research database has been established to structure data collection and to enable multinational investigations into the development of children and adults with PWS. As part of a joint basic science and clinical study of PWS funded through Framework 6 of the European Union (EU), an expert multidisciplinary group was established that included clinicians involved in PWS research and clinical practice, expert database software developers, and representatives from two national PWS Associations. This group identified the key issues that required resolution and the data fields necessary for a comprehensive database to support PWS research. The database consists of six 'index' entry points and branching panels and sub-panels and over 1200 data 'fields'. It is Internet-based and designed to support multi-site clinical research in PWS. An algorithm ensures that participant data are anonymous. Access to data is controlled in a manner that is compatible with EU and national laws. The database determines the assessments to be used to collect data thereby enabling the combining of data from different groups under specifically agreed conditions. The data collected at any one time will be determined by individual research groups, who retain control of the data. Over time the database will accumulate data on participants with PWS that will support future research by avoiding the need for repeat data collection of fixed data and it will also enable longitudinal studies and treatment trials. The development of the database has proved to be complex with various administrative and ethical issues to be addressed. At an early stage, it was important to clarify the exact function of the database. It was agreed that it was primarily to support grant-funded research rather than clinical practice. The most complex issues that had to be addressed were concerned with data ownership and establishing the rules for data entry, retrieval and sharing that are compatible with data protection laws, and which are likely to be acceptable to participants and their families and to individual research groups.
-
Palmieri, Gaspare; Evans, Chris; Hansen, Vidje; Brancaleoni, Greta; Ferrari, Silvia; Porcelli, Piero; Reitano, Francesco; Rigatelli, Marco
2009-01-01
The Clinical Outcomes in Routine Evaluation--Outcome Measure (CORE-OM) was translated into Italian and tested in non-clinical (n = 263) and clinical (n = 647) samples. The translation showed good acceptability, internal consistency and convergent validity in both samples. There were large and statistically significant differences between clinical and non-clinical datasets on all scores. The reliable change criteria were similar to those for the UK referential data. Some of the clinically significant change criteria, particularly for the men, were moderately different from the UK cutting points. The Italian version of the CORE-OM showed respectable psychometric parameters. However, it seemed plausible that non-clinical and clinical distributions of self-report scores on psychopathology and functioning measures may differ by language and culture. *A good quality Italian translation of the CORE-OM, and hence the GP-CORE, CORE-10 and CORE-5 measures also, is now available for use by practitioners and anyone surveying or exploring general psychological state. The measures can be obtained from CORE-IMS or yourself and practitioners are encouraged to share anonymised data so that good clinical and non-clinical referential databases can be established for Italy.
-
Abou El Hassan, Mohamed; Stoianov, Alexandra; Araújo, Petra A T; Sadeghieh, Tara; Chan, Man Khun; Chen, Yunqi; Randell, Edward; Nieuwesteeg, Michelle; Adeli, Khosrow
2015-11-01
The CALIPER program has established a comprehensive database of pediatric reference intervals using largely the Abbott ARCHITECT biochemical assays. To expand clinical application of CALIPER reference standards, the present study is aimed at transferring CALIPER reference intervals from the Abbott ARCHITECT to Beckman Coulter AU assays. Transference of CALIPER reference intervals was performed based on the CLSI guidelines C28-A3 and EP9-A2. The new reference intervals were directly verified using up to 100 reference samples from the healthy CALIPER cohort. We found a strong correlation between Abbott ARCHITECT and Beckman Coulter AU biochemical assays, allowing the transference of the vast majority (94%; 30 out of 32 assays) of CALIPER reference intervals previously established using Abbott assays. Transferred reference intervals were, in general, similar to previously published CALIPER reference intervals, with some exceptions. Most of the transferred reference intervals were sex-specific and were verified using healthy reference samples from the CALIPER biobank based on CLSI criteria. It is important to note that the comparisons performed between the Abbott and Beckman Coulter assays make no assumptions as to assay accuracy or which system is more correct/accurate. The majority of CALIPER reference intervals were transferrable to Beckman Coulter AU assays, allowing the establishment of a new database of pediatric reference intervals. This further expands the utility of the CALIPER database to clinical laboratories using the AU assays; however, each laboratory should validate these intervals for their analytical platform and local population as recommended by the CLSI. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.
-
A Data Analysis Expert System For Large Established Distributed Databases
NASA Astrophysics Data System (ADS)
Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick
1987-05-01
The purpose of this work is to analyze the applicability of artificial intelligence techniques for developing a user-friendly, parallel interface to large isolated, incompatible NASA databases for the purpose of assisting the management decision process. To carry out this work, a survey was conducted to establish the data access requirements of several key NASA user groups. In addition, current NASA database access methods were evaluated. The results of this work are presented in the form of a design for a natural language database interface system, called the Deductively Augmented NASA Management Decision Support System (DANMDS). This design is feasible principally because of recently announced commercial hardware and software product developments which allow cross-vendor compatibility. The goal of the DANMDS system is commensurate with the central dilemma confronting most large companies and institutions in America, the retrieval of information from large, established, incompatible database systems. The DANMDS system implementation would represent a significant first step toward this problem's resolution.
-
The Top 50 Articles on Minimally Invasive Spine Surgery.
Virk, Sohrab S; Yu, Elizabeth
2017-04-01
Bibliometric study of current literature. To catalog the most important minimally invasive spine (MIS) surgery articles using the amount of citations as a marker of relevance. MIS surgery is a relatively new tool used by spinal surgeons. There is a dynamic and evolving field of research related to MIS techniques, clinical outcomes, and basic science research. To date, there is no comprehensive review of the most cited articles related to MIS surgery. A systematic search was performed over three widely used literature databases: Web of Science, Scopus, and Google Scholar. There were four searches performed using the terms "minimally invasive spine surgery," "endoscopic spine surgery," "percutaneous spinal surgery," and "lateral interbody surgery." The amount of citations included was averaged amongst the three databases to rank each article. The query of the three databases was performed in November 2015. Fifty articles were selected based upon the amount of citations each averaged amongst the three databases. The most cited article was titled "Extreme Lateral Interbody Fusion (XLIF): a novel surgical technique for anterior lumbar interbody fusion" by Ozgur et al and was credited with 447, 239, and 279 citations in Google Scholar, Web of Science, and Scopus, respectively. Citations ranged from 27 to 239 for Web of Science, 60 to 279 for Scopus, and 104 to 462 for Google Scholar. There was a large variety of articles written spanning over 14 different topics with the majority dealing with clinical outcomes related to MIS surgery. The majority of the most cited articles were level III and level IV studies. This is likely due to the relatively recent nature of technological advances in the field. Furthermore level I and level II studies are required in MIS surgery in the years ahead. 5.
-
HMDB 4.0: the human metabolome database for 2018.
Wishart, David S; Feunang, Yannick Djoumbou; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vázquez-Fresno, Rosa; Sajed, Tanvir; Johnson, Daniel; Li, Carin; Karu, Naama; Sayeeda, Zinat; Lo, Elvis; Assempour, Nazanin; Berjanskii, Mark; Singhal, Sandeep; Arndt, David; Liang, Yonjie; Badran, Hasan; Grant, Jason; Serra-Cayuela, Arnau; Liu, Yifeng; Mandal, Rupa; Neveu, Vanessa; Pon, Allison; Knox, Craig; Wilson, Michael; Manach, Claudine; Scalbert, Augustin
2018-01-04
The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB's chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC-MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
-
A new method for the automatic retrieval of medical cases based on the RadLex ontology.
Spanier, A B; Cohen, D; Joskowicz, L
2017-03-01
The goal of medical case-based image retrieval (M-CBIR) is to assist radiologists in the clinical decision-making process by finding medical cases in large archives that most resemble a given case. Cases are described by radiology reports comprised of radiological images and textual information on the anatomy and pathology findings. The textual information, when available in standardized terminology, e.g., the RadLex ontology, and used in conjunction with the radiological images, provides a substantial advantage for M-CBIR systems. We present a new method for incorporating textual radiological findings from medical case reports in M-CBIR. The input is a database of medical cases, a query case, and the number of desired relevant cases. The output is an ordered list of the most relevant cases in the database. The method is based on a new case formulation, the Augmented RadLex Graph and an Anatomy-Pathology List. It uses a new case relatedness metric [Formula: see text] that prioritizes more specific medical terms in the RadLex tree over less specific ones and that incorporates the length of the query case. An experimental study on 8 CT queries from the 2015 VISCERAL 3D Case Retrieval Challenge database consisting of 1497 volumetric CT scans shows that our method has accuracy rates of 82 and 70% on the first 10 and 30 most relevant cases, respectively, thereby outperforming six other methods. The increasing amount of medical imaging data acquired in clinical practice constitutes a vast database of untapped diagnostically relevant information. This paper presents a new hybrid approach to retrieving the most relevant medical cases based on textual and image information.
-
Ben-Ari Fuchs, Shani; Lieder, Iris; Stelzer, Gil; Mazor, Yaron; Buzhor, Ella; Kaplan, Sergey; Bogoch, Yoel; Plaschkes, Inbar; Shitrit, Alina; Rappaport, Noa; Kohn, Asher; Edgar, Ron; Shenhav, Liraz; Safran, Marilyn; Lancet, Doron; Guan-Golan, Yaron; Warshawsky, David; Shtrichman, Ronit
2016-03-01
Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from "data-to-knowledge-to-innovation," a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data. Prominent among the emerging remedies to this challenge are the gene set enrichment tools. This study reports on GeneAnalytics™ ( geneanalytics.genecards.org ), a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics' differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science's GeneCards suite, including the GeneCards®--the human gene database; the MalaCards-the human diseases database; and the PathCards--the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®--the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene-tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell "cards" in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics, and others yet to emerge on the postgenomics horizon.
-
Use of Patient Registries and Administrative Datasets for the Study of Pediatric Cancer
Rice, Henry E.; Englum, Brian R.; Gulack, Brian C.; Adibe, Obinna O.; Tracy, Elizabeth T.; Kreissman, Susan G.; Routh, Jonathan C.
2015-01-01
Analysis of data from large administrative databases and patient registries is increasingly being used to study childhood cancer care, although the value of these data sources remains unclear to many clinicians. Interpretation of large databases requires a thorough understanding of how the dataset was designed, how data were collected, and how to assess data quality. This review will detail the role of administrative databases and registry databases for the study of childhood cancer, tools to maximize information from these datasets, and recommendations to improve the use of these databases for the study of pediatric oncology. PMID:25807938
-
DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu, X; Fatyga, M; Vora, S
Purpose: To determine if differences in patient positioning methods have an impact on the incidence and modeling of grade >=2 acute rectal toxicity in prostate cancer patients who were treated with Intensity Modulated Radiation Therapy (IMRT). Methods: We compared two databases of patients treated with radiation therapy for prostate cancer: a database of 79 patients who were treated with 7 field IMRT and daily image guided positioning based on implanted gold markers (IGRTdb), and a database of 302 patients who were treated with 5 field IMRT and daily positioning using a trans-abdominal ultrasound system (USdb). Complete planning dosimetry was availablemore » for IGRTdb patients while limited planning dosimetry, recorded at the time of planning, was available for USdb patients. We fit Lyman-Kutcher-Burman (LKB) model to IGRTdb only, and Univariate Logistic Regression (ULR) NTCP model to both databases. We perform Receiver Operating Characteristics analysis to determine the predictive power of NTCP models. Results: The incidence of grade >= 2 acute rectal toxicity in IGRTdb was 20%, while the incidence in USdb was 54%. Fits of both LKB and ULR models yielded predictive NTCP models for IGRTdb patients with Area Under the Curve (AUC) in the 0.63 – 0.67 range. Extrapolation of the ULR model from IGRTdb to planning dosimetry in USdb predicts that the incidence of acute rectal toxicity in USdb should not exceed 40%. Fits of the ULR model to the USdb do not yield predictive NTCP models and their AUC is consistent with AUC = 0.5. Conclusion: Accuracy of a patient positioning system affects clinically observed toxicity rates and the quality of NTCP models that can be derived from toxicity data. Poor correlation between planned and clinically delivered dosimetry may lead to erroneous or poorly performing NTCP models, even if the number of patients in a database is large.« less
-
INCIDENCE AND PREVALENCE OF ACROMEGALY IN THE UNITED STATES: A CLAIMS-BASED ANALYSIS.
Broder, Michael S; Chang, Eunice; Cherepanov, Dasha; Neary, Maureen P; Ludlam, William H
2016-11-01
Acromegaly, a rare endocrine disorder, results from excessive growth hormone secretion, leading to multisystem-associated morbidities. Using 2 large nationwide databases, we estimated the annual incidence and prevalence of acromegaly in the U.S. We used 2008 to 2013 data from the Truven Health MarketScan ® Commercial Claims and Encounters Database and IMS Health PharMetrics healthcare insurance claims databases, with health plan enrollees <65 years of age. Study patients had ≥2 claims with acromegaly (International Classification of Diseases, 9th Revision, Clinical Modification Code [ICD-9CM] 253.0), or 1 claim with acromegaly and 1 claim for pituitary tumor, pituitary surgery, or cranial stereotactic radiosurgery. Annual incidence was calculated for each year from 2009 to 2013, and prevalence in 2013. Estimates were stratified by age and sex. Incidence was up to 11.7 cases per million person-years (PMPY) in MarketScan and 9.6 cases PMPY in PharMetrics. Rates were similar by sex but typically lowest in ≤17 year olds and higher in >24 year olds. The prevalence estimates were 87.8 and 71.0 per million per year in MarketScan and PharMetrics, respectively. Prevalence consistently increased with age but was similar by sex in each database. The current U.S. incidence of acromegaly may be up to 4 times higher and prevalence may be up to 50% higher than previously reported in European studies. Our findings correspond with the estimates reported by a recent U.S. study that used a single managed care database, supporting the robustness of these estimates in this population. Our study indicates there are approximately 3,000 new cases of acromegaly per year, with a prevalence of about 25,000 acromegaly patients in the U.S. CT = computed tomography GH = growth hormone IGF-1 = insulin-like growth factor 1 ICD-9-CM Code = International Classification of Diseases, 9th Revision, Clinical Modification Codes MRI = magnetic resonance imaging PMPY = per million person-years.
-
Caron, Alexandre; Chazard, Emmanuel; Muller, Joris; Perichon, Renaud; Ferret, Laurie; Koutkias, Vassilis; Beuscart, Régis; Beuscart, Jean-Baptiste; Ficheur, Grégoire
2017-03-01
The significant risk of adverse events following medical procedures supports a clinical epidemiological approach based on the analyses of collections of electronic medical records. Data analytical tools might help clinical epidemiologists develop more appropriate case-crossover designs for monitoring patient safety. To develop and assess the methodological quality of an interactive tool for use by clinical epidemiologists to systematically design case-crossover analyses of large electronic medical records databases. We developed IT-CARES, an analytical tool implementing case-crossover design, to explore the association between exposures and outcomes. The exposures and outcomes are defined by clinical epidemiologists via lists of codes entered via a user interface screen. We tested IT-CARES on data from the French national inpatient stay database, which documents diagnoses and medical procedures for 170 million inpatient stays between 2007 and 2013. We compared the results of our analysis with reference data from the literature on thromboembolic risk after delivery and bleeding risk after total hip replacement. IT-CARES provides a user interface with 3 columns: (i) the outcome criteria in the left-hand column, (ii) the exposure criteria in the right-hand column, and (iii) the estimated risk (odds ratios, presented in both graphical and tabular formats) in the middle column. The estimated odds ratios were consistent with the reference literature data. IT-CARES may enhance patient safety by facilitating clinical epidemiological studies of adverse events following medical procedures. The tool's usability must be evaluated and improved in further research. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association.
-
Determining conserved metabolic biomarkers from a million database queries.
Kurczy, Michael E; Ivanisevic, Julijana; Johnson, Caroline H; Uritboonthai, Winnie; Hoang, Linh; Fang, Mingliang; Hicks, Matthew; Aldebot, Anthony; Rinehart, Duane; Mellander, Lisa J; Tautenhahn, Ralf; Patti, Gary J; Spilker, Mary E; Benton, H Paul; Siuzdak, Gary
2015-12-01
Metabolite databases provide a unique window into metabolome research allowing the most commonly searched biomarkers to be catalogued. Omic scale metabolite profiling, or metabolomics, is finding increased utility in biomarker discovery largely driven by improvements in analytical technologies and the concurrent developments in bioinformatics. However, the successful translation of biomarkers into clinical or biologically relevant indicators is limited. With the aim of improving the discovery of translatable metabolite biomarkers, we present search analytics for over one million METLIN metabolite database queries. The most common metabolites found in METLIN were cross-correlated against XCMS Online, the widely used cloud-based data processing and pathway analysis platform. Analysis of the METLIN and XCMS common metabolite data has two primary implications: these metabolites, might indicate a conserved metabolic response to stressors and, this data may be used to gauge the relative uniqueness of potential biomarkers. METLIN can be accessed by logging on to: https://metlin.scripps.edu siuzdak@scripps.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
-
LONI visualization environment.
Dinov, Ivo D; Valentino, Daniel; Shin, Bae Cheol; Konstantinidis, Fotios; Hu, Guogang; MacKenzie-Graham, Allan; Lee, Erh-Fang; Shattuck, David; Ma, Jeff; Schwartz, Craig; Toga, Arthur W
2006-06-01
Over the past decade, the use of informatics to solve complex neuroscientific problems has increased dramatically. Many of these research endeavors involve examining large amounts of imaging, behavioral, genetic, neurobiological, and neuropsychiatric data. Superimposing, processing, visualizing, or interpreting such a complex cohort of datasets frequently becomes a challenge. We developed a new software environment that allows investigators to integrate multimodal imaging data, hierarchical brain ontology systems, on-line genetic and phylogenic databases, and 3D virtual data reconstruction models. The Laboratory of Neuro Imaging visualization environment (LONI Viz) consists of the following components: a sectional viewer for imaging data, an interactive 3D display for surface and volume rendering of imaging data, a brain ontology viewer, and an external database query system. The synchronization of all components according to stereotaxic coordinates, region name, hierarchical ontology, and genetic labels is achieved via a comprehensive BrainMapper functionality, which directly maps between position, structure name, database, and functional connectivity information. This environment is freely available, portable, and extensible, and may prove very useful for neurobiologists, neurogenetisists, brain mappers, and for other clinical, pedagogical, and research endeavors.
-
Puerarin injection for treatment of unstable angina pectoris: a meta-analysis and systematic review
Gao, Zhisheng; Wei, Baozhu; Qian, Cheng
2015-01-01
Background: Puerarin is an effective ingredient isolated from Radix Puerariae, a leguminous plant. In China, a large number of early studies suggest that puerarin may be used in the treatment of coronary heart disease. In recent years, puerarin injection has been widely used to treat coronary heart disease and angina pectoris. Objective: To systematically evaluate the clinical efficacy and safety of puerarin injection in the treatment of unstable angina pectoris (UAP). Methods: Data were retrieved from digital databases, including PubMed, Excerpt Medica Database (EMBASE), China Biology Medicine (CBM), the Cochrane Library, and Chinese databases. Results: Compared with patients who were treated with conventional Western medicines alone, the patients who were treated with conventional Western medicines in combination with puerarin injection exhibited significant improvements in the incidence of angina pectoris, electrocardiogram findings, nitroglycerin consumption and plasma endothelin levels. Conclusions: Strong evidence suggests that, the use of puerarin in combination with conventional Western medicines is a better treatment option for treating UAP, compared with the use of conventional Western medicines alone. PMID:26628941
-
Creating databases for biological information: an introduction.
Stein, Lincoln
2013-06-01
The essence of bioinformatics is dealing with large quantities of information. Whether it be sequencing data, microarray data files, mass spectrometric data (e.g., fingerprints), the catalog of strains arising from an insertional mutagenesis project, or even large numbers of PDF files, there inevitably comes a time when the information can simply no longer be managed with files and directories. This is where databases come into play. This unit briefly reviews the characteristics of several database management systems, including flat file, indexed file, relational databases, and NoSQL databases. It compares their strengths and weaknesses and offers some general guidelines for selecting an appropriate database management system. Copyright 2013 by JohnWiley & Sons, Inc.
-
Design and implementation of a fault-tolerant and dynamic metadata database for clinical trials
NASA Astrophysics Data System (ADS)
Lee, J.; Zhou, Z.; Talini, E.; Documet, J.; Liu, B.
2007-03-01
In recent imaging-based clinical trials, quantitative image analysis (QIA) and computer-aided diagnosis (CAD) methods are increasing in productivity due to higher resolution imaging capabilities. A radiology core doing clinical trials have been analyzing more treatment methods and there is a growing quantity of metadata that need to be stored and managed. These radiology centers are also collaborating with many off-site imaging field sites and need a way to communicate metadata between one another in a secure infrastructure. Our solution is to implement a data storage grid with a fault-tolerant and dynamic metadata database design to unify metadata from different clinical trial experiments and field sites. Although metadata from images follow the DICOM standard, clinical trials also produce metadata specific to regions-of-interest and quantitative image analysis. We have implemented a data access and integration (DAI) server layer where multiple field sites can access multiple metadata databases in the data grid through a single web-based grid service. The centralization of metadata database management simplifies the task of adding new databases into the grid and also decreases the risk of configuration errors seen in peer-to-peer grids. In this paper, we address the design and implementation of a data grid metadata storage that has fault-tolerance and dynamic integration for imaging-based clinical trials.
-
Archetype relational mapping - a practical openEHR persistence solution.
Wang, Li; Min, Lingtong; Wang, Rui; Lu, Xudong; Duan, Huilong
2015-11-05
One of the primary obstacles to the widespread adoption of openEHR methodology is the lack of practical persistence solutions for future-proof electronic health record (EHR) systems as described by the openEHR specifications. This paper presents an archetype relational mapping (ARM) persistence solution for the archetype-based EHR systems to support healthcare delivery in the clinical environment. First, the data requirements of the EHR systems are analysed and organized into archetype-friendly concepts. The Clinical Knowledge Manager (CKM) is queried for matching archetypes; when necessary, new archetypes are developed to reflect concepts that are not encompassed by existing archetypes. Next, a template is designed for each archetype to apply constraints related to the local EHR context. Finally, a set of rules is designed to map the archetypes to data tables and provide data persistence based on the relational database. A comparison study was conducted to investigate the differences among the conventional database of an EHR system from a tertiary Class A hospital in China, the generated ARM database, and the Node + Path database. Five data-retrieving tests were designed based on clinical workflow to retrieve exams and laboratory tests. Additionally, two patient-searching tests were designed to identify patients who satisfy certain criteria. The ARM database achieved better performance than the conventional database in three of the five data-retrieving tests, but was less efficient in the remaining two tests. The time difference of query executions conducted by the ARM database and the conventional database is less than 130 %. The ARM database was approximately 6-50 times more efficient than the conventional database in the patient-searching tests, while the Node + Path database requires far more time than the other two databases to execute both the data-retrieving and the patient-searching tests. The ARM approach is capable of generating relational databases using archetypes and templates for archetype-based EHR systems, thus successfully adapting to changes in data requirements. ARM performance is similar to that of conventionally-designed EHR systems, and can be applied in a practical clinical environment. System components such as ARM can greatly facilitate the adoption of openEHR architecture within EHR systems.
-
Viereck, Christopher; Boudes, Pol
2009-07-01
We compared the clinical trial transparency practices of US/European pharma by analyzing the publicly-accessible clinical trial results databases of major drugs (doripenem, varenicline, lapatinib, zoledronic acid, adalimumab, insulin glargine, raltegravir, gefitinib). We evaluated their accessibility and utility from the perspective of the lay public. We included databases on company websites, http://www.clinicalstudyresults.org, http://www.clinicaltrials.gov and http://clinicaltrials.ifpma.org. Only 2 of 8 company homepages provide a direct link to the results. While the use of common terms on company search engines led to results for 5 of the 8 drugs following 2-4 clicks, no logical pathway was identified. The number of clinical trials in the databases was inconsistent: 0 for doripenem to 45 for insulin glargine. Results from all phases of clinical development were provided for 2 (insulin glargine and gefitinib) of the 8 drugs. Analyses of phase III reports revealed that most critical elements of the International Conference of Harmonization E3 Structure and Content of Synopses for Clinical Trial Reports were provided for 2 (varenicline, lapatinib) of the 8 drugs. For adalimumab and zoledronic acid, only citations were provided, which the lay public would be unable to access. None of the clinical trial reports was written in lay language. User-friendly support, when provided, was of marginal benefit. Only 1 of the databases (gefitinib) permitted the user to find the most recently updated reports. None of the glossaries included explanations for adverse events or statistical methodology. In conclusion, our study indicates that the public faces significant hurdles in finding and understanding clinical trial results databases.
-
Evaluating the Impact of Database Heterogeneity on Observational Study Results
Madigan, David; Ryan, Patrick B.; Schuemie, Martijn; Stang, Paul E.; Overhage, J. Marc; Hartzema, Abraham G.; Suchard, Marc A.; DuMouchel, William; Berlin, Jesse A.
2013-01-01
Clinical studies that use observational databases to evaluate the effects of medical products have become commonplace. Such studies begin by selecting a particular database, a decision that published papers invariably report but do not discuss. Studies of the same issue in different databases, however, can and do generate different results, sometimes with strikingly different clinical implications. In this paper, we systematically study heterogeneity among databases, holding other study methods constant, by exploring relative risk estimates for 53 drug-outcome pairs and 2 widely used study designs (cohort studies and self-controlled case series) across 10 observational databases. When holding the study design constant, our analysis shows that estimated relative risks range from a statistically significant decreased risk to a statistically significant increased risk in 11 of 53 (21%) of drug-outcome pairs that use a cohort design and 19 of 53 (36%) of drug-outcome pairs that use a self-controlled case series design. This exceeds the proportion of pairs that were consistent across databases in both direction and statistical significance, which was 9 of 53 (17%) for cohort studies and 5 of 53 (9%) for self-controlled case series. Our findings show that clinical studies that use observational databases can be sensitive to the choice of database. More attention is needed to consider how the choice of data source may be affecting results. PMID:23648805
-
Lau, Christine S. M.; Zywot, Aleksander; Mahendraraj, Krishnaraj
2017-01-01
Introduction Gallbladder carcinoma (GBC) is the most common malignancy of the biliary tract and the third most common gastrointestinal tract malignancy. This study examines a large cohort of GBC patients in the United States in an effort to define demographics, clinical, and pathologic features impacting clinical outcomes. Methods Demographic and clinical data on 22,343 GBC patients was abstracted from the SEER database (1973–2013). Results GBC was presented most often among Caucasian (63.9%) females (70.7%) as poorly or moderately differentiated (42.5% and 38.2%) tumors, with lymph node involvement (88.2%). Surgery alone was the most common treatment modality for GBC patients (55.0%). Combination surgery and radiation (10.6%) achieved significantly longer survival rates compared to surgery alone (4.0 ± 0.2 versus 3.7 ± 0.1 years, p = 0.004). Overall mortality was 87.0% and cancer-specific mortality was 75.4%. Conclusions GBC is an uncommon malignancy that presents most often among females in their 8th decade of life, with over a third of cases presenting with distant metastasis. The incidence of GBC has doubled in the last decade concurrent with increases in cholecystectomy rates attributable in part to improved histopathological detection, as well as laparoscopic advances and enhanced endoscopic techniques. Surgical resection confers significant survival benefit in GBC patients. PMID:28638176
-
Mosunjac, Marina B; Sundstrom, J Bruce; Mosunjac, Mario I
2008-10-01
To describe a subset of cases with the unusual clinical and histomorphological presentation of anaplastic large cell lymphoma (ALCL) mimicking fever of unknown origin (FUO) and sepsis. A pathology database was searched using full term Systematized Nomenclature of Medicine codes for ALCL to identify 23ALCL cases from the period 1999-2006. Of those, five cases that did not have a correct premortem diagnosis were further analyzed to elucidate the reasons for delayed and incorrect pre-mortem diagnosis. The analyzed data included clinical presentation, duration of symptoms, duration of hospital stay, premortem presumed cause of death, white blood cell count, platelet count, anion gap and blood pH, liver enzymes (alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, alkaline phosphatase), lactate, coagulation tests (prothrombin time, partial thromboplastin time, fibrinogen, D-dimers), microbiology cultures, and radiology and surgical pathology reports. Autopsy reports were reviewed for description of major gross findings, initial clinical diagnosis, and cause of death. Five fatal and pre-mortem unrecognized ALCL cases were characterized by rapid decline, with histologic findings showing predominantly extranodal involvement, intravascular lymphomatosis, and hemophagocytosis. The cases were also characterized by unusual clinical manifestations including a FUO, sepsis, and disseminated intravascular coagulation-like picture, lactic acidosis, hepatosplenomegaly, and absence of significant peripheral adenopathy. There is a distinct group of ALCLs with unique and specific clinical, gross autopsy, and histopathologic findings. Recognition of this clinical variant may facilitate early detection and potentially timely diagnosis and therapy.
-
The 2010-2015 Prevalence of Eosinophilic Esophagitis in the USA: A Population-Based Study.
Mansoor, Emad; Cooper, Gregory S
2016-10-01
Eosinophilic esophagitis (EoE) is a chronic inflammatory disorder with increasing prevalence. However, epidemiologic data have mostly been acquired from small studies. We sought to describe the epidemiology of EoE in the USA, utilizing a large database. We queried a commercial database (Explorys Inc, Cleveland, OH, USA), an aggregate of electronic health record data from 26 major integrated US healthcare systems from 1999 to July 2015. We identified an aggregated patient cohort of eligible patients with EoE and a history of proton-pump inhibitor use between July 2010 and July 2015, based on Systematized Nomenclature of Medicine-Clinical Terms. We calculated the prevalence of EoE among different patient groups. Of the 30,301,440 individuals in the database, we identified 7840 patients with EoE with an overall prevalence of 25.9/100,000 persons. Prevalence was higher in males than females [odds ratio (OR) 2.00; 95 % CI 1.92-2.10, p < 0.0001], Caucasians versus African-Americans and Asians (OR 2.00; 95 % CI 1.86-2.14, p < 0.0001), and adults (18-65 years) versus elderly (>65 years) and children (<18 years) (OR 1.63; 95 % CI 1.54-1.71, p < 0.0001). Compared with controls (individuals in database without EoE), individuals with EoE were more likely to have other gastrointestinal diagnoses such as dysphagia and at least one allergic condition. In this large study, we found that the estimated prevalence of EoE in the USA is 25.9/100,000, which is at the lower end of prevalence rates reported in the USA and other industrial countries. We confirmed that EoE has a strong association with allergic and gastrointestinal diagnoses.
-
Validating abortion procedure coding in Canadian administrative databases.
Samiedaluie, Saied; Peterson, Sandra; Brant, Rollin; Kaczorowski, Janusz; Norman, Wendy V
2016-07-12
The British Columbia (BC) Ministry of Health collects abortion procedure data in the Medical Services Plan (MSP) physician billings database and in the hospital information Discharge Abstracts Database (DAD). Our study seeks to validate abortion procedure coding in these databases. Two randomized controlled trials enrolled a cohort of 1031 women undergoing abortion. The researcher collected database includes both enrollment and follow up chart review data. The study cohort was linked to MSP and DAD data to identify all abortions events captured in the administrative databases. We compared clinical chart data on abortion procedures with health administrative data. We considered a match to occur if an abortion related code was found in administrative data within 30 days of the date of the same event documented in a clinical chart. Among 1158 abortion events performed during enrollment and follow-up period, 99.1 % were found in at least one of the administrative data sources. The sensitivities for the two databases, evaluated using a gold standard, were 97.7 % (95 % confidence interval (CI): 96.6-98.5) for the MSP database and 91.9 % (95 % CI: 90.0-93.4) for the DAD. Abortion events coded in the BC health administrative databases are highly accurate. Single-payer health administrative databases at the provincial level in Canada have the potential to offer valid data reflecting abortion events. ClinicalTrials.gov Identifier NCT01174225 , Current Controlled Trials ISRCTN19506752 .
-
Very Large Data Volumes Analysis of Collaborative Systems with Finite Number of States
ERIC Educational Resources Information Center
Ivan, Ion; Ciurea, Cristian; Pavel, Sorin
2010-01-01
The collaborative system with finite number of states is defined. A very large database is structured. Operations on large databases are identified. Repetitive procedures for collaborative systems operations are derived. The efficiency of such procedures is analyzed. (Contains 6 tables, 5 footnotes and 3 figures.)
-
An alternative database approach for management of SNOMED CT and improved patient data queries.
Campbell, W Scott; Pedersen, Jay; McClay, James C; Rao, Praveen; Bastola, Dhundy; Campbell, James R
2015-10-01
SNOMED CT is the international lingua franca of terminologies for human health. Based in Description Logics (DL), the terminology enables data queries that incorporate inferences between data elements, as well as, those relationships that are explicitly stated. However, the ontologic and polyhierarchical nature of the SNOMED CT concept model make it difficult to implement in its entirety within electronic health record systems that largely employ object oriented or relational database architectures. The result is a reduction of data richness, limitations of query capability and increased systems overhead. The hypothesis of this research was that a graph database (graph DB) architecture using SNOMED CT as the basis for the data model and subsequently modeling patient data upon the semantic core of SNOMED CT could exploit the full value of the terminology to enrich and support advanced data querying capability of patient data sets. The hypothesis was tested by instantiating a graph DB with the fully classified SNOMED CT concept model. The graph DB instance was tested for integrity by calculating the transitive closure table for the SNOMED CT hierarchy and comparing the results with transitive closure tables created using current, validated methods. The graph DB was then populated with 461,171 anonymized patient record fragments and over 2.1 million associated SNOMED CT clinical findings. Queries, including concept negation and disjunction, were then run against the graph database and an enterprise Oracle relational database (RDBMS) of the same patient data sets. The graph DB was then populated with laboratory data encoded using LOINC, as well as, medication data encoded with RxNorm and complex queries performed using LOINC, RxNorm and SNOMED CT to identify uniquely described patient populations. A graph database instance was successfully created for two international releases of SNOMED CT and two US SNOMED CT editions. Transitive closure tables and descriptive statistics generated using the graph database were identical to those using validated methods. Patient queries produced identical patient count results to the Oracle RDBMS with comparable times. Database queries involving defining attributes of SNOMED CT concepts were possible with the graph DB. The same queries could not be directly performed with the Oracle RDBMS representation of the patient data and required the creation and use of external terminology services. Further, queries of undefined depth were successful in identifying unknown relationships between patient cohorts. The results of this study supported the hypothesis that a patient database built upon and around the semantic model of SNOMED CT was possible. The model supported queries that leveraged all aspects of the SNOMED CT logical model to produce clinically relevant query results. Logical disjunction and negation queries were possible using the data model, as well as, queries that extended beyond the structural IS_A hierarchy of SNOMED CT to include queries that employed defining attribute-values of SNOMED CT concepts as search parameters. As medical terminologies, such as SNOMED CT, continue to expand, they will become more complex and model consistency will be more difficult to assure. Simultaneously, consumers of data will increasingly demand improvements to query functionality to accommodate additional granularity of clinical concepts without sacrificing speed. This new line of research provides an alternative approach to instantiating and querying patient data represented using advanced computable clinical terminologies. Copyright © 2015 Elsevier Inc. All rights reserved.
-
Digital hand atlas and computer-aided bone age assessment via the Web
NASA Astrophysics Data System (ADS)
Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente
1999-07-01
A frequently used assessment method of bone age is atlas matching by a radiological examination of a hand image against a reference set of atlas patterns of normal standards. We are in a process of developing a digital hand atlas with a large standard set of normal hand and wrist images that reflect the skeletal maturity, race and sex difference, and current child development. The digital hand atlas will be used for a computer-aided bone age assessment via Web. We have designed and partially implemented a computer-aided diagnostic (CAD) system for Web-based bone age assessment. The system consists of a digital hand atlas, a relational image database and a Web-based user interface. The digital atlas is based on a large standard set of normal hand an wrist images with extracted bone objects and quantitative features. The image database uses a content- based indexing to organize the hand images and their attributes and present to users in a structured way. The Web-based user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, will be extracted and compared with patterns from the atlas database to assess the bone age. The relevant reference imags and the final assessment report will be sent back to the user's browser via Web. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. In this paper, we present the system design and Web-based client-server model for computer-assisted bone age assessment and our initial implementation of the digital atlas database.
-
Benchmarking distributed data warehouse solutions for storing genomic variant information
Wiewiórka, Marek S.; Wysakowicz, Dawid P.; Okoniewski, Michał J.
2017-01-01
Abstract Genomic-based personalized medicine encompasses storing, analysing and interpreting genomic variants as its central issues. At a time when thousands of patientss sequenced exomes and genomes are becoming available, there is a growing need for efficient database storage and querying. The answer could be the application of modern distributed storage systems and query engines. However, the application of large genomic variant databases to this problem has not been sufficiently far explored so far in the literature. To investigate the effectiveness of modern columnar storage [column-oriented Database Management System (DBMS)] and query engines, we have developed a prototypic genomic variant data warehouse, populated with large generated content of genomic variants and phenotypic data. Next, we have benchmarked performance of a number of combinations of distributed storages and query engines on a set of SQL queries that address biological questions essential for both research and medical applications. In addition, a non-distributed, analytical database (MonetDB) has been used as a baseline. Comparison of query execution times confirms that distributed data warehousing solutions outperform classic relational DBMSs. Moreover, pre-aggregation and further denormalization of data, which reduce the number of distributed join operations, significantly improve query performance by several orders of magnitude. Most of distributed back-ends offer a good performance for complex analytical queries, while the Optimized Row Columnar (ORC) format paired with Presto and Parquet with Spark 2 query engines provide, on average, the lowest execution times. Apache Kudu on the other hand, is the only solution that guarantees a sub-second performance for simple genome range queries returning a small subset of data, where low-latency response is expected, while still offering decent performance for running analytical queries. In summary, research and clinical applications that require the storage and analysis of variants from thousands of samples can benefit from the scalability and performance of distributed data warehouse solutions. Database URL: https://github.com/ZSI-Bio/variantsdwh PMID:29220442
-
Vaccarino, Anthony L; Dharsee, Moyez; Strother, Stephen; Aldridge, Don; Arnott, Stephen R; Behan, Brendan; Dafnas, Costas; Dong, Fan; Edgecombe, Kenneth; El-Badrawi, Rachad; El-Emam, Khaled; Gee, Tom; Evans, Susan G; Javadi, Mojib; Jeanson, Francis; Lefaivre, Shannon; Lutz, Kristen; MacPhee, F Chris; Mikkelsen, Jordan; Mikkelsen, Tom; Mirotchnick, Nicholas; Schmah, Tanya; Studzinski, Christa M; Stuss, Donald T; Theriault, Elizabeth; Evans, Kenneth R
2018-01-01
Historically, research databases have existed in isolation with no practical avenue for sharing or pooling medical data into high dimensional datasets that can be efficiently compared across databases. To address this challenge, the Ontario Brain Institute's "Brain-CODE" is a large-scale neuroinformatics platform designed to support the collection, storage, federation, sharing and analysis of different data types across several brain disorders, as a means to understand common underlying causes of brain dysfunction and develop novel approaches to treatment. By providing researchers access to aggregated datasets that they otherwise could not obtain independently, Brain-CODE incentivizes data sharing and collaboration and facilitates analyses both within and across disorders and across a wide array of data types, including clinical, neuroimaging and molecular. The Brain-CODE system architecture provides the technical capabilities to support (1) consolidated data management to securely capture, monitor and curate data, (2) privacy and security best-practices, and (3) interoperable and extensible systems that support harmonization, integration, and query across diverse data modalities and linkages to external data sources. Brain-CODE currently supports collaborative research networks focused on various brain conditions, including neurodevelopmental disorders, cerebral palsy, neurodegenerative diseases, epilepsy and mood disorders. These programs are generating large volumes of data that are integrated within Brain-CODE to support scientific inquiry and analytics across multiple brain disorders and modalities. By providing access to very large datasets on patients with different brain disorders and enabling linkages to provincial, national and international databases, Brain-CODE will help to generate new hypotheses about the biological bases of brain disorders, and ultimately promote new discoveries to improve patient care.
-
Vaccarino, Anthony L.; Dharsee, Moyez; Strother, Stephen; Aldridge, Don; Arnott, Stephen R.; Behan, Brendan; Dafnas, Costas; Dong, Fan; Edgecombe, Kenneth; El-Badrawi, Rachad; El-Emam, Khaled; Gee, Tom; Evans, Susan G.; Javadi, Mojib; Jeanson, Francis; Lefaivre, Shannon; Lutz, Kristen; MacPhee, F. Chris; Mikkelsen, Jordan; Mikkelsen, Tom; Mirotchnick, Nicholas; Schmah, Tanya; Studzinski, Christa M.; Stuss, Donald T.; Theriault, Elizabeth; Evans, Kenneth R.
2018-01-01
Historically, research databases have existed in isolation with no practical avenue for sharing or pooling medical data into high dimensional datasets that can be efficiently compared across databases. To address this challenge, the Ontario Brain Institute’s “Brain-CODE” is a large-scale neuroinformatics platform designed to support the collection, storage, federation, sharing and analysis of different data types across several brain disorders, as a means to understand common underlying causes of brain dysfunction and develop novel approaches to treatment. By providing researchers access to aggregated datasets that they otherwise could not obtain independently, Brain-CODE incentivizes data sharing and collaboration and facilitates analyses both within and across disorders and across a wide array of data types, including clinical, neuroimaging and molecular. The Brain-CODE system architecture provides the technical capabilities to support (1) consolidated data management to securely capture, monitor and curate data, (2) privacy and security best-practices, and (3) interoperable and extensible systems that support harmonization, integration, and query across diverse data modalities and linkages to external data sources. Brain-CODE currently supports collaborative research networks focused on various brain conditions, including neurodevelopmental disorders, cerebral palsy, neurodegenerative diseases, epilepsy and mood disorders. These programs are generating large volumes of data that are integrated within Brain-CODE to support scientific inquiry and analytics across multiple brain disorders and modalities. By providing access to very large datasets on patients with different brain disorders and enabling linkages to provincial, national and international databases, Brain-CODE will help to generate new hypotheses about the biological bases of brain disorders, and ultimately promote new discoveries to improve patient care. PMID:29875648
-
Adapting a large database of point of care summarized guidelines: a process description.
Delvaux, Nicolas; Van de Velde, Stijn; Aertgeerts, Bert; Goossens, Martine; Fauquert, Benjamin; Kunnamo, Ilka; Van Royen, Paul
2017-02-01
Questions posed at the point of care (POC) can be answered using POC summarized guidelines. To implement a national POC information resource, we subscribed to a large database of POC summarized guidelines to complement locally available guidelines. Our challenge was in developing a sustainable strategy for adapting almost 1000 summarized guidelines. The aim of this paper was to describe our process for adapting a database of POC summarized guidelines. An adaptation process based on the ADAPTE framework was tailored to be used by a heterogeneous group of participants. Guidelines were assessed on content and on applicability to the Belgian context. To improve efficiency, we chose to first aim our efforts towards those guidelines most important to primary care doctors. Over a period of 3 years, we screened about 80% of 1000 international summarized guidelines. For those guidelines identified as most important for primary care doctors, we noted that in about half of the cases, remarks were made concerning content. On the other hand, at least two-thirds of all screened guidelines required no changes when evaluating their local usability. Adapting a large body of POC summarized guidelines using a formal adaptation process is possible, even when faced with limited resources. This can be done by creating an efficient and collaborative effort and ensuring user-friendly procedures. Our experiences show that even though in most cases guidelines can be adopted without adaptations, careful review of guidelines developed in a different context remains necessary. Streamlining international efforts in adapting international POC information resources and adopting similar adaptation processes may lessen duplication efforts and prove more cost-effective. © 2015 The Authors. Journal of Evaluation in Clinical Practice published by John Wiley & Sons, Ltd.
-
Royle, P; Waugh, N
2003-01-01
To contribute to making searching for Technology Assessment Reports (TARs) more cost-effective by suggesting an optimum literature retrieval strategy. A sample of 20 recent TARs. All sources used to search for clinical and cost-effectiveness studies were recorded. In addition, all studies that were included in the clinical and cost-effectiveness sections of the TARs were identified, and their characteristics recorded, including author, journal, year, study design, study size and quality score. Each was also classified by publication type, and then checked to see whether it was indexed in the following databases: MEDLINE, EMBASE, and then either the Cochrane Controlled Trials Register (CCTR) for clinical effectiveness studies or the NHS Economic Evaluation Database (NHS EED) for the cost-effectiveness studies. Any study not found in at least one of these databases was checked to see whether it was indexed in the Science Citation Index (SCI) and BIOSIS, and the American Society of Clinical Oncology (ASCO) Online if a cancer review. Any studies still not found were checked to see whether they were in a number of additional databases. The median number of sources searched per TAR was 20, and the range was from 13 to 33 sources. Six sources (CCTR, DARE, EMBASE, MEDLINE, NHS EED and sponsor/industry submissions to National Institute for Clinical Excellence) were used in all reviews. After searching the MEDLINE, EMBASE and NHS EED databases, 87.3% of the clinical effectiveness studies and 94.8% of the cost-effectiveness studies were found, rising to 98.2% when SCI, BIOSIS and ASCO Online and 97.9% when SCI and ASCO Online, respectively, were added. The median number of sources searched for the 14 TARs that included an economic model was 9.0 per TAR. A sensitive search filter for identifying non-randomised controlled trials (RCT), constructed for MEDLINE and using the search terms from the bibliographic records in the included studies, retrieved only 85% of the known sample. Therefore, it is recommended that when searching for non-RCT studies a search is done for the intervention alone, and records are then scanned manually for those that look relevant. Searching additional databases beyond the Cochrane Library (which includes CCTR, NHS EED and the HTA database), MEDLINE, EMBASE and SCI, plus BIOSIS limited to meeting abstracts only, was seldom found to be effective in retrieving additional studies for inclusion in the clinical and cost-effectiveness sections of TARs (apart from reviews of cancer therapies, where a search of the ASCO database is recommended). A more selective approach to database searching would suffice in most cases and would save resources, thereby making the TAR process more efficient. However, searching non-database sources (including submissions from manufacturers, recent meeting abstracts, contact with experts and checking reference lists) does appear to be a productive way of identifying further studies.
-
Bréant, C; Borst, F; Campi, D; Griesser, V; Momjian, S
1999-01-01
The use of a controlled vocabulary set in a hospital-wide clinical information system is of crucial importance for many departmental database systems to communicate and exchange information. In the absence of an internationally recognized clinical controlled vocabulary set, a new extension of the International statistical Classification of Diseases (ICD) is proposed. It expands the scope of the standard ICD beyond diagnosis and procedures to clinical terminology. In addition, the common Clinical Findings Dictionary (CFD) further records the definition of clinical entities. The construction of the vocabulary set and the CFD is incremental and manual. Tools have been implemented to facilitate the tasks of defining/maintaining/publishing dictionary versions. The design of database applications in the integrated clinical information system is driven by the CFD which is part of the Medical Questionnaire Designer tool. Several integrated clinical database applications in the field of diabetes and neuro-surgery have been developed at the HUG.
-
Bréant, C.; Borst, F.; Campi, D.; Griesser, V.; Momjian, S.
1999-01-01
The use of a controlled vocabulary set in a hospital-wide clinical information system is of crucial importance for many departmental database systems to communicate and exchange information. In the absence of an internationally recognized clinical controlled vocabulary set, a new extension of the International statistical Classification of Diseases (ICD) is proposed. It expands the scope of the standard ICD beyond diagnosis and procedures to clinical terminology. In addition, the common Clinical Findings Dictionary (CFD) further records the definition of clinical entities. The construction of the vocabulary set and the CFD is incremental and manual. Tools have been implemented to facilitate the tasks of defining/maintaining/publishing dictionary versions. The design of database applications in the integrated clinical information system is driven by the CFD which is part of the Medical Questionnaire Designer tool. Several integrated clinical database applications in the field of diabetes and neuro-surgery have been developed at the HUG. Images Figure 1 PMID:10566451
-
Teaching Case: Adapting the Access Northwind Database to Support a Database Course
ERIC Educational Resources Information Center
Dyer, John N.; Rogers, Camille
2015-01-01
A common problem encountered when teaching database courses is that few large illustrative databases exist to support teaching and learning. Most database textbooks have small "toy" databases that are chapter objective specific, and thus do not support application over the complete domain of design, implementation and management concepts…
-
Large-Scale 1:1 Computing Initiatives: An Open Access Database
ERIC Educational Resources Information Center
Richardson, Jayson W.; McLeod, Scott; Flora, Kevin; Sauers, Nick J.; Kannan, Sathiamoorthy; Sincar, Mehmet
2013-01-01
This article details the spread and scope of large-scale 1:1 computing initiatives around the world. What follows is a review of the existing literature around 1:1 programs followed by a description of the large-scale 1:1 database. Main findings include: 1) the XO and the Classmate PC dominate large-scale 1:1 initiatives; 2) if professional…
-
A Database as a Service for the Healthcare System to Store Physiological Signal Data.
Chang, Hsien-Tsung; Lin, Tsai-Huei
2016-01-01
Wearable devices that measure physiological signals to help develop self-health management habits have become increasingly popular in recent years. These records are conducive for follow-up health and medical care. In this study, based on the characteristics of the observed physiological signal records- 1) a large number of users, 2) a large amount of data, 3) low information variability, 4) data privacy authorization, and 5) data access by designated users-we wish to resolve physiological signal record-relevant issues utilizing the advantages of the Database as a Service (DaaS) model. Storing a large amount of data using file patterns can reduce database load, allowing users to access data efficiently; the privacy control settings allow users to store data securely. The results of the experiment show that the proposed system has better database access performance than a traditional relational database, with a small difference in database volume, thus proving that the proposed system can improve data storage performance.
-
A Database as a Service for the Healthcare System to Store Physiological Signal Data
Lin, Tsai-Huei
2016-01-01
Wearable devices that measure physiological signals to help develop self-health management habits have become increasingly popular in recent years. These records are conducive for follow-up health and medical care. In this study, based on the characteristics of the observed physiological signal records– 1) a large number of users, 2) a large amount of data, 3) low information variability, 4) data privacy authorization, and 5) data access by designated users—we wish to resolve physiological signal record-relevant issues utilizing the advantages of the Database as a Service (DaaS) model. Storing a large amount of data using file patterns can reduce database load, allowing users to access data efficiently; the privacy control settings allow users to store data securely. The results of the experiment show that the proposed system has better database access performance than a traditional relational database, with a small difference in database volume, thus proving that the proposed system can improve data storage performance. PMID:28033415
-
Watanabe, Yoshinori; Hirano, Yoko; Asami, Yuko; Okada, Maki; Fujita, Kazuya
2017-11-01
A unique database named 'AN-SAPO' was developed by Iwato Corp. and Japan Brain Corp. in collaboration with the psychiatric clinics run by Himorogi Group in Japan. The AN-SAPO database includes patients' depression/anxiety score data from a mobile app named AN-SAPO and medical records from medical prescription software named 'ORCA'. On the mobile app, depression/anxiety severity can be evaluated by answering 20 brief questions and the scores are transferred to the AN-SAPO database together with the patients' medical records on ORCA. Currently, this database is used at the Himorogi Group's psychiatric clinics and has over 2000 patients' records accumulated since November 2013. Since the database covers patients' demographic data, prescribed drugs, and the efficacy and safety information, it could be a useful supporting tool for decision-making in clinical practice. We expect it to be utilised in wider areas of medical fields and for future pharmacovigilance and pharmacoepidemiological studies.
-
Guideline.gov: A Database of Clinical Specialty Guidelines.
El-Khayat, Yamila M; Forbes, Carrie S; Coghill, Jeffrey G
2017-01-01
The National Guidelines Clearinghouse (NGC), also known as Guideline.gov, is a database of resources to assist health care providers with a central depository of guidelines for clinical specialty areas in medicine. The database is provided free of charge and is sponsored by the U.S. Department of Health and Human Services and the Agency for Healthcare Research and Quality. The guidelines for treatment are updated regularly, with new guidelines replacing older guidelines every five years. There are hundreds of current guidelines with more added each week. The purpose and goal of NGC is to provide physicians, nurses, and other health care providers, insurance companies, and others in the field of health care with a unified database of the most current, detailed, relevant, and objective clinical practice guidelines.
-
The liver tissue bank and clinical database in China.
Yang, Yuan; Liu, Yi-Min; Wei, Ming-Yue; Wu, Yi-Fei; Gao, Jun-Hui; Liu, Lei; Zhou, Wei-Ping; Wang, Hong-Yang; Wu, Meng-Chao
2010-12-01
To develop a standardized and well-rounded material available for hepatology research, the National Liver Tissue Bank (NLTB) Project began in 2008 in China to make well-characterized and optimally preserved liver tumor tissue and clinical database. From Dec 2008 to Jun 2010, over 3000 individuals have been enrolled as liver tumor donors to the NLTB, including 2317 cases of newly diagnosed hepatocellular carcinoma (HCC) and about 1000 cases of diagnosed benign or malignant liver tumors. The clinical database and sample store can be managed easily and correctly with the data management platform used. We believe that the high-quality samples with detailed information database will become the cornerstone of hepatology research especially in studies exploring the diagnosis and new treatments for HCC and other liver diseases.
-
HomeBank: An Online Repository of Daylong Child-Centered Audio Recordings
VanDam, Mark; Warlaumont, Anne S.; Bergelson, Elika; Cristia, Alejandrina; Soderstrom, Melanie; De Palma, Paul; MacWhinney, Brian
2017-01-01
HomeBank is introduced here. It is a public, permanent, extensible, online database of daylong audio recorded in naturalistic environments. HomeBank serves two primary purposes. First, it is a repository for raw audio and associated files: one database requires special permissions, and another redacted database allows unrestricted public access. Associated files include metadata such as participant demographics and clinical diagnostics, automated annotations, and human-generated transcriptions and annotations. Many recordings use the child-perspective LENA recorders (LENA Research Foundation, Boulder, Colorado, United States), but various recordings and metadata can be accommodated. The HomeBank database can have both vetted and unvetted recordings, with different levels of accessibility. Additionally, HomeBank is an open repository for processing and analysis tools for HomeBank or similar data sets. HomeBank is flexible for users and contributors, making primary data available to researchers, especially those in child development, linguistics, and audio engineering. HomeBank facilitates researchers’ access to large-scale data and tools, linking the acoustic, auditory, and linguistic characteristics of children’s environments with a variety of variables including socioeconomic status, family characteristics, language trajectories, and disorders. Automated processing applied to daylong home audio recordings is now becoming widely used in early intervention initiatives, helping parents to provide richer speech input to at-risk children. PMID:27111272
-
Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu
2017-12-12
Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA's complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform.
-
Fifteen hundred guidelines and growing: the UK database of clinical guidelines.
van Loo, John; Leonard, Niamh
2006-06-01
The National Library for Health offers a comprehensive searchable database of nationally approved clinical guidelines, called the Guidelines Finder. This resource, commissioned in 2002, is managed and developed by the University of Sheffield Health Sciences Library. The authors introduce the historical and political dimension of guidelines and the nature of guidelines as a mechanism to ensure clinical effectiveness in practice. The article then outlines the maintenance and organisation of the Guidelines Finder database itself, the criteria for selection, who publishes guidelines and guideline formats, usage of the Guidelines Finder service and finally looks at some lessons learnt from a local library offering a national service. Clinical guidelines are central to effective clinical practice at the national, organisational and individual level. The Guidelines Finder is one of the most visited resources within the National Library for Health and is successful in answering information needs related to specific patient care, clinical research, guideline development and education.
-
Seamless lesion insertion in digital mammography: methodology and reader study
NASA Astrophysics Data System (ADS)
Pezeshk, Aria; Petrick, Nicholas; Sahiner, Berkman
2016-03-01
Collection of large repositories of clinical images containing verified cancer locations is costly and time consuming due to difficulties associated with both the accumulation of data and establishment of the ground truth. This problem poses a significant challenge to the development of machine learning algorithms that require large amounts of data to properly train and avoid overfitting. In this paper we expand the methods in our previous publications by making several modifications that significantly increase the speed of our insertion algorithms, thereby allowing them to be used for inserting lesions that are much larger in size. These algorithms have been incorporated into an image composition tool that we have made publicly available. This tool allows users to modify or supplement existing datasets by seamlessly inserting a real breast mass or micro-calcification cluster extracted from a source digital mammogram into a different location on another mammogram. We demonstrate examples of the performance of this tool on clinical cases taken from the University of South Florida Digital Database for Screening Mammography (DDSM). Finally, we report the results of a reader study evaluating the realism of inserted lesions compared to clinical lesions. Analysis of the radiologist scores in the study using receiver operating characteristic (ROC) methodology indicates that inserted lesions cannot be reliably distinguished from clinical lesions.
-
Design and implementation of a distributed large-scale spatial database system based on J2EE
NASA Astrophysics Data System (ADS)
Gong, Jianya; Chen, Nengcheng; Zhu, Xinyan; Zhang, Xia
2003-03-01
With the increasing maturity of distributed object technology, CORBA, .NET and EJB are universally used in traditional IT field. However, theories and practices of distributed spatial database need farther improvement in virtue of contradictions between large scale spatial data and limited network bandwidth or between transitory session and long transaction processing. Differences and trends among of CORBA, .NET and EJB are discussed in details, afterwards the concept, architecture and characteristic of distributed large-scale seamless spatial database system based on J2EE is provided, which contains GIS client application, web server, GIS application server and spatial data server. Moreover the design and implementation of components of GIS client application based on JavaBeans, the GIS engine based on servlet, the GIS Application server based on GIS enterprise JavaBeans(contains session bean and entity bean) are explained.Besides, the experiments of relation of spatial data and response time under different conditions are conducted, which proves that distributed spatial database system based on J2EE can be used to manage, distribute and share large scale spatial data on Internet. Lastly, a distributed large-scale seamless image database based on Internet is presented.
-
Vener, David F; Gaies, Michael; Jacobs, Jeffrey P; Pasquali, Sara K
2017-01-01
The growth in large-scale data management capabilities and the successful care of patients with congenital heart defects have coincidentally paralleled each other for the last three decades, and participation in multicenter congenital heart disease databases and registries is now a fundamental component of cardiac care. This manuscript attempts for the first time to consolidate in one location all of the relevant databases worldwide, including target populations, specialties, Web sites, and participation information. Since at least 1,992 cardiac surgeons and cardiologists began leveraging this burgeoning technology to create multi-institutional data collections addressing a variety of specialties within this field. Pediatric heart diseases are particularly well suited to this methodology because each individual care location has access to only a relatively limited number of diagnoses and procedures in any given calendar year. Combining multiple institutions data therefore allows for a far more accurate contemporaneous assessment of treatment modalities and adverse outcomes. Additionally, the data can be used to develop outcome benchmarks by which individual institutions can measure their progress against the field as a whole and focus quality improvement efforts in a more directed fashion, and there is increasing utilization combining clinical research efforts within existing data structures. Efforts are ongoing to support better collaboration and integration across data sets, to improve efficiency, further the utility of the data collection infrastructure and information collected, and to enhance return on investment for participating institutions.
-
TabSQL: a MySQL tool to facilitate mapping user data to public databases.
Xia, Xiao-Qin; McClelland, Michael; Wang, Yipeng
2010-06-23
With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.
-
TabSQL: a MySQL tool to facilitate mapping user data to public databases
2010-01-01
Background With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. Results We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. Conclusions TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data. PMID:20573251
-
Creating databases for biological information: an introduction.
Stein, Lincoln
2002-08-01
The essence of bioinformatics is dealing with large quantities of information. Whether it be sequencing data, microarray data files, mass spectrometric data (e.g., fingerprints), the catalog of strains arising from an insertional mutagenesis project, or even large numbers of PDF files, there inevitably comes a time when the information can simply no longer be managed with files and directories. This is where databases come into play. This unit briefly reviews the characteristics of several database management systems, including flat file, indexed file, and relational databases, as well as ACeDB. It compares their strengths and weaknesses and offers some general guidelines for selecting an appropriate database management system.
-
Effectiveness of 'rehabilitation in the home' service.
Bharadwaj, Sneha; Bruce, David
2014-11-01
Rehabilitation in the home (RITH) services increasingly provide hospital substitution services. This study examines clinical outcomes in a large metropolitan RITH service in Western Australia. The 2010 database of Fremantle Hospital RITH service was interrogated to identify the clinical profile of cases, length of stay (LOS) and clinical outcomes. Negative outcomes included death or unexpected hospital readmission. Multiple logistic regression modelling was used to explore associations with negative outcomes. This study was reviewed by the Institutional Review Board which deemed it not to require ethics approval. There were 1348 cases managed by RITH: 70.6% were aged≥65 years; elective joint replacement (29.7%), medical conditions (20%), stroke (13%), hip fractures (10%) were major contributors. The majority (93.3%) were discharged after a median of 9 days. Negative outcomes occurred in 90 cases (6.7%), including five deaths (0.4%) and 85 readmissions (6.3%). Independent associations with negative outcomes included older age (odds ratio (OR) (95% CI); 1.02, P=0.006), orthopaedic conditions (OR 1.91, P=0.004) and longer inpatient LOS (OR 1.96, P=0.003). Age above 80 years was independently associated with risk of negative outcome (OR 2.99, P=0.004). RITH had a low rate of negative outcomes. The database proved useful for monitoring quality of service provision. WHAT IS KNOWN ABOUT THE TOPIC?: Rehabilitation in the home environment has proven cost effective for multiple conditions, particularly stroke and elective joint surgery, among others, facilitating better quality of life, with reduced rates of delirium and mortality. Overall there are few negative outcomes and death is rare. WHAT DOES THIS PAPER ADD?: Although RITH services are widely utilised as bed substitution services, there is scant literature on clinical outcomes while within the service. This study focuses on frequency of good and poor clinical outcomes in a well-established RITH service in Western Australia, suggesting pattern recognition of an at-risk cohort by identifying potentially useful predictors of poor outcome. WHAT ARE THE IMPLICATIONS FOR PRACTITIONERS?: RITH services are a safe alternative for many, including older people. Health administration databases are useful tools to monitor clinical outcomes. Clinical indicators such as older age, long hospital stay and orthopaedic diagnoses may be useful predictors of poor outcomes in such services.
-
A Four-Dimensional Probabilistic Atlas of the Human Brain
Mazziotta, John; Toga, Arthur; Evans, Alan; Fox, Peter; Lancaster, Jack; Zilles, Karl; Woods, Roger; Paus, Tomas; Simpson, Gregory; Pike, Bruce; Holmes, Colin; Collins, Louis; Thompson, Paul; MacDonald, David; Iacoboni, Marco; Schormann, Thorsten; Amunts, Katrin; Palomero-Gallagher, Nicola; Geyer, Stefan; Parsons, Larry; Narr, Katherine; Kabani, Noor; Le Goualher, Georges; Feidler, Jordan; Smith, Kenneth; Boomsma, Dorret; Pol, Hilleke Hulshoff; Cannon, Tyrone; Kawashima, Ryuta; Mazoyer, Bernard
2001-01-01
The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype– phenotype–behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders. PMID:11522763
-
Colen, Sascha; van den Bekerom, Michel P J; Mulier, Michiel; Haverkamp, Daniël
2012-08-01
Although accepted as a conservative treatment option for knee osteoarthritis, the debate about the effectiveness of intra-articular treatment with hyaluronic acid (HA) is still ongoing because of contrasting outcomes in different clinical studies. Several well designed clinical studies showed a significant improvement in pain at follow-up compared with baseline but no significant improvement comparing the efficacy of HA with placebo (saline) or with other conservative treatment options. Notwithstanding the effectiveness of different types of intra-articular HA products, the question of whether one HA product is better than another is still unanswered. In this systematic review we compare the effects of intra-articularly administered HA with intra-articularly administered placebo in general and, more specifically, the effects of individual HA products with placebo. We also compare the efficacy of different HA products. A systematic review of randomized controlled trials (RCTs) was conducted using databases including MEDLINE, Cochrane Database of Systematic Reviews, Cochrane Clinical Trial Register and EMBASE. Seventy-four RCTs were included in this systematic review. HA improves pain by approximately 40-50% compared with baseline levels. However, when compared with saline the difference in efficacy is not that large. Due to a large 'placebo effect' of saline (approximately 30% pain reduction, persisting for at least 3 months) we determined a weighted mean difference between the efficacy of HA and saline of just 10.20 using the visual analog scale for pain. It is debatable whether this difference reaches the minimum clinically important difference. Comparing the different HA products, which vary in the molecular weight, concentration, and volume of HA, we were not able to conclude that one brand has a better efficacy than another due to the heterogeneity of the studies and outcomes. In the future it will be important to determine the exact mechanism of action of placebo as this may give us an idea of how to treat osteoarthritis more efficiently. Due to the limitations of this review (follow-up of just 3 months and large heterogeneity of the included studies), it is also important to compare the different HA products to determine which product(s), or which molecular weight range, concentration, or volume of HA is the best option to treat osteoarthritis. Our recommendation is to start large (multicenter) RCTs to give us more evidence about the efficacy of the different HA products.
-
Kuhn, Jens H.; Andersen, Kristian G.; Baize, Sylvain; Bào, Yīmíng; Bavari, Sina; Berthet, Nicolas; Blinkova, Olga; Brister, J. Rodney; Clawson, Anna N.; Fair, Joseph; Gabriel, Martin; Garry, Robert F.; Gire, Stephen K.; Goba, Augustine; Gonzalez, Jean-Paul; Günther, Stephan; Happi, Christian T.; Jahrling, Peter B.; Kapetshi, Jimmy; Kobinger, Gary; Kugelman, Jeffrey R.; Leroy, Eric M.; Maganga, Gael Darren; Mbala, Placide K.; Moses, Lina M.; Muyembe-Tamfum, Jean-Jacques; N’Faly, Magassouba; Nichol, Stuart T.; Omilabu, Sunday A.; Palacios, Gustavo; Park, Daniel J.; Paweska, Janusz T.; Radoshitzky, Sheli R.; Rossi, Cynthia A.; Sabeti, Pardis C.; Schieffelin, John S.; Schoepp, Randal J.; Sealfon, Rachel; Swanepoel, Robert; Towner, Jonathan S.; Wada, Jiro; Wauquier, Nadia; Yozwiak, Nathan L.; Formenty, Pierre
2014-01-01
In 2014, Ebola virus (EBOV) was identified as the etiological agent of a large and still expanding outbreak of Ebola virus disease (EVD) in West Africa and a much more confined EVD outbreak in Middle Africa. Epidemiological and evolutionary analyses confirmed that all cases of both outbreaks are connected to a single introduction each of EBOV into human populations and that both outbreaks are not directly connected. Coding-complete genomic sequence analyses of isolates revealed that the two outbreaks were caused by two novel EBOV variants, and initial clinical observations suggest that neither of them should be considered strains. Here we present consensus decisions on naming for both variants (West Africa: “Makona”, Middle Africa: “Lomela”) and provide database-compatible full, shortened, and abbreviated names that are in line with recently established filovirus sub-species nomenclatures. PMID:25421896
-
Computers and the orthopaedic office.
Berumen, Edmundo; Barllow, Fidel Dobarganes; Fong, Fransisco Javier; Lopez, Jorge Arturo
2002-01-01
The advance of today's medicine could be linked very closely to the history of computers through the last twenty years. In the beginning the first attempt to build a computer was trying to help us with mathematical calculations. This has changed recently and computers are now linked to x-ray machines, CT scanners, and MRIs. Being able to share information is one of the goals of the future. Today's computer technology has helped a great deal to allow orthopaedic surgeons from around the world to consult on a difficult case or to become a part of a large database. Obtaining the results from a method of treatment using a multicentric information study can be done on a regular basis. In the future, computers will help us to retrieve information from patients' clinical history directly from a hospital database or by portable memory cards that will carry every radiograph or video from previous surgeries.
-
IDOMAL: an ontology for malaria.
Topalis, Pantelis; Mitraka, Elvira; Bujila, Ioana; Deligianni, Elena; Dialynas, Emmanuel; Siden-Kiamos, Inga; Troye-Blomberg, Marita; Louis, Christos
2010-08-10
Ontologies are rapidly becoming a necessity for the design of efficient information technology tools, especially databases, because they permit the organization of stored data using logical rules and defined terms that are understood by both humans and machines. This has as consequence both an enhanced usage and interoperability of databases and related resources. It is hoped that IDOMAL, the ontology of malaria will prove a valuable instrument when implemented in both malaria research and control measures. The OBOEdit2 software was used for the construction of the ontology. IDOMAL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. The first version of the malaria ontology covers both clinical and epidemiological aspects of the disease, as well as disease and vector biology. IDOMAL is meant to later become the nucleation site for a much larger ontology of vector borne diseases, which will itself be an extension of a large ontology of infectious diseases (IDO). The latter is currently being developed in the frame of a large international collaborative effort. IDOMAL, already freely available in its first version, will form part of a suite of ontologies that will be used to drive IT tools and databases specifically constructed to help control malaria and, later, other vector-borne diseases. This suite already consists of the ontology described here as well as the one on insecticide resistance that has been available for some time. Additional components are being developed and introduced into IDOMAL.
-
High Performance Semantic Factoring of Giga-Scale Semantic Graph Databases
DOE Office of Scientific and Technical Information (OSTI.GOV)
Joslyn, Cliff A.; Adolf, Robert D.; Al-Saffar, Sinan
2010-10-04
As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to bring high performance computational resources to bear on their analysis, interpretation, and visualization, especially with respect to their innate semantic structure. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multithreaded architecture of the Cray XMT platform, conventional clusters, and large data stores. In this paper we describe that architecture, and present the results of our deployingmore » that for the analysis of the Billion Triple dataset with respect to its semantic factors.« less
-
Bueno, Anibal; Rodríguez-López, Rocío; Reyes-Palomares, Armando; Rojano, Elena; Corpas, Manuel; Nevado, Julián; Lapunzina, Pablo; Sánchez-Jiménez, Francisca; Ranea, Juan A G
2018-06-26
Copy number variations (CNVs) are genomic structural variations (deletions, duplications, or translocations) that represent the 4.8-9.5% of human genome variation in healthy individuals. In some cases, CNVs can also lead to disease, being the etiology of many known rare genetic/genomic disorders. Despite the last advances in genomic sequencing and diagnosis, the pathological effects of many rare genetic variations remain unresolved, largely due to the low number of patients available for these cases, making it difficult to identify consistent patterns of genotype-phenotype relationships. We aimed to improve the identification of statistically consistent genotype-phenotype relationships by integrating all the genetic and clinical data of thousands of patients with rare genomic disorders (obtained from the DECIPHER database) into a phenotype-patient-genotype tripartite network. Then we assessed how our network approach could help in the characterization and diagnosis of novel cases in clinical genetics. The systematic approach implemented in this work is able to better define the relationships between phenotypes and specific loci, by exploiting large-scale association networks of phenotypes and genotypes in thousands of rare disease patients. The application of the described methodology facilitated the diagnosis of novel clinical cases, ranking phenotypes by locus specificity and reporting putative new clinical features that may suggest additional clinical follow-ups. In this work, the proof of concept developed over a set of novel clinical cases demonstrates that this network-based methodology might help improve the precision of patient clinical records and the characterization of rare syndromes.
-
Gershenwald, Jeffrey E; Scolyer, Richard A; Hess, Kenneth R; Sondak, Vernon K; Long, Georgina V; Ross, Merrick I; Lazar, Alexander J; Faries, Mark B; Kirkwood, John M; McArthur, Grant A; Haydu, Lauren E; Eggermont, Alexander M M; Flaherty, Keith T; Balch, Charles M; Thompson, John F
2017-11-01
Answer questions and earn CME/CNE To update the melanoma staging system of the American Joint Committee on Cancer (AJCC) a large database was assembled comprising >46,000 patients from 10 centers worldwide with stages I, II, and III melanoma diagnosed since 1998. Based on analyses of this new database, the existing seventh edition AJCC stage IV database, and contemporary clinical trial data, the AJCC Melanoma Expert Panel introduced several important changes to the Tumor, Nodes, Metastasis (TNM) classification and stage grouping criteria. Key changes in the eighth edition AJCC Cancer Staging Manual include: 1) tumor thickness measurements to be recorded to the nearest 0.1 mm, not 0.01 mm; 2) definitions of T1a and T1b are revised (T1a, <0.8 mm without ulceration; T1b, 0.8-1.0 mm with or without ulceration or <0.8 mm with ulceration), with mitotic rate no longer a T category criterion; 3) pathological (but not clinical) stage IA is revised to include T1b N0 M0 (formerly pathologic stage IB); 4) the N category descriptors "microscopic" and "macroscopic" for regional node metastasis are redefined as "clinically occult" and "clinically apparent"; 5) prognostic stage III groupings are based on N category criteria and T category criteria (ie, primary tumor thickness and ulceration) and increased from 3 to 4 subgroups (stages IIIA-IIID); 6) definitions of N subcategories are revised, with the presence of microsatellites, satellites, or in-transit metastases now categorized as N1c, N2c, or N3c based on the number of tumor-involved regional lymph nodes, if any; 7) descriptors are added to each M1 subcategory designation for lactate dehydrogenase (LDH) level (LDH elevation no longer upstages to M1c); and 8) a new M1d designation is added for central nervous system metastases. This evidence-based revision of the AJCC melanoma staging system will guide patient treatment, provide better prognostic estimates, and refine stratification of patients entering clinical trials. CA Cancer J Clin 2017;67:472-492. © 2017 American Cancer Society. © 2017 American Cancer Society.
-
Gershenwald, Jeffrey E.; Scolyer, Richard A.; Hess, Kenneth R.; Sondak, Vernon K.; Long, Georgina V.; Ross, Merrick I.; Lazar, Alexander J.; Faries, Mark B.; Kirkwood, John M.; McArthur, Grant A.; Haydu, Lauren E.; Eggermont, Alexander M. M.; Flaherty, Keith T.; Balch, Charles M.; Thompson, John F.
2018-01-01
To update the melanoma staging system of the American Joint Committee on Cancer (AJCC) a large database was assembled comprising >46,000 patients from 10 centers worldwide with stages I, II, and III melanoma diagnosed since 1998. Based on analyses of this new database, the existing seventh edition AJCC stage IV database, and contemporary clinical trial data, the AJCC Melanoma Expert Panel introduced several important changes to the Tumor, Nodes, Metastasis (TNM) classification and stage grouping criteria. Key changes in the eighth edition AJCC Cancer Staging Manual include: 1) tumor thickness measurements to be recorded to the nearest 0.1 mm, not 0.01 mm; 2) definitions of T1a and T1b are revised (T1a, <0.8 mm without ulceration; T1b, 0.8–1.0 mm with or without ulceration or <0.8 mm with ulceration), with mitotic rate no longer a T category criterion; 3) pathological (but not clinical) stage IA is revised to include T1b N0 M0 (formerly pathologic stage IB); 4) the N category descriptors “microscopic” and “macroscopic” for regional node metastasis are redefined as “clinically occult” and “clinically apparent”; 5) prognostic stage III groupings are based on N category criteria and T category criteria (ie, primary tumor thickness and ulceration) and increased from 3 to 4 subgroups (stages IIIA–IIID); 6) definitions of N subcategories are revised, with the presence of microsatellites, satellites, or in-transit metastases now categorized as N1c, N2c, or N3c based on the number of tumor-involved regional lymph nodes, if any; 7) descriptors are added to each M1 subcategory designation for lactate dehydrogenase (LDH) level (LDH elevation no longer upstages to M1c); and 8) a new M1d designation is added for central nervous system metastases. This evidence-based revision of the AJCC melanoma staging system will guide patient treatment, provide better prognostic estimates, and refine stratification of patients entering clinical trials. PMID:29028110
-
Rapid learning: a breakthrough agenda.
Etheredge, Lynn M
2014-07-01
A "rapid-learning health system" was proposed in a 2007 thematic issue of Health Affairs. The system was envisioned as one that uses evidence-based medicine to quickly determine the best possible treatments for patients. It does so by drawing on electronic health records and the power of big data to access large volumes of information from a variety of sources at high speed. The foundation for a rapid-learning health system was laid during 2007-13 by workshops, policy papers, large public investments in databases and research programs, and developing learning systems. Challenges now include implementing a new clinical research system with several hundred million patients, modernizing clinical trials and registries, devising and funding research on national priorities, and analyzing genetic and other factors that influence diseases and responses to treatment. Next steps also should aim to improve comparative effectiveness research; build on investments in health information technology to standardize handling of genetic information and support information exchange through apps and software modules; and develop new tools, data, and information for clinical decision support. Further advances will require commitment, leadership, and public-private and global collaboration. Project HOPE—The People-to-People Health Foundation, Inc.
-
Nieder, Carsten; Andratschke, Nicolaus H; Grosu, Anca L
2014-09-01
Radiation therapy is one of the cornerstones of modern multidisciplinary cancer treatment. Normal tissue tolerance is critical as radiation-induced side effects may compromise organ function and quality of life. The importance of normal tissue research is reflected by the large number of scientific articles, which have been published between 2006 and 2010. The present study identified important areas of research as well as seminal publications. The article citation rate is among the potential indicators of scientific impact. Highly cited articles, arbitrarily defined as those with ≥15 citations, were identified via a systematic search of the citation database, Scopus. Up to 608 articles per year were published between 2006 and 2010, however, <10% of publications in each year accumulated ≥15 citations. This figure is notably low, when compared with other oncology studies. A large variety of preclinical and clinical topics, including toxicity prediction, the dose-volume relationship and radioprotectors, accumulated ≥15 citations. However, clinical prevention or mitigation studies were underrepresented. The following conclusion may be drawn from the present study; despite the improved technology that has resulted in superior dose distribution, clinical prevention or mitigation studies are critical and must receive higher priority, funding and attention.
-
Integrated radiologist's workstation enabling the radiologist as an effective clinical consultant
NASA Astrophysics Data System (ADS)
McEnery, Kevin W.; Suitor, Charles T.; Hildebrand, Stan; Downs, Rebecca; Thompson, Stephen K.; Shepard, S. Jeff
2002-05-01
Since February 2000, radiologists at the M. D. Anderson Cancer Center have accessed clinical information through an internally developed radiologist's clinical interpretation workstation called RadStation. This project provides a fully integrated digital dictation workstation with clinical data review. RadStation enables the radiologist as an effective clinical consultant with access to pertinent sources of clinical information at the time of dictation. Data sources not only include prior radiology reports from the radiology information system (RIS) but access to pathology data, laboratory data, history and physicals, clinic notes, and operative reports. With integrated clinical information access, a radiologists's interpretation not only comments on morphologic findings but also can enable evaluation of study findings in the context of pertinent clinical presentation and history. Image access is enabled through the integration of an enterprise image archive (Stentor, San Francisco). Database integration is achieved by a combination of real time HL7 messaging and queries to SQL-based legacy databases. A three-tier system architecture accommodates expanding access to additional databases including real-time patient schedule as well as patient medications and allergies.
-
Roberts, Michael C; Ilardi, Stephen S; Johnson, Rebecca J
2006-07-01
This study tested the folkloristic belief that doctoral degree recipients who pursue academic careers typically wind up at institutions ranked lower in prestige than the institutions at which they trained (the step-down thesis). We used a database of faculty members in 150 clinical psychology doctoral programs accredited by the American Psychological Association, and compared each faculty member's training institution with the current employing institution on three distinct reputation ranking systems: The Center (University of Florida, Gainesville) for overall university reputation, the National Research Council (Washington, DC) for doctoral degree department reputation, and the news magazine, U.S. News and World Report ranking for clinical psychology training program reputation. Although support for the step-down thesis was found across all three ranking systems, a disproportionately large number of professors were also observed to move laterally in terms of their employing institution's reputation.
-
Optimal medication dosing from suboptimal clinical examples: a deep reinforcement learning approach.
Nemati, Shamim; Ghassemi, Mohammad M; Clifford, Gari D
2016-08-01
Misdosing medications with sensitive therapeutic windows, such as heparin, can place patients at unnecessary risk, increase length of hospital stay, and lead to wasted hospital resources. In this work, we present a clinician-in-the-loop sequential decision making framework, which provides an individualized dosing policy adapted to each patient's evolving clinical phenotype. We employed retrospective data from the publicly available MIMIC II intensive care unit database, and developed a deep reinforcement learning algorithm that learns an optimal heparin dosing policy from sample dosing trails and their associated outcomes in large electronic medical records. Using separate training and testing datasets, our model was observed to be effective in proposing heparin doses that resulted in better expected outcomes than the clinical guidelines. Our results demonstrate that a sequential modeling approach, learned from retrospective data, could potentially be used at the bedside to derive individualized patient dosing policies.
-
Patients' Positive and Negative Responses to Reading Mental Health Clinical Notes Online.
Denneson, Lauren M; Chen, Jason I; Pisciotta, Maura; Tuepker, Anais; Dobscha, Steven K
2018-05-01
This study describes responses to OpenNotes, clinical notes available online, among patients receiving mental health care and explores whether responses vary by patient demographic or clinical characteristics. Survey data from 178 veterans receiving mental health treatment at a large Veterans Affairs medical center included patient-reported health self-efficacy, health knowledge, alliance with clinicians, and negative emotional responses after reading OpenNotes. Health care data were extracted from the patient care database. Reading OpenNotes helped many participants feel in control of their health care (49%) and have more trust in clinicians (45%), although a few (8%) frequently felt upset after reading their notes. In multivariate models, posttraumatic stress disorder was associated with increased patient-clinician alliance (p=.046) but also with negative emotional responses (p<.01). Patients receiving mental health care frequently reported benefits from reading OpenNotes, yet some experienced negative responses.
-
Monga, Ash K; Tracey, Michael R; Subbaroyan, Jeyakumar
2012-08-01
The aim of this manuscript was to provide a systematic literature review of clinical trial evidence for a range of electrical stimulation therapies in the treatment of lower urinary tract symptoms (LUTS). The databases MEDLINE, BIOSIS Previews, Inside Conferences, and EMBASE were searched. Original clinical studies with greater than 15 subjects were included. Seventy-three studies were included, representing implanted sacral nerve stimulation (SNS), percutaneous posterior tibial nerve stimulation (PTNS), and transcutaneous electrical stimulation (TENS) therapy modalities. Median mean reductions in incontinence episodes and voiding frequency were similar for implanted SNS and PTNS. However, long-term follow-up data to validate the sustained benefit of PTNS are lacking. Despite a substantial body of research devoted to SNS validation, it is not possible to definitively define the appropriate role of this therapy owing largely to study design flaws that inhibited rigorous intention to treat analyses for the majority of these studies.
-
Zamami, Yoshito; Niimura, Takahiro; Takechi, Kenshi; Imanishi, Masaki; Koyama, Toshihiro; Ishizawa, Keisuke
2017-01-01
Approximately 100000 people suffer cardiopulmonary arrest in Japan every year, and the aging of society means that this number is expected to increase. Worldwide, approximately 100 million develop cardiac arrest annually, making it an international issue. Although survival has improved thanks to advances in cardiopulmonary resuscitation, there is a high rate of postresuscitation encephalopathy after the return of spontaneous circulation, and the proportion of patients who can return to normal life is extremely low. Treatment for postresuscitation encephalopathy is long term, and if sequelae persist then nursing care is required, causing immeasurable economic burdens as a result of ballooning medical costs. As at present there is no drug treatment to improve postresuscitation encephalopathy as a complication of cardiopulmonary arrest, the development of novel drug treatments is desirable. In recent years, new efficacy for existing drugs used in the clinical setting has been discovered, and drug repositioning has been proposed as a strategy for developing those drugs as therapeutic agents for different diseases. This review describes a large-scale database study carried out following a discovery strategy for drug repositioning with the objective of improving survival rates after cardiopulmonary arrest and discusses future repositioning prospects.
-
Egbring, Marco; Kullak-Ublick, Gerd A; Russmann, Stefan
2010-01-01
To develop a software solution that supports management and clinical review of patient data from electronic medical records databases or claims databases for pharmacoepidemiological drug safety studies. We used open source software to build a data management system and an internet application with a Flex client on a Java application server with a MySQL database backend. The application is hosted on Amazon Elastic Compute Cloud. This solution named Phynx supports data management, Web-based display of electronic patient information, and interactive review of patient-level information in the individual clinical context. This system was applied to a dataset from the UK General Practice Research Database (GPRD). Our solution can be setup and customized with limited programming resources, and there is almost no extra cost for software. Access times are short, the displayed information is structured in chronological order and visually attractive, and selected information such as drug exposure can be blinded. External experts can review patient profiles and save evaluations and comments via a common Web browser. Phynx provides a flexible and economical solution for patient-level review of electronic medical information from databases considering the individual clinical context. It can therefore make an important contribution to an efficient validation of outcome assessment in drug safety database studies.
-
The role of boldness in psychopathy: A study of academic and clinical perceptions.
Berg, Joanna M; Lilienfeld, Scott O; Sellbom, Martin
2017-10-01
The relevance of boldness to psychopathy has recently become a major flashpoint of scientific controversy. Although some authors have contended that boldness is a necessary (although insufficient) component of psychopathy, others have asserted that it is largely or entirely irrelevant to psychopathy. We addressed this issue by examining clinical perceptions of the relevance of the 3 triarchic dimensions (boldness, disinhibition, and meanness) to psychopathy among a sample of mental health professionals and graduate students (N = 228) using a vignette-based, person-centered methodology. A vignette comprising boldness descriptors afforded statistically significant and moderate to large (Cohen's ds ranged from .47 to .99) increases in perceived resemblance to overall psychopathy above and beyond the other triarchic dimensions, both singly and jointly; these findings extended largely to clinical perceptions of Factor 1 (i.e., interpersonal and affective aspects of psychopathy) but not Factor 2 (i.e., impulsive and antisocial aspects of psychopathy) resemblance. Contrary to the claims of some recent authors, boldness alone was perceived as being as relevant to psychopathy as was disinhibition, although both dimensions were perceived as less relevant to psychopathy than was meanness. These findings offer strong support for the contention that boldness is regarded as a key feature of classical psychopathy and are broadly consistent with interpersonal models of psychopathy. (PsycINFO Database Record (c) 2017 APA, all rights reserved).
-
Grolez, G; Moreau, C; Danel-Brunaud, V; Delmaire, C; Lopes, R; Pradat, P F; El Mendili, M M; Defebvre, L; Devos, D
2016-08-27
Amyotrophic lateral sclerosis (ALS) is a fatal, rapidly progressive neurodegenerative disease that mainly affects the motor system. A number of potentially neuroprotective and neurorestorative disease-modifying drugs are currently in clinical development. At present, the evaluation of a drug's clinical efficacy in ALS is based on the ALS Functional Rating Scale Revised, motor tests and survival. However, these endpoints are general, variable and late-stage measures of the ALS disease process and thus require the long-term assessment of large cohorts. Hence, there is a need for more sensitive radiological biomarkers. Various sequences for magnetic resonance imaging (MRI) of the brain and spinal cord have may have value as surrogate biomarkers for use in future clinical trials. Here, we review the MRI findings in ALS, their clinical correlations, and their limitations and potential role as biomarkers. The PubMed database was screened to identify studies using MRI in ALS. We included general MRI studies with a control group and an ALS group and longitudinal studies even if a control group was lacking. A total of 116 studies were analysed with MRI data and clinical correlations. The most disease-sensitive MRI patterns are in motor regions but the brain is more broadly affected. Despite the existing MRI biomarkers, there is a need for large cohorts with long term MRI and clinical follow-up. MRI assessment could be improved by standardized MRI protocols with multicentre studies.
-
Clinical utility of RapidArc™ radiotherapy technology
Infusino, Erminia
2015-01-01
RapidArc™ is a radiation technique that delivers highly conformal dose distributions through the complete rotation (360°) and speed variation of the linear accelerator gantry. This technique, called volumetric modulated arc therapy (VMAT), compared with conventional radiotherapy techniques, can achieve high-target volume coverage and sparing damage to normal tissues. RapidArc delivers precise dose distribution and conformity similar to or greater than intensity-modulated radiation therapy in a short time, generally a few minutes, to which image-guided radiation therapy is added. RapidArc has become a currently used technology in many centers, which use RapidArc technology to treat a large number of patients. Large and small hospitals use it to treat the most challenging cases, but more and more frequently for the most common cancers. The clinical use of RapidArc and VMAT technology is constantly growing. At present, a limited number of clinical data are published, mostly concerning planning and feasibility studies. Clinical outcome data are increasing for a few tumor sites, even if only a little. The purpose of this work is to discuss the current status of VMAT techniques in clinical use through a review of the published data of planning systems and clinical outcomes in several tumor sites. The study consisted of a systematic review based on analysis of manuscripts retrieved from the PubMed, BioMed Central, and Scopus databases by searching for the keywords “RapidArc”, “Volumetric modulated arc radiotherapy”, and “Intensity-modulated radiotherapy”. PMID:26648755
-
DOE Office of Scientific and Technical Information (OSTI.GOV)
Roberts, D
Purpose: A unified database system was developed to allow accumulation, review and analysis of quality assurance (QA) data for measurement, treatment, imaging and simulation equipment in our department. Recording these data in a database allows a unified and structured approach to review and analysis of data gathered using commercial database tools. Methods: A clinical database was developed to track records of quality assurance operations on linear accelerators, a computed tomography (CT) scanner, high dose rate (HDR) afterloader and imaging systems such as on-board imaging (OBI) and Calypso in our department. The database was developed using Microsoft Access database and visualmore » basic for applications (VBA) programming interface. Separate modules were written for accumulation, review and analysis of daily, monthly and annual QA data. All modules were designed to use structured query language (SQL) as the basis of data accumulation and review. The SQL strings are dynamically re-written at run time. The database also features embedded documentation, storage of documents produced during QA activities and the ability to annotate all data within the database. Tests are defined in a set of tables that define test type, specific value, and schedule. Results: Daily, Monthly and Annual QA data has been taken in parallel with established procedures to test MQA. The database has been used to aggregate data across machines to examine the consistency of machine parameters and operations within the clinic for several months. Conclusion: The MQA application has been developed as an interface to a commercially available SQL engine (JET 5.0) and a standard database back-end. The MQA system has been used for several months for routine data collection.. The system is robust, relatively simple to extend and can be migrated to a commercial SQL server.« less
-
Jagtap, Pratik; Goslinga, Jill; Kooren, Joel A; McGowan, Thomas; Wroblewski, Matthew S; Seymour, Sean L; Griffin, Timothy J
2013-04-01
Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
-
FARME DB: a functional antibiotic resistance element database
Wallace, James C.; Port, Jesse A.; Smith, Marissa N.; Faustman, Elaine M.
2017-01-01
Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates. Database URL: http://staff.washington.edu/jwallace/farme PMID:28077567
-
Kaspar, Mathias; Ertl, Maximilian; Fette, Georg; Dietrich, Georg; Toepfer, Martin; Angermann, Christiane; Störk, Stefan; Puppe, Frank
2016-08-05
Data that needs to be documented for clinical studies has often been acquired and documented in clinical routine. Usually this data is manually transferred to Case Report Forms (CRF) and/or directly into an electronic data capture (EDC) system. To enhance the documentation process of a large clinical follow-up study targeting patients admitted for acutely decompensated heart failure by accessing the data created during routine and study visits from a hospital information system (HIS) and by transferring it via a data warehouse (DWH) into the study's EDC system. This project is based on the clinical DWH developed at the University of Würzburg. The DWH was extended by several new data domains including data created by the study team itself. An R user interface was developed for the DWH that allows to access its source data in all its detail, to transform data as comprehensively as possible by R into study-specific variables and to support the creation of data and catalog tables. A data flow was established that starts with labeling patients as study patients within the HIS and proceeds with updating the DWH with this label and further data domains at a daily rate. Several study-specific variables were defined using the implemented R user interface of the DWH. This system was then used to export these variables as data tables ready for import into our EDC system. The data tables were then used to initialize the first 296 patients within the EDC system by pseudonym, visit and data values. Afterwards, these records were filled with clinical data on heart failure, vital parameters and time spent on selected wards. This solution focuses on the comprehensive access and transformation of data for a DWH-EDC system linkage. Using this system in a large clinical study has demonstrated the feasibility of this approach for a study with a complex visit schedule.
-
Liu, Xiaoyu; Chen, Pinyi; Liu, Ling; Zhang, Yanqi; Wu, Yazhou; Pettigrew, Julia Christine; Cheng, Dixiang; Yi, Dong
2014-01-01
Background In East Asia, numerous reports describe the utilization of traditional Chinese herbal decoctions to treat gout. However, the reported clinical effects vary. Objectives In this study, we reviewed and analyzed a large number of randomized controlled clinical trials to systematically assess the clinical efficacy and adverse reactions of Chinese herbal decoctions for treating gout. Methods We performed a comprehensive search of databases, such as PubMed, EMBASE, the Cochrane Central Register of Controlled Trials, Chinese biomedical literature database, et al. In addition, we manually searched the relevant meeting information in the library of the Third Military Medical University. Results Finally, 17 randomized controlled trials with a sample size of 1,402 cases met the criteria and were included in the study. The results of the meta-analysis showed that when gout had progressed to the stage of acute arthritis, there was no significant difference in clinical efficacy between Chinese herbal decoctions and traditional Western medicine, as indicated based on the following parameters: serum uric acid (standardized mean difference (SMD):0.35, 95% confidence interval (CI): 0.03 to 0.67), C reactive protein (SMD: 0.25, 95% CI: −0.18 to 0.69), erythrocyte sedimentation rate (SMD: 0.21, 95% CI: −0.02 to 0.45) and overall clinical response (relative risk (RR): 1.05, 95% CI: 1.01 to 1.10). However, the Chinese herbal decoction was significantly better than traditional Western medicine in controlling adverse drug reactions (RR: 0.06, 95% CI: 0.03 to 0.13). Conclusions Through a systematic review of the clinical efficacy and safety of Chinese herbal decoctions and traditional Western medicine for the treatment of gout, we found that Chinese herbal decoction and traditional Western medicine led to similar clinical efficacy, but the Chinese herbal decoctions were superior to Western medicine in terms of controlling adverse drug reactions. PMID:24465466
-
Bruland, Philipp; Doods, Justin; Storck, Michael; Dugas, Martin
2017-01-01
Data dictionaries provide structural meta-information about data definitions in health information technology (HIT) systems. In this regard, reusing healthcare data for secondary purposes offers several advantages (e.g. reduce documentation times or increased data quality). Prerequisites for data reuse are its quality, availability and identical meaning of data. In diverse projects, research data warehouses serve as core components between heterogeneous clinical databases and various research applications. Given the complexity (high number of data elements) and dynamics (regular updates) of electronic health record (EHR) data structures, we propose a clinical metadata warehouse (CMDW) based on a metadata registry standard. Metadata of two large hospitals were automatically inserted into two CMDWs containing 16,230 forms and 310,519 data elements. Automatic updates of metadata are possible as well as semantic annotations. A CMDW allows metadata discovery, data quality assessment and similarity analyses. Common data models for distributed research networks can be established based on similarity analyses.
-
Internet and cardiovascular research: the present and its future potentials and limits.
2002-03-01
The Internet and the World Wide Web have been proposed as tools to improve medical and cardiovascular research. These new technologies have been mainly applied to large-scale clinical trials, with the development of clinical-trial websites. They include tools for the management of some aspects of clinical trials, such as the dissemination of information on trial progress; randomisation and the monitoring processes; the distribution and accountability of study drugs; and remote data-entry. Several clinical-trial websites have been developed in the cardiovascular field over the last few years, but few have been designed to conduct trials fully online. Advantages of such systems include greater interaction between the coordinating centre and investigators, availability of a clean database in a short time, and cost reduction. Website developers need to take care of security issues and to use security tools (data encryption, firewalls, passwords and electronic signatures) in order to prevent unauthorised users from accessing the system and patient data.
-
Orthographic and Phonological Neighborhood Databases across Multiple Languages.
Marian, Viorica
2017-01-01
The increased globalization of science and technology and the growing number of bilinguals and multilinguals in the world have made research with multiple languages a mainstay for scholars who study human function and especially those who focus on language, cognition, and the brain. Such research can benefit from large-scale databases and online resources that describe and measure lexical, phonological, orthographic, and semantic information. The present paper discusses currently-available resources and underscores the need for tools that enable measurements both within and across multiple languages. A general review of language databases is followed by a targeted introduction to databases of orthographic and phonological neighborhoods. A specific focus on CLEARPOND illustrates how databases can be used to assess and compare neighborhood information across languages, to develop research materials, and to provide insight into broad questions about language. As an example of how using large-scale databases can answer questions about language, a closer look at neighborhood effects on lexical access reveals that not only orthographic, but also phonological neighborhoods can influence visual lexical access both within and across languages. We conclude that capitalizing upon large-scale linguistic databases can advance, refine, and accelerate scientific discoveries about the human linguistic capacity.
-
Asiimwe, Innocent Gerald; Rumona, Dickson
2016-01-01
To limit selective and incomplete publication of the results of clinical trials, registries including ClinicalTrials.gov were introduced. The ClinicalTrials.gov registry added a results database in 2008 to enable researchers to post the results of their trials as stipulated by the Food and Drug Administration Amendment Act of 2007. This study aimed to determine the direction and magnitude of any change in publication proportions of registered breast cancer trials that occurred since the inception of the ClinicalTrials.gov results database. A cross-sectional study design was employed using ClinicalTrials.gov, a publicly available registry/results database as the primary data source. Registry contents under the subcategories 'Breast Neoplasms' and 'Breast Neoplasms, Male' were downloaded on 1 August 2015. A literature search for included trials was afterwards conducted using MEDLINE and DISCOVER databases to determine publication status of the registered breast cancer trials. Nearly half (168/340) of the listed trials had been published, with a median time to publication of 24 months (Q1 = 14 months, Q3 = 42 months). Only 86 trials were published within 24 months of completion. There was no significant increase in publication proportions of trials that were completed before the introduction of the results database compared to those completed after (OR = 1.00, 95 % CI = .61 to 1.63; adjusted OR = 0.84, 95 % CI = .51 to 1.39). Characteristics associated with publication included trial type (observational versus interventional adjusted OR = .28, 95 % CI = .10 to .74) and completion/termination status (terminated versus completed adjusted OR = .22, 95 % CI = .09 to .51). Less than a half of breast cancer trials registered in ClinicalTrials.gov are published in peer-reviewed journals.
-
Large Scale Landslide Database System Established for the Reservoirs in Southern Taiwan
NASA Astrophysics Data System (ADS)
Tsai, Tsai-Tsung; Tsai, Kuang-Jung; Shieh, Chjeng-Lun
2017-04-01
Typhoon Morakot seriously attack southern Taiwan awaken the public awareness of large scale landslide disasters. Large scale landslide disasters produce large quantity of sediment due to negative effects on the operating functions of reservoirs. In order to reduce the risk of these disasters within the study area, the establishment of a database for hazard mitigation / disaster prevention is necessary. Real time data and numerous archives of engineering data, environment information, photo, and video, will not only help people make appropriate decisions, but also bring the biggest concern for people to process and value added. The study tried to define some basic data formats / standards from collected various types of data about these reservoirs and then provide a management platform based on these formats / standards. Meanwhile, in order to satisfy the practicality and convenience, the large scale landslide disasters database system is built both provide and receive information abilities, which user can use this large scale landslide disasters database system on different type of devices. IT technology progressed extreme quick, the most modern system might be out of date anytime. In order to provide long term service, the system reserved the possibility of user define data format /standard and user define system structure. The system established by this study was based on HTML5 standard language, and use the responsive web design technology. This will make user can easily handle and develop this large scale landslide disasters database system.
-
Large-scale annotation of small-molecule libraries using public databases.
Zhou, Yingyao; Zhou, Bin; Chen, Kaisheng; Yan, S Frank; King, Frederick J; Jiang, Shumei; Winzeler, Elizabeth A
2007-01-01
While many large publicly accessible databases provide excellent annotation for biological macromolecules, the same is not true for small chemical compounds. Commercial data sources also fail to encompass an annotation interface for large numbers of compounds and tend to be cost prohibitive to be widely available to biomedical researchers. Therefore, using annotation information for the selection of lead compounds from a modern day high-throughput screening (HTS) campaign presently occurs only under a very limited scale. The recent rapid expansion of the NIH PubChem database provides an opportunity to link existing biological databases with compound catalogs and provides relevant information that potentially could improve the information garnered from large-scale screening efforts. Using the 2.5 million compound collection at the Genomics Institute of the Novartis Research Foundation (GNF) as a model, we determined that approximately 4% of the library contained compounds with potential annotation in such databases as PubChem and the World Drug Index (WDI) as well as related databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and ChemIDplus. Furthermore, the exact structure match analysis showed 32% of GNF compounds can be linked to third party databases via PubChem. We also showed annotations such as MeSH (medical subject headings) terms can be applied to in-house HTS databases in identifying signature biological inhibition profiles of interest as well as expediting the assay validation process. The automated annotation of thousands of screening hits in batch is becoming feasible and has the potential to play an essential role in the hit-to-lead decision making process.
-
Comparison of the Frontier Distributed Database Caching System to NoSQL Databases
NASA Astrophysics Data System (ADS)
Dykstra, Dave
2012-12-01
One of the main attractions of non-relational “NoSQL” databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It also compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.
-
Comparison of the Frontier Distributed Database Caching System to NoSQL Databases
DOE Office of Scientific and Technical Information (OSTI.GOV)
Dykstra, Dave
One of the main attractions of non-relational NoSQL databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It alsomore » compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.« less
-
de Souza, Gustavo A.; Arntzen, Magnus Ø.; Fortuin, Suereta; Schürch, Anita C.; Målen, Hiwa; McEvoy, Christopher R. E.; van Soolingen, Dick; Thiede, Bernd; Warren, Robin M.; Wiker, Harald G.
2011-01-01
Precise annotation of genes or open reading frames is still a difficult task that results in divergence even for data generated from the same genomic sequence. This has an impact in further proteomic studies, and also compromises the characterization of clinical isolates with many specific genetic variations that may not be represented in the selected database. We recently developed software called multistrain mass spectrometry prokaryotic database builder (MSMSpdbb) that can merge protein databases from several sources and be applied on any prokaryotic organism, in a proteomic-friendly approach. We generated a database for the Mycobacterium tuberculosis complex (using three strains of Mycobacterium bovis and five of M. tuberculosis), and analyzed data collected from two laboratory strains and two clinical isolates of M. tuberculosis. We identified 2561 proteins, of which 24 were present in M. tuberculosis H37Rv samples, but not annotated in the M. tuberculosis H37Rv genome. We were also able to identify 280 nonsynonymous single amino acid polymorphisms and confirm 367 translational start sites. As a proof of concept we applied the database to whole-genome DNA sequencing data of one of the clinical isolates, which allowed the validation of 116 predicted single amino acid polymorphisms and the annotation of 131 N-terminal start sites. Moreover we identified regions not present in the original M. tuberculosis H37Rv sequence, indicating strain divergence or errors in the reference sequence. In conclusion, we demonstrated the potential of using a merged database to better characterize laboratory or clinical bacterial strains. PMID:21030493
-
Wu, Li-Tzy; Gersing, Ken; Burchett, Bruce; Woody, George E; Blazer, Dan G
2011-11-01
This study examined the prevalence of substance use disorders (SUDs) among psychiatric patients aged 2-17 years in an electronic health records database (N=11,457) and determined patterns of comorbid diagnoses among patients with a SUD to inform emerging comparative effectiveness research (CER) efforts. DSM-IV diagnoses of all inpatients and outpatients at a large university-based hospital and its associated psychiatric clinics were systematically captured between 2000 and 2010: SUD, anxiety (AD), mood (MD), conduct (CD), attention deficit/hyperactivity (ADHD), personality (PD), adjustment, eating, impulse-control, psychotic, learning, mental retardation, and relational disorders. The prevalence of SUD in the 2-12-year age group (n=6210) was 1.6% and increased to 25% in the 13-17-year age group (n=5247). Cannabis diagnosis was the most prevalent SUD, accounting for more than 80% of all SUD cases. Among patients with a SUD (n=1423), children aged 2-12 years (95%) and females (75-100%) showed high rates of comorbidities; blacks were more likely than whites to be diagnosed with CD, impulse-control, and psychotic diagnoses, while whites had elevated odds of having AD, ADHD, MD, PD, relational, and eating diagnoses. Patients with a SUD used more inpatient treatment than patients without a SUD (43% vs. 21%); children, females, and blacks had elevated odds of inpatient psychiatric treatment. Collectively, results add clinical evidence on treatment needs and diagnostic patterns for understudied diagnoses. Copyright © 2011 Elsevier Ltd. All rights reserved.
-
Building an Ontology-driven Database for Clinical Immune Research
Ma, Jingming
2006-01-01
The clinical researches of immune response usually generate a huge amount of biomedical testing data over a certain period of time. The user-friendly data management systems based on the relational database will help immunologists/clinicians to fully manage the data. On the other hand, the same biological assays such as ELISPOT and flow cytometric assays are involved in immunological experiments no matter of different study purposes. The reuse of biological knowledge is one of driving forces behind this ontology-driven data management. Therefore, an ontology-driven database will help to handle different clinical immune researches and help immunologists/clinicians easily understand the immunological data from each other. We will discuss some outlines for building an ontology-driven data management for clinical immune researches (ODMim). PMID:17238637
-
Use of national clinical databases for informing and for evaluating health care policies.
Black, Nick; Tan, Stefanie
2013-02-01
Policy-makers and analysts could make use of national clinical databases either to inform or to evaluate meso-level (organisation and delivery of health care) and macro-level (national) policies. Reviewing the use of 15 of the best established databases in England, we identify and describe four published examples of each use. These show that policy-makers can either make use of the data itself or of research based on the database. For evaluating policies, the major advantages are the huge sample sizes available, the generalisability of the data, its immediate availability and historic information. The principal methodological challenges involve the need for risk adjustment and time-series analysis. Given their usefulness in the policy arena, there are several reasons why national clinical databases have not been used more, some due to a lack of 'push' by their custodians and some to the lack of 'pull' by policy-makers. Greater exploitation of these valuable resources would be facilitated by policy-makers' and custodians' increased awareness, minimisation of legal restrictions on data use, improvements in the quality of databases and a library of examples of applications to policy. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
-
HepSEQ: International Public Health Repository for Hepatitis B
Gnaneshan, Saravanamuttu; Ijaz, Samreen; Moran, Joanne; Ramsay, Mary; Green, Jonathan
2007-01-01
HepSEQ is a repository for an extensive library of public health and molecular data relating to hepatitis B virus (HBV) infection collected from international sources. It is hosted by the Centre for Infections, Health Protection Agency (HPA), England, United Kingdom. This repository has been developed as a web-enabled, quality-controlled database to act as a tool for surveillance, HBV case management and for research. The web front-end for the database system can be accessed from . The format of the database system allows for comprehensive molecular, clinical and epidemiological data to be deposited into a functional database, to search and manipulate the stored data and to extract and visualize the information on epidemiological, virological, clinical, nucleotide sequence and mutational aspects of HBV infection through web front-end. Specific tools, built into the database, can be utilized to analyse deposited data and provide information on HBV genotype, identify mutations with known clinical significance (e.g. vaccine escape, precore and antiviral-resistant mutations) and carry out sequence homology searches against other deposited strains. Further mechanisms are also in place to allow specific tailored searches of the database to be undertaken. PMID:17130143
-
Gallagher, Sarah A; Smith, Angela B; Matthews, Jonathan E; Potter, Clarence W; Woods, Michael E; Raynor, Mathew; Wallen, Eric M; Rathmell, W Kimryn; Whang, Young E; Kim, William Y; Godley, Paul A; Chen, Ronald C; Wang, Andrew; You, Chaochen; Barocas, Daniel A; Pruthi, Raj S; Nielsen, Matthew E; Milowsky, Matthew I
2014-01-01
The management of genitourinary malignancies requires a multidisciplinary care team composed of urologists, medical oncologists, and radiation oncologists. A genitourinary (GU) oncology clinical database is an invaluable resource for patient care and research. Although electronic medical records provide a single web-based record used for clinical care, billing, and scheduling, information is typically stored in a discipline-specific manner and data extraction is often not applicable to a research setting. A GU oncology database may be used for the development of multidisciplinary treatment plans, analysis of disease-specific practice patterns, and identification of patients for research studies. Despite the potential utility, there are many important considerations that must be addressed when developing and implementing a discipline-specific database. The creation of the GU oncology database including prostate, bladder, and kidney cancers with the identification of necessary variables was facilitated by meetings of stakeholders in medical oncology, urology, and radiation oncology at the University of North Carolina (UNC) at Chapel Hill with a template data dictionary provided by the Department of Urologic Surgery at Vanderbilt University Medical Center. Utilizing Research Electronic Data Capture (REDCap, version 4.14.5), the UNC Genitourinary OncoLogy Database (UNC GOLD) was designed and implemented. The process of designing and implementing a discipline-specific clinical database requires many important considerations. The primary consideration is determining the relationship between the database and the Institutional Review Board (IRB) given the potential applications for both clinical and research uses. Several other necessary steps include ensuring information technology security and federal regulation compliance; determination of a core complete dataset; creation of standard operating procedures; standardizing entry of free text fields; use of data exports, queries, and de-identification strategies; inclusion of individual investigators' data; and strategies for prioritizing specific projects and data entry. A discipline-specific database requires a buy-in from all stakeholders, meticulous development, and data entry resources to generate a unique platform for housing information that may be used for clinical care and research with IRB approval. The steps and issues identified in the development of UNC GOLD provide a process map for others interested in developing a GU oncology database. Copyright © 2014 Elsevier Inc. All rights reserved.
-
From ClinicalTrials.gov trial registry to an analysis-ready database of clinical trial results.
Cepeda, M Soledad; Lobanov, Victor; Berlin, Jesse A
2013-04-01
The ClinicalTrials.gov web site provides a convenient interface to look up study results, but it does not allow downloading data in a format that can be readily used for quantitative analyses. To develop a system that automatically downloads study results from ClinicalTrials.gov and provides an interface to retrieve study results in a spreadsheet format ready for analysis. Sherlock(®) identifies studies by intervention, population, or outcome of interest and in seconds creates an analytic database of study results ready for analyses. The outcome classification algorithms used in Sherlock were validated against a classification by an expert. Having a database ready for analysis that can be updated automatically, dramatically extends the utility of the ClinicalTrials.gov trial registry. It increases the speed of comparative research, reduces the need for manual extraction of data, and permits answering a vast array of questions.
-
High performance semantic factoring of giga-scale semantic graph databases.
DOE Office of Scientific and Technical Information (OSTI.GOV)
al-Saffar, Sinan; Adolf, Bob; Haglin, David
2010-10-01
As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to bring high performance computational resources to bear on their analysis, interpretation, and visualization, especially with respect to their innate semantic structure. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multithreaded architecture of the Cray XMT platform, conventional clusters, and large data stores. In this paper we describe that architecture, and present the results of our deployingmore » that for the analysis of the Billion Triple dataset with respect to its semantic factors, including basic properties, connected components, namespace interaction, and typed paths.« less
-
NASA Astrophysics Data System (ADS)
Borisova, E.; Pavlova, E.; Kundurjiev, T.; Troyanova, P.; Genova, Ts.; Avramov, L.
2014-05-01
We investigated more than 500 clinical cases to receive the spectral properties of basal cell (136 patients) and squamous cell carcinoma (28), malignant melanoma (41) and different cutaneous dysplastic and benign cutaneous lesions. Excitation at 365, 385 and 405 nm using LEDs sources is applied to obtain autofluorescence spectra, and broad-band illumination in the region of 400-900 nm is used to detect diffuse reflectance spectra of all pathologies investigated. USB4000 microspectrometer (Ocean Optics Inc, USA) is applied as a detector and fiber-optic probe is used for delivery of the light. In the case of in vivo tumor measurements spectral shape and intensity changes are observed that are specific for a given type of lesion. Autofluorescence origins of the signals coming from skin tissues are mainly due to proteins, such as collagen, elastin, keratin, their cross-links, co-enzimes - NADH and flavins and endogenous porphyrins. Spectral features significant into diffuse spectroscopy diagnosis are related to the effects of re-absorption of hemoglobin and its forms, as well as melanin and its concentration in different pathologies. We developed significant database and revealed specific features for a large class of cutaneous neoplasia, using about 30 different spectral peculiarities to differentiate cutaneous tumors. Sensitivity and specificity obtained exceed 90%, which make optical biopsy very useful tool for clinical practice. These results are obtained in the frames of clinical investigations for development of significant "spectral features" database for the most common cutaneous malignant, dysplastic and benign lesions. In the forthcoming plans, our group tries to optimize the existing experimental system for optical biopsy of skin, and to introduce it and the diagnostic algorithms developed into clinical practice, based on the high diagnostic accuracy achieved.
-
Slutsky, Jeremiah; Singh, Nilkamal; Khalsa, Sat Bir S.
2015-01-01
Abstract Objective: A comprehensive bibliometric analysis was conducted on publications for yoga therapy research in clinical populations. Methods: Major electronic databases were searched for articles in all languages published between 1967 and 2013. Databases included PubMed, PsychInfo, MEDLINE, IndMed, Indian Citation Index, Index Medicus for South-East Asia Region, Web of Knowledge, Embase, EBSCO, and Google Scholar. Nonindexed journals were searched manually. Key search words included yoga, yoga therapy, pranayama, asana. All studies met the definition of a clinical trial. All styles of yoga were included. The authors extracted the data. Results: A total of 486 articles met the inclusion criteria and were published in 217 different peer-reviewed journals from 29 different countries on 28,080 study participants. The primary result observed is the three-fold increase in number of publications seen in the last 10 years, inclusive of all study designs. Overall, 45% of the studies published were randomized controlled trials, 18% were controlled studies, and 37% were uncontrolled studies. Most publications originated from India (n=258), followed by the United States (n=122) and Canada (n=13). The top three disorders addressed by yoga interventions were mental health, cardiovascular disease, and respiratory disease. Conclusion: A surge in publications on yoga to mitigate disease-related symptoms in clinical populations has occurred despite challenges facing the field of yoga research, which include standardization and limitations in funding, time, and resources. The population at large has observed a parallel surge in the use of yoga outside of clinical practice. The use of yoga as a complementary therapy in clinical practice may lead to health benefits beyond traditional treatment alone; however, to effect changes in health care policy, more high-quality, evidence-based research is needed. PMID:26196166
-
Winters, Brian R; Mossanen, Matthew; Holt, Sarah K; Lin, Daniel W; Wright, Jonathan L
2016-10-01
To examine the risk factors associated with upstaging at inguinal lymph node dissection (ILND) in men with penile cancer and clinically negative lymph nodes (cN0) using a large US cancer database. The National Cancer Data Base was queried from 1998 to 2012 to identify men with penile cancer who underwent ILND and had complete clinical or pathologic node status available. Lymphovascular invasion (LVI) was available after 2010. Multivariate logistic regression evaluated factors (cT stage, grade, LVI) associated with pathologic nodal upstaging in those with cN0 disease. Correlations between clinical and pathologic node status were also calculated with weighted kappa statistics. Complete clinical and pathologic LN status was available for 875 patients. Of these, 461 (53%) were cN0. Upstaging occurred in 111 (24%). When stratified by low, intermediate, and high-risk groups, the proportion with pathologically positive LNs was 16%, 20%, and 27%, respectively (P = .12). On multivariate analysis, limited to men with LVI data available (N = 206), LVI (odds ratio 3.10, 95% confidence interval 1.39-6.92), but not increasing stage (univariate only) or grade (univariate only), was significantly associated with upstaging at ILND. In this analysis, of 461 patients with node-negative penile cancer undergoing ILND, upstaging was observed in 24%. LVI was the strongest independent predictor of occult lymph node disease. These findings corroborate the presence of LVI as the significant risk factor for occult micrometastases and suggest a possible improvement in existing risk stratification groupings, with the presence of LVI, regardless of stage or grade, to be considered high-risk disease. Copyright © 2016 Elsevier Inc. All rights reserved.
-
Planas, M; Rodríguez, T; Lecha, M
2004-01-01
Decisions have to be made about what data on patient characteristics and processes and outcome need to be collected, and standard definitions of these data items need to be developed to identify data quality concerns as promptly as possible and to establish ways to improve data quality. The usefulness of any clinical database depends strongly on the quality of the collected data. If the data quality is poor, the results of studies using the database might be biased and unreliable. Furthermore, if the quality of the database has not been verified, the results might be given little credence, especially if they are unwelcome or unexpected. To assure the quality of clinical database is essential the clear definition of the uses to which the database is going to be put; the database should to be developed that is comprehensive in terms of its usefulness but limited in its size.
-
[Benefits of large healthcare databases for drug risk research].
Garbe, Edeltraut; Pigeot, Iris
2015-08-01
Large electronic healthcare databases have become an important worldwide data resource for drug safety research after approval. Signal generation methods and drug safety studies based on these data facilitate the prospective monitoring of drug safety after approval, as has been recently required by EU law and the German Medicines Act. Despite its large size, a single healthcare database may include insufficient patients for the study of a very small number of drug-exposed patients or the investigation of very rare drug risks. For that reason, in the United States, efforts have been made to work on models that provide the linkage of data from different electronic healthcare databases for monitoring the safety of medicines after authorization in (i) the Sentinel Initiative and (ii) the Observational Medical Outcomes Partnership (OMOP). In July 2014, the pilot project Mini-Sentinel included a total of 178 million people from 18 different US databases. The merging of the data is based on a distributed data network with a common data model. In the European Network of Centres for Pharmacoepidemiology and Pharmacovigilance (ENCEPP) there has been no comparable merging of data from different databases; however, first experiences have been gained in various EU drug safety projects. In Germany, the data of the statutory health insurance providers constitute the most important resource for establishing a large healthcare database. Their use for this purpose has so far been severely restricted by the Code of Social Law (Section 75, Book 10). Therefore, a reform of this section is absolutely necessary.
-
Hirata, Makoto; Kamatani, Yoichiro; Nagai, Akiko; Kiyohara, Yutaka; Ninomiya, Toshiharu; Tamakoshi, Akiko; Yamagata, Zentaro; Kubo, Michiaki; Muto, Kaori; Mushiroda, Taisei; Murakami, Yoshinori; Yuji, Koichiro; Furukawa, Yoichi; Zembutsu, Hitoshi; Tanaka, Toshihiro; Ohnishi, Yozo; Nakamura, Yusuke; Matsuda, Koichi
2017-03-01
To implement personalized medicine, we established a large-scale patient cohort, BioBank Japan, in 2003. BioBank Japan contains DNA, serum, and clinical information derived from approximately 200,000 patients with 47 diseases. Serum and clinical information were collected annually until 2012. We analyzed clinical information of participants at enrollment, including age, sex, body mass index, hypertension, and smoking and drinking status, across 47 diseases, and compared the results with the Japanese database on Patient Survey and National Health and Nutrition Survey. We conducted multivariate logistic regression analysis, adjusting for sex and age, to assess the association between family history and disease development. Distribution of age at enrollment reflected the typical age of disease onset. Analysis of the clinical information revealed strong associations between smoking and chronic obstructive pulmonary disease, drinking and esophageal cancer, high body mass index and metabolic disease, and hypertension and cardiovascular disease. Logistic regression analysis showed that individuals with a family history of keloid exhibited a higher odds ratio than those without a family history, highlighting the strong impact of host genetic factor(s) on disease onset. Cross-sectional analysis of the clinical information of participants at enrollment revealed characteristics of the present cohort. Analysis of family history revealed the impact of host genetic factors on each disease. BioBank Japan, by publicly distributing DNA, serum, and clinical information, could be a fundamental infrastructure for the implementation of personalized medicine. Copyright © 2017 The Authors. Production and hosting by Elsevier B.V. All rights reserved.
-
Bussmann, Hermann; Wester, C William; Ndwapi, Ndwapi; Vanderwarker, Chris; Gaolathe, Tendani; Tirelo, Geoffrey; Avalos, Ava; Moffat, Howard; Marlink, Richard G
2006-02-01
Individual patient care and programme evaluation are pivotal for the success of antiretroviral treatment programmes in resource-limited countries. While computer-aided documentation and data storage are indispensable for any large programme, several important issues need to be addressed including which data are to be collected, who collects it and how it is entered into an electronic database. We describe a patient-monitoring approach, which uses patient encounter forms (in hybrid paper + electronic format) based on optical character recognition, piloted at Princess Marina Hospital in Gaborone, Botswana's first public highly active antiretroviral therapy (HAART) outpatient clinic. Our novel data capture approach collects "key" data for tracking patient and programme outcomes. It saves physician time and does not detract from clinical care.
-
Bussmann, Hermann; Wester, C. William; Ndwapi, Ndwapi; Vanderwarker, Chris; Gaolathe, Tendani; Tirelo, Geoffrey; Avalos, Ava; Moffat, Howard; Marlink, Richard G.
2006-01-01
Individual patient care and programme evaluation are pivotal for the success of antiretroviral treatment programmes in resource-limited countries. While computer-aided documentation and data storage are indispensable for any large programme, several important issues need to be addressed including which data are to be collected, who collects it and how it is entered into an electronic database. We describe a patient-monitoring approach, which uses patient encounter forms (in hybrid paper + electronic format) based on optical character recognition, piloted at Princess Marina Hospital in Gaborone, Botswana's first public highly active antiretroviral therapy (HAART) outpatient clinic. Our novel data capture approach collects "key" data for tracking patient and programme outcomes. It saves physician time and does not detract from clinical care. PMID:16501730
-
Visualizing the semantic content of large text databases using text maps
NASA Technical Reports Server (NTRS)
Combs, Nathan
1993-01-01
A methodology for generating text map representations of the semantic content of text databases is presented. Text maps provide a graphical metaphor for conceptualizing and visualizing the contents and data interrelationships of large text databases. Described are a set of experiments conducted against the TIPSTER corpora of Wall Street Journal articles. These experiments provide an introduction to current work in the representation and visualization of documents by way of their semantic content.
-
Realization of Real-Time Clinical Data Integration Using Advanced Database Technology
Yoo, Sooyoung; Kim, Boyoung; Park, Heekyong; Choi, Jinwook; Chun, Jonghoon
2003-01-01
As information & communication technologies have advanced, interest in mobile health care systems has grown. In order to obtain information seamlessly from distributed and fragmented clinical data from heterogeneous institutions, we need solutions that integrate data. In this article, we introduce a method for information integration based on real-time message communication using trigger and advanced database technologies. Messages were devised to conform to HL7, a standard for electronic data exchange in healthcare environments. The HL7 based system provides us with an integrated environment in which we are able to manage the complexities of medical data. We developed this message communication interface to generate and parse HL7 messages automatically from the database point of view. We discuss how easily real time data exchange is performed in the clinical information system, given the requirement for minimum loading of the database system. PMID:14728271
-
Schober, E; Rami, B; Grabert, M; Thon, A; Kapellen, Th; Reinehr, Th; Holl, R W
2009-05-01
To analyse and compare clinical characteristics in young patients with maturity-onset diabetes of the young (MODY) and Type 2 diabetes mellitus (T2DM). We conducted an observational investigation using the DPV-Wiss database containing clinical data on 40 757 diabetic patients < 20 years of age from Germany and Austria. Three hundred and thirty-nine cases were clinically categorized as MODY (0.83%); 562 patients were diagnosed as T2DM (1.4%). In 20% of cases, the diagnosis of MODY was based on clinical findings only. Of the 272 subjects where genetic testing was available, 3% did not carry mutations in the three examined MODY genes. Glucokinase-MODY was commoner than HNF1A-MODY and HNF4A-MODY. Age at diagnosis was younger in MODY patients. The body mass index of T2DM was significantly higher compared with all MODY subgroups. Macrovascular risk factors such as dyslipidaemia and hypertension were commoner in T2DM, but 23% of MODY patients had dyslipidaemia and 10% hypertension. Glycaemic control was within the therapeutic target (HbA(1c) < 7.5%) in 86% of MODY and 70% of T2DM patients. The prevalence of MODY in children and adolescents in Germany and Austria is lower than that of T2DM in this age group. Dyslipidaemia and hypertension are less frequent in MODY compared with T2DM patients, but do occur.
-
Gainotti, Sabina; Torreri, Paola; Wang, Chiuhui Mary; Reihs, Robert; Mueller, Heimo; Heslop, Emma; Roos, Marco; Badowska, Dorota Mazena; de Paulis, Federico; Kodra, Yllka; Carta, Claudio; Martìn, Estrella Lopez; Miller, Vanessa Rangel; Filocamo, Mirella; Mora, Marina; Thompson, Mark; Rubinstein, Yaffa; Posada de la Paz, Manuel; Monaco, Lucia; Lochmüller, Hanns; Taruscio, Domenica
2018-05-01
In rare disease (RD) research, there is a huge need to systematically collect biomaterials, phenotypic, and genomic data in a standardized way and to make them findable, accessible, interoperable and reusable (FAIR). RD-Connect is a 6 years global infrastructure project initiated in November 2012 that links genomic data with patient registries, biobanks, and clinical bioinformatics tools to create a central research resource for RDs. Here, we present RD-Connect Registry & Biobank Finder, a tool that helps RD researchers to find RD biobanks and registries and provide information on the availability and accessibility of content in each database. The finder concentrates information that is currently sparse on different repositories (inventories, websites, scientific journals, technical reports, etc.), including aggregated data and metadata from participating databases. Aggregated data provided by the finder, if appropriately checked, can be used by researchers who are trying to estimate the prevalence of a RD, to organize a clinical trial on a RD, or to estimate the volume of patients seen by different clinical centers. The finder is also a portal to other RD-Connect tools, providing a link to the RD-Connect Sample Catalogue, a large inventory of RD biological samples available in participating biobanks for RD research. There are several kinds of users and potential uses for the RD-Connect Registry & Biobank Finder, including researchers collaborating with academia and the industry, dealing with the questions of basic, translational, and/or clinical research. As of November 2017, the finder is populated with aggregated data for 222 registries and 21 biobanks.
-
The EpiSLI Database: A Publicly Available Database on Speech and Language
ERIC Educational Resources Information Center
Tomblin, J. Bruce
2010-01-01
Purpose: This article describes a database that was created in the process of conducting a large-scale epidemiologic study of specific language impairment (SLI). As such, this database will be referred to as the EpiSLI database. Children with SLI have unexpected and unexplained difficulties learning and using spoken language. Although there is no…
-
The role of insurance claims databases in drug therapy outcomes research.
Lewis, N J; Patwell, J T; Briesacher, B A
1993-11-01
The use of insurance claims databases in drug therapy outcomes research holds great promise as a cost-effective alternative to post-marketing clinical trials. Claims databases uniquely capture information about episodes of care across healthcare services and settings. They also facilitate the examination of drug therapy effects on cohorts of patients and specific patient subpopulations. However, there are limitations to the use of insurance claims databases including incomplete diagnostic and provider identification data. The characteristics of the population included in the insurance plan, the plan benefit design, and the variables of the database itself can influence the research results. Given the current concerns regarding the completeness of insurance claims databases, and the validity of their data, outcomes research usually requires original data to validate claims data or to obtain additional information. Improvements to claims databases such as standardisation of claims information reporting, addition of pertinent clinical and economic variables, and inclusion of information relative to patient severity of illness, quality of life, and satisfaction with provided care will enhance the benefit of such databases for outcomes research.
-
Weng, W; Liang, Y; Kimball, E S; Hobbs, T; Kong, S; Sakurada, B; Bouchard, J
2016-07-01
Objective To explore trends in demographics, comorbidities, anti-diabetic drug usage, and healthcare utilization costs in patients with newly-diagnosed type 2 diabetes mellitus (T2DM) using a large US claims database. Methods For the years 2007 and 2012, Truven Health Marketscan Research Databases were used to identify adults with newly-diagnosed T2DM and continuous 12-month enrollment with prescription benefits. Variables examined included patient demographics, comorbidities, inpatient utilization patterns, healthcare costs (inpatient and outpatient), drug costs, and diabetes drug claim patterns. Results Despite an increase in the overall database population between 2007-2012, the incidence of newly-diagnosed T2DM decreased from 1.1% (2007) to 0.65% (2012). Hyperlipidemia and hypertension were the most common comorbidities and increased in prevalence from 2007 to 2012. In 2007, 48.3% of newly-diagnosed T2DM patients had no claims for diabetes medications, compared with 36.2% of patients in 2012. The use of a single oral anti-diabetic drug (OAD) was the most common diabetes medication-related claim (46.2% of patients in 2007; 56.7% of patients in 2012). Among OAD monotherapy users, metformin was the most commonly used and increased from 2007 (74.7% of OAD monotherapy users) to 2012 (90.8%). Decreases were observed for sulfonylureas (14.1% to 6.2%) and thiazolidinediones (7.3% to 0.6%). Insulin, predominantly basal insulin, was used by 3.9% of patients in 2007 and 5.3% of patients in 2012. Mean total annual healthcare costs increased from $13,744 in 2007 to $15,175 in 2012, driven largely by outpatient services, although costs in all individual categories of healthcare services (inpatient and outpatient) increased. Conversely, total drug costs per patient were lower in 2012 compared with 2007. Conclusions Despite a drop in the rate of newly-diagnosed T2DM from 2007 to 2012 in the US, increased total medical costs and comorbidities per individual patient suggest that the clinical and economic trends for T2DM are not declining.
-
Lin, Yimo; Pan, I-Wen; Mayer, Rory R; Lam, Sandi
2015-12-01
OBJECT Research conducted using large administrative data sets has increased in recent decades, but reports on the fidelity and reliability of such data have been mixed. The goal of this project was to compare data from a large, administrative claims data set with a quality improvement registry in order to ascertain similarities and differences in content. METHODS Data on children younger than 12 months with nonsyndromic craniosynostosis who underwent surgery in 2012 were queried in both the Kids' Inpatient Database (KID) and the American College of Surgeons Pediatric National Surgical Quality Improvement Program (Peds NSQIP). Data from published clinical craniosynostosis surgery series are reported for comparison. RESULTS Among patients younger than 12 months of age, a total of 1765 admissions were identified in KID and 391 in Peds NSQIP in 2012. Only nonsyndromic patients were included. The mean length of stay was 3.2 days in KID and 4 days in Peds NSQIP. The rates of cardiac events (0.5% in KID, 0.3% in Peds NSQIP, and 0.4%-2.2% in the literature), stroke/intracranial bleeds (0.4% in KID, 0.5% in Peds NSQIP, and 0.3%-1.2% in the literature), infection (0.2% in KID, 0.8% in Peds NSQIP, and 0%-8% in the literature), wound disruption (0.2% in KID, 0.5% in Peds NSQIP, 0%-4% in the literature), and seizures (0.7% in KID, 0.8% in Peds NSQIP, 0%-0.8% in the literature) were low and similar between the 2 data sets. The reported rates of blood transfusion (36% in KID, 64% in Peds NSQIP, and 1.7%-100% in the literature) varied between the 2 data sets. CONCLUSIONS Both the KID and Peds NSQIP databases provide large samples of surgical patients, with more cases reported in KID. The rates of complications studied were similar between the 2 data sets, with the exception of blood transfusion events where the retrospective chart review process of Peds NSQIP captured almost double the rate reported in KID.
-
Grand Challenges in Clinical Decision Support v10
Sittig, Dean F.; Wright, Adam; Osheroff, Jerome A.; Middleton, Blackford; Teich, Jonathan M.; Ash, Joan S.; Campbell, Emily; Bates, David W.
2008-01-01
There is a pressing need for high-quality, effective means of designing, developing, presenting, implementing, evaluating, and maintaining all types of clinical decision support capabilities for clinicians, patients and consumers. Using an iterative, consensus-building process we identified a rank-ordered list of the top 10 grand challenges in clinical decision support. This list was created to educate and inspire researchers, developers, funders, and policy-makers. The list of challenges in order of importance that they be solved if patients and organizations are to begin realizing the fullest benefits possible of these systems consists of: Improve the human-computer interface; Disseminate best practices in CDS design, development, and implementation; Summarize patient-level information; Prioritize and filter recommendations to the user; Create an architecture for sharing executable CDS modules and services; Combine recommendations for patients with co-morbidities; Prioritize CDS content development and implementation; Create internet-accessible clinical decision support repositories; Use freetext information to drive clinical decision support; Mine large clinical databases to create new CDS. Identification of solutions to these challenges is critical if clinical decision support is to achieve its potential and improve the quality, safety and efficiency of healthcare. PMID:18029232
-
USDA-ARS?s Scientific Manuscript database
Tomato Functional Genomics Database (TFGD; http://ted.bti.cornell.edu) provides a comprehensive systems biology resource to store, mine, analyze, visualize and integrate large-scale tomato functional genomics datasets. The database is expanded from the previously described Tomato Expression Database...
-
Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency.
Aniceto, Rodrigo; Xavier, Rene; Guimarães, Valeria; Hondo, Fernanda; Holanda, Maristela; Walter, Maria Emilia; Lifschitz, Sérgio
2015-01-01
Rapid advances in high-throughput sequencing techniques have created interesting computational challenges in bioinformatics. One of them refers to management of massive amounts of data generated by automatic sequencers. We need to deal with the persistency of genomic data, particularly storing and analyzing these large-scale processed data. To find an alternative to the frequently considered relational database model becomes a compelling task. Other data models may be more effective when dealing with a very large amount of nonconventional data, especially for writing and retrieving operations. In this paper, we discuss the Cassandra NoSQL database approach for storing genomic data. We perform an analysis of persistency and I/O operations with real data, using the Cassandra database system. We also compare the results obtained with a classical relational database system and another NoSQL database approach, MongoDB.
-
Clinical research in a hospital--from the lone rider to teamwork.
Hannisdal, E
1996-01-01
Clinical research of high international standard is very demanding and requires clinical data of high quality, software, hardware and competence in research design and statistical treatment of data. Most busy clinicians have little time allocated for clinical research and this increases the need for a potent infrastructure. This paper describes how the Norwegian Radium Hospital, a specialized cancer hospital, has reorganized the clinical research process. This includes a new department, the Clinical Research Office, which serves the formal framework, a central Diagnosis Registry, clinical databases and multicentre studies. The department assists about 120 users, mainly clinicians. Installation of a network software package with over 10 programs has strongly provided an internal standardization, reduced the costs and saved clinicians a great deal of time. The hospital is building up about 40 diagnosis-specific clinical databases with up to 200 variables registered. These databases are shared by the treatment group and seem to be important tools for quality assurance. We conclude that the clinical research process benefits from a firm infrastructure facilitating teamwork through extensive use of modern information technology. We are now ready for the next phase, which is to work for a better external technical framework for cooperation with other institutions throughout the world.
-
Wang, Shirley V; Schneeweiss, Sebastian; Berger, Marc L; Brown, Jeffrey; de Vries, Frank; Douglas, Ian; Gagne, Joshua J; Gini, Rosa; Klungel, Olaf; Mullins, C Daniel; Nguyen, Michael D; Rassen, Jeremy A; Smeeth, Liam; Sturkenboom, Miriam
2017-09-01
Defining a study population and creating an analytic dataset from longitudinal healthcare databases involves many decisions. Our objective was to catalogue scientific decisions underpinning study execution that should be reported to facilitate replication and enable assessment of validity of studies conducted in large healthcare databases. We reviewed key investigator decisions required to operate a sample of macros and software tools designed to create and analyze analytic cohorts from longitudinal streams of healthcare data. A panel of academic, regulatory, and industry experts in healthcare database analytics discussed and added to this list. Evidence generated from large healthcare encounter and reimbursement databases is increasingly being sought by decision-makers. Varied terminology is used around the world for the same concepts. Agreeing on terminology and which parameters from a large catalogue are the most essential to report for replicable research would improve transparency and facilitate assessment of validity. At a minimum, reporting for a database study should provide clarity regarding operational definitions for key temporal anchors and their relation to each other when creating the analytic dataset, accompanied by an attrition table and a design diagram. A substantial improvement in reproducibility, rigor and confidence in real world evidence generated from healthcare databases could be achieved with greater transparency about operational study parameters used to create analytic datasets from longitudinal healthcare databases. © 2017 The Authors. Pharmacoepidemiology & Drug Safety Published by John Wiley & Sons Ltd.
-
Human Variome Project Quality Assessment Criteria for Variation Databases.
Vihinen, Mauno; Hancock, John M; Maglott, Donna R; Landrum, Melissa J; Schaafsma, Gerard C P; Taschner, Peter
2016-06-01
Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. © 2016 WILEY PERIODICALS, INC.
-
Establishment of an international database for genetic variants in esophageal cancer.
Vihinen, Mauno
2016-10-01
The establishment of a database has been suggested in order to collect, organize, and distribute genetic information about esophageal cancer. The World Organization for Specialized Studies on Diseases of the Esophagus and the Human Variome Project will be in charge of a central database of information about esophageal cancer-related variations from publications, databases, and laboratories; in addition to genetic details, clinical parameters will also be included. The aim will be to get all the central players in research, clinical, and commercial laboratories to contribute. The database will follow established recommendations and guidelines. The database will require a team of dedicated curators with different backgrounds. Numerous layers of systematics will be applied to facilitate computational analyses. The data items will be extensively integrated with other information sources. The database will be distributed as open access to ensure exchange of the data with other databases. Variations will be reported in relation to reference sequences on three levels--DNA, RNA, and protein-whenever applicable. In the first phase, the database will concentrate on genetic variations including both somatic and germline variations for susceptibility genes. Additional types of information can be integrated at a later stage. © 2016 New York Academy of Sciences.
-
The thyrotropin receptor mutation database: update 2003.
Führer, Dagmar; Lachmund, Peter; Nebel, Istvan-Tibor; Paschke, Ralf
2003-12-01
In 1999 we have created a TSHR mutation database compiling TSHR mutations with their basic characteristics and associated clinical conditions (www.uni-leipzig.de/innere/tshr). Since then, more than 2887 users from 36 countries have logged into the TSHR mutation database and have contributed several valuable suggestions for further improvement of the database. We now present an updated and extended version of the TSHR database to which several novel features have been introduced: 1. detailed functional characteristics on all 65 mutations (43 activating and 22 inactivating mutations) reported to date, 2. 40 pedigrees with detailed information on molecular aspects, clinical courses and treatment options in patients with gain-of-function and loss-of-function germline TSHR mutations, 3. a first compilation of site-directed mutagenesis studies, 4. references with Medline links, 5. a user friendly search tool for specific database searches, user-specific database output and 6. an administrator tool for the submission of novel TSHR mutations. The TSHR mutation database is installed as one of the locus specific HUGO mutation databases. It is listed under index TSHR 603372 (http://ariel.ucs.unimelb.edu.au/~cotton/glsdbq.htm) and can be accessed via www.uni-leipzig.de/innere/tshr.
-
Prevalence rates for depression by industry: a claims database analysis.
Wulsin, Lawson; Alterman, Toni; Timothy Bushnell, P; Li, Jia; Shen, Rui
2014-11-01
To estimate and interpret differences in depression prevalence rates among industries, using a large, group medical claims database. Depression cases were identified by ICD-9 diagnosis code in a population of 214,413 individuals employed during 2002-2005 by employers based in western Pennsylvania. Data were provided by Highmark, Inc. (Pittsburgh and Camp Hill, PA). Rates were adjusted for age, gender, and employee share of health care costs. National industry measures of psychological distress, work stress, and physical activity at work were also compiled from other data sources. Rates for clinical depression in 55 industries ranged from 6.9 to 16.2 %, (population rate = 10.45 %). Industries with the highest rates tended to be those which, on the national level, require frequent or difficult interactions with the public or clients, and have high levels of stress and low levels of physical activity. Additional research is needed to help identify industries with relatively high rates of depression in other regions and on the national level, and to determine whether these differences are due in part to specific work stress exposures and physical inactivity at work. Claims database analyses may provide a cost-effective way to identify priorities for depression treatment and prevention in the workplace.
-
Federal Register 2010, 2011, 2012, 2013, 2014
2013-04-09
... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health Submission for OMB Review; 30-day Comment Request: The Clinical Trials Reporting Program (CTRP) Database (NCI) SUMMARY: Under... Program (CTRP) Database, 0925-0600, Expiration Date 3/31/2013--REINSTATEMENT WITH CHANGE, National Cancer...
-
Parkhill, Anne; Hill, Kelvin
2009-03-01
The Australian National Stroke Foundation appointed a search specialist to find the best available evidence for the second edition of its Clinical Guidelines for Acute Stroke Management. To identify the relative effectiveness of differing evidence sources for the guideline update. We searched and reviewed references from five valid evidence sources for clinical and economic questions: (i) electronic databases; (ii) reference lists of relevant systematic reviews, guidelines, and/or primary studies; (iii) table of contents of a number of key journals for the last 6 months; (iv) internet/grey literature; and (v) experts. Reference sources were recorded, quantified, and analysed. In the clinical portion of the guidelines document, there was a greater use of previous knowledge and sources other than electronic databases for evidence, while there was a greater use of electronic databases for the economic section. The results confirmed that searchers need to be aware of the context and range of sources for evidence searches. For best available evidence, searchers cannot rely solely on electronic databases and need to encompass many different media and sources.
-
Bakshi, Sonal R; Shukla, Shilin N; Shah, Pankaj M
2009-01-01
We developed a Microsoft Access-based laboratory management system to facilitate database management of leukemia patients referred for cytogenetic tests in regards to karyotyping and fluorescence in situ hybridization (FISH). The database is custom-made for entry of patient data, clinical details, sample details, cytogenetics test results, and data mining for various ongoing research areas. A number of clinical research laboratoryrelated tasks are carried out faster using specific "queries." The tasks include tracking clinical progression of a particular patient for multiple visits, treatment response, morphological and cytogenetics response, survival time, automatic grouping of patient inclusion criteria in a research project, tracking various processing steps of samples, turn-around time, and revenue generated. Since 2005 we have collected of over 5,000 samples. The database is easily updated and is being adapted for various data maintenance and mining needs.
-
Bousquet, P-J; Demoly, P; Romano, A; Aberer, W; Bircher, A; Blanca, M; Brockow, K; Pichler, W; Torres, M J; Terreehorst, I; Arnoux, B; Atanaskovic-Markovic, M; Barbaud, A; Bijl, A; Bonadonna, P; Burney, P G; Caimmi, S; Canonica, G W; Cernadas, J; Dahlen, B; Daures, J-P; Fernandez, J; Gomes, E; Gueant, J-L; Kowalski, M L; Kvedariene, V; Mertes, P-M; Martins, P; Nizankowska-Mogilnicka, E; Papadopoulos, N; Ponvert, C; Pirmohamed, M; Ring, J; Salapatas, M; Sanz, M L; Szczeklik, A; Van Ganse, E; De Weck, A L; Zuberbier, T; Merk, H F; Sachs, B; Sidoroff, A
2009-02-01
Nonallergic hypersensitivity and allergic reactions are part of the many different types of adverse drug reactions (ADRs). Databases exist for the collection of ADRs. Spontaneous reporting makes up the core data-generating system of pharmacovigilance, but there is a large under-estimation of allergy/hypersensitivity drug reactions. A specific database is therefore required for drug allergy and hypersensitivity using standard operating procedures (SOPs), as the diagnosis of drug allergy/hypersensitivity is difficult and current pharmacovigilance algorithms are insufficient. Although difficult, the diagnosis of drug allergy/hypersensitivity has been standardized by the European Network for Drug Allergy (ENDA) under the aegis of the European Academy of Allergology and Clinical Immunology and SOPs have been published. Based on ENDA and Global Allergy and Asthma European Network (GA(2)LEN, EU Framework Programme 6) SOPs, a Drug Allergy and Hypersensitivity Database (DAHD((R))) has been established under FileMaker((R)) Pro 9. It is already available online in many different languages and can be accessed using a personal login. GA(2)LEN is a European network of 27 partners (16 countries) and 59 collaborating centres (26 countries), which can coordinate and implement the DAHD across Europe. The GA(2)LEN-ENDA-DAHD platform interacting with a pharmacovigilance network appears to be of great interest for the reporting of allergy/hypersensitivity ADRs in conjunction with other pharmacovigilance instruments.
-
Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu
2017-01-01
Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA’s complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform. PMID:29312567
-
Gradishar, William; Johnson, KariAnne; Brown, Krystal; Mundt, Erin; Manley, Susan
2017-07-01
There is a growing move to consult public databases following receipt of a genetic test result from a clinical laboratory; however, the well-documented limitations of these databases call into question how often clinicians will encounter discordant variant classifications that may introduce uncertainty into patient management. Here, we evaluate discordance in BRCA1 and BRCA2 variant classifications between a single commercial testing laboratory and a public database commonly consulted in clinical practice. BRCA1 and BRCA2 variant classifications were obtained from ClinVar and compared with the classifications from a reference laboratory. Full concordance and discordance were determined for variants whose ClinVar entries were of the same pathogenicity (pathogenic, benign, or uncertain). Variants with conflicting ClinVar classifications were considered partially concordant if ≥1 of the listed classifications agreed with the reference laboratory classification. Four thousand two hundred and fifty unique BRCA1 and BRCA2 variants were available for analysis. Overall, 73.2% of classifications were fully concordant and 12.3% were partially concordant. The remaining 14.5% of variants had discordant classifications, most of which had a definitive classification (pathogenic or benign) from the reference laboratory compared with an uncertain classification in ClinVar (14.0%). Here, we show that discrepant classifications between a public database and single reference laboratory potentially account for 26.7% of variants in BRCA1 and BRCA2 . The time and expertise required of clinicians to research these discordant classifications call into question the practicality of checking all test results against a database and suggest that discordant classifications should be interpreted with these limitations in mind. With the increasing use of clinical genetic testing for hereditary cancer risk, accurate variant classification is vital to ensuring appropriate medical management. There is a growing move to consult public databases following receipt of a genetic test result from a clinical laboratory; however, we show that up to 26.7% of variants in BRCA1 and BRCA2 have discordant classifications between ClinVar and a reference laboratory. The findings presented in this paper serve as a note of caution regarding the utility of database consultation. © AlphaMed Press 2017.
-
SEER Linked Databases - SEER Datasets
SEER-Medicare database of elderly persons with cancer is useful for epidemiologic and health services research. SEER-MHOS has health-related quality of life information about elderly persons with cancer. SEER-CAHPS database has clinical, survey, and health services information on people with cancer.
-
Development and Operation of a Database Machine for Online Access and Update of a Large Database.
ERIC Educational Resources Information Center
Rush, James E.
1980-01-01
Reviews the development of a fault tolerant database processor system which replaced OCLC's conventional file system. A general introduction to database management systems and the operating environment is followed by a description of the hardware selection, software processes, and system characteristics. (SW)
-
Hypersonic and Supersonic Flow Roadmaps Using Bibliometrics and Database Tomography.
ERIC Educational Resources Information Center
Kostoff, R. N.; Eberhart, Henry J.; Toothman, Darrell Ray
1999-01-01
Database Tomography (DT) is a textual database-analysis system consisting of algorithms for extracting multiword phrase frequencies and proximities from a large textual database, to augment interpretative capabilities of the expert human analyst. Describes use of the DT process, supplemented by literature bibliometric analyses, to derive technical…
-
Comparison of the NCI open database with seven large chemical structural databases.
Voigt, J H; Bienfait, B; Wang, S; Nicklaus, M C
2001-01-01
Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.
-
Becker, Pierre T; de Bel, Annelies; Martiny, Delphine; Ranque, Stéphane; Piarroux, Renaud; Cassagne, Carole; Detandt, Monique; Hendrickx, Marijke
2014-11-01
The identification of filamentous fungi by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) relies mainly on a robust and extensive database of reference spectra. To this end, a large in-house library containing 760 strains and representing 472 species was built and evaluated on 390 clinical isolates by comparing MALDI-TOF MS with the classical identification method based on morphological observations. The use of MALDI-TOF MS resulted in the correct identification of 95.4% of the isolates at species level, without considering LogScore values. Taking into account the Brukers' cutoff value for reliability (LogScore >1.70), 85.6% of the isolates were correctly identified. For a number of isolates, microscopic identification was limited to the genus, resulting in only 61.5% of the isolates correctly identified at species level while the correctness reached 94.6% at genus level. Using this extended in-house database, MALDI-TOF MS thus appears superior to morphology in order to obtain a robust and accurate identification of filamentous fungi. A continuous extension of the library is however necessary to further improve its reliability. Indeed, 15 isolates were still not represented while an additional three isolates were not recognized, probably because of a lack of intraspecific variability of the corresponding species in the database. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
-
Accuracy of blood transfusion in postpartum hemorrhage to assess maternal morbidity.
Sagot, P; Mourtialon, P; Benzenine, E; Bardou, M; Ferdynus, C; Morel, P; Quantin, C
2012-06-01
To measure the accuracy of blood transfusion (timing and number of blood units) in postpartum hemorrhage (PPH) in a perinatal network. (1) The ANONYMAT software system was used for anonymization and linkage of two large stand-alone databases, the Burgundy Perinatal Network (BPN) and the National Blood Centre (EFS) databases, which contain, respectively, clinical data from hospital discharges and information concerning any blood transfusion in France (considered as the gold standard database for identifying any transfusion). (2) Identification of prescriptions of at least one red blood cell (RBC) unit at the day of delivery (≥22 weeks) and up to 42 days, with manual reviewing of medical records in case of discordant recording. (3) Assessing the sensitivity and positive predictive value of data from the BPN database. Among the 9736 women receiving at least one blood product dispensed between 01/01/2006 and 12/31/2007 and the 35,779 women who delivered, 233 women (0.65% of deliveries) received at least one RBC unit for post partum hemorrhage. In the BPN database according to the type of hospital stay in our perinatal network (delivery stay only, delivery and post-delivery stays), sensitivity and positive predictive value for RBC transfusion ranged from 61.4% (55.1-67.6) to 67.8% (61.8-73.8) and 82.2% (76.5-87.9) to 83.2% (77.8-88.5), respectively. Linkage of both BPN and EFS databases allowed accurate recording of all but one RBC transfusion. Our approach allowed 100% electronic recording of PPH requiring blood transfusion, making it an important sentinel event of maternal morbidity to assess the perinatal network. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
-
Wang, Julia; Al-Ouran, Rami; Hu, Yanhui; Kim, Seon-Young; Wan, Ying-Wooi; Wangler, Michael F; Yamamoto, Shinya; Chao, Hsiao-Tuan; Comjean, Aram; Mohr, Stephanie E; Perrimon, Norbert; Liu, Zhandong; Bellen, Hugo J
2017-06-01
One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format. To this end, we created MARRVEL (model organism aggregated resources for rare variant exploration). MARRVEL is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER. Importantly, it curates model organism-specific databases to concurrently display a concise summary regarding the human gene homologs in budding and fission yeast, worm, fly, fish, mouse, and rat on a single webpage. Experiment-based information on tissue expression, protein subcellular localization, biological process, and molecular function for the human gene and homologs in the seven model organisms are arranged into a concise output. Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. Altogether, MARRVEL dramatically improves efficiency and accessibility to data collection and facilitates analysis of human genes and variants by cross-disciplinary integration of 18 million records available in public databases to facilitate clinical diagnosis and basic research. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
-
Will the future of knowledge work automation transform personalized medicine?
Naik, Gauri; Bhide, Sanika S
2014-09-01
Today, we live in a world of 'information overload' which demands high level of knowledge-based work. However, advances in computer hardware and software have opened possibilities to automate 'routine cognitive tasks' for knowledge processing. Engineering intelligent software systems that can process large data sets using unstructured commands and subtle judgments and have the ability to learn 'on the fly' are a significant step towards automation of knowledge work. The applications of this technology for high throughput genomic analysis, database updating, reporting clinically significant variants, and diagnostic imaging purposes are explored using case studies.
-
Workflow based framework for life science informatics.
Tiwari, Abhishek; Sekhar, Arvind K T
2007-10-01
Workflow technology is a generic mechanism to integrate diverse types of available resources (databases, servers, software applications and different services) which facilitate knowledge exchange within traditionally divergent fields such as molecular biology, clinical research, computational science, physics, chemistry and statistics. Researchers can easily incorporate and access diverse, distributed tools and data to develop their own research protocols for scientific analysis. Application of workflow technology has been reported in areas like drug discovery, genomics, large-scale gene expression analysis, proteomics, and system biology. In this article, we have discussed the existing workflow systems and the trends in applications of workflow based systems.
-
A Database of Supercooled Large Droplet Ice Accretions [Supplement
NASA Technical Reports Server (NTRS)
VanZante, Judith Foss
2007-01-01
A unique, publicly available database regarding supercooled large droplet (SLD) ice accretions has been developed in NASA Glenn's Icing Research Tunnel. Identical cloud and flight conditions were generated for five different airfoil models. The models chosen represent a variety of aircraft types from the horizontal stabilizer of a large transport aircraft to the wings of regional, business, and general aviation aircraft. In addition to the standard documentation methods of 2D ice shape tracing and imagery, ice mass measurements were also taken. This database will also be used to validate and verify the extension of the ice accretion code, LEWICE, into the SLD realm.
-
A Database of Supercooled Large Droplet Ice Accretions
NASA Technical Reports Server (NTRS)
VanZante, Judith Foss
2007-01-01
A unique, publicly available database regarding supercooled large droplet ice accretions has been developed in NASA Glenn's Icing Research Tunnel. Identical cloud and flight conditions were generated for five different airfoil models. The models chosen represent a variety of aircraft types from the horizontal stabilizer of a large trans-port aircraft to the wings of regional, business, and general aviation aircraft. In addition to the standard documentation methods of 2D ice shape tracing and imagery, ice mass measurements were also taken. This database will also be used to validate and verify the extension of the ice accretion code, LEWICE, into the SLD realm.
-
A Review of Stellar Abundance Databases and the Hypatia Catalog Database
NASA Astrophysics Data System (ADS)
Hinkel, Natalie Rose
2018-01-01
The astronomical community is interested in elements from lithium to thorium, from solar twins to peculiarities of stellar evolution, because they give insight into different regimes of star formation and evolution. However, while some trends between elements and other stellar or planetary properties are well known, many other trends are not as obvious and are a point of conflict. For example, stars that host giant planets are found to be consistently enriched in iron, but the same cannot be definitively said for any other element. Therefore, it is time to take advantage of large stellar abundance databases in order to better understand not only the large-scale patterns, but also the more subtle, small-scale trends within the data.In this overview to the special session, I will present a review of large stellar abundance databases that are both currently available (i.e. RAVE, APOGEE) and those that will soon be online (i.e. Gaia-ESO, GALAH). Additionally, I will discuss the Hypatia Catalog Database (www.hypatiacatalog.com) -- which includes abundances from individual literature sources that observed stars within 150pc. The Hypatia Catalog currently contains 72 elements as measured within ~6000 stars, with a total of ~240,000 unique abundance determinations. The online database offers a variety of solar normalizations, stellar properties, and planetary properties (where applicable) that can all be viewed through multiple interactive plotting interfaces as well as in a tabular format. By analyzing stellar abundances for large populations of stars and from a variety of different perspectives, a wealth of information can be revealed on both large and small scales.
-
Outpatient clinic visits during heat waves: findings from a large family medicine clinical database.
Vashishtha, Devesh; Sieber, William; Hailey, Brittany; Guirguis, Kristen; Gershunov, Alexander; Al-Delaimy, Wael K
2018-03-10
The purpose of this study was to determine whether heat waves are associated with increased frequency of clinic visits for ICD-9 codes of illnesses traditionally associated with heat waves. During 4 years of family medicine clinic data between 2012 and 2016, we identified six heat wave events in San Diego County. For each heat wave event, we selected a control period in the same season that was twice as long. Scheduling a visit on a heat wave day (versus a non-heat wave day) was the primary predictor, and receiving a primary ICD-9 disease code related to heat waves was the outcome. Analyses were adjusted for age, gender, race/ethnicity and marital status. Of the 5448 visits across the heat wave and control periods, 6.4% of visits (n = 346) were for heat wave-related diagnoses. Scheduling a visit on heat wave day was not associated with receiving a heat wave-related ICD code as compared with the control period (adjusted odds ratio: 1.35; 95% confidence interval: 0.86-1.36; P = 0.51). We show that in a relatively large and demographically diverse population, patients who schedule appointments during heat waves are not being more frequently seen for diagnoses typically associated with heat waves in the acute setting. Given that heat waves are increasing in frequency due to climate change, there is an opportunity to increase utilization of primary care clinics during heat waves.
-
NASA Technical Reports Server (NTRS)
Handley, Thomas H., Jr.; Collins, Donald J.; Doyle, Richard J.; Jacobson, Allan S.
1991-01-01
Viewgraphs on DataHub knowledge based assistance for science visualization and analysis using large distributed databases. Topics covered include: DataHub functional architecture; data representation; logical access methods; preliminary software architecture; LinkWinds; data knowledge issues; expert systems; and data management.
-
Nørrelund, Helene; Mazin, Wiktor; Pedersen, Lars
2014-01-01
Denmark is facing a reduction in clinical trial activity as the pharmaceutical industry has moved trials to low-cost emerging economies. Competitiveness in industry-sponsored clinical research depends on speed, quality, and cost. Because Denmark is widely recognized as a region that generates high quality data, an enhanced ability to attract future trials could be achieved if speed can be improved by taking advantage of the comprehensive national and regional registries. A "single point-of-entry" system has been established to support collaboration between hospitals and industry. When assisting industry in early-stage feasibility assessments, potential trial participants are identified by use of registries to shorten the clinical trial startup times. The Aarhus University Clinical Trial Candidate Database consists of encrypted data from the Danish National Registry of Patients allowing an immediate estimation of the number of patients with a specific discharge diagnosis in each hospital department or outpatient specialist clinic in the Central Denmark Region. The free access to health care, thorough monitoring of patients who are in contact with the health service, completeness of registration at the hospital level, and ability to link all databases are competitive advantages in an increasingly complex clinical trial environment.
-
Alternative therapies for chronic rhinosinusitis: A review.
Griffin, Aaron S; Cabot, Peter; Wallwork, Ben; Panizza, Ben
2018-03-01
The use of alternative medicine in chronic rhinosinusitis (CRS) continues to increase in popularity, for the most part without meeting the burden of being based on sound clinical evidence. New and emerging treatments, both natural and developed, are numerous, and it remains a challenge for otolaryngologists as well as general practitioners to keep up to date with these therapies and their efficacy. In this systematic review, we discuss a number of alternative therapies for CRS, their proposed physiologic mechanisms, and evidence supporting their use. This analysis is based on our review of the English-language literature on alternative therapies for CRS (we did not include any therapies that are already recommended by accepted professional bodies). Data collection was performed using the PubMed database (not restricted to MEDLINE due to the nature of the subject matter), the Cochrane databases, and bibliography searches. We found that while many of the alternative therapies we reviewed might have a firm basis in science, they lack any clinical evidence to support their use specifically for CRS. Some emerging therapies, such as therapeutic ultrasonography and phonophoresis, show some promise, based on a growing body of positive evidence. In addition, the use of baby shampoo, thyme honey, and bromelain additives to saline lavage in CRS are all supported by clinical evidence, as is Sinupret, an oral preparation that contains echinacea. However, higher levels of evidence gleaned from large, well-designed, prospective, randomized, controlled trials are needed before any of these therapies can be recommended.
-
Clinical and Epidemiological Aspects of Scorpionism in the World: A Systematic Review.
Santos, Maria S V; Silva, Cláudio G L; Neto, Basílio Silva; Grangeiro Júnior, Cícero R P; Lopes, Victor H G; Teixeira Júnior, Antônio G; Bezerra, Deryk A; Luna, João V C P; Cordeiro, Josué B; Júnior, Jucier Gonçalves; Lima, Marcos A P
2016-12-01
Scorpion stings are registered worldwide, but the incidence and the features of the envenomations vary depending on the region. The aim of this review was to summarize the epidemiological, clinical, diagnostic, and therapeutic data worldwide regarding humans stung by scorpions. A systematic review of the literature was conducted through the online databases of the Virtual Health Library (VHL), which hosts Medline and the Latin American and Caribbean Center on Health Sciences Informational (LILACS) database. We selected articles published between January 1, 2002 and July 31, 2014. Scorpion envenomation reports were found throughout the world, mainly in subtropical and tropical regions. The clinical manifestations were sympathetically and parasympathetically mediated, depending on the species of scorpion. Some of the most common severe complications of scorpionism included respiratory distress syndrome, pulmonary edema, cardiac dysfunction, impaired hemostasis, pancreatitis, and multiple organ failure. Scorpion envenomation could be classified as mild, moderate, and severe, and the therapeutic approach was based on the case severity. The treatment comprised 3 components: symptomatic measures, vital functions support, and injection of antivenom. Moreover, the time that elapsed between the sting and administration of the appropriate medical care was extremely important to the patient's prognosis. The large number of scorpion stings worldwide is concerning and reaffirms the need for new prevention measures and policies to reduce the incidence, prevalence, morbidity, and mortality rates from these poisonous arachnids. Copyright © 2016 Wilderness Medical Society. Published by Elsevier Inc. All rights reserved.
-
Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency
Aniceto, Rodrigo; Xavier, Rene; Guimarães, Valeria; Hondo, Fernanda; Holanda, Maristela; Walter, Maria Emilia; Lifschitz, Sérgio
2015-01-01
Rapid advances in high-throughput sequencing techniques have created interesting computational challenges in bioinformatics. One of them refers to management of massive amounts of data generated by automatic sequencers. We need to deal with the persistency of genomic data, particularly storing and analyzing these large-scale processed data. To find an alternative to the frequently considered relational database model becomes a compelling task. Other data models may be more effective when dealing with a very large amount of nonconventional data, especially for writing and retrieving operations. In this paper, we discuss the Cassandra NoSQL database approach for storing genomic data. We perform an analysis of persistency and I/O operations with real data, using the Cassandra database system. We also compare the results obtained with a classical relational database system and another NoSQL database approach, MongoDB. PMID:26558254
-
Wain, Karen E; Riggs, Erin; Hanson, Karen; Savage, Melissa; Riethmaier, Darlene; Muirhead, Andrea; Mitchell, Elyse; Packard, Bethanny Smith; Faucett, W Andrew
2012-10-01
The International Standards for Cytogenomic Arrays (ISCA) Consortium is a worldwide collaborative effort dedicated to optimizing patient care by improving the quality of chromosomal microarray testing. The primary effort of the ISCA Consortium has been the development of a database of copy number variants (CNVs) identified during the course of clinical microarray testing. This database is a powerful resource for clinicians, laboratories, and researchers, and can be utilized for a variety of applications, such as facilitating standardized interpretations of certain CNVs across laboratories or providing phenotypic information for counseling purposes when published data is sparse. A recognized limitation to the clinical utility of this database, however, is the quality of clinical information available for each patient. Clinical genetic counselors are uniquely suited to facilitate the communication of this information to the laboratory by virtue of their existing clinical responsibilities, case management skills, and appreciation of the evolving nature of scientific knowledge. We intend to highlight the critical role that genetic counselors play in ensuring optimal patient care through contributing to the clinical utility of the ISCA Consortium's database, as well as the quality of individual patient microarray reports provided by contributing laboratories. Current tools, paper and electronic forms, created to maximize this collaboration are shared. In addition to making a professional commitment to providing complete clinical information, genetic counselors are invited to become ISCA members and to become involved in the discussions and initiatives within the Consortium.
-
The ClinicalTrials.gov results database--update and key issues.
Zarin, Deborah A; Tse, Tony; Williams, Rebecca J; Califf, Robert M; Ide, Nicholas C
2011-03-03
The ClinicalTrials.gov trial registry was expanded in 2008 to include a database for reporting summary results. We summarize the structure and contents of the results database, provide an update of relevant policies, and show how the data can be used to gain insight into the state of clinical research. We analyzed ClinicalTrials.gov data that were publicly available between September 2009 and September 2010. As of September 27, 2010, ClinicalTrials.gov received approximately 330 new and 2000 revised registrations each week, along with 30 new and 80 revised results submissions. We characterized the 79,413 registry and 2178 results of trial records available as of September 2010. From a sample cohort of results records, 78 of 150 (52%) had associated publications within 2 years after posting. Of results records available publicly, 20% reported more than two primary outcome measures and 5% reported more than five. Of a sample of 100 registry record outcome measures, 61% lacked specificity in describing the metric used in the planned analysis. In a sample of 700 results records, the mean number of different analysis populations per study group was 2.5 (median, 1; range, 1 to 25). Of these trials, 24% reported results for 90% or less of their participants. ClinicalTrials.gov provides access to study results not otherwise available to the public. Although the database allows examination of various aspects of ongoing and completed clinical trials, its ultimate usefulness depends on the research community to submit accurate, informative data.
-
Clauson, Kevin A; Polen, Hyla H; Peak, Amy S; Marsh, Wallace A; DiScala, Sandra L
2008-11-01
Clinical decision support tools (CDSTs) on personal digital assistants (PDAs) and online databases assist healthcare practitioners who make decisions about dietary supplements. To assess and compare the content of PDA dietary supplement databases and their online counterparts used as CDSTs. A total of 102 question-and-answer pairs were developed within 10 weighted categories of the most clinically relevant aspects of dietary supplement therapy. PDA versions of AltMedDex, Lexi-Natural, Natural Medicines Comprehensive Database, and Natural Standard and their online counterparts were assessed by scope (percent of correct answers present), completeness (3-point scale), ease of use, and a composite score integrating all 3 criteria. Descriptive statistics and inferential statistics, including a chi(2) test, Scheffé's multiple comparison test, McNemar's test, and the Wilcoxon signed rank test were used to analyze data. The scope scores for PDA databases were: Natural Medicines Comprehensive Database 84.3%, Natural Standard 58.8%, Lexi-Natural 50.0%, and AltMedDex 36.3%, with Natural Medicines Comprehensive Database statistically superior (p < 0.01). Completeness scores were: Natural Medicines Comprehensive Database 78.4%, Natural Standard 51.0%, Lexi-Natural 43.5%, and AltMedDex 29.7%. Lexi-Natural was superior in ease of use (p < 0.01). Composite scores for PDA databases were: Natural Medicines Comprehensive Database 79.3, Natural Standard 53.0, Lexi-Natural 48.0, and AltMedDex 32.5, with Natural Medicines Comprehensive Database superior (p < 0.01). There was no difference between the scope for PDA and online database pairs with Lexi-Natural (50.0% and 53.9%, respectively) or Natural Medicines Comprehensive Database (84.3% and 84.3%, respectively) (p > 0.05), whereas differences existed for AltMedDex (36.3% vs 74.5%, respectively) and Natural Standard (58.8% vs 80.4%, respectively) (p < 0.01). For composite scores, AltMedDex and Natural Standard online were better than their PDA counterparts (p < 0.01). Natural Medicines Comprehensive Database achieved significantly higher scope, completeness, and composite scores compared with other dietary supplement PDA CDSTs in this study. There was no difference between the PDA and online databases for Lexi-Natural and Natural Medicines Comprehensive Database, whereas online versions of AltMedDex and Natural Standard were significantly better than their PDA counterparts.
-
ERIC Educational Resources Information Center
Justice, Laura M.; Breit-Smith, Allison; Rogers, Margaret
2010-01-01
Purpose: This clinical forum was organized to provide a means for informing the research and clinical communities of one mechanism through which research capacity might be enhanced within the field of speech-language pathology. Specifically, forum authors describe the process of conducting secondary analyses of extant databases to answer questions…
-
Brief Report: The Negev Hospital-University-Based (HUB) Autism Database
ERIC Educational Resources Information Center
Meiri, Gal; Dinstein, Ilan; Michaelowski, Analya; Flusser, Hagit; Ilan, Michal; Faroy, Michal; Bar-Sinai, Asif; Manelis, Liora; Stolowicz, Dana; Yosef, Lili Lea; Davidovitch, Nadav; Golan, Hava; Arbelle, Shosh; Menashe, Idan
2017-01-01
Elucidating the heterogeneous etiologies of autism will require investment in comprehensive longitudinal data acquisition from large community based cohorts. With this in mind, we have established a hospital-university-based (HUB) database of autism which incorporates prospective and retrospective data from a large and ethnically diverse…
-
ERIC Educational Resources Information Center
Johnson, Doug
2004-01-01
Schools gather, store and use an increasingly large amount of data. Keeping track of everything from bus routes to building access codes to test scores to sports equipment is done with the help of electronic database programs. Large databases designed for budgeting and student record keeping have long been an integral part of the educational…
-
Kash, Melissa J
2016-01-01
In an era where physicians rely on point-of-care databases that provide filtered, pre-appraised, and quickly accessible clinical information by smartphone applications, it is difficult to teach medical students the importance of knowing not only when it is appropriate to search the primary medical literature but also how to do it. This column will describe how librarians at an academic health sciences library use an unusual clinical case to make demonstrations of searching primary medical literature real and meaningful to medical students, and to illustrate vividly the importance of knowing what to do when the answer to a clinical question cannot be found in a point-of-care database.
-
The BiolAD-DB system : an informatics system for clinical and genetic data.
Nielsen, David A; Leidner, Marty; Haynes, Chad; Krauthammer, Michael; Kreek, Mary Jeanne
2007-01-01
The Biology of Addictive Diseases-Database (BiolAD-DB) system is a research bioinformatics system for archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password-protected BiolAD-DB SQL compliant server and database. BiolAD-DB tools further provide functionalities for generating customized reports and views. The BiolAD-DB system schema, client, and installation instructions are freely available at http://www.rockefeller.edu/biolad-db/.
-
Semantic processing of EHR data for clinical research.
Sun, Hong; Depraetere, Kristof; De Roo, Jos; Mels, Giovanni; De Vloed, Boris; Twagirumukiza, Marc; Colaert, Dirk
2015-12-01
There is a growing need to semantically process and integrate clinical data from different sources for clinical research. This paper presents an approach to integrate EHRs from heterogeneous resources and generate integrated data in different data formats or semantics to support various clinical research applications. The proposed approach builds semantic data virtualization layers on top of data sources, which generate data in the requested semantics or formats on demand. This approach avoids upfront dumping to and synchronizing of the data with various representations. Data from different EHR systems are first mapped to RDF data with source semantics, and then converted to representations with harmonized domain semantics where domain ontologies and terminologies are used to improve reusability. It is also possible to further convert data to application semantics and store the converted results in clinical research databases, e.g. i2b2, OMOP, to support different clinical research settings. Semantic conversions between different representations are explicitly expressed using N3 rules and executed by an N3 Reasoner (EYE), which can also generate proofs of the conversion processes. The solution presented in this paper has been applied to real-world applications that process large scale EHR data. Copyright © 2015 Elsevier Inc. All rights reserved.
-
Efficiency of inpatient orthopedic surgery in Japan: a medical claims database analysis.
Nakata, Yoshinori; Yoshimura, Tatsuya; Watanabe, Yuichi; Otake, Hiroshi; Oiso, Giichiro; Sawa, Tomohiro
2017-07-10
Purpose The purpose of this paper is to determine the characteristics of healthcare facilities that produce the most efficient inpatient orthopedic surgery using a large-scale medical claims database in Japan. Design/methodology/approach Reimbursement claims data were obtained from April 1 through September 30, 2014. Input-oriented Banker-Charnes-Cooper model of data envelopment analysis (DEA) was employed. The decision-making unit was defined as a healthcare facility where orthopedic surgery was performed. Inputs were defined as the length of stay, the number of beds, and the total costs of expensive surgical devices. Output was defined as total surgical fees for each surgery. Efficiency scores of healthcare facilities were compared among different categories of healthcare facilities. Findings The efficiency scores of healthcare facilities with a diagnosis-procedure combination (DPC) reimbursement were significantly lower than those without DPC ( p=0.0000). All the efficiency scores of clinics with beds were 1. Their efficiency scores were significantly higher than those of university hospitals, public hospitals, and other hospitals ( p=0.0000). Originality/value This is the first research that applied DEA for orthopedic surgery in Japan. The healthcare facilities with DPC reimbursement were less efficient than those without DPC. The clinics with beds were the most efficient among all types of management bodies of healthcare facilities.
-
Buske, Orion J.; Schiettecatte, François; Hutton, Benjamin; Dumitriu, Sergiu; Misyura, Andriy; Huang, Lijia; Hartley, Taila; Girdea, Marta; Sobreira, Nara; Mungall, Chris; Brudno, Michael
2016-01-01
Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously-identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis. PMID:26255989
-
Genetic Variation in Cardiomyopathy and Cardiovascular Disorders.
McNally, Elizabeth M; Puckelwartz, Megan J
2015-01-01
With the wider deployment of massively-parallel, next-generation sequencing, it is now possible to survey human genome data for research and clinical purposes. The reduced cost of producing short-read sequencing has now shifted the burden to data analysis. Analysis of genome sequencing remains challenged by the complexity of the human genome, including redundancy and the repetitive nature of genome elements and the large amount of variation in individual genomes. Public databases of human genome sequences greatly facilitate interpretation of common and rare genetic variation, although linking database sequence information to detailed clinical information is limited by privacy and practical issues. Genetic variation is a rich source of knowledge for cardiovascular disease because many, if not all, cardiovascular disorders are highly heritable. The role of rare genetic variation in predicting risk and complications of cardiovascular diseases has been well established for hypertrophic and dilated cardiomyopathy, where the number of genes that are linked to these disorders is growing. Bolstered by family data, where genetic variants segregate with disease, rare variation can be linked to specific genetic variation that offers profound diagnostic information. Understanding genetic variation in cardiomyopathy is likely to help stratify forms of heart failure and guide therapy. Ultimately, genetic variation may be amenable to gene correction and gene editing strategies.
-
Buske, Orion J; Schiettecatte, François; Hutton, Benjamin; Dumitriu, Sergiu; Misyura, Andriy; Huang, Lijia; Hartley, Taila; Girdea, Marta; Sobreira, Nara; Mungall, Chris; Brudno, Michael
2015-10-01
Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis. © 2015 WILEY PERIODICALS, INC.
-
[Characteristics of clinical trials in Hungary based on the analysis of an international database].
Tóth, Tamás; Pollner, Péter; Palla, Gergely; Dinya, Elek
2017-03-01
Intorduction: The ClinicalTrials.gov website, which is operated by the US government, collects data about clinical trials. We have processed data related to Hungary by downloading from the website as XML files. Most of the data describe trials performed after 2000, so we got an overview about the clinical research of the last 10 to 15 years. As the majority of the data fields are collected as free text, significant data cleaning was needed. The database contained 2863 trials related to Hungary from 189 settlements. Only 20 per cent of the actual research organizations could have been identified as many times only an "id" number or a general name was given, thus this information was anonymised in many cases. Besides the analysis of the information obtained from this database, our study points out the relevant issues that may influence the international view of the Hungarian clinical research. Orv. Hetil., 2017, 158(9), 345-351.
-
Teaching Advanced SQL Skills: Text Bulk Loading
ERIC Educational Resources Information Center
Olsen, David; Hauser, Karina
2007-01-01
Studies show that advanced database skills are important for students to be prepared for today's highly competitive job market. A common task for database administrators is to insert a large amount of data into a database. This paper illustrates how an up-to-date, advanced database topic, namely bulk insert, can be incorporated into a database…
-
Sagace: A web-based search engine for biomedical databases in Japan
2012-01-01
Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816
-
Functional evaluation of out-of-the-box text-mining tools for data-mining tasks
Jung, Kenneth; LePendu, Paea; Iyer, Srinivasan; Bauer-Mehren, Anna; Percha, Bethany; Shah, Nigam H
2015-01-01
Objective The trade-off between the speed and simplicity of dictionary-based term recognition and the richer linguistic information provided by more advanced natural language processing (NLP) is an area of active discussion in clinical informatics. In this paper, we quantify this trade-off among text processing systems that make different trade-offs between speed and linguistic understanding. We tested both types of systems in three clinical research tasks: phase IV safety profiling of a drug, learning adverse drug–drug interactions, and learning used-to-treat relationships between drugs and indications. Materials We first benchmarked the accuracy of the NCBO Annotator and REVEAL in a manually annotated, publically available dataset from the 2008 i2b2 Obesity Challenge. We then applied the NCBO Annotator and REVEAL to 9 million clinical notes from the Stanford Translational Research Integrated Database Environment (STRIDE) and used the resulting data for three research tasks. Results There is no significant difference between using the NCBO Annotator and REVEAL in the results of the three research tasks when using large datasets. In one subtask, REVEAL achieved higher sensitivity with smaller datasets. Conclusions For a variety of tasks, employing simple term recognition methods instead of advanced NLP methods results in little or no impact on accuracy when using large datasets. Simpler dictionary-based methods have the advantage of scaling well to very large datasets. Promoting the use of simple, dictionary-based methods for population level analyses can advance adoption of NLP in practice. PMID:25336595
-
A high performance, ad-hoc, fuzzy query processing system for relational databases
NASA Technical Reports Server (NTRS)
Mansfield, William H., Jr.; Fleischman, Robert M.
1992-01-01
Database queries involving imprecise or fuzzy predicates are currently an evolving area of academic and industrial research. Such queries place severe stress on the indexing and I/O subsystems of conventional database environments since they involve the search of large numbers of records. The Datacycle architecture and research prototype is a database environment that uses filtering technology to perform an efficient, exhaustive search of an entire database. It has recently been modified to include fuzzy predicates in its query processing. The approach obviates the need for complex index structures, provides unlimited query throughput, permits the use of ad-hoc fuzzy membership functions, and provides a deterministic response time largely independent of query complexity and load. This paper describes the Datacycle prototype implementation of fuzzy queries and some recent performance results.
-
Integration of NASA/GSFC and USGS Rock Magnetic Databases.
NASA Astrophysics Data System (ADS)
Nazarova, K. A.; Glen, J. M.
2004-05-01
A global Magnetic Petrology Database (MPDB) was developed and continues to be updated at NASA/Goddard Space Flight Center. The purpose of this database is to provide the geomagnetic community with a comprehensive and user-friendly method of accessing magnetic petrology data via the Internet for a more realistic interpretation of satellite (as well as aeromagnetic and ground) lithospheric magnetic anomalies. The MPDB contains data on rocks from localities around the world (about 19,000 samples) including the Ukranian and Baltic Shields, Kamchatka, Iceland, Urals Mountains, etc. The MPDB is designed, managed and presented on the web as a research oriented database. Several database applications have been specifically developed for data manipulation and analysis of the MPDB. The geophysics unit at the USGS in Menlo Park has over 17,000 rock-property data, largely from sites within the western U.S. This database contains rock-density and rock-magnetic parameters collected for use in gravity and magnetic field modeling, and paleomagnetic studies. Most of these data were taken from surface outcrops and together they span a broad range of rock types. Measurements were made either in-situ at the outcrop, or in the laboratory on hand samples and paleomagnetic cores acquired in the field. The USGS and NASA/GSFC data will be integrated as part of an effort to provide public access to a single, uniformly maintained database. Due to the large number of data and the very large area sampled, the database can yield rock-property statistics on a broad range of rock types; it is thus applicable to study areas beyond the geographic scope of the database. The intent of this effort is to provide incentive for others to further contribute to the database, and a tool with which the geophysical community can entertain studies formerly precluded.
-
Compressing DNA sequence databases with coil.
White, W Timothy J; Hendy, Michael D
2008-05-20
Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression - an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression - the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.
-
Compressing DNA sequence databases with coil
White, W Timothy J; Hendy, Michael D
2008-01-01
Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work. PMID:18489794
-
Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS
Stingu, Catalina S.; Borgmann, Toralf; Rodloff, Arne C.; Vielkind, Paul; Jentsch, Holger; Schellenberger, Wolfgang; Eschrich, Klaus
2015-01-01
Background Actinomyces are a common part of the residential flora of the human intestinal tract, genitourinary system and skin. Isolation and identification of Actinomyces by conventional methods is often difficult and time consuming. In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has become a rapid and simple method to identify bacteria. Objective The present study evaluated a new in-house algorithm using MALDI-TOF-MS for rapid identification of different species of oral Actinomyces cultivated from subgingival biofilm. Design Eleven reference strains and 674 clinical strains were used in this study. All the strains were preliminarily identified using biochemical methods and then subjected to MALDI-TOF-MS analysis using both similarity-based analysis and classification methods (support vector machine [SVM]). The genotype of the reference strains and of 232 clinical strains was identified by sequence analysis of the 16S ribosomal RNA (rRNA). Results The sequence analysis of the 16S rRNA gene of all references strains confirmed their previous identification. The MALDI-TOF-MS spectra obtained from the reference strains and the other clinical strains undoubtedly identified as Actinomyces by 16S rRNA sequencing were used to create the mass spectra reference database. Already a visual inspection of the mass spectra of different species reveals both similarities and differences. However, the differences between them are not large enough to allow a reliable differentiation by similarity analysis. Therefore, classification methods were applied as an alternative approach for differentiation and identification of Actinomyces at the species level. A cross-validation of the reference database representing 14 Actinomyces species yielded correct results for all species which were represented by more than two strains in the database. Conclusions Our results suggest that a combination of MALDI-TOF-MS with powerful classification algorithms, such as SVMs, provide a useful tool for the differentiation and identification of oral Actinomyces. PMID:25597306
-
Chaplin, Beth; Meloni, Seema; Eisen, Geoffrey; Jolayemi, Toyin; Banigbe, Bolanle; Adeola, Juliette; Wen, Craig; Reyes Nieva, Harry; Chang, Charlotte; Okonkwo, Prosper; Kanki, Phyllis
2015-01-01
The implementation of PEPFAR programs in resource-limited settings was accompanied by the need to document patient care on a scale unprecedented in environments where paper-based records were the norm. We describe the development of an electronic medical records system (EMRS) put in place at the beginning of a large HIV/AIDS care and treatment program in Nigeria. Databases were created to record laboratory results, medications prescribed and dispensed, and clinical assessments, using a relational database program. A collection of stand-alone files recorded different elements of patient care, linked together by utilities that aggregated data on national standard indicators and assessed patient care for quality improvement, tracked patients requiring follow-up, generated counts of ART regimens dispensed, and provided 'snapshots' of a patient's response to treatment. A secure server was used to store patient files for backup and transfer. By February 2012, when the program transitioned to local in-country management by APIN, the EMRS was used in 33 hospitals across the country, with 4,947,433 adult, pediatric and PMTCT records that had been created and continued to be available for use in patient care. Ongoing trainings for data managers, along with an iterative process of implementing changes to the databases and forms based on user feedback, were needed. As the program scaled up and the volume of laboratory tests increased, results were produced in a digital format, wherever possible, that could be automatically transferred to the EMRS. Many larger clinics began to link some or all of the databases to local area networks, making them available to a larger group of staff members, or providing the ability to enter information simultaneously where needed. The EMRS improved patient care, enabled efficient reporting to the Government of Nigeria and to U.S. funding agencies, and allowed program managers and staff to conduct quality control audits. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
-
Varrone, Andrea; Dickson, John C; Tossici-Bolt, Livia; Sera, Terez; Asenbaum, Susanne; Booij, Jan; Kapucu, Ozlem L; Kluge, Andreas; Knudsen, Gitte M; Koulibaly, Pierre Malick; Nobili, Flavio; Pagani, Marco; Sabri, Osama; Vander Borght, Thierry; Van Laere, Koen; Tatsch, Klaus
2013-01-01
Dopamine transporter (DAT) imaging with [(123)I]FP-CIT (DaTSCAN) is an established diagnostic tool in parkinsonism and dementia. Although qualitative assessment criteria are available, DAT quantification is important for research and for completion of a diagnostic evaluation. One critical aspect of quantification is the availability of normative data, considering possible age and gender effects on DAT availability. The aim of the European Normal Control Database of DaTSCAN (ENC-DAT) study was to generate a large database of [(123)I]FP-CIT SPECT scans in healthy controls. SPECT data from 139 healthy controls (74 men, 65 women; age range 20-83 years, mean 53 years) acquired in 13 different centres were included. Images were reconstructed using the ordered-subset expectation-maximization algorithm without correction (NOACSC), with attenuation correction (AC), and with both attenuation and scatter correction using the triple-energy window method (ACSC). Region-of-interest analysis was performed using the BRASS software (caudate and putamen), and the Southampton method (striatum). The outcome measure was the specific binding ratio (SBR). A significant effect of age on SBR was found for all data. Gender had a significant effect on SBR in the caudate and putamen for the NOACSC and AC data, and only in the left caudate for the ACSC data (BRASS method). Significant effects of age and gender on striatal SBR were observed for all data analysed with the Southampton method. Overall, there was a significant age-related decline in SBR of between 4 % and 6.7 % per decade. This study provides a large database of [(123)I]FP-CIT SPECT scans in healthy controls across a wide age range and with balanced gender representation. Higher DAT availability was found in women than in men. An average age-related decline in DAT availability of 5.5 % per decade was found for both genders, in agreement with previous reports. The data collected in this study may serve as a reference database for nuclear medicine centres and for clinical trials using [(123)I]FP-CIT SPECT as the imaging marker.
-
Privacy considerations in the context of an Australian observational database.
Duszynski, K M; Beilby, J J; Marley, J E; Walker, D C; Pratt, N L
2001-12-01
Observational databases are increasingly acknowledged for their value in clinical investigation. Australian general practice in particular presents an exciting opportunity to examine treatment in a natural setting. The paper explores issues such as privacy and confidentiality--foremost considerations when conducting this form of pharmacoepidemiological research. Australian legislation is currently addressing these exact issues in order to establish clear directives regarding ethical concerns. The development of a pharmacoepidemiological database arising from the integration of computerized Australian general practice records is described in addition, to the challenges associated with creating a database which considers patient privacy. The database known as 'Medic-GP', presently contains more than 950,000 clinical notes (including consultations, pathology, diagnostic imaging and adverse reactions) over a 5-year time period and relates to 55,000 patients. The paper then details a retrospective study which utilized the database to examine the interaction between antibiotic prescribing and patient outcomes from a community perspective, following a policy intervention. This study illustrates the application of computerized general practice records in research.
-
BioMart: a data federation framework for large collaborative projects.
Zhang, Junjun; Haider, Syed; Baran, Joachim; Cros, Anthony; Guberman, Jonathan M; Hsu, Jack; Liang, Yong; Yao, Long; Kasprzyk, Arek
2011-01-01
BioMart is a freely available, open source, federated database system that provides a unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework. BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects between different research groups. BioMart contains several levels of query optimization to efficiently manage large data sets and offers a diverse selection of graphical user interfaces and application programming interfaces to ensure that queries can be performed in whatever manner is most convenient for the user. The software has now been adopted by a large number of different biological databases spanning a wide range of data types and providing a rich source of annotation available to bioinformaticians and biologists alike.
-
Interhospital network system using the worldwide web and the common gateway interface.
Oka, A; Harima, Y; Nakano, Y; Tanaka, Y; Watanabe, A; Kihara, H; Sawada, S
1999-05-01
We constructed an interhospital network system using the worldwide web (WWW) and the Common Gateway Interface (CGI). Original clinical images are digitized and stored as a database for educational and research purposes. Personal computers (PCs) are available for data treatment and browsing. Our system is simple, as digitized images are stored into a Unix server machine. Images of important and interesting clinical cases are selected and registered into the image database using CGI. The main image format is 8- or 12-bit Joint Photographic Experts Group (JPEG) image. Original clinical images are finally stored in CD-ROM using a CD recorder. The image viewer can browse all of the images for one case at once as thumbnail pictures; image quality can be selected depending on the user's purpose. Using the network system, clinical images of interesting cases can be rapidly transmitted and discussed with other related hospitals. Data transmission from relational hospitals takes 1 to 2 minutes per 500 Kbyte of data. More distant hospitals (e.g., Rakusai Hospital, Kyoto) takes 1 minute more. The mean number of accesses our image database in a recent 3-month period was 470. There is a total about 200 cases in our image database, acquired over the past 2 years. Our system is useful for communication and image treatment between hospitals and we will describe the elements of our system and image database.
-
Systematic review of interventional sickle cell trials registered in ClinicalTrials.gov.
Lebensburger, Jeffrey D; Hilliard, Lee M; Pair, Lauren E; Oster, Robert; Howard, Thomas H; Cutter, Gary R
2015-12-01
The registry ClinicalTrials.gov was created to provide investigators and patients an accessible database of relevant clinical trials. To understand the state of sickle cell disease clinical trials, a comprehensive review of all 174 "closed," "interventional" sickle cell trials registered at ClinicalTrials.gov was completed in January 2015. The majority of registered sickle cell disease clinical trials listed an academic center as the primary sponsor and were an early phase trial. The primary outcome for sickle cell disease trials focused on pain (23%), bone marrow transplant (BMT) (13%), hydroxyurea (8%), iron overload (8%), and pulmonary hypertension (8%). A total of 52 trials were listed as terminated or withdrawn, including 25 (14% of all trials) terminated for failure to enroll participants. At the time of this review, only 19 trials uploaded results and 29 trials uploaded a manuscript in the ClinicalTrials.gov database. A systematic review of pubmed.gov revealed that only 35% of sickle cell studies completed prior to 2014 resulted in an identified manuscript. In comparison, of 80 thalassemia trials registered in ClinicalTrials.gov, four acknowledged failure to enroll participants as a reason for trial termination or withdrawal, and 48 trials (60%) completed prior to 2014 resulted in a currently identified manuscript. ClinicalTrials.gov can be an important database for investigators and patients with sickle cell disease to understand the current available research trials. To enhance the validity of the website, investigators must update their trial results and upload trial manuscripts into the database. This study, for the first time, quantifies outcomes of sickle cell disease trials and provides support to the belief that barriers exist to successful completion, publication, and dissemination of sickle cell trial results. © The Author(s) 2015.
-
Chen-Ying Hung; Wei-Chen Chen; Po-Tsun Lai; Ching-Heng Lin; Chi-Chun Lee
2017-07-01
Electronic medical claims (EMCs) can be used to accurately predict the occurrence of a variety of diseases, which can contribute to precise medical interventions. While there is a growing interest in the application of machine learning (ML) techniques to address clinical problems, the use of deep-learning in healthcare have just gained attention recently. Deep learning, such as deep neural network (DNN), has achieved impressive results in the areas of speech recognition, computer vision, and natural language processing in recent years. However, deep learning is often difficult to comprehend due to the complexities in its framework. Furthermore, this method has not yet been demonstrated to achieve a better performance comparing to other conventional ML algorithms in disease prediction tasks using EMCs. In this study, we utilize a large population-based EMC database of around 800,000 patients to compare DNN with three other ML approaches for predicting 5-year stroke occurrence. The result shows that DNN and gradient boosting decision tree (GBDT) can result in similarly high prediction accuracies that are better compared to logistic regression (LR) and support vector machine (SVM) approaches. Meanwhile, DNN achieves optimal results by using lesser amounts of patient data when comparing to GBDT method.
-
3D marker-controlled watershed for kidney segmentation in clinical CT exams.
Wieclawek, Wojciech
2018-02-27
Image segmentation is an essential and non trivial task in computer vision and medical image analysis. Computed tomography (CT) is one of the most accessible medical examination techniques to visualize the interior of a patient's body. Among different computer-aided diagnostic systems, the applications dedicated to kidney segmentation represent a relatively small group. In addition, literature solutions are verified on relatively small databases. The goal of this research is to develop a novel algorithm for fully automated kidney segmentation. This approach is designed for large database analysis including both physiological and pathological cases. This study presents a 3D marker-controlled watershed transform developed and employed for fully automated CT kidney segmentation. The original and the most complex step in the current proposition is an automatic generation of 3D marker images. The final kidney segmentation step is an analysis of the labelled image obtained from marker-controlled watershed transform. It consists of morphological operations and shape analysis. The implementation is conducted in a MATLAB environment, Version 2017a, using i.a. Image Processing Toolbox. 170 clinical CT abdominal studies have been subjected to the analysis. The dataset includes normal as well as various pathological cases (agenesis, renal cysts, tumors, renal cell carcinoma, kidney cirrhosis, partial or radical nephrectomy, hematoma and nephrolithiasis). Manual and semi-automated delineations have been used as a gold standard. Wieclawek Among 67 delineated medical cases, 62 cases are 'Very good', whereas only 5 are 'Good' according to Cohen's Kappa interpretation. The segmentation results show that mean values of Sensitivity, Specificity, Dice, Jaccard, Cohen's Kappa and Accuracy are 90.29, 99.96, 91.68, 85.04, 91.62 and 99.89% respectively. All 170 medical cases (with and without outlines) have been classified by three independent medical experts as 'Very good' in 143-148 cases, as 'Good' in 15-21 cases and as 'Moderate' in 6-8 cases. An automatic kidney segmentation approach for CT studies to compete with commonly known solutions was developed. The algorithm gives promising results, that were confirmed during validation procedure done on a relatively large database, including 170 CTs with both physiological and pathological cases.
-
The Determinants of the Technical Efficiency of Acute Inpatient Care in Canada.
Wang, Li; Grignon, Michel; Perry, Sheril; Chen, Xi-Kuan; Ytsma, Alison; Allin, Sara; Gapanenko, Katerina
2018-04-17
To evaluate the technical efficiency of acute inpatient care at the pan-Canadian level and to explore the factors associated with inefficiency-why hospitals are not on their production frontier. Canadian Management Information System (MIS) database (CMDB) and Discharge Abstract Database (DAD) for the fiscal year of 2012-2013. We use a nonparametric approach (data envelopment analysis) applied to three peer groups (teaching, large, and medium hospitals, focusing on their acute inpatient care only). The double bootstrap procedure (Simar and Wilson 2007) is adopted in the regression. Information on inpatient episodes of care (number and quality of outcomes) was extracted from the DAD. The cost of the inpatient care was extracted from the CMDB. On average, acute hospitals in Canada are operating at about 75 percent efficiency, and this could thus potentially increase their level of outcomes (quantity and quality) by addressing inefficiencies. In some cases, such as for teaching hospitals, the factors significantly correlated with efficiency scores were not related to management but to the social composition of the caseload. In contrast, for large and medium nonteaching hospitals, efficiency related more to the ability to discharge patients to postacute care facilities. The efficiency of medium hospitals is also positively related to treating more clinically noncomplex patients. The main drivers of efficiency of acute inpatient care vary by hospital peer groups. Thus, the results provide different policy and managerial implications for teaching, large, and medium hospitals to achieve efficiency gains. © Health Research and Educational Trust.
-
PS1-41: Just Add Data: Implementing an Event-Based Data Model for Clinical Trial Tracking
Fuller, Sharon; Carrell, David; Pardee, Roy
2012-01-01
Background/Aims Clinical research trials often have similar fundamental tracking needs, despite being quite variable in their specific logic and activities. A model tracking database that can be quickly adapted by a variety of studies has the potential to achieve significant efficiencies in database development and maintenance. Methods Over the course of several different clinical trials, we have developed a database model that is highly adaptable to a variety of projects. Rather than hard-coding each specific event that might occur in a trial, along with its logical consequences, this model considers each event and its parameters to be a data record in its own right. Each event may have related variables (metadata) describing its prerequisites, subsequent events due, associated mailings, or events that it overrides. The metadata for each event is stored in the same record with the event name. When changes are made to the study protocol, no structural changes to the database are needed. One has only to add or edit events and their metadata. Changes in the event metadata automatically determine any related logic changes. In addition to streamlining application code, this model simplifies communication between the programmer and other team members. Database requirements can be phrased as changes to the underlying data, rather than to the application code. The project team can review a single report of events and metadata and easily see where changes might be needed. In addition to benefitting from streamlined code, the front end database application can also implement useful standard features such as automated mail merges and to do lists. Results The event-based data model has proven itself to be robust, adaptable and user-friendly in a variety of study contexts. We have chosen to implement it as a SQL Server back end and distributed Access front end. Interested readers may request a copy of the Access front end and scripts for creating the back end database. Discussion An event-based database with a consistent, robust set of features has the potential to significantly reduce development time and maintenance expense for clinical trial tracking databases.
-
Application of Large-Scale Database-Based Online Modeling to Plant State Long-Term Estimation
NASA Astrophysics Data System (ADS)
Ogawa, Masatoshi; Ogai, Harutoshi
Recently, attention has been drawn to the local modeling techniques of a new idea called “Just-In-Time (JIT) modeling”. To apply “JIT modeling” to a large amount of database online, “Large-scale database-based Online Modeling (LOM)” has been proposed. LOM is a technique that makes the retrieval of neighboring data more efficient by using both “stepwise selection” and quantization. In order to predict the long-term state of the plant without using future data of manipulated variables, an Extended Sequential Prediction method of LOM (ESP-LOM) has been proposed. In this paper, the LOM and the ESP-LOM are introduced.
-
Generation and validation of a universal perinatal database and biospecimen repository: PeriBank.
Antony, K M; Hemarajata, P; Chen, J; Morris, J; Cook, C; Masalas, D; Gedminas, M; Brown, A; Versalovic, J; Aagaard, K
2016-11-01
There is a dearth of biospecimen repositories available to perinatal researchers. In order to address this need, here we describe the methodology used to establish such a resource. With the collaboration of MedSci.net, we generated an online perinatal database with 847 fields of clinical information. Simultaneously, we established a biospecimen repository of the same clinical participants. The demographic and clinical outcomes data are described for the first 10 000 participants enrolled. The demographic characteristics are consistent with the demographics of the delivery hospitals. Quality analysis of the biospecimens reveals variation in very few analytes. Furthermore, since the creation of PeriBank, we have demonstrated validity of the database and tissue integrity of the biospecimen repository. Here we establish that the creation of a universal perinatal database and biospecimen collection is not only possible, but allows for the performance of state-of-the-science translational perinatal research and is a potentially valuable resource to academic perinatal researchers.
-
Tiedemann Svendsen, Mathias; Henningsen, Emil; Hertz, Jens Michael; Vestergaard Grejsen, Dorthe; Bygum, Anette
2014-09-01
Ectodermal dysplasias form a complex, nosologic group of diseases with defects in at least 2 ectodermal structures. A retrospective study of patients with ectodermal dysplasia seen at our department over a period of 19 years (1994-2013) was performed. The study population consisted of 67 patients covering 17 different diagnoses. Forty-five families were identified of which 26 were sporadic cases with no affected family members. In 27 tested families a disease-causing mutation was identified in 23 families. Eleven mutations were novel mutations. To our knowledge, we present the first large ectodermal dysplasia cohort focusing on clinical manifestations in combination with mutational analysis. We recommend a nationwide study to estimate the prevalence of the ectodermal dysplasia and to ensure relevant molecular genetic testing which may form the basis of a national ectodermal dysplasia database.
-
Reproducing a Prospective Clinical Study as a Computational Retrospective Study in MIMIC-II.
Kury, Fabrício S P; Huser, Vojtech; Cimino, James J
2015-01-01
In this paper we sought to reproduce, as a computational retrospective study in an EHR database (MIMIC-II), a recent large prospective clinical study: the 2013 publication, by the Japanese Association for Acute Medicine (JAAM), about disseminated intravascular coagulation, in the journal Critical Care (PMID: 23787004). We designed in SQL and Java a set of electronic phenotypes that reproduced the study's data sampling, and used R to perform the same statistical inference procedures. All produced source code is available online at https://github.com/fabkury/paamia2015. Our program identified 2,257 eligible patients in MIMIC-II, and the results remarkably agreed with the prospective study. A minority of the needed data elements was not found in MIMIC-II, and statistically significant inferences were possible in the majority of the cases.
-
Capturing Key NANDA-I Nursing Diagnoses From Actual Clinical Data for Patients With Heart Failure.
Park, Hyejin; Tucker, Denise A
2017-01-01
The purpose of the study was to identify key nursing diagnoses with related factors and signs/symptoms using NANDA-I for patients with heart failure (HF). A retrospective descriptive design was used to address the research questions. Data were obtained from the records of patients discharged for 1 year with the medical diagnoses of HF from a Midwestern community hospital. A total of 272 inpatient records were analyzed to describe the frequency and percentage of NANDA-I diagnosis with related factors and signs/symptoms. The top 10 NANDA-I diagnoses associated with related factors and signs/symptoms were identified. Further research related to standardized nursing terminologies such as NANDA-I using large clinical databases from health information systems is needed to support evidence-based nursing diagnosis decision making. © 2015 NANDA International, Inc.