FORWARD: A Registry and Longitudinal Clinical Database to Study Fragile X Syndrome.

PubMed

Sherman, Stephanie L; Kidd, Sharon A; Riley, Catharine; Berry-Kravis, Elizabeth; Andrews, Howard F; Miller, Robert M; Lincoln, Sharyn; Swanson, Mark; Kaufmann, Walter E; Brown, W Ted

2017-06-01

Advances in the care of patients with fragile X syndrome (FXS) have been hampered by lack of data. This deficiency has produced fragmentary knowledge regarding the natural history of this condition, healthcare needs, and the effects of the disease on caregivers. To remedy this deficiency, the Fragile X Clinic and Research Consortium was established to facilitate research. Through a collective effort, the Fragile X Clinic and Research Consortium developed the Fragile X Online Registry With Accessible Research Database (FORWARD) to facilitate multisite data collection. This report describes FORWARD and the way it can be used to improve health and quality of life of FXS patients and their relatives and caregivers. FORWARD collects demographic information on individuals with FXS and their family members (affected and unaffected) through a 1-time registry form. The longitudinal database collects clinician- and parent-reported data on individuals diagnosed with FXS, focused on those who are 0 to 24 years of age, although individuals of any age can participate. The registry includes >2300 registrants (data collected September 7, 2009 to August 31, 2014). The longitudinal database includes data on 713 individuals diagnosed with FXS (data collected September 7, 2012 to August 31, 2014). Longitudinal data continue to be collected on enrolled patients along with baseline data on new patients. FORWARD represents the largest resource of clinical and demographic data for the FXS population in the United States. These data can be used to advance our understanding of FXS: the impact of cooccurring conditions, the impact on the day-to-day lives of individuals living with FXS and their families, and short-term and long-term outcomes. Copyright © 2017 by the American Academy of Pediatrics.

The Cardiac Safety Research Consortium ECG database.

PubMed

Kligfield, Paul; Green, Cynthia L

2012-01-01

The Cardiac Safety Research Consortium (CSRC) ECG database was initiated to foster research using anonymized, XML-formatted, digitized ECGs with corresponding descriptive variables from placebo- and positive-control arms of thorough QT studies submitted to the US Food and Drug Administration (FDA) by pharmaceutical sponsors. The database can be expanded to other data that are submitted directly to CSRC from other sources, and currently includes digitized ECGs from patients with genotyped varieties of congenital long-QT syndrome; this congenital long-QT database is also linked to ambulatory electrocardiograms stored in the Telemetric and Holter ECG Warehouse (THEW). Thorough QT data sets are available from CSRC for unblinded development of algorithms for analysis of repolarization and for blinded comparative testing of algorithms developed for the identification of moxifloxacin, as used as a positive control in thorough QT studies. Policies and procedures for access to these data sets are available from CSRC, which has developed tools for statistical analysis of blinded new algorithm performance. A recently approved CSRC project will create a data set for blinded analysis of automated ECG interval measurements, whose initial focus will include comparison of four of the major manufacturers of automated electrocardiographs in the United States. CSRC welcomes application for use of the ECG database for clinical investigation. Copyright © 2012 Elsevier Inc. All rights reserved.

PRESENTED AT TRIANGLE CONSORTIUM FOR REPRODUCTIVE BIOLOGY MEETING IN CHAPEL HILL, NC ON 2/11/2006: SPERM COUNT DISTRIBUTIONS IN FERTILE MEN

EPA Science Inventory

Sperm concentration and count are often used as indicators of environmental impacts on male reproductive health. Existing clinical databases may be biased towards sub-fertile men with low sperm counts and less is known about expected sperm count distributions in cohorts of ferti...

Development of a model web-based system to support a statewide quality consortium in radiation oncology.

PubMed

Moran, Jean M; Feng, Mary; Benedetti, Lisa A; Marsh, Robin; Griffith, Kent A; Matuszak, Martha M; Hess, Michael; McMullen, Matthew; Fisher, Jennifer H; Nurushev, Teamour; Grubb, Margaret; Gardner, Stephen; Nielsen, Daniel; Jagsi, Reshma; Hayman, James A; Pierce, Lori J

A database in which patient data are compiled allows analytic opportunities for continuous improvements in treatment quality and comparative effectiveness research. We describe the development of a novel, web-based system that supports the collection of complex radiation treatment planning information from centers that use diverse techniques, software, and hardware for radiation oncology care in a statewide quality collaborative, the Michigan Radiation Oncology Quality Consortium (MROQC). The MROQC database seeks to enable assessment of physician- and patient-reported outcomes and quality improvement as a function of treatment planning and delivery techniques for breast and lung cancer patients. We created tools to collect anonymized data based on all plans. The MROQC system representing 24 institutions has been successfully deployed in the state of Michigan. Since 2012, dose-volume histogram and Digital Imaging and Communications in Medicine-radiation therapy plan data and information on simulation, planning, and delivery techniques have been collected. Audits indicated >90% accurate data submission and spurred refinements to data collection methodology. This model web-based system captures detailed, high-quality radiation therapy dosimetry data along with patient- and physician-reported outcomes and clinical data for a radiation therapy collaborative quality initiative. The collaborative nature of the project has been integral to its success. Our methodology can be applied to setting up analogous consortiums and databases. Copyright © 2016 American Society for Radiation Oncology. Published by Elsevier Inc. All rights reserved.

Military Suicide Research Consortium

DTIC Science & Technology

2014-10-01

increasing and decreasing (or even ceasing entirely) across different periods of time but still building on itself with each progressive episode...community from suicide. One study found that social norms, high levels of support, identification with role models , and high self-esteem help pro - tect...in follow-up. o Conducted quality control checks of clinical data . Monitored safety, adverse events for DSMB reporting. Initiated Database

Understanding Differences in Administrative and Audited Patient Data in Cardiac Surgery: Comparison of the University HealthSystem Consortium and Society of Thoracic Surgeons Databases.

PubMed

Prasad, Anjali; Helder, Meghana R; Brown, Dwight A; Schaff, Hartzell V

2016-10-01

The University HealthSystem Consortium (UHC) administrative database has been used increasingly as a quality indicator for hospitals and even individual surgeons. We aimed to determine the accuracy of cardiac surgical data in the administrative UHC database vs data in the clinical Society of Thoracic Surgeons database. We reviewed demographic and outcomes information of patients with aortic valve replacement (AVR), mitral valve replacement (MVR), and coronary artery bypass grafting (CABG) surgery between January 1, 2012, and December 31, 2013. Data collected in aggregate and compared across the databases included case volume, physician specialty coding, patient age and sex, comorbidities, mortality rate, and postoperative complications. In these 2 years, the UHC database recorded 1,270 AVRs, 355 MVRs, and 1,473 CABGs. The Society of Thoracic Surgeons database case volumes were less by 2% to 12% (1,219 AVRs; 316 MVRs; and 1,442 CABGs). Errors in physician specialty coding occurred in UHC data (AVR, 0.6%; MVR, 0.8%; and CABG, 0.7%). In matched patients from each database, demographic age and sex information was identical. Although definitions differed in the databases, percentages of patients with at least one comorbidity were similar. Hospital mortality rates were similar as well, but postoperative recorded complications differed greatly. In comparing the 2 databases, we found similarity in patient demographic information and percentage of patients with comorbidities. The small difference in volumes of each operation type and the larger disparity in postoperative complications between the databases were related to differences in data definition, data collection, and coding errors. Copyright © 2016 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Developing knowledge resources to support precision medicine: principles from the Clinical Pharmacogenetics Implementation Consortium (CPIC).

PubMed

Hoffman, James M; Dunnenberger, Henry M; Kevin Hicks, J; Caudle, Kelly E; Whirl Carrillo, Michelle; Freimuth, Robert R; Williams, Marc S; Klein, Teri E; Peterson, Josh F

2016-07-01

To move beyond a select few genes/drugs, the successful adoption of pharmacogenomics into routine clinical care requires a curated and machine-readable database of pharmacogenomic knowledge suitable for use in an electronic health record (EHR) with clinical decision support (CDS). Recognizing that EHR vendors do not yet provide a standard set of CDS functions for pharmacogenetics, the Clinical Pharmacogenetics Implementation Consortium (CPIC) Informatics Working Group is developing and systematically incorporating a set of EHR-agnostic implementation resources into all CPIC guidelines. These resources illustrate how to integrate pharmacogenomic test results in clinical information systems with CDS to facilitate the use of patient genomic data at the point of care. Based on our collective experience creating existing CPIC resources and implementing pharmacogenomics at our practice sites, we outline principles to define the key features of future knowledge bases and discuss the importance of these knowledge resources for pharmacogenomics and ultimately precision medicine. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The role of expert searching in the Family Physicians' Inquiries Network (FPIN)*

PubMed Central

Ward, Deborah; Meadows, Susan E.; Nashelsky, Joan E.

2005-01-01

Objective: This article describes the contributions of medical librarians, as members of the Family Physicians' Inquiries Network (FPIN), to the creation of a database of clinical questions and answers that allows family physicians to practice evidence-based medicine using high-quality information at the point of care. The medical librarians have contributed their evidence-based search expertise and knowledge of information systems that support the processes and output of the consortium. Methods: Since its inception, librarians have been included as valued members of the FPIN community. FPIN recognizes the search expertise of librarians, and each FPIN librarian must meet qualifications demonstrating appropriate experience and training in evidence-based medicine. The consortium works collaboratively to produce the Clinical Inquiries series published in family medicine publications. Results: Over 170 Clinical Inquiries have appeared in Journal of Family Practice (JFP) and American Family Physician (AFP). Surveys have shown that this series has become the most widely read part of the JFP Website. As a result, FPIN has formalized specific librarian roles that have helped build the organizational infrastructure. Conclusions: All of the activities of the consortium are highly collaborative, and the librarian community reflects that. The FPIN librarians are valuable and equal contributors to the process of creating, updating, and maintaining high-quality clinical information for practicing primary care physicians. Of particular value is the skill of expert searching that the librarians bring to FPIN's products. PMID:15685280

Assessment methodologies and statistical issues for computer-aided diagnosis of lung nodules in computed tomography: contemporary research topics relevant to the lung image database consortium.

PubMed

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.

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

PubMed Central

Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Josée; Laroche, Jérôme; Larose, Stéphane; Maaroufi, Halim; Fothergill, Joanne L.; Moore, Matthew; Winsor, Geoffrey L.; Aaron, Shawn D.; Barbeau, Jean; Bell, Scott C.; Burns, Jane L.; Camara, Miguel; Cantin, André; Charette, Steve J.; Dewar, Ken; Déziel, Éric; Grimwood, Keith; Hancock, Robert E. W.; Harrison, Joe J.; Heeb, Stephan; Jelsbak, Lars; Jia, Baofeng; Kenna, Dervla T.; Kidd, Timothy J.; Klockgether, Jens; Lam, Joseph S.; Lamont, Iain L.; Lewenza, Shawn; Loman, Nick; Malouin, François; Manos, Jim; McArthur, Andrew G.; McKeown, Josie; Milot, Julie; Naghra, Hardeep; Nguyen, Dao; Pereira, Sheldon K.; Perron, Gabriel G.; Pirnay, Jean-Paul; Rainey, Paul B.; Rousseau, Simon; Santos, Pedro M.; Stephenson, Anne; Taylor, Véronique; Turton, Jane F.; Waglechner, Nicholas; Williams, Paul; Thrane, Sandra W.; Wright, Gerard D.; Brinkman, Fiona S. L.; Tucker, Nicholas P.; Tümmler, Burkhard; Winstanley, Craig; Levesque, Roger C.

2015-01-01

The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care. PMID:26483767

Rationale of the FIBROTARGETS study designed to identify novel biomarkers of myocardial fibrosis

PubMed Central

Ferreira, João Pedro; Machu, Jean‐Loup; Girerd, Nicolas; Jaisser, Frederic; Thum, Thomas; Butler, Javed; González, Arantxa; Diez, Javier; Heymans, Stephane; McDonald, Kenneth; Gyöngyösi, Mariann; Firat, Hueseyin; Rossignol, Patrick; Pizard, Anne

2017-01-01

Abstract Aims Myocardial fibrosis alters the cardiac architecture favouring the development of cardiac dysfunction, including arrhythmias and heart failure. Reducing myocardial fibrosis may improve outcomes through the targeted diagnosis and treatment of emerging fibrotic pathways. The European‐Commission‐funded ‘FIBROTARGETS’ is a multinational academic and industrial consortium with the main aims of (i) characterizing novel key mechanistic pathways involved in the metabolism of fibrillary collagen that may serve as biotargets, (ii) evaluating the potential anti‐fibrotic properties of novel or repurposed molecules interfering with the newly identified biotargets, and (iii) characterizing bioprofiles based on distinct mechanistic phenotypes involving the aforementioned biotargets. These pathways will be explored by performing a systematic and collaborative search for mechanisms and targets of myocardial fibrosis. These mechanisms will then be translated into individualized diagnostic tools and specific therapeutic pharmacological options for heart failure. Methods and results The FIBROTARGETS consortium has merged data from 12 patient cohorts in a common database available to individual consortium partners. The database consists of >12 000 patients with a large spectrum of cardiovascular clinical phenotypes. It integrates community‐based population cohorts, cardiovascular risk cohorts, and heart failure cohorts. Conclusions The FIBROTARGETS biomarker programme is aimed at exploring fibrotic pathways allowing the bioprofiling of patients into specific ‘fibrotic’ phenotypes and identifying new therapeutic targets that will potentially enable the development of novel and tailored anti‐fibrotic therapies for heart failure. PMID:28988439

Development of a personalized training system using the Lung Image Database Consortium and Image Database resource Initiative Database.

PubMed

Lin, Hongli; Wang, Weisheng; Luo, Jiawei; Yang, Xuedong

2014-12-01

The aim of this study was to develop a personalized training system using the Lung Image Database Consortium (LIDC) and Image Database resource Initiative (IDRI) Database, because collecting, annotating, and marking a large number of appropriate computed tomography (CT) scans, and providing the capability of dynamically selecting suitable training cases based on the performance levels of trainees and the characteristics of cases are critical for developing a efficient training system. A novel approach is proposed to develop a personalized radiology training system for the interpretation of lung nodules in CT scans using the Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) database, which provides a Content-Boosted Collaborative Filtering (CBCF) algorithm for predicting the difficulty level of each case of each trainee when selecting suitable cases to meet individual needs, and a diagnostic simulation tool to enable trainees to analyze and diagnose lung nodules with the help of an image processing tool and a nodule retrieval tool. Preliminary evaluation of the system shows that developing a personalized training system for interpretation of lung nodules is needed and useful to enhance the professional skills of trainees. The approach of developing personalized training systems using the LIDC/IDRL database is a feasible solution to the challenges of constructing specific training program in terms of cost and training efficiency. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Resources | Division of Cancer Prevention

Cancer.gov

Manual of Operations Version 3, 12/13/2012 (PDF, 162KB) Database Sources Consortium for Functional Glycomics databases Design Studies Related to the Development of Distributed, Web-based European Carbohydrate Databases (EUROCarbDB) |

Consortia for Engineering, Science and Technology Libraries in India: A Case Study of INDEST Consortium

NASA Astrophysics Data System (ADS)

Pathak, S. K.; Deshpande, N. J.

2007-10-01

The present scenario of the INDEST Consortium among engineering, science and technology (including astronomy and astrophysics) libraries in India is discussed. The Indian National Digital Library in Engineering Sciences & Technology (INDEST) Consortium is a major initiative of the Ministry of Human Resource Development, Government of India. The INDEST Consortium provides access to 16 full text e-resources and 7 bibliographic databases for 166 institutions as members who are taking advantage of cost effective access to premier resources in engineering, science and technology, including astronomy and astrophysics. Member institutions can access over 6500 e-journals from 1092 publishers. Out of these, over 150 e-journals are exclusively for the astronomy and physics community. The current study also presents a comparative analysis of the key features of nine major services, viz. ACM Digital Library, ASCE Journals, ASME Journals, EBSCO Databases (Business Source Premier), Elsevier's Science Direct, Emerald Full Text, IEEE/IEE Electronic Library Online (IEL), ProQuest ABI/INFORM and Springer Verlag's Link. In this paper, the limitations of this consortium are also discussed.

Prostate Cancer Clinical Consortium Clinical Research Site:Targeted Therapies

DTIC Science & Technology

2015-10-01

AWARD NUMBER: W81XWH-14-2-0159 TITLE: Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies PRINCIPAL INVESTIGATOR...Sep 2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies 5b. GRANT NUMBER... therapy resistance/sensitivity, identification of new therapeutic targets through high quality genomic analyses, providing access to the highest quality

Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies

DTIC Science & Technology

2017-10-01

AWARD NUMBER: W81XWH-14-2-0159 TITLE: Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies PRINCIPAL INVESTIGATOR...Annual PREPARED FOR: U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702-5012 DISTRIBUTION STATEMENT: Approved for...AND SUBTITLE Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

ICONE: An International Consortium of Neuro Endovascular Centres.

PubMed

Raymond, J; White, P; Kallmes, D F; Spears, J; Marotta, T; Roy, D; Guilbert, F; Weill, A; Nguyen, T; Molyneux, A J; Cloft, H; Cekirge, S; Saatci, I; Bracard, S; Meder, J F; Moret, J; Cognard, C; Qureshi, A I; Turk, A S; Berenstein, A

2008-06-30

The proliferation of new endovascular devices and therapeutic strategies calls for a prudentand rational evaluation of their clinical benefit. This evaluation must be done in an effective manner and in collaboration with industry. Such research initiative requires organisation a land methodological support to survive and thrive in a competitive environment. We propose the formation of an international consortium, an academic alliance committed to the pursuit of effective neurovascular therapies. Such a consortium would be dedicated to the designand execution of basic science, device developmentand clinical trials. The Consortium is owned and operated by its members. Members are international leaders in neurointerventional research and clinical practice. The Consortium brings competency, knowledge, and expertise to industry as well as to its membership across aspectrum of research initiatives such as: expedited review of clinical trials, protocol development, surveys and systematic reviews; laboratory expertise and support for research design and grant applications to public agencies. Once objectives and protocols are approved, the Consortium provides a stable network of centers capable of timely realization of clinical trials or pre clinical investigations in an optimal environment. The Consortium is a non-profit organization. The potential revenue generated from clientsponsored financial agreements will be redirected to the academic and research objectives of the organization. The Consortium wishes to work inconcert with industry, to support emerging trends in neurovascular therapeutic development. The Consortium is a realistic endeavour optimally structured to promote excellence through scientific appraisal of our treatments, and to accelerate technical progress while maximizing patients' safety and welfare.

Establishment of Kawasaki disease database based on metadata standard.

PubMed

Park, Yu Rang; Kim, Jae-Jung; Yoon, Young Jo; Yoon, Young-Kwang; Koo, Ha Yeong; Hong, Young Mi; Jang, Gi Young; Shin, Soo-Yong; Lee, Jong-Keuk

2016-07-01

Kawasaki disease (KD) is a rare disease that occurs predominantly in infants and young children. To identify KD susceptibility genes and to develop a diagnostic test, a specific therapy, or prevention method, collecting KD patients' clinical and genomic data is one of the major issues. For this purpose, Kawasaki Disease Database (KDD) was developed based on the efforts of Korean Kawasaki Disease Genetics Consortium (KKDGC). KDD is a collection of 1292 clinical data and genomic samples of 1283 patients from 13 KKDGC-participating hospitals. Each sample contains the relevant clinical data, genomic DNA and plasma samples isolated from patients' blood, omics data and KD-associated genotype data. Clinical data was collected and saved using the common data elements based on the ISO/IEC 11179 metadata standard. Two genome-wide association study data of total 482 samples and whole exome sequencing data of 12 samples were also collected. In addition, KDD includes the rare cases of KD (16 cases with family history, 46 cases with recurrence, 119 cases with intravenous immunoglobulin non-responsiveness, and 52 cases with coronary artery aneurysm). As the first public database for KD, KDD can significantly facilitate KD studies. All data in KDD can be searchable and downloadable. KDD was implemented in PHP, MySQL and Apache, with all major browsers supported.Database URL: http://www.kawasakidisease.kr. © The Author(s) 2016. Published by Oxford University Press.

Dictionary as Database.

ERIC Educational Resources Information Center

Painter, Derrick

1996-01-01

Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline

PubMed Central

Rudnick, Paul A.; Markey, Sanford P.; Roth, Jeri; Mirokhin, Yuri; Yan, Xinjian; Tchekhovskoi, Dmitrii V.; Edwards, Nathan J.; Thangudu, Ratna R.; Ketchum, Karen A.; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Stein, Stephen E.

2016-01-01

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics datasets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and non-reference markers of cancer. The CPTAC labs have focused on colon, breast, and ovarian tissues in the first round of analyses; spectra from these datasets were produced from 2D LC-MS/MS analyses and represent deep coverage. To reduce the variability introduced by disparate data analysis platforms (e.g., software packages, versions, parameters, sequence databases, etc.), the CPTAC Common Data Analysis Platform (CDAP) was created. The CDAP produces both peptide-spectrum-match (PSM) reports and gene-level reports. The pipeline processes raw mass spectrometry data according to the following: (1) Peak-picking and quantitative data extraction, (2) database searching, (3) gene-based protein parsimony, and (4) false discovery rate (FDR)-based filtering. The pipeline also produces localization scores for the phosphopeptide enrichment studies using the PhosphoRS program. Quantitative information for each of the datasets is specific to the sample processing, with PSM and protein reports containing the spectrum-level or gene-level (“rolled-up”) precursor peak areas and spectral counts for label-free or reporter ion log-ratios for 4plex iTRAQ™. The reports are available in simple tab-delimited formats and, for the PSM-reports, in mzIdentML. The goal of the CDAP is to provide standard, uniform reports for all of the CPTAC data, enabling comparisons between different samples and cancer types as well as across the major ‘omics fields. PMID:26860878

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline.

PubMed

Rudnick, Paul A; Markey, Sanford P; Roth, Jeri; Mirokhin, Yuri; Yan, Xinjian; Tchekhovskoi, Dmitrii V; Edwards, Nathan J; Thangudu, Ratna R; Ketchum, Karen A; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Stein, Stephen E

2016-03-04

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics data sets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and nonreference markers of cancer. The CPTAC laboratories have focused on colon, breast, and ovarian tissues in the first round of analyses; spectra from these data sets were produced from 2D liquid chromatography-tandem mass spectrometry analyses and represent deep coverage. To reduce the variability introduced by disparate data analysis platforms (e.g., software packages, versions, parameters, sequence databases, etc.), the CPTAC Common Data Analysis Platform (CDAP) was created. The CDAP produces both peptide-spectrum-match (PSM) reports and gene-level reports. The pipeline processes raw mass spectrometry data according to the following: (1) peak-picking and quantitative data extraction, (2) database searching, (3) gene-based protein parsimony, and (4) false-discovery rate-based filtering. The pipeline also produces localization scores for the phosphopeptide enrichment studies using the PhosphoRS program. Quantitative information for each of the data sets is specific to the sample processing, with PSM and protein reports containing the spectrum-level or gene-level ("rolled-up") precursor peak areas and spectral counts for label-free or reporter ion log-ratios for 4plex iTRAQ. The reports are available in simple tab-delimited formats and, for the PSM-reports, in mzIdentML. The goal of the CDAP is to provide standard, uniform reports for all of the CPTAC data to enable comparisons between different samples and cancer types as well as across the major omics fields.

Metro-Minnesota Community Clinical Oncology Program (MM-CCOP) | Division of Cancer Prevention

Cancer.gov

The Metro-Minnesota Community Clinical Oncology (MMCCOP) program has a long-standing history which clearly demonstrates the success of the consortium, as demonstrated by both the ongoing commitment of the original consortium members and the growth of the consortium from 1979 through 2014. The MMCCOP consortium represents an established community program base which began in

Acute pancreatitis patient registry to examine novel therapies in clinical experience (APPRENTICE): an international, multicenter consortium for the study of acute pancreatitis.

PubMed

Papachristou, Georgios I; Machicado, Jorge D; Stevens, Tyler; Goenka, Mahesh Kumar; Ferreira, Miguel; Gutierrez, Silvia C; Singh, Vikesh K; Kamal, Ayesha; Gonzalez-Gonzalez, Jose A; Pelaez-Luna, Mario; Gulla, Aiste; Zarnescu, Narcis O; Triantafyllou, Konstantinos; Barbu, Sorin T; Easler, Jeffrey; Ocampo, Carlos; Capurso, Gabriele; Archibugi, Livia; Cote, Gregory A; Lambiase, Louis; Kochhar, Rakesh; Chua, Tiffany; Tiwari, Subhash Ch; Nawaz, Haq; Park, Walter G; de-Madaria, Enrique; Lee, Peter J; Wu, Bechien U; Greer, Phil J; Dugum, Mohannad; Koutroumpakis, Efstratios; Akshintala, Venkata; Gougol, Amir

2017-01-01

We have established a multicenter international consortium to better understand the natural history of acute pancreatitis (AP) worldwide and to develop a platform for future randomized clinical trials. The AP patient registry to examine novel therapies in clinical experience (APPRENTICE) was formed in July 2014. Detailed web-based questionnaires were then developed to prospectively capture information on demographics, etiology, pancreatitis history, comorbidities, risk factors, severity biomarkers, severity indices, health-care utilization, management strategies, and outcomes of AP patients. Between November 2015 and September 2016, a total of 20 sites (8 in the United States, 5 in Europe, 3 in South America, 2 in Mexico and 2 in India) prospectively enrolled 509 AP patients. All data were entered into the REDCap (Research Electronic Data Capture) database by participating centers and systematically reviewed by the coordinating site (University of Pittsburgh). The approaches and methodology are described in detail, along with an interim report on the demographic results. APPRENTICE, an international collaboration of tertiary AP centers throughout the world, has demonstrated the feasibility of building a large, prospective, multicenter patient registry to study AP. Analysis of the collected data may provide a greater understanding of AP and APPRENTICE will serve as a future platform for randomized clinical trials.

Massage Therapy for Health Purposes

MedlinePlus

... Web site: www.nih.gov/health/clinicaltrials/ Cochrane Database of Systematic Reviews The Cochrane Database of Systematic ... Licensed Complementary and Alternative Healthcare Professions. Seattle, WA: Academic Consortium for Complementary and Alternative Health Care; 2009. ...

Drug development and nonclinical to clinical translational databases: past and current efforts.

PubMed

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).

The Génolevures database.

PubMed

Martin, Tiphaine; Sherman, David J; Durrens, Pascal

2011-01-01

The Génolevures online database (URL: http://www.genolevures.org) stores and provides the data and results obtained by the Génolevures Consortium through several campaigns of genome annotation of the yeasts in the Saccharomycotina subphylum (hemiascomycetes). This database is dedicated to large-scale comparison of these genomes, storing not only the different chromosomal elements detected in the sequences, but also the logical relations between them. The database is divided into a public part, accessible to anyone through Internet, and a private part where the Consortium members make genome annotations with our Magus annotation system; this system is used to annotate several related genomes in parallel. The public database is widely consulted and offers structured data, organized using a REST web site architecture that allows for automated requests. The implementation of the database, as well as its associated tools and methods, is evolving to cope with the influx of genome sequences produced by Next Generation Sequencing (NGS). Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Completed | Office of Cancer Clinical Proteomics Research

Cancer.gov

Prior to the current Clinical Proteomic Tumor Analysis Consortium (CPTAC), previously funded initiatives associated with clinical proteomics research included: Clinical Proteomic Tumor Analysis Consortium (CPTAC 2.0) Clinical Proteomic Technologies for Cancer Initiative (CPTC) Mouse Proteomic Technologies Initiative

Current nonclinical testing paradigm enables safe entry to First-In-Human clinical trials: The IQ consortium nonclinical to clinical translational database.

PubMed

Monticello, Thomas M; Jones, Thomas W; Dambach, Donna M; Potter, David M; Bolt, Michael W; Liu, Maggie; Keller, Douglas A; Hart, Timothy K; Kadambi, Vivek J

2017-11-01

The contribution of animal testing in drug development has been widely debated and challenged. An industry-wide nonclinical to clinical translational database was created to determine how safety assessments in animal models translate to First-In-Human clinical risk. The blinded database was composed of 182 molecules and contained animal toxicology data coupled with clinical observations from phase I human studies. Animal and clinical data were categorized by organ system and correlations determined. The 2×2 contingency table (true positive, false positive, true negative, false negative) was used for statistical analysis. Sensitivity was 48% with a 43% positive predictive value (PPV). The nonhuman primate had the strongest performance in predicting adverse effects, especially for gastrointestinal and nervous system categories. When the same target organ was identified in both the rodent and nonrodent, the PPV increased. Specificity was 84% with an 86% negative predictive value (NPV). The beagle dog had the strongest performance in predicting an absence of clinical adverse effects. If no target organ toxicity was observed in either test species, the NPV increased. While nonclinical studies can demonstrate great value in the PPV for certain species and organ categories, the NPV was the stronger predictive performance measure across test species and target organs indicating that an absence of toxicity in animal studies strongly predicts a similar outcome in the clinic. These results support the current regulatory paradigm of animal testing in supporting safe entry to clinical trials and provide context for emerging alternate models. Copyright © 2017 Elsevier Inc. All rights reserved.

Acute pancreatitis patient registry to examine novel therapies in clinical experience (APPRENTICE): an international, multicenter consortium for the study of acute pancreatitis

PubMed Central

Papachristou, Georgios I.; Machicado, Jorge D.; Stevens, Tyler; Goenka, Mahesh Kumar; Ferreira, Miguel; Gutierrez, Silvia C.; Singh, Vikesh K.; Kamal, Ayesha; Gonzalez-Gonzalez, Jose A.; Pelaez-Luna, Mario; Gulla, Aiste; Zarnescu, Narcis O.; Triantafyllou, Konstantinos; Barbu, Sorin T.; Easler, Jeffrey; Ocampo, Carlos; Capurso, Gabriele; Archibugi, Livia; Cote, Gregory A.; Lambiase, Louis; Kochhar, Rakesh; Chua, Tiffany; Tiwari, Subhash Ch.; Nawaz, Haq; Park, Walter G.; de-Madaria, Enrique; Lee, Peter J.; Wu, Bechien U.; Greer, Phil J.; Dugum, Mohannad; Koutroumpakis, Efstratios; Akshintala, Venkata; Gougol, Amir

2017-01-01

Background We have established a multicenter international consortium to better understand the natural history of acute pancreatitis (AP) worldwide and to develop a platform for future randomized clinical trials. Methods The AP patient registry to examine novel therapies in clinical experience (APPRENTICE) was formed in July 2014. Detailed web-based questionnaires were then developed to prospectively capture information on demographics, etiology, pancreatitis history, comorbidities, risk factors, severity biomarkers, severity indices, health-care utilization, management strategies, and outcomes of AP patients. Results Between November 2015 and September 2016, a total of 20 sites (8 in the United States, 5 in Europe, 3 in South America, 2 in Mexico and 2 in India) prospectively enrolled 509 AP patients. All data were entered into the REDCap (Research Electronic Data Capture) database by participating centers and systematically reviewed by the coordinating site (University of Pittsburgh). The approaches and methodology are described in detail, along with an interim report on the demographic results. Conclusion APPRENTICE, an international collaboration of tertiary AP centers throughout the world, has demonstrated the feasibility of building a large, prospective, multicenter patient registry to study AP. Analysis of the collected data may provide a greater understanding of AP and APPRENTICE will serve as a future platform for randomized clinical trials. PMID:28042246

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

Enhancing Transfer Effectiveness: A Model for the 1990's. First Year Report to the National Effective Transfer Consortium. Executive Summary.

ERIC Educational Resources Information Center

Berman, Paul; And Others

This first-year report of the National Effective Transfer Consortium (NETC) summarizes the progress made by the member colleges in creating standardized measures of actual and expected transfer rates and of transfer effectiveness, and establishing a database that would enable valid comparisons among NETC colleges. Following background information…

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

PubMed

Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

A novel cross-disciplinary multi-institute approach to translational cancer research: lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC).

PubMed

Patel, Ashokkumar A; Gilbertson, John R; Showe, Louise C; London, Jack W; Ross, Eric; Ochs, Michael F; Carver, Joseph; Lazarus, Andrea; Parwani, Anil V; Dhir, Rajiv; Beck, J Robert; Liebman, Michael; Garcia, Fernando U; Prichard, Jeff; Wilkerson, Myra; Herberman, Ronald B; Becich, Michael J

2007-06-08

The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu) is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1) for bioinformatics and a repository of serum and tissue samples; (2) a data model for biomarker data storage; and (3) a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium's intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancer-specific biomarkers and encourage collaborative research efforts among the participating centers. The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission. The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual property/tech transfer agreements, and material transfer agreements that have been approved by each of the member institutions. This was the foundational work that has led to the development of a centralized data warehouse that has met each of the institutions' IRB/HIPAA standards. Currently, this "virtual biorepository" has over 58,000 annotated samples from 11,467 cancer patients available for research purposes. The clinical annotation of tissue samples is either done manually over the internet or semi-automated batch modes through mapping of local data elements with PCABC common data elements. The database currently holds information on 7188 cases (associated with 9278 specimens and 46,666 annotated blocks and blood samples) of prostate cancer, 2736 cases (associated with 3796 specimens and 9336 annotated blocks and blood samples) of breast cancer and 1543 cases (including 1334 specimens and 2671 annotated blocks and blood samples) of melanoma. These numbers continue to grow, and plans to integrate new tumor sites are in progress. Furthermore, the group has also developed a central web-based tool that allows investigators to share their translational (genomics/proteomics) experiment data on research evaluating potential biomarkers via a central location on the Consortium's web site. The technological achievements and the statewide informatics infrastructure that have been established by the Consortium will enable robust and efficient studies of biomarkers and their relevance to the clinical course of cancer. Studies resulting from the creation of the Consortium may allow for better classification of cancer types, more accurate assessment of disease prognosis, a better ability to identify the most appropriate individuals for clinical trial participation, and better surrogate markers of disease progression and/or response to therapy.

77 FR 43237 - Genome in a Bottle Consortium-Work Plan Review Workshop

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-24

... in human whole genome variant calls. A principal motivation for this consortium is to enable... principal motivation for this consortium is to enable science-based regulatory oversight of clinical...

Pediatric post-marketing safety systems in North America: assessment of the current status.

PubMed

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.

Notice of Pre-Application Webinar (RFA-CA-15-021, RFA-CA-15-022, RFA-CA-15-023) | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute will hold a public pre-application webinar on Friday, December 11 at 12:00 p.m. (EST) for the Funding Opportunity Announcements (FOAs) RFA-CA-15-021 entitled “Proteome Characterization Centers for Clinical Proteomic Tumor Analysis Consortium (U24), RFA-CA-15-022 entitled “Proteogenomic Translational Research Centers for Clinical Proteomic Tumor Analysis Consortium (U01)”, and RFA-CA-15-023 entitled “Proteogenomic Data Analysis Centers for Clinical Proteomic Tumor Analysis Consortium (U24)”.

Completion of the National Land Cover Database (NLCD) 1992-2001 Land Cover Change Retrofit Product

EPA Science Inventory

The Multi-Resolution Land Characteristics Consortium has supported the development of two national digital land cover products: the National Land Cover Dataset (NLCD) 1992 and National Land Cover Database (NLCD) 2001. Substantial differences in imagery, legends, and methods betwe...

Cancer Core Europe: a consortium to address the cancer care-cancer research continuum challenge.

PubMed

Eggermont, Alexander M M; Caldas, Carlos; Ringborg, Ulrik; Medema, René; Tabernero, Josep; Wiestler, Otmar

2014-11-01

European cancer research for a transformative initiative by creating a consortium of six leading excellent comprehensive cancer centres that will work together to address the cancer care-cancer research continuum. Prerequisites for joint translational and clinical research programs are very demanding. These require the creation of a virtual single 'e-hospital' and a powerful translational platform, inter-compatible clinical molecular profiling laboratories with a robust underlying computational biology pipeline, standardised functional and molecular imaging, commonly agreed Standard Operating Procedures (SOPs) for liquid and tissue biopsy procurement, storage and processing, for molecular diagnostics, 'omics', functional genetics, immune-monitoring and other assessments. Importantly also it requires a culture of data collection and data storage that provides complete longitudinal data sets to allow for: effective data sharing and common database building, and to achieve a level of completeness of data that is required for conducting outcome research, taking into account our current understanding of cancers as communities of evolving clones. Cutting edge basic research and technology development serve as an important driving force for innovative translational and clinical studies. Given the excellent track records of the six participants in these areas, Cancer Core Europe will be able to support the full spectrum of research required to address the cancer research- cancer care continuum. Cancer Core Europe also constitutes a unique environment to train the next generation of talents in innovative translational and clinical oncology. Copyright © 2014. Published by Elsevier Ltd.

Completion of the 2006 National Land Cover Database Update for the Conterminous United States

EPA Science Inventory

Under the organization of the Multi-Resolution Land Characteristics (MRLC) Consortium, the National Land Cover Database (NLCD) has been updated to characterize both land cover and land cover change from 2001 to 2006. An updated version of NLCD 2001 (Version 2.0) is also provided....

Identifying complications of interventional procedures from UK routine healthcare databases: a systematic search for methods using clinical codes.

PubMed

Keltie, Kim; Cole, Helen; Arber, Mick; Patrick, Hannah; Powell, John; Campbell, Bruce; Sims, Andrew

2014-11-28

Several authors have developed and applied methods to routine data sets to identify the nature and rate of complications following interventional procedures. But, to date, there has been no systematic search for such methods. The objective of this article was to find, classify and appraise published methods, based on analysis of clinical codes, which used routine healthcare databases in a United Kingdom setting to identify complications resulting from interventional procedures. A literature search strategy was developed to identify published studies that referred, in the title or abstract, to the name or acronym of a known routine healthcare database and to complications from procedures or devices. The following data sources were searched in February and March 2013: Cochrane Methods Register, Conference Proceedings Citation Index - Science, Econlit, EMBASE, Health Management Information Consortium, Health Technology Assessment database, MathSciNet, MEDLINE, MEDLINE in-process, OAIster, OpenGrey, Science Citation Index Expanded and ScienceDirect. Of the eligible papers, those which reported methods using clinical coding were classified and summarised in tabular form using the following headings: routine healthcare database; medical speciality; method for identifying complications; length of follow-up; method of recording comorbidity. The benefits and limitations of each approach were assessed. From 3688 papers identified from the literature search, 44 reported the use of clinical codes to identify complications, from which four distinct methods were identified: 1) searching the index admission for specified clinical codes, 2) searching a sequence of admissions for specified clinical codes, 3) searching for specified clinical codes for complications from procedures and devices within the International Classification of Diseases 10th revision (ICD-10) coding scheme which is the methodology recommended by NHS Classification Service, and 4) conducting manual clinical review of diagnostic and procedure codes. The four distinct methods identifying complication from codified data offer great potential in generating new evidence on the quality and safety of new procedures using routine data. However the most robust method, using the methodology recommended by the NHS Classification Service, was the least frequently used, highlighting that much valuable observational data is being ignored.

Department of Defense prostate cancer clinical trials consortium: a new instrument for prostate cancer clinical research.

PubMed

Morris, Michael J; Basch, Ethan M; Wilding, George; Hussain, Maha; Carducci, Michael A; Higano, Celestia; Kantoff, Philip; Oh, William K; Small, Eric J; George, Daniel; Mathew, Paul; Beer, Tomasz M; Slovin, Susan F; Ryan, Charles; Logothetis, Christopher; Scher, Howard I

2009-01-01

In 2005, the US Department of Defense, through the US Army Medical Research and Materiel Command, Office of the Congressionally Directed Medical Research Programs, created a funding mechanism to form a clinical trials consortium to conduct phase I and II studies in prostate cancer. This is the first report of the Prostate Cancer Clinical Trials Consortium (PCCTC). The Department of Defense award supports a consortium of 10 prostate cancer research centers. Memorial Sloan-Kettering Cancer Center was awarded the Coordinating Center grant for the consortium and charged with creating an infrastructure to conduct early-phase multicenter clinical trials. Each participating center was required to introduce >or=1 clinical trial per year and maintain accrual of a minimum of 35 patients per year. The PCCTC was launched in 2006 and now encompasses 10 leading prostate cancer research centers. Fifty-one trials have been opened, and 1386 patients have been accrued at member sites. Members share an online clinical trial management system for protocol tracking, electronic data capture, and data storage. A legal framework has been instituted, and standard operating procedures, an administrative structure, editorial support, centralized budgeting, and mechanisms for scientific review are established. The PCCTC fulfills a congressional directive to create a clinical trials instrument dedicated to early-phase prostate cancer studies. The member institutions have built an administrative, informatics, legal, financial, statistical, and scientific infrastructure to support this endeavor. Clinical trials are open and accruing in excess of federally mandated goals.

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

Xie, Sharon X.; Baek, Young; Grossman, Murray; Arnold, Steven E.; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M.-Y.; Trojanowski, John Q.

2010-01-01

Background It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). These comparative studies rely on powerful database tools to quickly generate data sets which match diverse and complementary criteria set by the studies. Methods In this paper, we present a novel Integrated NeuroDegenerative Disease (INDD) database developed at the University of Pennsylvania (Penn) through a consortium of Penn investigators. Since these investigators work on AD, PD, ALS and FTLD, this allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used Microsoft SQL Server as the platform with built-in “backwards” functionality to provide Access as a front-end client to interface with the database. We used PHP hypertext Preprocessor to create the “front end” web interface and then integrated individual neurodegenerative disease databases using a master lookup table. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Results We compare the results of a biomarker study using the INDD database to those using an alternative approach by querying individual database separately. Conclusions We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies across several neurodegenerative diseases. PMID:21784346

Legacy Clinical Data from the Mission Connect Mild TBI Translational Research Consortium

DTIC Science & Technology

2017-10-01

mTBI) Translational Research Consortium was to improve the diagnosis and treatment of mTBI. We enrolled a total of 88 mTBI patients and 73 orthopedic ...AWARD NUMBER: W81XWH-16-2-0026 TITLE: Legacy Clinical Data from the Mission Connect Mild TBI Translational Research Consortium PRINCIPAL...Annual PREPARED FOR: U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702-5012 DISTRIBUTION STATEMENT: Approved for

Prostate Cancer Clinical Trials Group: The University of Michigan Site

DTIC Science & Technology

2012-04-01

and fusion-negative strata. UM will be the lead site for this trial with the Univ. of Chicago N01 Phase II consortium as the coordinating center. Ten...sensitive prostate cancer: a University of Chicago Phase II Consortium/Department of Defense Prostate Cancer Clinical Trials Consortium study. JE Ward, T...N01 contract with CTEP (University of Chicago – Early Therapeutics Development with Phase II emphasis group). The Program is committed to creating

Legal Agreements and the Governance of Research Commons: Lessons from Materials Sharing in Mouse Genomics

PubMed Central

Mishra, Amrita

2014-01-01

Abstract Omics research infrastructure such as databases and bio-repositories requires effective governance to support pre-competitive research. Governance includes the use of legal agreements, such as Material Transfer Agreements (MTAs). We analyze the use of such agreements in the mouse research commons, including by two large-scale resource development projects: the International Knockout Mouse Consortium (IKMC) and International Mouse Phenotyping Consortium (IMPC). We combine an analysis of legal agreements and semi-structured interviews with 87 members of the mouse model research community to examine legal agreements in four contexts: (1) between researchers; (2) deposit into repositories; (3) distribution by repositories; and (4) exchanges between repositories, especially those that are consortium members of the IKMC and IMPC. We conclude that legal agreements for the deposit and distribution of research reagents should be kept as simple and standard as possible, especially when minimal enforcement capacity and resources exist. Simple and standardized legal agreements reduce transactional bottlenecks and facilitate the creation of a vibrant and sustainable research commons, supported by repositories and databases. PMID:24552652

Cognitive Challenges

MedlinePlus

... Find Local Resources Publications Webinars and Videos Biosample Repository Patient-Focused Drug Development Learn Engage Donate Healthcare ... and Funding Preclinical Research Natural History Database Biosample ... Research Consortium Research Conferences Research Resources International ...

Southeast Clinical Oncology Research Consortium, Inc. (SCOR) | Division of Cancer Prevention

Cancer.gov

The SCCC-Upstate is a merger of two successful legacy CCOPs known as Southeast Cancer Control Consortium, Inc. (SCCC) and Upstate Carolina (hereafter the Consortium) comprised of 23 components and 63 sub-components, located in a five-state area of the Southeast US (GA, NC, SC, TN, and VA) with a nonclinical Administrative Office (AO) in Winston-Salem, NC. The Consortium

New Funding Opportunity Announcements (FOAs): Reissuance of Clinical Proteomic Tumor Analysis Consortium (CPTAC) | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute is soliciting applications for the reissuance of its Clinical Proteomic Tumor Analysis Consortium (CPTAC) program.   CPTAC will support broad efforts focused on several cancer types to explore further the complexities of cancer proteomes and their connections to abnormalities in cancer genomes.

Lungs in TSC

MedlinePlus

... Find Local Resources Publications Webinars and Videos Biosample Repository Patient-Focused Drug Development Learn Engage Donate Healthcare ... and Funding Preclinical Research Natural History Database Biosample ... Research Consortium Research Conferences Research Resources International ...

Changes in classification of genetic variants in BRCA1 and BRCA2.

PubMed

Kast, Karin; Wimberger, Pauline; Arnold, Norbert

2018-02-01

Classification of variants of unknown significance (VUS) in the breast cancer genes BRCA1 and BRCA2 changes with accumulating evidence for clinical relevance. In most cases down-staging towards neutral variants without clinical significance is possible. We searched the database of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) for changes in classification of genetic variants as an update to our earlier publication on genetic variants in the Centre of Dresden. Changes between 2015 and 2017 were recorded. In the group of variants of unclassified significance (VUS, Class 3, uncertain), only changes of classification towards neutral genetic variants were noted. In BRCA1, 25% of the Class 3 variants (n = 2/8) changed to Class 2 (likely benign) and Class 1 (benign). In BRCA2, in 50% of the Class 3 variants (n = 16/32), a change to Class 2 (n = 10/16) or Class 1 (n = 6/16) was observed. No change in classification was noted in Class 4 (likely pathogenic) and Class 5 (pathogenic) genetic variants in both genes. No up-staging from Class 1, Class 2 or Class 3 to more clinical significance was observed. All variants with a change in classification in our cohort were down-staged towards no clinical significance by a panel of experts of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC). Prevention in families with Class 3 variants should be based on pedigree based risks and should not be guided by the presence of a VUS.

Call for participation in the neurogenetics consortium within the Human Variome Project.

PubMed

Haworth, Andrea; Bertram, Lars; Carrera, Paola; Elson, Joanna L; Braastad, Corey D; Cox, Diane W; Cruts, Marc; den Dunnen, Johann T; Farrer, Matthew J; Fink, John K; Hamed, Sherifa A; Houlden, Henry; Johnson, Dennis R; Nuytemans, Karen; Palau, Francesc; Rayan, Dipa L Raja; Robinson, Peter N; Salas, Antonio; Schüle, Birgitt; Sweeney, Mary G; Woods, Michael O; Amigo, Jorge; Cotton, Richard G H; Sobrido, Maria-Jesus

2011-08-01

The rate of DNA variation discovery has accelerated the need to collate, store and interpret the data in a standardised coherent way and is becoming a critical step in maximising the impact of discovery on the understanding and treatment of human disease. This particularly applies to the field of neurology as neurological function is impaired in many human disorders. Furthermore, the field of neurogenetics has been proven to show remarkably complex genotype-to-phenotype relationships. To facilitate the collection of DNA sequence variation pertaining to neurogenetic disorders, we have initiated the "Neurogenetics Consortium" under the umbrella of the Human Variome Project. The Consortium's founding group consisted of basic researchers, clinicians, informaticians and database creators. This report outlines the strategic aims established at the preliminary meetings of the Neurogenetics Consortium and calls for the involvement of the wider neurogenetic community in enabling the development of this important resource.

Eye Involvement in TSC

MedlinePlus

... Find Local Resources Publications Webinars and Videos Biosample Repository Patient-Focused Drug Development Learn Engage Donate Healthcare ... and Funding Preclinical Research Natural History Database Biosample ... Research Consortium Research Conferences Research Resources International ...

Scientific Use Cases for the Virtual Atomic and Molecular Data Center

NASA Astrophysics Data System (ADS)

Dubernet, M. L.; Aboudarham, J.; Ba, Y. A.; Boiziot, M.; Bottinelli, S.; Caux, E.; Endres, C.; Glorian, J. M.; Henry, F.; Lamy, L.; Le Sidaner, P.; Møller, T.; Moreau, N.; Rénié, C.; Roueff, E.; Schilke, P.; Vastel, C.; Zwoelf, C. M.

2014-12-01

VAMDC Consortium is a worldwide consortium which federates interoperable Atomic and Molecular databases through an e-science infrastructure. The contained data are of the highest scientific quality and are crucial for many applications: astrophysics, atmospheric physics, fusion, plasma and lighting technologies, health, etc. In this paper we present astrophysical scientific use cases in relation to the use of the VAMDC e-infrastructure. Those will cover very different applications such as: (i) modeling the spectra of interstellar objects using the myXCLASS software tool implemented in the Common Astronomy Software Applications package (CASA) or using the CASSIS software tool, in its stand-alone version or implemented in the Herschel Interactive Processing Environment (HIPE); (ii) the use of Virtual Observatory tools accessing VAMDC databases; (iii) the access of VAMDC from the Paris solar BASS2000 portal; (iv) the combination of tools and database from the APIS service (Auroral Planetary Imaging and Spectroscopy); (v) combination of heterogeneous data for the application to the interstellar medium from the SPECTCOL tool.

NRA8-21 Cycle 2 RBCC Turbopump Risk Reduction

NASA Technical Reports Server (NTRS)

Ferguson, Thomas V.; Williams, Morgan; Marcu, Bogdan

2004-01-01

This project was composed of three sub-tasks. The objective of the first task was to use the CFD code INS3D to generate both on- and off-design predictions for the consortium optimized impeller flowfield. The results of the flow simulations are given in the first section. The objective of the second task was to construct a turbomachinery testing database comprised of measurements made on several different impellers, an inducer and a diffuser. The data was in the form of static pressure measurements as well as laser velocimeter measurements of velocities and flow angles within the stated components. Several databases with this information were created for these components. The third subtask objective was two-fold: first, to validate the Enigma CFD code for pump diffuser analysis, and secondly, to perform steady and unsteady analyses on some wide flow range diffuser concepts using Enigma. The code was validated using the consortium optimized impeller database and then applied to two different concepts for wide flow diffusers.

Development of Pain Endpoint Models for Use in Prostate Cancer Clinical Trials and Drug Approval

DTIC Science & Technology

2016-10-01

consensus meeting, with input from investigators in the Prostate Cancer Clinical Trials Consortium, FDA Office of Oncology Drug Products, FDA Study...Cancer Clinical Trials Consortium, FDA Office of Oncology Drug Products, FDA Study Endpoint and Label Development Team, and FDA Division of...Abstract. American Society of Clinical Oncology . Chicago IL, June 1-5, 2013. INVENTIONS, PATENTS AND LICENSES None 11 REPORTABLE OUTCOMES

Building an integrated neurodegenerative disease database at an academic health center.

PubMed

Xie, Sharon X; Baek, Young; Grossman, Murray; Arnold, Steven E; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M-Y; Trojanowski, John Q

2011-07-01

It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration. These comparative studies rely on powerful database tools to quickly generate data sets that match diverse and complementary criteria set by them. In this article, we present a novel integrated neurodegenerative disease (INDD) database, which was developed at the University of Pennsylvania (Penn) with the help of a consortium of Penn investigators. Because the work of these investigators are based on Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration, it allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used the Microsoft SQL server as a platform, with built-in "backwards" functionality to provide Access as a frontend client to interface with the database. We used PHP Hypertext Preprocessor to create the "frontend" web interface and then used a master lookup table to integrate individual neurodegenerative disease databases. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Using the INDD database, we compared the results of a biomarker study with those using an alternative approach by querying individual databases separately. We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies on several neurodegenerative diseases. Copyright © 2011 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

Validation of post-operative residual contrast enhancing tumor volume as an independent prognostic factor for overall survival in newly diagnosed glioblastoma.

PubMed

Ellingson, Benjamin M; Abrey, Lauren E; Nelson, Sarah J; Kaufmann, Timothy J; Garcia, Josep; Chinot, Olivier; Saran, Frank; Nishikawa, Ryo; Henriksson, Roger; Mason, Warren P; Wick, Wolfgang; Butowski, Nicholas; Ligon, Keith L; Gerstner, Elizabeth R; Colman, Howard; de Groot, John; Chang, Susan; Mellinghoff, Ingo; Young, Robert J; Alexander, Brian M; Colen, Rivka; Taylor, Jennie W; Arrillaga-Romany, Isabel; Mehta, Arnav; Huang, Raymond Y; Pope, Whitney B; Reardon, David; Batchelor, Tracy; Prados, Michael; Galanis, Evanthia; Wen, Patrick Y; Cloughesy, Timothy F

2018-04-05

In the current study, we pooled imaging data in newly diagnosed GBM patients from international multicenter clinical trials, single institution databases, and multicenter clinical trial consortiums to identify the relationship between post-operative residual enhancing tumor volume and overall survival (OS). Data from 1,511 newly diagnosed GBM patients from 5 data sources were included in the current study: 1) a single institution database from UCLA (N=398; Discovery); 2) patients from the Ben and Cathy Ivy Foundation for Early Phase Clinical Trials Network Radiogenomics Database (N=262 from 8 centers; Confirmation); 3) the chemoradiation placebo arm from an international phase III trial (AVAglio; N=394 from 120 locations in 23 countries; Validation); 4) the experimental arm from AVAglio examining chemoradiation plus bevacizumab (N=404 from 120 locations in 23 countries; Exploratory Set 1); and 5) an Alliance (N0874) Phase I/II trial of vorinostat plus chemoradiation (N=53; Exploratory Set 2). Post-surgical, residual enhancing disease was quantified using T1 subtraction maps. Multivariate Cox regression models were used to determine influence of clinical variables, MGMT status, and residual tumor volume on OS. A log-linear relationship was observed between post-operative, residual enhancing tumor volume and OS in newly diagnosed GBM treated with standard chemoradiation. Post-operative tumor volume is a prognostic factor for OS (P<0.01), regardless of therapy, age, and MGMT promoter methylation status. Post-surgical, residual contrast-enhancing disease significantly negatively influences survival in patients with newly diagnosed glioblastoma treated with chemoradiation with or without concomitant experimental therapy.

78 FR 47674 - Genome in a Bottle Consortium-Progress and Planning Workshop

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-06

... quantitative performance metrics for confidence in variant calling. These standards and quantitative..., reproducible research and regulated applications in the clinic. On April 13, 2012, NIST convened the workshop... consortium. No proprietary information will be shared as part of the consortium, and all research results...

SU-E-T-544: A Radiation Oncology-Specific Multi-Institutional Federated Database: Initial Implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hendrickson, K; Phillips, M; Fishburn, M

Purpose: To implement a common database structure and user-friendly web-browser based data collection tools across several medical institutions to better support evidence-based clinical decision making and comparative effectiveness research through shared outcomes data. Methods: A consortium of four academic medical centers agreed to implement a federated database, known as Oncospace. Initial implementation has addressed issues of differences between institutions in workflow and types and breadth of structured information captured. This requires coordination of data collection from departmental oncology information systems (OIS), treatment planning systems, and hospital electronic medical records in order to include as much as possible the multi-disciplinary clinicalmore » data associated with a patients care. Results: The original database schema was well-designed and required only minor changes to meet institution-specific data requirements. Mobile browser interfaces for data entry and review for both the OIS and the Oncospace database were tailored for the workflow of individual institutions. Federation of database queries--the ultimate goal of the project--was tested using artificial patient data. The tests serve as proof-of-principle that the system as a whole--from data collection and entry to providing responses to research queries of the federated database--was viable. The resolution of inter-institutional use of patient data for research is still not completed. Conclusions: The migration from unstructured data mainly in the form of notes and documents to searchable, structured data is difficult. Making the transition requires cooperation of many groups within the department and can be greatly facilitated by using the structured data to improve clinical processes and workflow. The original database schema design is critical to providing enough flexibility for multi-institutional use to improve each institution s ability to study outcomes, determine best practices, and support research. The project has demonstrated the feasibility of deploying a federated database environment for research purposes to multiple institutions.« less

Legal Medicine Information System using CDISC ODM.

PubMed

Kiuchi, Takahiro; Yoshida, Ken-ichi; Kotani, Hirokazu; Tamaki, Keiji; Nagai, Hisashi; Harada, Kazuki; Ishikawa, Hirono

2013-11-01

We have developed a new database system for forensic autopsies, called the Legal Medicine Information System, using the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM). This system comprises two subsystems, namely the Institutional Database System (IDS) located in each institute and containing personal information, and the Central Anonymous Database System (CADS) located in the University Hospital Medical Information Network Center containing only anonymous information. CDISC ODM is used as the data transfer protocol between the two subsystems. Using the IDS, forensic pathologists and other staff can register and search for institutional autopsy information, print death certificates, and extract data for statistical analysis. They can also submit anonymous autopsy information to the CADS semi-automatically. This reduces the burden of double data entry, the time-lag of central data collection, and anxiety regarding legal and ethical issues. Using the CADS, various studies on the causes of death can be conducted quickly and easily, and the results can be used to prevent similar accidents, diseases, and abuse. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry

PubMed Central

Kessler, Michael D.; Yerges-Armstrong, Laura; Taub, Margaret A.; Shetty, Amol C.; Maloney, Kristin; Jeng, Linda Jo Bone; Ruczinski, Ingo; Levin, Albert M.; Williams, L. Keoki; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Boorgula, Meher Preethi; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Scott, Alan F.; Vergara, Candelaria; Gao, Jingjing; Hu, Yijuan; Johnston, Henry Richard; Qin, Zhaohui S.; Padhukasahasram, Badri; Dunston, Georgia M.; Faruque, Mezbah U.; Kenny, Eimear E.; Gietzen, Kimberly; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-YounA; Kumar, Rajesh; Schleimer, Robert; Bustamante, Carlos; De La Vega, Francisco M.; Gignoux, Chris R.; Shringarpure, Suyash S.; Musharoff, Shaila; Wojcik, Genevieve; Burchard, Esteban G.; Eng, Celeste; Gourraud, Pierre-Antoine; Hernandez, Ryan D.; Lizee, Antoine; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O.; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Abecasis, Goncalo; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Pissamai, Maul R. N.; Trevor, Maul R. N.; Watson, Harold; Araujo, Maria Ilma; Oliveira, Ricardo Riccio; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Herrera-Paz, Edwin Francisco; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Vasquez, Olga Marina; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria; O'Connor, Timothy D.

2016-01-01

To characterize the extent and impact of ancestry-related biases in precision genomic medicine, we use 642 whole-genome sequences from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) project to evaluate typical filters and databases. We find significant correlations between estimated African ancestry proportions and the number of variants per individual in all variant classification sets but one. The source of these correlations is highlighted in more detail by looking at the interaction between filtering criteria and the ClinVar and Human Gene Mutation databases. ClinVar's correlation, representing African ancestry-related bias, has changed over time amidst monthly updates, with the most extreme switch happening between March and April of 2014 (r=0.733 to r=−0.683). We identify 68 SNPs as the major drivers of this change in correlation. As long as ancestry-related bias when using these clinical databases is minimally recognized, the genetics community will face challenges with implementation, interpretation and cost-effectiveness when treating minority populations. PMID:27725664

Guidelines for Assessment of Gait and Reference Values for Spatiotemporal Gait Parameters in Older Adults: The Biomathics and Canadian Gait Consortiums Initiative

PubMed Central

Beauchet, Olivier; Allali, Gilles; Sekhon, Harmehr; Verghese, Joe; Guilain, Sylvie; Steinmetz, Jean-Paul; Kressig, Reto W.; Barden, John M.; Szturm, Tony; Launay, Cyrille P.; Grenier, Sébastien; Bherer, Louis; Liu-Ambrose, Teresa; Chester, Vicky L.; Callisaya, Michele L.; Srikanth, Velandai; Léonard, Guillaume; De Cock, Anne-Marie; Sawa, Ryuichi; Duque, Gustavo; Camicioli, Richard; Helbostad, Jorunn L.

2017-01-01

Background: Gait disorders, a highly prevalent condition in older adults, are associated with several adverse health consequences. Gait analysis allows qualitative and quantitative assessments of gait that improves the understanding of mechanisms of gait disorders and the choice of interventions. This manuscript aims (1) to give consensus guidance for clinical and spatiotemporal gait analysis based on the recorded footfalls in older adults aged 65 years and over, and (2) to provide reference values for spatiotemporal gait parameters based on the recorded footfalls in healthy older adults free of cognitive impairment and multi-morbidities. Methods: International experts working in a network of two different consortiums (i.e., Biomathics and Canadian Gait Consortium) participated in this initiative. First, they identified items of standardized information following the usual procedure of formulation of consensus findings. Second, they merged databases including spatiotemporal gait assessments with GAITRite® system and clinical information from the “Gait, cOgnitiOn & Decline” (GOOD) initiative and the Generation 100 (Gen 100) study. Only healthy—free of cognitive impairment and multi-morbidities (i.e., ≤ 3 therapeutics taken daily)—participants aged 65 and older were selected. Age, sex, body mass index, mean values, and coefficients of variation (CoV) of gait parameters were used for the analyses. Results: Standardized systematic assessment of three categories of items, which were demographics and clinical information, and gait characteristics (clinical and spatiotemporal gait analysis based on the recorded footfalls), were selected for the proposed guidelines. Two complementary sets of items were distinguished: a minimal data set and a full data set. In addition, a total of 954 participants (mean age 72.8 ± 4.8 years, 45.8% women) were recruited to establish the reference values. Performance of spatiotemporal gait parameters based on the recorded footfalls declined with increasing age (mean values and CoV) and demonstrated sex differences (mean values). Conclusions: Based on an international multicenter collaboration, we propose consensus guidelines for gait assessment and spatiotemporal gait analysis based on the recorded footfalls, and reference values for healthy older adults. PMID:28824393

Clinicians' experiences with the fragile X clinical and research consortium.

PubMed

Liu, Jessica A; Hagerman, Randi J; Miller, Robert M; Craft, Lisa T; Finucane, Brenda; Tartaglia, Nicole; Berry-Kravis, Elizabeth M; Sherman, Stephanie L; Kidd, Sharon A; Cohen, Jeffrey

2016-12-01

The objectives of the study were to assess the attitudes and experiences of clinicians involved in a consortium of clinics serving people with fragile X-associated disorders to gauge satisfaction with the consortium and its efforts to improve quality of life for patients and the community. An internet survey was sent to 26 fragile X (FX) clinic directors participating in the Fragile X Clinical and Research Consortium (FXCRC). Respondents were asked to complete 19 questions on consortium performance and outcomes relevant for their own clinic. The response rate was 84% (22/26), with two surveys providing incomplete data. Assistance with clinic establishment, opportunities for research collaborations, and access to colleagues and information were highly valued. Approximately 76% of clinicians reported improvements in patient care and 60% reported an increase in patient services. There was a 57% increase in participation in a FX-related clinical trial among clinics since joining the FXCRC (24% vs. 81%). Overall, respondents reported primarily positive experiences from participation in the FXCRC. Common suggestions for improvement included additional financial support and increased utilization of collected patient data for research purposes. Additionally, a Clinic Services Checklist was administered annually to examine changes in services offered over time. There were several important changes regarding the provision of services by clinics, often with multiple clinics changing with respect to a service. In conclusion, the FXCRC has led to the establishment and sustainment of fragile X clinics in the U.S., fostered cooperation among fragile X clinicians, and provided clinics with a platform to share recommendations and best practices to maximize quality of life for their patients and the overall fragile X community. The results from the survey and checklist also provide suggestions to strengthen the FXCRC and enhance future collaborations among FXCRC members. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Establishing a Consortium for the Study of Rare Diseases: The Urea Cycle Disorders Consortium

PubMed Central

Seminara, Jennifer; Tuchman, Mendel; Krivitzky, Lauren; Krischer, Jeffrey; Lee, Hye-Seung; LeMons, Cynthia; Baumgartner, Matthias; Cederbaum, Stephen; Diaz, George A.; Feigenbaum, Annette; Gallagher, Renata C.; Harding, Cary O.; Kerr, Douglas S.; Lanpher, Brendan; Lee, Brendan; Lichter-Konecki, Uta; McCandless, Shawn E.; Merritt, J. Lawrence; Oster-Granite, Mary Lou; Seashore, Margretta R.; Stricker, Tamar; Summar, Marshall; Waisbren, Susan; Yudkoff, Marc; Batshaw, Mark L.

2010-01-01

The Urea Cycle Disorders Consortium (UCDC) was created as part of a larger network established by the National Institutes of Health to study rare diseases. This paper reviews the UCDC’s accomplishments over the first six years, including how the Consortium was developed and organized, clinical research studies initiated, and the importance of creating partnerships with patient advocacy groups, philanthropic foundations and biotech and pharmaceutical companies. PMID:20188616

Types of Seizures Affecting Individuals with TSC

MedlinePlus

... Find Local Resources Publications Webinars and Videos Biosample Repository Patient-Focused Drug Development Learn Engage Donate Healthcare ... and Funding Preclinical Research Natural History Database Biosample ... Research Consortium Research Conferences Research Resources International ...

Completion of the 2011 National Land Cover Database for the conterminous United States – Representing a decade of land cover change information

USGS Publications Warehouse

Homer, Collin G.; Dewitz, Jon; Yang, Limin; Jin, Suming; Danielson, Patrick; Xian, George Z.; Coulston, John; Herold, Nathaniel; Wickham, James; Megown, Kevin

2015-01-01

The National Land Cover Database (NLCD) provides nationwide data on land cover and land cover change at the native 30-m spatial resolution of the Landsat Thematic Mapper (TM). The database is designed to provide five-year cyclical updating of United States land cover and associated changes. The recent release of NLCD 2011 products now represents a decade of consistently produced land cover and impervious surface for the Nation across three periods: 2001, 2006, and 2011 (Homer et al., 2007; Fry et al., 2011). Tree canopy cover has also been produced for 2011 (Coluston et al., 2012; Coluston et al., 2013). With the release of NLCD 2011, the database provides the ability to move beyond simple change detection to monitoring and trend assessments. NLCD 2011 represents the latest evolution of NLCD products, continuing its focus on consistency, production, efficiency, and product accuracy. NLCD products are designed for widespread application in biology, climate, education, land management, hydrology, environmental planning, risk and disease analysis, telecommunications and visualization, and are available for no cost at http://www.mrlc.gov. NLCD is produced by a Federal agency consortium called the Multi-Resolution Land Characteristics Consortium (MRLC) (Wickham et al., 2014). In the consortium arrangement, the U.S. Geological Survey (USGS) leads NLCD land cover and imperviousness production for the bulk of the Nation; the National Oceanic and Atmospheric Administration (NOAA) completes NLCD land cover for the conterminous U.S. (CONUS) coastal zones; and the U.S. Forest Service (USFS) designs and produces the NLCD tree canopy cover product. Other MRLC partners collaborate through resource or data contribution to ensure NLCD products meet their respective program needs (Wickham et al., 2014).

Microsoft Enterprise Consortium: A Resource for Teaching Data Warehouse, Business Intelligence and Database Management Systems

ERIC Educational Resources Information Center

Kreie, Jennifer; Hashemi, Shohreh

2012-01-01

Data is a vital resource for businesses; therefore, it is important for businesses to manage and use their data effectively. Because of this, businesses value college graduates with an understanding of and hands-on experience working with databases, data warehouses and data analysis theories and tools. Faculty in many business disciplines try to…

A 30-meter spatial database for the nation's forests

Treesearch

Raymond L. Czaplewski

2002-01-01

The FIA vision for remote sensing originated in 1992 with the Blue Ribbon Panel on FIA, and it has since evolved into an ambitious performance target for 2003. FIA is joining a consortium of Federal agencies to map the Nation's land cover. FIA field data will help produce a seamless, standardized, national geospatial database for forests at the scale of 30-m...

Medical informatics in medical research - the Severe Malaria in African Children (SMAC) Network's experience.

PubMed

Olola, C H O; Missinou, M A; Issifou, S; Anane-Sarpong, E; Abubakar, I; Gandi, J N; Chagomerana, M; Pinder, M; Agbenyega, T; Kremsner, P G; Newton, C R J C; Wypij, D; Taylor, T E

2006-01-01

Computers are widely used for data management in clinical trials in the developed countries, unlike in developing countries. Dependable systems are vital for data management, and medical decision making in clinical research. Monitoring and evaluation of data management is critical. In this paper we describe database structures and procedures of systems used to implement, coordinate, and sustain data management in Africa. We outline major lessons, challenges and successes achieved, and recommendations to improve medical informatics application in biomedical research in sub-Saharan Africa. A consortium of experienced research units at five sites in Africa in studying children with disease formed a new clinical trials network, Severe Malaria in African Children. In December 2000, the network introduced an observational study involving these hospital-based sites. After prototyping, relational database management systems were implemented for data entry and verification, data submission and quality assurance monitoring. Between 2000 and 2005, 25,858 patients were enrolled. Failure to meet data submission deadline and data entry errors correlated positively (correlation coefficient, r = 0.82), with more errors occurring when data was submitted late. Data submission lateness correlated inversely with hospital admissions (r = -0.62). Developing and sustaining dependable DBMS, ongoing modifications to optimize data management is crucial for clinical studies. Monitoring and communication systems are vital in multi-center networks for good data management. Data timeliness is associated with data quality and hospital admissions.

The Blue Cross Blue Shield of Michigan Cardiovascular Consortium (BMC2) collaborative quality improvement initiative in percutaneous coronary interventions.

PubMed

Moscucci, Mauro; Share, David; Kline-Rogers, Eva; O'Donnell, Michael; Maxwell-Eward, Ann; Meengs, William L; Clark, Vivian L; Kraft, Phillip; De Franco, Anthony C; Chambers, James L; Patel, Kirit; McGinnity, John G; Eagle, Kim A

2002-10-01

The past decade has been characterized by increased scrutiny of outcomes of surgical and percutaneous coronary interventions (PCIs). This increased scrutiny has led to the development of regional, state, and national databases for outcome assessment and for public reporting. This report describes the initial development of a regional, collaborative, cardiovascular consortium and the progress made so far by this collaborative group. In 1997, a group of hospitals in the state Michigan agreed to create a regional collaborative consortium for the development of a quality improvement program in interventional cardiology. The project included the creation of a comprehensive database of PCIs to be used for risk assessment, feedback on absolute and risk-adjusted outcomes, and sharing of information. To date, information from nearly 20,000 PCIs have been collected. A risk prediction tool for death in the hospital and additional risk prediction tools for other outcomes have been developed from the data collected, and are currently used by the participating centers for risk assessment and for quality improvement. As the project enters into year 5, the participating centers are deeply engaged in the quality improvement phase, and expansion to a total of 17 hospitals with active PCI programs is in process. In conclusion, the Blue Cross Blue Shield of Michigan Cardiovascular Consortium is an example of a regional collaborative effort to assess and improve quality of care and outcomes that overcome the barriers of traditional market and academic competition.

Standardized End Point Definitions for Coronary Intervention Trials: The Academic Research Consortium-2 Consensus Document.

PubMed

Garcia-Garcia, Hector M; McFadden, Eugène P; Farb, Andrew; Mehran, Roxana; Stone, Gregg W; Spertus, John; Onuma, Yoshinobu; Morel, Marie-Angèle; van Es, Gerrit-Anne; Zuckerman, Bram; Fearon, William F; Taggart, David; Kappetein, Arie-Pieter; Krucoff, Mitchell W; Vranckx, Pascal; Windecker, Stephan; Cutlip, Donald; Serruys, Patrick W

2018-06-14

The Academic Research Consortium (ARC)-2 initiative revisited the clinical and angiographic end point definitions in coronary device trials, proposed in 2007, to make them more suitable for use in clinical trials that include increasingly complex lesion and patient populations and incorporate novel devices such as bioresorbable vascular scaffolds. In addition, recommendations for the incorporation of patient-related outcomes in clinical trials are proposed. Academic Research Consortium-2 is a collaborative effort between academic research organizations in the United States and Europe, device manufacturers, and European, US, and Asian regulatory bodies. Several in-person meetings were held to discuss the changes that have occurred in the device landscape and in clinical trials and regulatory pathways in the last decade. The consensus-based end point definitions in this document are endorsed by the stakeholders of this document and strongly advocated for clinical trial purposes. This Academic Research Consortium-2 document provides further standardization of end point definitions for coronary device trials, incorporating advances in technology and knowledge. Their use will aid interpretation of trial outcomes and comparison among studies, thus facilitating the evaluation of the safety and effectiveness of these devices.

NCI Pediatric Preclinical Testing Consortium

Cancer.gov

NCI has awarded grants to five research teams to participate in its Pediatric Preclinical Testing Consortium, which is intended to help to prioritize which agents to pursue in pediatric clinical trials.

A Four-Dimensional Probabilistic Atlas of the Human Brain

PubMed Central

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

Targeted mutation screening panels expose systematic population bias in detection of cystic fibrosis risk.

PubMed

Lim, Regine M; Silver, Ari J; Silver, Maxwell J; Borroto, Carlos; Spurrier, Brett; Petrossian, Tanya C; Larson, Jessica L; Silver, Lee M

2016-02-01

Carrier screening for mutations contributing to cystic fibrosis (CF) is typically accomplished with panels composed of variants that are clinically validated primarily in patients of European descent. This approach has created a static genetic and phenotypic profile for CF. An opportunity now exists to reevaluate the disease profile of CFTR at a global population level. CFTR allele and genotype frequencies were obtained from a nonpatient cohort with more than 60,000 unrelated personal genomes collected by the Exome Aggregation Consortium. Likely disease-contributing mutations were identified with the use of public database annotations and computational tools. We identified 131 previously described and likely pathogenic variants and another 210 untested variants with a high probability of causing protein damage. None of the current genetic screening panels or existing CFTR mutation databases covered a majority of deleterious variants in any geographical population outside of Europe. Both clinical annotation and mutation coverage by commercially available targeted screening panels for CF are strongly biased toward detection of reproductive risk in persons of European descent. South and East Asian populations are severely underrepresented, in part because of a definition of disease that preferences the phenotype associated with European-typical CFTR alleles.

The MRI-Linear Accelerator Consortium: Evidence-Based Clinical Introduction of an Innovation in Radiation Oncology Connecting Researchers, Methodology, Data Collection, Quality Assurance, and Technical Development.

PubMed

Kerkmeijer, Linda G W; Fuller, Clifton D; Verkooijen, Helena M; Verheij, Marcel; Choudhury, Ananya; Harrington, Kevin J; Schultz, Chris; Sahgal, Arjun; Frank, Steven J; Goldwein, Joel; Brown, Kevin J; Minsky, Bruce D; van Vulpen, Marco

2016-01-01

An international research consortium has been formed to facilitate evidence-based introduction of MR-guided radiotherapy (MR-linac) and to address how the MR-linac could be used to achieve an optimized radiation treatment approach to improve patients' survival, local, and regional tumor control and quality of life. The present paper describes the organizational structure of the clinical part of the MR-linac consortium. Furthermore, it elucidates why collaboration on this large project is necessary, and how a central data registry program will be implemented.

National Maternal and Child Oral Health Resource Center

MedlinePlus

... the Organizations Database Center for Oral Health Systems Integration and Improvement (COHSII) COHSII is a consortium promoting ... to e-mail lists Featured Resources Consensus Statement Integration Framework Bright Futures Pocket Guide Consumer Materials Special ...

Construction of 3-D Earth Models for Station Specific Path Corrections by Dynamic Ray Tracing

DTIC Science & Technology

2001-10-01

the numerical eikonal solution method of Vidale (1988) being used by the MIT led consortium. The model construction described in this report relies...assembled. REFERENCES Barazangi, M., Fielding, E., Isacks, B. & Seber, D., (1996), Geophysical And Geological Databases And Ctbt...preprint download6). Fielding, E., Isacks, B.L., and Baragangi. M. (1992), A Network Accessible Geological and Geophysical Database for

International Cancer Proteogenome Consortium | Office of Cancer Clinical Proteomics Research

Cancer.gov

The International Cancer Proteogenome Consortium (ICPC), is a voluntary scientific organization that provides a forum for collaboration among some of the world's leading cancer and proteogenomic research centers.

Clinical Trial Principles and Endpoint Definitions for Paravalvular Leaks in Surgical Prosthesis: An Expert Statement.

PubMed

Ruiz, Carlos E; Hahn, Rebecca T; Berrebi, Alain; Borer, Jeffrey S; Cutlip, Donald E; Fontana, Greg; Gerosa, Gino; Ibrahim, Reda; Jelnin, Vladimir; Jilaihawi, Hasan; Jolicoeur, E Marc; Kliger, Chad; Kronzon, Itzhak; Leipsic, Jonathon; Maisano, Francesco; Millan, Xavier; Nataf, Patrick; O'Gara, Patrick T; Pibarot, Philippe; Ramee, Stephen R; Rihal, Charanjit S; Rodes-Cabau, Josep; Sorajja, Paul; Suri, Rakesh; Swain, Julie A; Turi, Zoltan G; Tuzcu, E Murat; Weissman, Neil J; Zamorano, Jose L; Serruys, Patrick W; Leon, Martin B

2017-04-25

The VARC (Valve Academic Research Consortium) for transcatheter aortic valve replacement set the standard for selecting appropriate clinical endpoints reflecting safety and effectiveness of transcatheter devices, and defining single and composite clinical endpoints for clinical trials. No such standardization exists for circumferentially sutured surgical valve paravalvular leak (PVL) closure. This document seeks to provide core principles, appropriate clinical endpoints, and endpoint definitions to be used in clinical trials of PVL closure devices. The PVL Academic Research Consortium met to review evidence and make recommendations for assessment of disease severity, data collection, and updated endpoint definitions. A 5-class grading scheme to evaluate PVL was developed in concordance with VARC recommendations. Unresolved issues in the field are outlined. The current PVL Academic Research Consortium provides recommendations for assessment of disease severity, data collection, and endpoint definitions. Future research in the field is warranted. Copyright © 2017 American College of Cardiology Foundation and European Society of Cardiology. Published by Elsevier Inc. All rights reserved.

The clinical implications of immunogenomics in colorectal cancer: A path for precision medicine.

PubMed

Riley, Jenny M; Cross, Ashley W; Paulos, Chrystal M; Rubinstein, Mark P; Wrangle, John; Camp, E Ramsay

2018-04-15

Colorectal cancer (CRC) remains the third most common malignancy and the second-leading cause of cancer-related deaths in the United States. Large multi-omic databases, such as The Cancer Genome Atlas and the International Colorectal Cancer Subtyping Consortium, have identified distinct molecular subtypes related to anatomy. The identification of genomic alterations in CRC is now critical because of the recent success and US Food and Drug Administration approval of pembrolizumab and nivolumab for microsatellite-instable tumors. In parallel, landmark studies have established the prognostic significance of the CRC tumor-infiltrating lymphocyte and the clinical impact of the tumor immune microenvironment. As a result, there is a growing appreciation for immunogenomics, the interconnected relation between tumor genomics and the immune microenvironment. The clinical implications of CRC immunogenomics continue to expand, and it will likely serve as a guide for next-generation immunotherapy strategies for improving outcomes for this disease. Cancer 2018;124:1650-9. © 2018 American Cancer Society. © 2018 American Cancer Society.

Improvements to the Magnetics Information Consortium (MagIC) Paleo and Rock Magnetic Database

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Tauxe, L.; Koppers, A. A. P.; Constable, C.; Jonestrask, L.

2015-12-01

The Magnetic Information Consortium (MagIC) database (http://earthref.org/MagIC/) continues to improve the ease of data uploading and editing, the creation of complex searches, data visualization, and data downloads for the paleomagnetic, geomagnetic, and rock magnetic communities. Online data editing is now available and the need for proprietary spreadsheet software is therefore entirely negated. The data owner can change values in the database or delete entries through an HTML 5 web interface that resembles typical spreadsheets in behavior and uses. Additive uploading now allows for additions to data sets to be uploaded with a simple drag and drop interface. Searching the database has improved with the addition of more sophisticated search parameters and with the facility to use them in complex combinations. A comprehensive summary view of a search result has been added for increased quick data comprehension while a raw data view is available if one desires to see all data columns as stored in the database. Data visualization plots (ARAI, equal area, demagnetization, Zijderveld, etc.) are presented with the data when appropriate to aid the user in understanding the dataset. MagIC data associated with individual contributions or from online searches may be downloaded in the tab delimited MagIC text file format for susbsequent offline use and analysis. With input from the paleomagnetic, geomagnetic, and rock magnetic communities, the MagIC database will continue to improve as a data warehouse and resource.

A New Interface for the Magnetics Information Consortium (MagIC) Paleo and Rock Magnetic Database

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Koppers, A. A. P.; Tauxe, L.; Constable, C.; Shaar, R.; Jonestrask, L.

2014-12-01

The Magnetic Information Consortium (MagIC) database (http://earthref.org/MagIC/) continues to improve the ease of uploading data, the creation of complex searches, data visualization, and data downloads for the paleomagnetic, geomagnetic, and rock magnetic communities. Data uploading has been simplified and no longer requires the use of the Excel SmartBook interface. Instead, properly formatted MagIC text files can be dragged-and-dropped onto an HTML 5 web interface. Data can be uploaded one table at a time to facilitate ease of uploading and data error checking is done online on the whole dataset at once instead of incrementally in an Excel Console. Searching the database has improved with the addition of more sophisticated search parameters and with the ability to use them in complex combinations. Searches may also be saved as permanent URLs for easy reference or for use as a citation in a publication. Data visualization plots (ARAI, equal area, demagnetization, Zijderveld, etc.) are presented with the data when appropriate to aid the user in understanding the dataset. Data from the MagIC database may be downloaded from individual contributions or from online searches for offline use and analysis in the tab delimited MagIC text file format. With input from the paleomagnetic, geomagnetic, and rock magnetic communities, the MagIC database will continue to improve as a data warehouse and resource.

Clinical assessment of acute lateral ankle sprain injuries (ROAST): 2019 consensus statement and recommendations of the International Ankle Consortium.

PubMed

Delahunt, Eamonn; Bleakley, Chris M; Bossard, Daniela S; Caulfield, Brian M; Docherty, Carrie L; Doherty, Cailbhe; Fourchet, François; Fong, Daniel T; Hertel, Jay; Hiller, Claire E; Kaminski, Thomas W; McKeon, Patrick O; Refshauge, Kathryn M; Remus, Alexandria; Verhagen, Evert; Vicenzino, Bill T; Wikstrom, Erik A; Gribble, Phillip A

2018-06-09

Lateral ankle sprain injury is the most common musculoskeletal injury incurred by individuals who participate in sports and recreational physical activities. Following initial injury, a high proportion of individuals develop long-term injury-associated symptoms and chronic ankle instability. The development of chronic ankle instability is consequent on the interaction of mechanical and sensorimotor insufficiencies/impairments that manifest following acute lateral ankle sprain injury. To reduce the propensity for developing chronic ankle instability, clinical assessments should evaluate whether patients in the acute phase following lateral ankle sprain injury exhibit any mechanical and/or sensorimotor impairments. This modified Delphi study was undertaken under the auspices of the executive committee of the International Ankle Consortium. The primary aim was to develop recommendations, based on expert (n=14) consensus, for structured clinical assessment of acute lateral ankle sprain injuries. After two modified Delphi rounds, consensus was achieved on the clinical assessment of acute lateral ankle sprain injuries. Consensus was reached on a minimum standard clinical diagnostic assessment. Key components of this clinical diagnostic assessment include: establishing the mechanism of injury, as well as the assessment of ankle joint bones and ligaments. Through consensus, the expert panel also developed the International Ankle Consortium Rehabilitation-Oriented ASsessmenT (ROAST). The International Ankle Consortium ROAST will help clinicians identify mechanical and/or sensorimotor impairments that are associated with chronic ankle instability. This consensus statement from the International Ankle Consortium aims to be a key resource for clinicians who regularly assess individuals with acute lateral ankle sprain injuries. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Standardized End Point Definitions for Coronary Intervention Trials: The Academic Research Consortium-2 Consensus Document.

PubMed

Garcia-Garcia, Hector M; McFadden, Eugène P; Farb, Andrew; Mehran, Roxana; Stone, Gregg W; Spertus, John; Onuma, Yoshinobu; Morel, Marie-Angèle; van Es, Gerrit-Anne; Zuckerman, Bram; Fearon, William F; Taggart, David; Kappetein, Arie-Pieter; Krucoff, Mitchell W; Vranckx, Pascal; Windecker, Stephan; Cutlip, Donald; Serruys, Patrick W

2018-06-12

The Academic Research Consortium (ARC)-2 initiative revisited the clinical and angiographic end point definitions in coronary device trials, proposed in 2007, to make them more suitable for use in clinical trials that include increasingly complex lesion and patient populations and incorporate novel devices such as bioresorbable vascular scaffolds. In addition, recommendations for the incorporation of patient-related outcomes in clinical trials are proposed. Academic Research Consortium-2 is a collaborative effort between academic research organizations in the United States and Europe, device manufacturers, and European, US, and Asian regulatory bodies. Several in-person meetings were held to discuss the changes that have occurred in the device landscape and in clinical trials and regulatory pathways in the last decade. The consensus-based end point definitions in this document are endorsed by the stakeholders of this document and strongly advocated for clinical trial purposes. This Academic Research Consortium-2 document provides further standardization of end point definitions for coronary device trials, incorporating advances in technology and knowledge. Their use will aid interpretation of trial outcomes and comparison among studies, thus facilitating the evaluation of the safety and effectiveness of these devices. © 2018 American Heart Association, Inc., and European Society of Cardiology.

The pediatric diabetes consortium: improving care of children with type 1 diabetes through collaborative research.

PubMed

2010-09-01

Although there are some interactions between the major pediatric diabetes programs in the United States, there has been no formal, independent structure for collaboration, the sharing of information, and the development of joint research projects that utilize common outcome measures. To fill this unmet clinical and research need, a consortium of seven pediatric diabetes centers in the United States has formed the Pediatric Diabetes Consortium (PDC) through an unrestricted grant from Novo Nordisk, Inc. (Princeton, NJ). This article describes the organizational structure of the PDC and the design of a study of important clinical outcomes in children and adolescents with new-onset, type 1 diabetes mellitus (T1DM). The outcomes study will describe the changes in A1c levels, the frequency of adverse events (diabetic ketoacidosis/severe hypoglycemia), and the frequency and timing of the "honeymoon" phase in newly diagnosed patients with T1DM over the first 12-24 months of the disease and examine the relationship between these clinical outcomes and demographic, socioeconomic, and treatment factors. This project will also allow the Consortium to develop a cohort of youth with T1DM whose clinical course has been well characterized and who wish to participate in future clinical trials and/or contribute to a repository of biological samples.

University of Washington Prostate Cancer Clinical Trials Consortium Application

DTIC Science & Technology

2011-04-01

13-25 Appendix 1: Protocol Evaluation Form Appendix 2: Community Symposia Flyer Appendix 3: Publications...Network Affiliate partners in the community . These and selected local practices receive quarterly correspondence that reviews our open clinical...studies: 09-002 (COU 301), 09-003 (AFFIRM), 09-004 (S0421), 09-005 (COU 302), 09-006 (doc dasatinib). Task 3. Maintain Communications with Consortium

Forest service contributions to the national land cover database (NLCD): Tree Canopy Cover Production

Treesearch

Bonnie Ruefenacht; Robert Benton; Vicky Johnson; Tanushree Biswas; Craig Baker; Mark Finco; Kevin Megown; John Coulston; Ken Winterberger; Mark Riley

2015-01-01

A tree canopy cover (TCC) layer is one of three elements in the National Land Cover Database (NLCD) 2011 suite of nationwide geospatial data layers. In 2010, the USDA Forest Service (USFS) committed to creating the TCC layer as a member of the Multi-Resolution Land Cover (MRLC) consortium. A general methodology for creating the TCC layer was reported at the 2012 FIA...

RNAcentral: an international database of ncRNA sequences

DOE PAGES

Williams, Kelly Porter

2014-10-28

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

Duchenne Regulatory Science Consortium Meeting on Disease Progression Modeling for Duchenne Muscular Dystrophy.

PubMed

Larkindale, Jane; Abresch, Richard; Aviles, Enrique; Bronson, Abby; Chin, Janice; Furlong, Pat; Gordish-Dressman, Heather; Habeeb-Louks, Elizabeth; Henricson, Erik; Kroger, Hans; Lynn, Charles; Lynn, Stephen; Martin, Dana; Nuckolls, Glen; Rooney, William; Romero, Klaus; Sweeney, Lee; Vandenborne, Krista; Walter, Glenn; Wolff, Jodi; Wong, Brenda; McDonald, Craig M; Duchenne Regulatory Science Consortium Imaging-Dmd Consortium And The Cinrg Investigators, Members Of The

2017-01-12

The Duchenne Regulatory Science Consortium (D-RSC) was established to develop tools to accelerate drug development for DMD.  The resulting tools are anticipated to meet validity requirements outlined by qualification/endorsement pathways at both the U.S. Food and Drug Administration (FDA) and European Medicines Administration (EMA), and will be made available to the drug development community. The initial goals of the consortium include the development of a disease progression model, with the goal of creating a model that would be used to forecast changes in clinically meaningful endpoints, which would inform clinical trial protocol development and data analysis.  Methods: In April of 2016 the consortium and other experts met to formulate plans for the development of the model.  Conclusions: Here we report the results of the meeting, and discussion as to the form of the model that we plan to move forward to develop, after input from the regulatory authorities.

CPTAC Launches Proteomics Data Portal | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) announces the launch of the CPTAC Data Portal. The Data Portal hosts all the data that is currently being produced by the consortium with additional historic data from CPTAC 1. The total amount of hosted data exceeds over 500 GB of RAW data in over 800 files.

LinkedOmics: analyzing multi-omics data within and across 32 cancer types.

PubMed

Vasaikar, Suhas V; Straub, Peter; Wang, Jing; Zhang, Bing

2018-01-04

The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. Using five case studies, we demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. LinkedOmics is freely available at http://www.linkedomics.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Residency training in physiatry during a time of change: funding of graduate medical education and other issues.

PubMed

DeLisa, J A; Jain, S S; Kirshblum, S

1998-01-01

Decision makers at the federal and state level are considering, and some states have enacted, a reduction in total United States residency positions, a shift in emphasis from specialist to generalist training, a need for programs to join together in training consortia to determine local residency position allocation strategy, a reduction in funding of international medical graduates, and a reduction in funding beyond the first certificate or a total of five years. A 5-page, 24-item questionnaire was sent to all physiatry residency training directors. The objective was to discern a descriptive database of physiatry training programs and how their institutions might respond to cuts in graduate medical education funding. Fifty-eight (73%) of the questionnaires were returned. Most training directors believe that their primary mission is to train general physiatrists and, to a much lesser extent, to train subspecialty or research fellows. Directors were asked how they might handle reductions in house staff such as using physician extenders, shifting clinical workload to faculty, hiring additional faculty, and funding physiatry residents from practice plans and endowments. Physiatry has had little experience (29%; 17/58) with voluntary graduate medical education consortiums, but most (67%; 34/58) seem to feel that if a consortium system is mandated, they would favor a local or regional over a national body because they do not believe the specialty has a strong enough national stature. The major barriers to a consortium for graduate medical education allocation were governance, academic, fiscal, bureaucratic, and competition.

Cohort profile: the Finnish Genetics of Pre-eclampsia Consortium (FINNPEC).

PubMed

Jääskeläinen, Tiina; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Kivinen, Katja; Pouta, Anneli; Laivuori, Hannele

2016-11-10

The Finnish Genetics of Pre-eclampsia Consortium (FINNPEC) Study was established to set up a nationwide clinical and DNA database on women with and without pre-eclampsia (PE), including their partners and infants, in order to identify genetic risk factors for PE. FINNPEC is a cross-sectional case-control cohort collected from 5 university hospitals in Finland during 2008-2011. A total of 1450 patients with PE and 1065 pregnant control women without PE (aged 18-47 years) were recruited. Altogether, there were 1377 full triads (625 PE and 752 control triads). The established cohort holds both clinical and genetic information of mother-infant-father triads representing a valuable resource for studying the pathogenesis of the disease. Furthermore, maternal biological samples (first and third trimester serum and placenta) will provide additional information for PE research. Until now, research has encompassed studies on candidate genes, Sanger and next-generation sequencing, and various studies on the placenta. FINNPEC has also participated in the InterPregGen study, which is the largest investigation on maternal and fetal genetic factors underlying PE until now. Ongoing studies focus on elucidating the role of immunogenetic and metabolic factors in PE. Data on morbidity and mortality will be collected from mothers and fathers through links to the nationwide health registers. 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/.

A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)

PubMed Central

Patel, Ashokkumar A.; Gilbertson, John R.; Showe, Louise C.; London, Jack W.; Ross, Eric; Ochs, Michael F.; Carver, Joseph; Lazarus, Andrea; Parwani, Anil V.; Dhir, Rajiv; Beck, J. Robert; Liebman, Michael; Garcia, Fernando U.; Prichard, Jeff; Wilkerson, Myra; Herberman, Ronald B.; Becich, Michael J.

2007-01-01

Background: The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu) is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1) for bioinformatics and a repository of serum and tissue samples; (2) a data model for biomarker data storage; and (3) a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium’s intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancer-specific biomarkers and encourage collaborative research efforts among the participating centers. Methods: The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission. The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual property/tech transfer agreements, and material transfer agreements that have been approved by each of the member institutions. This was the foundational work that has led to the development of a centralized data warehouse that has met each of the institutions’ IRB/HIPAA standards. Results: Currently, this “virtual biorepository” has over 58,000 annotated samples from 11,467 cancer patients available for research purposes. The clinical annotation of tissue samples is either done manually over the internet or semi-automated batch modes through mapping of local data elements with PCABC common data elements. The database currently holds information on 7188 cases (associated with 9278 specimens and 46,666 annotated blocks and blood samples) of prostate cancer, 2736 cases (associated with 3796 specimens and 9336 annotated blocks and blood samples) of breast cancer and 1543 cases (including 1334 specimens and 2671 annotated blocks and blood samples) of melanoma. These numbers continue to grow, and plans to integrate new tumor sites are in progress. Furthermore, the group has also developed a central web-based tool that allows investigators to share their translational (genomics/proteomics) experiment data on research evaluating potential biomarkers via a central location on the Consortium’s web site. Conclusions: The technological achievements and the statewide informatics infrastructure that have been established by the Consortium will enable robust and efficient studies of biomarkers and their relevance to the clinical course of cancer. Studies resulting from the creation of the Consortium may allow for better classification of cancer types, more accurate assessment of disease prognosis, a better ability to identify the most appropriate individuals for clinical trial participation, and better surrogate markers of disease progression and/or response to therapy. PMID:19455246

Glocal clinical registries: pacemaker registry design and implementation for global and local integration--methodology and case study.

PubMed

da Silva, Kátia Regina; Costa, Roberto; Crevelari, Elizabeth Sartori; Lacerda, Marianna Sobral; de Moraes Albertini, Caio Marcos; Filho, Martino Martinelli; Santana, José Eduardo; Vissoci, João Ricardo Nickenig; Pietrobon, Ricardo; Barros, Jacson V

2013-01-01

The ability to apply standard and interoperable solutions for implementing and managing medical registries as well as aggregate, reproduce, and access data sets from legacy formats and platforms to advanced standard formats and operating systems are crucial for both clinical healthcare and biomedical research settings. Our study describes a reproducible, highly scalable, standard framework for a device registry implementation addressing both local data quality components and global linking problems. We developed a device registry framework involving the following steps: (1) Data standards definition and representation of the research workflow, (2) Development of electronic case report forms using REDCap (Research Electronic Data Capture), (3) Data collection according to the clinical research workflow and, (4) Data augmentation by enriching the registry database with local electronic health records, governmental database and linked open data collections, (5) Data quality control and (6) Data dissemination through the registry Web site. Our registry adopted all applicable standardized data elements proposed by American College Cardiology / American Heart Association Clinical Data Standards, as well as variables derived from cardiac devices randomized trials and Clinical Data Interchange Standards Consortium. Local interoperability was performed between REDCap and data derived from Electronic Health Record system. The original data set was also augmented by incorporating the reimbursed values paid by the Brazilian government during a hospitalization for pacemaker implantation. By linking our registry to the open data collection repository Linked Clinical Trials (LinkedCT) we found 130 clinical trials which are potentially correlated with our pacemaker registry. This study demonstrates how standard and reproducible solutions can be applied in the implementation of medical registries to constitute a re-usable framework. Such approach has the potential to facilitate data integration between healthcare and research settings, also being a useful framework to be used in other biomedical registries.

Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for Pharmacogenetics-Guided Warfarin Dosing: 2017 Update.

PubMed

Johnson, J A; Caudle, K E; Gong, L; Whirl-Carrillo, M; Stein, C M; Scott, S A; Lee, M T; Gage, B F; Kimmel, S E; Perera, M A; Anderson, J L; Pirmohamed, M; Klein, T E; Limdi, N A; Cavallari, L H; Wadelius, M

2017-09-01

This document is an update to the 2011 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2C9 and VKORC1 genotypes and warfarin dosing. Evidence from the published literature is presented for CYP2C9, VKORC1, CYP4F2, and rs12777823 genotype-guided warfarin dosing to achieve a target international normalized ratio of 2-3 when clinical genotype results are available. In addition, this updated guideline incorporates recommendations for adult and pediatric patients that are specific to continental ancestry. © 2017 American Society for Clinical Pharmacology and Therapeutics.

Developing consistent Landsat data sets for large area applications: the MRLC 2001 protocol

USGS Publications Warehouse

Chander, G.; Huang, Chengquan; Yang, Limin; Homer, Collin G.; Larson, C.

2009-01-01

One of the major efforts in large area land cover mapping over the last two decades was the completion of two U.S. National Land Cover Data sets (NLCD), developed with nominal 1992 and 2001 Landsat imagery under the auspices of the MultiResolution Land Characteristics (MRLC) Consortium. Following the successful generation of NLCD 1992, a second generation MRLC initiative was launched with two primary goals: (1) to develop a consistent Landsat imagery data set for the U.S. and (2) to develop a second generation National Land Cover Database (NLCD 2001). One of the key enhancements was the formulation of an image preprocessing protocol and implementation of a consistent image processing method. The core data set of the NLCD 2001 database consists of Landsat 7 Enhanced Thematic Mapper Plus (ETM+) images. This letter details the procedures for processing the original ETM+ images and more recent scenes added to the database. NLCD 2001 products include Anderson Level II land cover classes, percent tree canopy, and percent urban imperviousness at 30-m resolution derived from Landsat imagery. The products are freely available for download to the general public from the MRLC Consortium Web site at http://www.mrlc.gov.

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa

PubMed Central

Manasa, Justen; Lessells, Richard; Rossouw, Theresa; Naidu, Kevindra; Van Vuuren, Cloete; Goedhals, Dominique; van Zyl, Gert; Bester, Armand; Skingsley, Andrew; Stott, Katharine; Danaviah, Siva; Chetty, Terusha; Singh, Lavanya; Moodley, Pravi; Iwuji, Collins; McGrath, Nuala; Seebregts, Christopher J.; de Oliveira, Tulio

2014-01-01

Abstract Substantial amounts of data have been generated from patient management and academic exercises designed to better understand the human immunodeficiency virus (HIV) epidemic and design interventions to control it. A number of specialized databases have been designed to manage huge data sets from HIV cohort, vaccine, host genomic and drug resistance studies. Besides databases from cohort studies, most of the online databases contain limited curated data and are thus sequence repositories. HIV drug resistance has been shown to have a great potential to derail the progress made thus far through antiretroviral therapy. Thus, a lot of resources have been invested in generating drug resistance data for patient management and surveillance purposes. Unfortunately, most of the data currently available relate to subtype B even though >60% of the epidemic is caused by HIV-1 subtype C. A consortium of clinicians, scientists, public health experts and policy markers working in southern Africa came together and formed a network, the Southern African Treatment and Resistance Network (SATuRN), with the aim of increasing curated HIV-1 subtype C and tuberculosis drug resistance data. This article describes the HIV-1 data curation process using the SATuRN Rega database. The data curation is a manual and time-consuming process done by clinical, laboratory and data curation specialists. Access to the highly curated data sets is through applications that are reviewed by the SATuRN executive committee. Examples of research outputs from the analysis of the curated data include trends in the level of transmitted drug resistance in South Africa, analysis of the levels of acquired resistance among patients failing therapy and factors associated with the absence of genotypic evidence of drug resistance among patients failing therapy. All these studies have been important for informing first- and second-line therapy. This database is a free password-protected open source database available on www.bioafrica.net. Database URL: http://www.bioafrica.net/regadb/ PMID:24504151

Incorporating Neutrophil-to-lymphocyte Ratio and Platelet-to-lymphocyte Ratio in Place of Neutrophil Count and Platelet Count Improves Prognostic Accuracy of the International Metastatic Renal Cell Carcinoma Database Consortium Model

PubMed Central

Chrom, Pawel; Stec, Rafal; Bodnar, Lubomir; Szczylik, Cezary

2018-01-01

Purpose The study investigated whether a replacement of neutrophil count and platelet count by neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) within the International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) model would improve its prognostic accuracy. Materials and Methods This retrospective analysis included consecutive patients with metastatic renal cell carcinoma treated with first-line tyrosine kinase inhibitors. The IMDC and modified-IMDC models were compared using: concordance index (CI), bias-corrected concordance index (BCCI), calibration plots, the Grønnesby and Borgan test, Bayesian Information Criterion (BIC), generalized R2, Integrated Discrimination Improvement (IDI), and continuous Net Reclassification Index (cNRI) for individual risk factors and the three risk groups. Results Three hundred and twenty-one patients were eligible for analyses. The modified-IMDC model with NLR value of 3.6 and PLR value of 157 was selected for comparison with the IMDC model. Both models were well calibrated. All other measures favoured the modified-IMDC model over the IMDC model (CI, 0.706 vs. 0.677; BCCI, 0.699 vs. 0.671; BIC, 2,176.2 vs. 2,190.7; generalized R2, 0.238 vs. 0.202; IDI, 0.044; cNRI, 0.279 for individual risk factors; and CI, 0.669 vs. 0.641; BCCI, 0.669 vs. 0.641; BIC, 2,183.2 vs. 2,198.1; generalized R2, 0.163 vs. 0.123; IDI, 0.045; cNRI, 0.165 for the three risk groups). Conclusion Incorporation of NLR and PLR in place of neutrophil count and platelet count improved prognostic accuracy of the IMDC model. These findings require external validation before introducing into clinical practice. PMID:28253564

Incorporating Neutrophil-to-lymphocyte Ratio and Platelet-to-lymphocyte Ratio in Place of Neutrophil Count and Platelet Count Improves Prognostic Accuracy of the International Metastatic Renal Cell Carcinoma Database Consortium Model.

PubMed

Chrom, Pawel; Stec, Rafal; Bodnar, Lubomir; Szczylik, Cezary

2018-01-01

The study investigated whether a replacement of neutrophil count and platelet count by neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) within the International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) model would improve its prognostic accuracy. This retrospective analysis included consecutive patients with metastatic renal cell carcinoma treated with first-line tyrosine kinase inhibitors. The IMDC and modified-IMDC models were compared using: concordance index (CI), bias-corrected concordance index (BCCI), calibration plots, the Grønnesby and Borgan test, Bayesian Information Criterion (BIC), generalized R 2 , Integrated Discrimination Improvement (IDI), and continuous Net Reclassification Index (cNRI) for individual risk factors and the three risk groups. Three hundred and twenty-one patients were eligible for analyses. The modified-IMDC model with NLR value of 3.6 and PLR value of 157 was selected for comparison with the IMDC model. Both models were well calibrated. All other measures favoured the modified-IMDC model over the IMDC model (CI, 0.706 vs. 0.677; BCCI, 0.699 vs. 0.671; BIC, 2,176.2 vs. 2,190.7; generalized R 2 , 0.238 vs. 0.202; IDI, 0.044; cNRI, 0.279 for individual risk factors; and CI, 0.669 vs. 0.641; BCCI, 0.669 vs. 0.641; BIC, 2,183.2 vs. 2,198.1; generalized R 2 , 0.163 vs. 0.123; IDI, 0.045; cNRI, 0.165 for the three risk groups). Incorporation of NLR and PLR in place of neutrophil count and platelet count improved prognostic accuracy of the IMDC model. These findings require external validation before introducing into clinical practice.

A cross-sectional view of the current state of treatment of youth with type 2 diabetes in the USA: Enrollment data from the Pediatric Diabetes Consortium type 2 diabetes registry

USDA-ARS?s Scientific Manuscript database

To describe the clinical characteristics, treatment approaches, clinical outcomes, and co-morbidities of youth with type 2 diabetes (T2D) enrolled in the Pediatric Diabetes Consortium (PDC) T2D Registry. PDC enrolled 598 youth <21 yr of age with T2D from February 2012 to July 2015 at eight centers. ...

OPAC Missing Record Retrieval.

ERIC Educational Resources Information Center

Johnson, Karl E.

1996-01-01

When the Higher Education Library Information Network of Rhode Island transferred members' bibliographic data into a shared online public access catalog (OPAC), 10% of the University of Rhode Island's monograph records were missing. This article describes the consortium's attempts to retrieve records from the database and the effectiveness of…

Overview of the Inland California Translational Consortium

NASA Astrophysics Data System (ADS)

Malkas, Linda H.

2017-05-01

The mission of the Inland California Translational Consortium (ICTC), an independent research consortium comprising a unique hub of regional institutions (City of Hope [COH], California Institute of Technology [Caltech], Jet Propulsion Laboratory [JPL], University of California Riverside [UCR], and Claremont Colleges Keck Graduate Institute [KGI], is to institute a new paradigm within the academic culture to accelerate translation of innovative biomedical discoveries into clinical applications that positively affect human health and life. The ICTC actively supports clinical translational research as well as the implementation and advancement of novel education and training models for the translation of basic discoveries into workable products and practices that preserve and improve human health while training and educating at all levels of the workforce using innovative forward-thinking approaches.

Duchenne Regulatory Science Consortium Meeting on Disease Progression Modeling for Duchenne Muscular Dystrophy

PubMed Central

Larkindale, Jane; Abresch, Richard; Aviles, Enrique; Bronson, Abby; Chin, Janice; Furlong, Pat; Gordish-Dressman, Heather; Habeeb-Louks, Elizabeth; Henricson, Erik; Kroger, Hans; Lynn, Charles; Lynn, Stephen; Martin, Dana; Nuckolls, Glen; Rooney, William; Romero, Klaus; Sweeney, Lee; Vandenborne, Krista; Walter, Glenn; Wolff, Jodi; Wong, Brenda; McDonald, Craig M.; Duchenne Regulatory Science Consortium, Imaging-DMD Consortium and the CINRG Investigators, members of the

2017-01-01

Introduction: The Duchenne Regulatory Science Consortium (D-RSC) was established to develop tools to accelerate drug development for DMD.  The resulting tools are anticipated to meet validity requirements outlined by qualification/endorsement pathways at both the U.S. Food and Drug Administration (FDA) and European Medicines Administration (EMA), and will be made available to the drug development community. The initial goals of the consortium include the development of a disease progression model, with the goal of creating a model that would be used to forecast changes in clinically meaningful endpoints, which would inform clinical trial protocol development and data analysis.  Methods: In April of 2016 the consortium and other experts met to formulate plans for the development of the model.  Conclusions: Here we report the results of the meeting, and discussion as to the form of the model that we plan to move forward to develop, after input from the regulatory authorities. PMID:28228973

Distributed Access View Integrated Database (DAVID) system

NASA Technical Reports Server (NTRS)

Jacobs, Barry E.

1991-01-01

The Distributed Access View Integrated Database (DAVID) System, which was adopted by the Astrophysics Division for their Astrophysics Data System, is a solution to the system heterogeneity problem. The heterogeneous components of the Astrophysics problem is outlined. The Library and Library Consortium levels of the DAVID approach are described. The 'books' and 'kits' level is discussed. The Universal Object Typer Management System level is described. The relation of the DAVID project with the Small Business Innovative Research (SBIR) program is explained.

Enhancing Transfer Effectiveness: A Model for the 1990s.

ERIC Educational Resources Information Center

Berman, Paul; And Others

In an effort to identify effective transfer practices appropriate to different community college circumstances, and to establish a quantitative database that would enable valid comparisons of transfer between their 28 member institutions, the National Effective Transfer Consortium (NETC) sponsored a survey of more than 30,000 students attending…

The ICPSR and Social Science Research

ERIC Educational Resources Information Center

Johnson, Wendell G.

2008-01-01

The Inter-university Consortium for Political and Social Research (ICPSR), a unit within the Institute for Social Research at the University of Michigan, is the world's largest social science data archive. The data sets in the ICPRS database give the social sciences librarian/subject specialist an opportunity of providing value-added bibliographic…

HYDROGEOLOGIC FOUNDATION IN SUPPORT OF ECOSYSTEM RESTORATION: BASE-FLOW LOADINGS OF NITRATE IN MID-ATLANTIC AGRICULTURAL WATERSHEDS

EPA Science Inventory

The study is a consortium between the U.S. Environmental Protection Agency (National Risk Management Research Laboratory) and the U.S. Geological Survey (Baltimore and Dover). The objectives of this study are: (1) to develop a geohydrological database for paired agricultural wate...

Consortial IT Services: Collaborating To Reduce the Pain.

ERIC Educational Resources Information Center

Klonoski, Ed

The Connecticut Distance Learning Consortium (CTDLC) provides its 32 members with Information Technologies (IT) services including a portal Web site, course management software, course hosting and development, faculty training, a help desk, online assessment, and a student financial aid database. These services are supplied to two- and four-year…

The CNES Gaia Data Processing Center: A Challenge and its Solutions

NASA Astrophysics Data System (ADS)

Chaoul, Laurence; Valette, Veronique

2011-08-01

After a brief reminder of the ESA Gaia project, this paper presents the data processing consortium (DPAC) and then the CNES data processing centre (DPCC). We focus on the challenge in terms of organisational aspects, processing capabilities, databases volumetry, and how we deal with these topics.

Distributed databases for materials study of thermo-kinetic properties

NASA Astrophysics Data System (ADS)

Toher, Cormac

2015-03-01

High-throughput computational materials science provides researchers with the opportunity to rapidly generate large databases of materials properties. To rapidly add thermal properties to the AFLOWLIB consortium and Materials Project repositories, we have implemented an automated quasi-harmonic Debye model, the Automatic GIBBS Library (AGL). This enables us to screen thousands of materials for thermal conductivity, bulk modulus, thermal expansion and related properties. The search and sort functions of the online database can then be used to identify suitable materials for more in-depth study using more precise computational or experimental techniques. AFLOW-AGL source code is public domain and will soon be released within the GNU-GPL license.

Highlights from the 2015 WIN Symposium: novel targets, innovative agents, and advanced technologies-a WINning strategy?

PubMed

Schilsky, Richard L

2015-01-01

The worldwide innovative networking (WIN) consortium comprises a global alliance of 28 academic and clinical cancer centres, 11 pharmaceutical and technology companies and five charitable or health payer organisations. Since its inception the consortium has striven to provide a forum for all of its members to network, share information and experience, and perform clinical trials with the overarching goal of advancing the care of patients with cancer through the use of precision medicine. The annual 2-day WIN Symposium is the most visible output of the consortium and provides an opportunity for around 400 experts and other delegates to meet and discuss the latest research and initiatives in personalised cancer medicine. The seventh WIN Symposium, held in Paris, France, 29-30 June 2015, consisted of nine plenary and eight poster sessions that covered the overarching theme of novel targets, innovative agents, and advanced technologies being a winning strategy. Highlights included discussions of immune mechanisms and ways to target the cancer immunome and systems biology approaches to supporting personalised cancer. The latest data from the BATTLE-2 and WINther trials were discussed, and round table discussions were held that focused on how best to design the next generation of clinical trials, which included SPRING, SUMMER, and BOOSTER being initiated by the WIN Consortium.

Increasing Nursing Faculty Research: The Iowa Gerontological Nursing Research and Regional Research Consortium Strategies

PubMed Central

Maas, Meridean L.; Conn, Vicki; Buckwalter, Kathleen C.; Herr, Keela; Tripp-Reimer, Toni

2012-01-01

Purpose Research development and regional consortium strategies are described to assist schools in all countries extend their gerontological nursing research productivity. The strategies, collaboration and mentoring experiences, and outcomes are also shared to illustrate a highly successful approach in increasing faculty programs of nursing research in a focused area of inquiry. Design A case description of gerontological nursing research development and regional consortium strategies in schools of nursing is used. The regional consortium included 17 schools of nursing that are working to increase faculty programs of gerontological nursing research. Survey responses describing publications, presentations, and research funding awards from 65 of 114 total faculty participants in consortium opportunities (pilot and mentoring grant participants, participants in summer scholars’ grantsmanship seminars) were collected annually from 1995 through 2008 to describe outcomes. Findings From 1994 through 2008, faculty participants from the consortium schools who responded to the annual surveys reported a total of 597 gerontological nursing publications, 527 presentations at research conferences, funding of 221 small and internal grants, and 130 external grant awards, including 47R-series grants and 4 K awards. Conclusions There is an urgent need for more nurse faculty with programs of research to inform the health care of persons and support the preparation of nurse clinicians and faculty. The shortage of nurse scientists with active programs of gerontological research is especially serious and limits the number of faculty who are needed to prepare future gerontological nurses, particularly those with doctoral degrees who will assume faculty positions. Further, junior faculty with a gerontological nursing research foci often lack the colleagues, mentors, and environments needed to develop successful research careers. The outcomes of the development and regional consortium strategies suggest that the principles of extending collaboration, mentoring, and resource sharing are useful to augment faculty research opportunities, networking and support, and to increase productivity in individual schools. Clinical Relevance Clinical relevance includes: (a) implications for preparing nurse scientists and academicians who are and will be needed to train nurses for clinical practice, and (b) development of more faculty programs of research to provide systematic evidence to inform nursing practice. PMID:19941587

Interdisciplinary Collaboration amongst Colleagues and between Initiatives with the Magnetics Information Consortium (MagIC) Database

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A. A. P.; Jarboe, N.; Tauxe, L.; Constable, C.; Jonestrask, L.; Shaar, R.

2014-12-01

Earth science grand challenges often require interdisciplinary and geographically distributed scientific collaboration to make significant progress. However, this organic collaboration between researchers, educators, and students only flourishes with the reduction or elimination of technological barriers. The Magnetics Information Consortium (http://earthref.org/MagIC/) is a grass-roots cyberinfrastructure effort envisioned by the geo-, paleo-, and rock magnetic scientific community to archive their wealth of peer-reviewed raw data and interpretations from studies on natural and synthetic samples. MagIC is dedicated to facilitating scientific progress towards several highly multidisciplinary grand challenges and the MagIC Database team is currently beta testing a new MagIC Search Interface and API designed to be flexible enough for the incorporation of large heterogeneous datasets and for horizontal scalability to tens of millions of records and hundreds of requests per second. In an effort to reduce the barriers to effective collaboration, the search interface includes a simplified data model and upload procedure, support for online editing of datasets amongst team members, commenting by reviewers and colleagues, and automated contribution workflows and data retrieval through the API. This web application has been designed to generalize to other databases in MagIC's umbrella website (EarthRef.org) so the Geochemical Earth Reference Model (http://earthref.org/GERM/) portal, Seamount Biogeosciences Network (http://earthref.org/SBN/), EarthRef Digital Archive (http://earthref.org/ERDA/) and EarthRef Reference Database (http://earthref.org/ERR/) will benefit from its development.

Using a centralised database system and server in the European Union Framework Programme 7 project SEPServer

NASA Astrophysics Data System (ADS)

Heynderickx, Daniel

2012-07-01

The main objective of the SEPServer project (EU FP7 project 262773) is to produce a new tool, which greatly facilitates the investigation of solar energetic particles (SEPs) and their origin: a server providing SEP data, related electromagnetic (EM) observations and analysis methods, a comprehensive catalogue of the observed SEP events, and educational/outreach material on solar eruptions. The project is coordinated by the University of Helsinki. The project will combine data and knowledge from 11 European partners and several collaborating parties from Europe and US. The datasets provided by the consortium partners are collected in a MySQL database (using the ESA Open Data Interface under licence) on a server operated by DH Consultancy, which also hosts a web interface providing browsing, plotting and post-processing and analysis tools developed by the consortium, as well as a Solar Energetic Particle event catalogue. At this stage of the project, a prototype server has been established, which is presently undergoing testing by users inside the consortium. Using a centralized database has numerous advantages, including: homogeneous storage of the data, which eliminates the need for dataset specific file access routines once the data are ingested in the database; a homogeneous set of metadata describing the datasets on both a global and detailed level, allowing for automated access to and presentation of the various data products; standardised access to the data in different programming environments (e.g. php, IDL); elimination of the need to download data for individual data requests. SEPServer will, thus, add value to several space missions and Earth-based observations by facilitating the coordinated exploitation of and open access to SEP data and related EM observations, and promoting correct use of these data for the entire space research community. This will lead to new knowledge on the production and transport of SEPs during solar eruptions and facilitate the development of models for predicting solar radiation storms and calculation of expected fluxes/fluences of SEPs encountered by spacecraft in the interplanetary medium.

Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene.

PubMed

Yohda, Masafumi; Yagi, Osami; Takechi, Ayane; Kitajima, Mizuki; Matsuda, Hisashi; Miyamura, Naoaki; Aizawa, Tomoko; Nakajima, Mutsuyasu; Sunairi, Michio; Daiba, Akito; Miyajima, Takashi; Teruya, Morimi; Teruya, Kuniko; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Juan, Ayaka; Nakano, Kazuma; Aoyama, Misako; Terabayashi, Yasunobu; Satou, Kazuhito; Hirano, Takashi

2015-07-01

A Dehalococcoides-containing bacterial consortium that performed dechlorination of 0.20 mM cis-1,2-dichloroethene to ethene in 14 days was obtained from the sediment mud of the lotus field. To obtain detailed information of the consortium, the metagenome was analyzed using the short-read next-generation sequencer SOLiD 3. Matching the obtained sequence tags with the reference genome sequences indicated that the Dehalococcoides sp. in the consortium was highly homologous to Dehalococcoides mccartyi CBDB1 and BAV1. Sequence comparison with the reference sequence constructed from 16S rRNA gene sequences in a public database showed the presence of Sedimentibacter, Sulfurospirillum, Clostridium, Desulfovibrio, Parabacteroides, Alistipes, Eubacterium, Peptostreptococcus and Proteocatella in addition to Dehalococcoides sp. After further enrichment, the members of the consortium were narrowed down to almost three species. Finally, the full-length circular genome sequence of the Dehalococcoides sp. in the consortium, D. mccartyi IBARAKI, was determined by analyzing the metagenome with the single-molecule DNA sequencer PacBio RS. The accuracy of the sequence was confirmed by matching it to the tag sequences obtained by SOLiD 3. The genome is 1,451,062 nt and the number of CDS is 1566, which includes 3 rRNA genes and 47 tRNA genes. There exist twenty-eight RDase genes that are accompanied by the genes for anchor proteins. The genome exhibits significant sequence identity with other Dehalococcoides spp. throughout the genome, but there exists significant difference in the distribution RDase genes. The combination of a short-read next-generation DNA sequencer and a long-read single-molecule DNA sequencer gives detailed information of a bacterial consortium. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Community-Supported Data Repositories in Paleobiology: A 'Middle Tail' Between the Geoscientific and Informatics Communities

NASA Astrophysics Data System (ADS)

Williams, J. W.; Ashworth, A. C.; Betancourt, J. L.; Bills, B.; Blois, J.; Booth, R.; Buckland, P.; Charles, D.; Curry, B. B.; Goring, S. J.; Davis, E.; Grimm, E. C.; Graham, R. W.; Smith, A. J.

2015-12-01

Community-supported data repositories (CSDRs) in paleoecology and paleoclimatology have a decades-long tradition and serve multiple critical scientific needs. CSDRs facilitate synthetic large-scale scientific research by providing open-access and curated data that employ community-supported metadata and data standards. CSDRs serve as a 'middle tail' or boundary organization between information scientists and the long-tail community of individual geoscientists collecting and analyzing paleoecological data. Over the past decades, a distributed network of CSDRs has emerged, each serving a particular suite of data and research communities, e.g. Neotoma Paleoecology Database, Paleobiology Database, International Tree Ring Database, NOAA NCEI for Paleoclimatology, Morphobank, iDigPaleo, and Integrated Earth Data Alliance. Recently, these groups have organized into a common Paleobiology Data Consortium dedicated to improving interoperability and sharing best practices and protocols. The Neotoma Paleoecology Database offers one example of an active and growing CSDR, designed to facilitate research into ecological and evolutionary dynamics during recent past global change. Neotoma combines a centralized database structure with distributed scientific governance via multiple virtual constituent data working groups. The Neotoma data model is flexible and can accommodate a variety of paleoecological proxies from many depositional contests. Data input into Neotoma is done by trained Data Stewards, drawn from their communities. Neotoma data can be searched, viewed, and returned to users through multiple interfaces, including the interactive Neotoma Explorer map interface, REST-ful Application Programming Interfaces (APIs), the neotoma R package, and the Tilia stratigraphic software. Neotoma is governed by geoscientists and provides community engagement through training workshops for data contributors, stewards, and users. Neotoma is engaged in the Paleobiological Data Consortium and other efforts to improve interoperability among cyberinfrastructure in the paleogeosciences.

Genetic variants of the DNA repair genes from Exome Aggregation Consortium (EXAC) database: significance in cancer.

PubMed

Das, Raima; Ghosh, Sankar Kumar

2017-04-01

DNA repair pathway is a primary defense system that eliminates wide varieties of DNA damage. Any deficiencies in them are likely to cause the chromosomal instability that leads to cell malfunctioning and tumorigenesis. Genetic polymorphisms in DNA repair genes have demonstrated a significant association with cancer risk. Our study attempts to give a glimpse of the overall scenario of the germline polymorphisms in the DNA repair genes by taking into account of the Exome Aggregation Consortium (ExAC) database as well as the Human Gene Mutation Database (HGMD) for evaluating the disease link, particularly in cancer. It has been found that ExAC DNA repair dataset (which consists of 228 DNA repair genes) comprises 30.4% missense, 12.5% dbSNP reported and 3.2% ClinVar significant variants. 27% of all the missense variants has the deleterious SIFT score of 0.00 and 6% variants carrying the most damaging Polyphen-2 score of 1.00, thus affecting the protein structure and function. However, as per HGMD, only a fraction (1.2%) of ExAC DNA repair variants was found to be cancer-related, indicating remaining variants reported in both the databases to be further analyzed. This, in turn, may provide an increased spectrum of the reported cancer linked variants in the DNA repair genes present in ExAC database. Moreover, further in silico functional assay of the identified vital cancer-associated variants, which is essential to get their actual biological significance, may shed some lights in the field of targeted drug development in near future. Copyright © 2017. Published by Elsevier B.V.

Glocal Clinical Registries: Pacemaker Registry Design and Implementation for Global and Local Integration – Methodology and Case Study

PubMed Central

da Silva, Kátia Regina; Costa, Roberto; Crevelari, Elizabeth Sartori; Lacerda, Marianna Sobral; de Moraes Albertini, Caio Marcos; Filho, Martino Martinelli; Santana, José Eduardo; Vissoci, João Ricardo Nickenig; Pietrobon, Ricardo; Barros, Jacson V.

2013-01-01

Background The ability to apply standard and interoperable solutions for implementing and managing medical registries as well as aggregate, reproduce, and access data sets from legacy formats and platforms to advanced standard formats and operating systems are crucial for both clinical healthcare and biomedical research settings. Purpose Our study describes a reproducible, highly scalable, standard framework for a device registry implementation addressing both local data quality components and global linking problems. Methods and Results We developed a device registry framework involving the following steps: (1) Data standards definition and representation of the research workflow, (2) Development of electronic case report forms using REDCap (Research Electronic Data Capture), (3) Data collection according to the clinical research workflow and, (4) Data augmentation by enriching the registry database with local electronic health records, governmental database and linked open data collections, (5) Data quality control and (6) Data dissemination through the registry Web site. Our registry adopted all applicable standardized data elements proposed by American College Cardiology / American Heart Association Clinical Data Standards, as well as variables derived from cardiac devices randomized trials and Clinical Data Interchange Standards Consortium. Local interoperability was performed between REDCap and data derived from Electronic Health Record system. The original data set was also augmented by incorporating the reimbursed values paid by the Brazilian government during a hospitalization for pacemaker implantation. By linking our registry to the open data collection repository Linked Clinical Trials (LinkedCT) we found 130 clinical trials which are potentially correlated with our pacemaker registry. Conclusion This study demonstrates how standard and reproducible solutions can be applied in the implementation of medical registries to constitute a re-usable framework. Such approach has the potential to facilitate data integration between healthcare and research settings, also being a useful framework to be used in other biomedical registries. PMID:23936257

Multicenter Approach to Recurrent Acute and Chronic Pancreatitis in the United States: The North American Pancreatitis Study 2 (NAPS2)

PubMed Central

Whitcomb, David C.; Yadav, Dhiraj; Adam, Slivka; Hawes, Robert H.; Brand, Randall E.; Anderson, Michelle A.; Money, Mary E.; Banks, Peter A.; Bishop, Michele D.; Baillie, John; Sherman, Stuart; DiSario, James; Burton, Frank R.; Gardner, Timothy B.; Amann, Stephen T.; Gelrud, Andres; Lo, Simon K.; DeMeo, Mark T.; Steinberg, William M.; Kochman, Michael L.; Etemad, Babak; Forsmark, Christopher E.; Elinoff, Beth; Greer, Julia B.; O’Connell, Michael; Lamb, Janette; Barmada, M. Michael

2008-01-01

Background Recurrent acute pancreatitis (RAP) and chronic pancreatitis (CP) are complex syndromes associated with numerous etiologies, clinical variables and complications. We developed the North American Pancreatitis Study 2 (NAPS2) to be sufficiently powered to understand the complex environmental, metabolic and genetic mechanisms underlying RAP and CP. Methods Between August 2000 and September 2006, a consortium of 20 expert academic and private sites prospectively ascertained 1,000 human subjects with RAP or CP, plus 695 controls (spouse, family, friend or unrelated). Standardized questionnaires were completed by both the physicians and study subjects and blood was drawn for genomic DNA and biomarker studies. All data were double-entered into a database and systematically reviewed to minimize errors and include missing data. Results A total of 1,000 subjects (460 RAP, 540 CP) and 695 controls who completed consent forms and questionnaires and donated blood samples comprised the final dataset. Data were organized according to diagnosis, supporting documentation, etiological classification, clinical signs and symptoms (including pain patterns and duration, and quality of life), past medical history, family history, environmental exposures (including alcohol and tobacco use), medication use and therapeutic interventions. Upon achieving the target enrollment, data were organized and classified to facilitate future analysis. The approaches, rationale and datasets are described, along with final demographic results. Conclusion The NAPS2 consortium has successfully completed a prospective ascertainment of 1,000 subjects with RAP and CP from the USA. These data will be useful in elucidating the environmental, metabolic and genetic conditions, and to investigate the complex interactions that underlie RAP and CP. PMID:18765957

Prader-Willi syndrome and early-onset morbid obesity NIH rare disease consortium: A review of natural history study.

PubMed

Butler, Merlin G; Kimonis, Virginia; Dykens, Elisabeth; Gold, June A; Miller, Jennifer; Tamura, Roy; Driscoll, Daniel J

2018-02-01

We describe the National Institutes of Health rare disease consortium for Prader-Willi syndrome (PWS) developed to address concerns regarding medical care, diagnosis, growth and development, awareness, and natural history. PWS results from errors in genomic imprinting leading to loss of paternally expressed genes due to 15q11-q13 deletion, maternal disomy 15 or imprinting defects. The 8 year study was conducted at four national sites on individuals with genetically confirmed PWS and early-onset morbid obesity (EMO) with data accumulated to gain a better understanding of the natural history, cause and treatment of PWS. Enrollment of 355 subjects with PWS and 36 subjects with EMO began in September 2006 with study completion in July 2014. Clinical, genetic, cognitive, behavior, and natural history data were systematically collected along with PWS genetic subtypes, pregnancy and birth history, mortality, obesity, and cognitive status with study details as important endpoints in both subject groups. Of the 355 individuals with PWS, 217 (61%) had the 15q11-q13 deletion, 127 (36%) had maternal disomy 15, and 11 (3%) had imprinting defects. Six deaths were reported in our PWS cohort with 598 cumulative years of study exposure and one death in the EMO group with 42 years of exposure. To our knowledge, this description of a longitudinal study in PWS represents the largest and most comprehensive cohort useful for investigators in planning comparable studies in other rare disorders. Ongoing studies utilizing this database should have a direct impact on care and services, diagnosis, treatment, genotype-phenotype correlations, and clinical outcomes in PWS. © 2017 Wiley Periodicals, Inc.

Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rasure, John, et. al.

Through past DOE funding, the MIND Research network has funded a national consortium effort that used multi-modal neuroimaging, genetics, and clinical assessment of subjects to study schizophrenia in both first episode and persistently ill patients. Although active recruitment of research participants is complete, this consortium remains active and productive in terms of analysis of this unique multi-modal data collected on over 320 subjects.

Federated or cached searches: Providing expected performance from multiple invasive species databases

NASA Astrophysics Data System (ADS)

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-06-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

Federated or cached searches: providing expected performance from multiple invasive species databases

USGS Publications Warehouse

Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

2011-01-01

Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

Ozone therapy in postgraduate theses in Egypt: systematic review.

PubMed

AlBedah, Abdullah M N; Khalil, Mohamed K M; Elolemy, Ahmed T; Alrasheid, Mohamed H S; Al Mudaiheem, Abdullah; Elolemy, Tawfik M B

2013-08-01

Systematic reviews of the studies published in the major medical data bases have not shown solid support for the use of ozone therapy. Unpublished or grey literature, including postgraduate theses, may solve this controversy. To review the postgraduate theses published in Egypt in order to assess the clinical safety and effectiveness of ozone therapy in specific medical conditions. The databases of the Egyptian Universities' Library Consortium and the databases of each university were searched for postgraduate theses that evaluated ozone therapy as an intervention for any disease or condition in any age group, compared with any or no other intervention and published before September 2010. A total of 28 quasi trials were included. The theses did not report any safety issues in terms of ozone therapy. With respect to its effectiveness, the studies suggested some benefits of ozone in the treatment of dental infection and recovery, musculoskeletal disorders, diabetes mellitus, chronic diseases, and obstetrics and gynaecology. However, the number of studies included was small and they were of limited quality. There is insufficient evidence to recommend the use of ozone in the treatment of dental infections, in facilitating faster dental recovery after extraction or implantation, in diabetes mellitus, musculoskeletal disorders, or obstetrics and gynaecology.

CTSA‐IP: A Solution to Identifying and Aggregating Intellectual Property across the NIH Clinical Translational Science Award (CTSA) Consortium of Biomedical Research Institutes

PubMed Central

Hazard, Mike; Steele, Scott; Wang, Dongwen; Pearson, Thomas; Scheideler, Mark; Dewhurst, Steve

2011-01-01

Abstract  One of the objectives of the Consortium of Institutions with Clinical and Translational Science Awards (CTSAs) is to enhance technology transfer among the CTSAs and with public and private sector partners. Clinical and Translational Sciences Award Intellectual Property (CTSA‐IP; http://www.CTSAIP.org) is a web‐based, open access IP search tool that aggregates and promotes technologies from member institutions of the National Institutes of Health’s (NIH) CTSAs consortium. Its ultimate aim is to stimulate collaborative research activity by encouraging the formation of public‐private partnerships with CTSA institutions and the NIH. First launched in 2009, CTSA‐IP has grown rapidly and met its first objectives of developing wide member institution participation and site usage. This communication will discuss the strategy employed in the initiative of aggregating IP across institutional boundaries, the promise that lies therein, as well as the challenges encountered and lessons learned in promoting CTSA‐wide engagement. Clin Trans Sci 2011; Volume 4: 328–331 PMID:22029803

The Ontological Perspectives of the Semantic Web and the Metadata Harvesting Protocol: Applications of Metadata for Improving Web Search.

ERIC Educational Resources Information Center

Fast, Karl V.; Campbell, D. Grant

2001-01-01

Compares the implied ontological frameworks of the Open Archives Initiative Protocol for Metadata Harvesting and the World Wide Web Consortium's Semantic Web. Discusses current search engine technology, semantic markup, indexing principles of special libraries and online databases, and componentization and the distinction between data and…

Clinical terminology support for a national ambulatory practice outcomes research network.

PubMed

Ricciardi, Thomas N; Lieberman, Michael I; Kahn, Michael G; Masarie, F E

2005-01-01

The Medical Quality Improvement Consortium (MQIC) is a nationwide collaboration of 74 healthcare delivery systems, consisting of 3755 clinicians, who contribute de-identified clinical data from the same commercial electronic medical record (EMR) for quality reporting, outcomes research and clinical research in public health and practice benchmarking. Despite the existence of a common, centrally-managed, shared terminology for core concepts (medications, problem lists, observation names), a substantial "back-end" information management process is required to ensure terminology and data harmonization for creating multi-facility clinically-acceptable queries and comparable results. We describe the information architecture created to support terminology harmonization across this data-sharing consortium and discuss the implications for large scale data sharing envisioned by proponents for the national adoption of ambulatory EMR systems.

Clinical Terminology Support for a National Ambulatory Practice Outcomes Research Network

PubMed Central

Ricciardi, Thomas N.; Lieberman, Michael I.; Kahn, Michael G.; Masarie, F.E. “Chip”

2005-01-01

The Medical Quality Improvement Consortium (MQIC) is a nationwide collaboration of 74 healthcare delivery systems, consisting of 3755 clinicians, who contribute de-identified clinical data from the same commercial electronic medical record (EMR) for quality reporting, outcomes research and clinical research in public health and practice benchmarking. Despite the existence of a common, centrally-managed, shared terminology for core concepts (medications, problem lists, observation names), a substantial “back-end” information management process is required to ensure terminology and data harmonization for creating multi-facility clinically-acceptable queries and comparable results. We describe the information architecture created to support terminology harmonization across this data-sharing consortium and discuss the implications for large scale data sharing envisioned by proponents for the national adoption of ambulatory EMR systems. PMID:16779116

Lessons learned from implementing service-oriented clinical decision support at four sites: A qualitative study.

PubMed

Wright, Adam; Sittig, Dean F; Ash, Joan S; Erickson, Jessica L; Hickman, Trang T; Paterno, Marilyn; Gebhardt, Eric; McMullen, Carmit; Tsurikova, Ruslana; Dixon, Brian E; Fraser, Greg; Simonaitis, Linas; Sonnenberg, Frank A; Middleton, Blackford

2015-11-01

To identify challenges, lessons learned and best practices for service-oriented clinical decision support, based on the results of the Clinical Decision Support Consortium, a multi-site study which developed, implemented and evaluated clinical decision support services in a diverse range of electronic health records. Ethnographic investigation using the rapid assessment process, a procedure for agile qualitative data collection and analysis, including clinical observation, system demonstrations and analysis and 91 interviews. We identified challenges and lessons learned in eight dimensions: (1) hardware and software computing infrastructure, (2) clinical content, (3) human-computer interface, (4) people, (5) workflow and communication, (6) internal organizational policies, procedures, environment and culture, (7) external rules, regulations, and pressures and (8) system measurement and monitoring. Key challenges included performance issues (particularly related to data retrieval), differences in terminologies used across sites, workflow variability and the need for a legal framework. Based on the challenges and lessons learned, we identified eight best practices for developers and implementers of service-oriented clinical decision support: (1) optimize performance, or make asynchronous calls, (2) be liberal in what you accept (particularly for terminology), (3) foster clinical transparency, (4) develop a legal framework, (5) support a flexible front-end, (6) dedicate human resources, (7) support peer-to-peer communication, (8) improve standards. The Clinical Decision Support Consortium successfully developed a clinical decision support service and implemented it in four different electronic health records and four diverse clinical sites; however, the process was arduous. The lessons identified by the Consortium may be useful for other developers and implementers of clinical decision support services. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

The International Childhood Cardiovascular Cohort (i3C) consortium outcomes study of childhood cardiovascular risk factors and adult cardiovascular morbidity and mortality: Design and recruitment.

PubMed

Sinaiko, Alan R; Jacobs, David R; Woo, Jessica G; Bazzano, Lydia; Burns, Trudy; Hu, Tian; Juonala, Markus; Prineas, Ronald; Raitakari, Olli; Steinberger, Julia; Urbina, Elaine; Venn, Alison; Jaquish, Cashell; Dwyer, Terry

2018-04-22

Although it is widely thought that childhood levels of cardiovascular (CV) risk factors are related to adult CV disease, longitudinal data directly linking the two are lacking. This paper describes the design and organization of the International Childhood Cardiovascular Cohort Consortium Outcomes Study (i3C Outcomes), the first longitudinal cohort study designed to locate adults with detailed, repeated, childhood biological, physical, and socioeconomic measurements and a harmonized database. I3C Outcomes uses a Heart Health Survey (HHS) to obtain information on adult CV endpoints, using mail, email, telephone, and clinic visits in the United States (U.S.) and Australia and a national health database in Finland. Microsoft Access, REsearch Data Capture (REDCap) (U.S.), LimeSurvey (Australia), and Medidata™ Rave data systems are used to collect, transfer and organize data. Self-reported CV events are adjudicated via hospital and doctor-released medical records. After the first two study years, participants (N = 10,968) were more likely to be female (56% vs. 48%), non-Hispanic white (90% vs. 80%), and older (10.4 ± 3.8 years vs. 9.4 ± 3.3 years) at their initial childhood study visit than the currently non-recruited cohort members. Over 48% of cohort members seen during both adulthood and childhood have been found and recruited, to date, vs. 5% of those not seen since childhood. Self-reported prevalences were 0.7% Type 1 Diabetes, 7.5% Type 2 Diabetes, 33% hypertension, and 12.8% CV event. 32% of CV events were judged to be true. I3C Outcomes is uniquely able to establish evidence-based guidelines for child health care and to clarify relations to adult CV disease. Copyright © 2018 Elsevier Inc. All rights reserved.

Cohort Profile Update: The TRacking Adolescents’ Individual Lives Survey (TRAILS)

PubMed Central

Oldehinkel, Albertine J; Rosmalen, Judith GM; Buitelaar, Jan K; Hoek, Hans W; Ormel, Johan; Raven, Dennis; Reijneveld, Sijmen A; Veenstra, René; Verhulst, Frank C; Vollebergh, Wilma AM; Hartman, Catharina A

2015-01-01

TRAILS consists of a population cohort (N = 2230) and a clinical cohort (N = 543), both of which were followed from about age 11 years onwards. To date, the population cohort has been assessed five times over a period of 11 years, with retention rates ranging between 80% and 96%. The clinical cohort has been assessed four times over a period of 8 years, with retention rates ranging between 77% and 85%. Since the IJE published a cohort profile on the TRAILS in 2008, the participants have matured from adolescents into young adults. The focus shifted from parents and school to entry into the labour market and family formation, including offspring. Furthermore, psychiatric diagnostic interviews were administered, the database was linked to a Psychiatric Case Registry, and the availability of genome-wide SNP variations opened the door to genome-wide association studies regarding a wide range of (endo)phenotypes. With some delay, TRAILS data are available to researchers outside the TRAILS consortium without costs; access can be obtained by submitting a publication proposal (see www.trails.nl). PMID:25431468

Understanding Gulf War Illness: An Integrative Modeling Approach

DTIC Science & Technology

2016-10-01

Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314 Centers for Disease Control, NIOSH, 1095 Willowdale Road, Morgantown, WV 26505...SUPPLEMENTARY NOTES 14. ABSTRACT The goal of the GWI consortium is to develop a better understanding of GWI and identify specific disease targets to...find treatments that will address the cause of the disease . The consortium will integrate our clinical understanding of the disease process with

Overview | Office of Cancer Genomics

Cancer.gov

The Human Cancer Model Initiative (HCMI) is an international consortium that is generating novel human tumor-derived culture models with associated genomic and clinical data. The HCMI consortium includes the US-National Cancer Institute, part of the National Institutes of Health, Cancer Research UK, foundation Hubrecht Organoid Technology, and Wellcome Sanger Institute. The goal of HCMI is to create up to one thousand cancer models from patient tumors.

The GED4GEM project: development of a Global Exposure Database for the Global Earthquake Model initiative

USGS Publications Warehouse

Gamba, P.; Cavalca, D.; Jaiswal, K.S.; Huyck, C.; Crowley, H.

2012-01-01

In order to quantify earthquake risk of any selected region or a country of the world within the Global Earthquake Model (GEM) framework (www.globalquakemodel.org/), a systematic compilation of building inventory and population exposure is indispensable. Through the consortium of leading institutions and by engaging the domain-experts from multiple countries, the GED4GEM project has been working towards the development of a first comprehensive publicly available Global Exposure Database (GED). This geospatial exposure database will eventually facilitate global earthquake risk and loss estimation through GEM’s OpenQuake platform. This paper provides an overview of the GED concepts, aims, datasets, and inference methodology, as well as the current implementation scheme, status and way forward.

Results From the John Glenn Biomedical Engineering Consortium. A Success Story for NASA and Northeast Ohio

NASA Technical Reports Server (NTRS)

Nall, Marsha M.; Barna, Gerald J.

2009-01-01

The John Glenn Biomedical Engineering Consortium was established by NASA in 2002 to formulate and implement an integrated, interdisciplinary research program to address risks faced by astronauts during long-duration space missions. The consortium is comprised of a preeminent team of Northeast Ohio institutions that include Case Western Reserve University, the Cleveland Clinic, University Hospitals Case Medical Center, The National Center for Space Exploration Research, and the NASA Glenn Research Center. The John Glenn Biomedical Engineering Consortium research is focused on fluid physics and sensor technology that addresses the critical risks to crew health, safety, and performance. Effectively utilizing the unique skills, capabilities and facilities of the consortium members is also of prime importance. Research efforts were initiated with a general call for proposals to the consortium members. The top proposals were selected for funding through a rigorous, peer review process. The review included participation from NASA's Johnson Space Center, which has programmatic responsibility for NASA's Human Research Program. The projects range in scope from delivery of prototype hardware to applied research that enables future development of advanced technology devices. All of the projects selected for funding have been completed and the results are summarized. Because of the success of the consortium, the member institutions have extended the original agreement to continue this highly effective research collaboration through 2011.

The future application of GML database in GIS

NASA Astrophysics Data System (ADS)

Deng, Yuejin; Cheng, Yushu; Jing, Lianwen

2006-10-01

In 2004, the Geography Markup Language (GML) Implementation Specification (version 3.1.1) was published by Open Geospatial Consortium, Inc. Now more and more applications in geospatial data sharing and interoperability depend on GML. The primary purpose of designing GML is for exchange and transportation of geo-information by standard modeling and encoding of geography phenomena. However, the problems of how to organize and access lots of GML data effectively arise in applications. The research on GML database focuses on these problems. The effective storage of GML data is a hot topic in GIS communities today. GML Database Management System (GDBMS) mainly deals with the problem of storage and management of GML data. Now two types of XML database, namely Native XML Database, and XML-Enabled Database are classified. Since GML is an application of the XML standard to geographic data, the XML database system can also be used for the management of GML. In this paper, we review the status of the art of XML database, including storage, index and query languages, management systems and so on, then move on to the GML database. At the end, the future prospect of GML database in GIS application is presented.

A data-driven algorithm integrating clinical and laboratory features for the diagnosis and prognosis of necrotizing enterocolitis.

PubMed

Ji, Jun; Ling, Xuefeng B; Zhao, Yingzhen; Hu, Zhongkai; Zheng, Xiaolin; Xu, Zhening; Wen, Qiaojun; Kastenberg, Zachary J; Li, Ping; Abdullah, Fizan; Brandt, Mary L; Ehrenkranz, Richard A; Harris, Mary Catherine; Lee, Timothy C; Simpson, B Joyce; Bowers, Corinna; Moss, R Lawrence; Sylvester, Karl G

2014-01-01

Necrotizing enterocolitis (NEC) is a major source of neonatal morbidity and mortality. Since there is no specific diagnostic test or risk of progression model available for NEC, the diagnosis and outcome prediction of NEC is made on clinical grounds. The objective in this study was to develop and validate new NEC scoring systems for automated staging and prognostic forecasting. A six-center consortium of university based pediatric teaching hospitals prospectively collected data on infants under suspicion of having NEC over a 7-year period. A database comprised of 520 infants was utilized to develop the NEC diagnostic and prognostic models by dividing the entire dataset into training and testing cohorts of demographically matched subjects. Developed on the training cohort and validated on the blind testing cohort, our multivariate analyses led to NEC scoring metrics integrating clinical data. Machine learning using clinical and laboratory results at the time of clinical presentation led to two nec models: (1) an automated diagnostic classification scheme; (2) a dynamic prognostic method for risk-stratifying patients into low, intermediate and high NEC scores to determine the risk for disease progression. We submit that dynamic risk stratification of infants with NEC will assist clinicians in determining the need for additional diagnostic testing and guide potential therapies in a dynamic manner. http://translationalmedicine.stanford.edu/cgi-bin/NEC/index.pl and smartphone application upon request.

CPTAC Prospective Biospecimen Collection Solicitation | Office of Cancer Clinical Proteomics Research

Cancer.gov

A new funding opportunity in support of the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) seeks to prospectively procure tumor samples, collected for proteomics investigation.

Global standardization measurement of cerebral spinal fluid for Alzheimer's disease: an update from the Alzheimer's Association Global Biomarkers Consortium.

PubMed

Carrillo, Maria C; Blennow, Kaj; Soares, Holly; Lewczuk, Piotr; Mattsson, Niklas; Oberoi, Pankaj; Umek, Robert; Vandijck, Manu; Salamone, Salvatore; Bittner, Tobias; Shaw, Leslie M; Stephenson, Diane; Bain, Lisa; Zetterberg, Henrik

2013-03-01

Recognizing that international collaboration is critical for the acceleration of biomarker standardization efforts and the efficient development of improved diagnosis and therapy, the Alzheimer's Association created the Global Biomarkers Standardization Consortium (GBSC) in 2010. The consortium brings together representatives of academic centers, industry, and the regulatory community with the common goal of developing internationally accepted common reference standards and reference methods for the assessment of cerebrospinal fluid (CSF) amyloid β42 (Aβ42) and tau biomarkers. Such standards are essential to ensure that analytical measurements are reproducible and consistent across multiple laboratories and across multiple kit manufacturers. Analytical harmonization for CSF Aβ42 and tau will help reduce confusion in the AD community regarding the absolute values associated with the clinical interpretation of CSF biomarker results and enable worldwide comparison of CSF biomarker results across AD clinical studies. Copyright © 2013 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

Segmentation of pulmonary nodules in computed tomography using a regression neural network approach and its application to the Lung Image Database Consortium and Image Database Resource Initiative dataset.

PubMed

Messay, Temesguen; Hardie, Russell C; Tuinstra, Timothy R

2015-05-01

We present new pulmonary nodule segmentation algorithms for computed tomography (CT). These include a fully-automated (FA) system, a semi-automated (SA) system, and a hybrid system. Like most traditional systems, the new FA system requires only a single user-supplied cue point. On the other hand, the SA system represents a new algorithm class requiring 8 user-supplied control points. This does increase the burden on the user, but we show that the resulting system is highly robust and can handle a variety of challenging cases. The proposed hybrid system starts with the FA system. If improved segmentation results are needed, the SA system is then deployed. The FA segmentation engine has 2 free parameters, and the SA system has 3. These parameters are adaptively determined for each nodule in a search process guided by a regression neural network (RNN). The RNN uses a number of features computed for each candidate segmentation. We train and test our systems using the new Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) data. To the best of our knowledge, this is one of the first nodule-specific performance benchmarks using the new LIDC-IDRI dataset. We also compare the performance of the proposed methods with several previously reported results on the same data used by those other methods. Our results suggest that the proposed FA system improves upon the state-of-the-art, and the SA system offers a considerable boost over the FA system. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Predictors for Perioperative Outcomes following Total Laryngectomy: A University HealthSystem Consortium Discharge Database Study.

PubMed

Rutledge, Jonathan W; Spencer, Horace; Moreno, Mauricio A

2014-07-01

The University HealthSystem Consortium (UHC) database collects discharge information on patients treated at academic health centers throughout the United States. We sought to use this database to identify outcome predictors for patients undergoing total laryngectomy. A secondary end point was to assess the validity of the UHC's predictive risk mortality model in this cohort of patients. Retrospective review. Academic medical centers (tertiary referral centers) and their affiliate hospitals in the United States. Using the UHC discharge database, we retrieved and analyzed data for 4648 patients undergoing total laryngectomy who were discharged between October 2007 and January 2011 from all of the member institutions. Demographics, comorbidities, institutional data, and outcomes were retrieved. The length of stay and overall costs were significantly higher among female patients (P < .0001), while age was a predictor of intensive care unit stay (P = .014). The overall complication rate was higher among Asians (P = .019) and in patients with anemia and diabetes compared with other comorbidities. The average institutional case load was 1.92 cases/mo; we found an inverse correlation (R = -0.47) between the institutional case load and length of stay (P < .0001). The UHC admit mortality risk estimator was found to be an accurate predictor not only of mortality (P < .0002) but also of intensive care unit admission and complication rate (P < .0001). This study provides an overview of laryngectomy outcomes in a contemporary cohort of patients treated at academic health centers. UHC admit mortality risk is an excellent outcome predictor and a valuable tool for risk stratification in these patients. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2014.

ENT COBRA (Consortium for Brachytherapy Data Analysis): interdisciplinary standardized data collection system for head and neck patients treated with interventional radiotherapy (brachytherapy).

PubMed

Tagliaferri, Luca; Kovács, György; Autorino, Rosa; Budrukkar, Ashwini; Guinot, Jose Luis; Hildebrand, Guido; Johansson, Bengt; Monge, Rafael Martìnez; Meyer, Jens E; Niehoff, Peter; Rovirosa, Angeles; Takàcsi-Nagy, Zoltàn; Dinapoli, Nicola; Lanzotti, Vito; Damiani, Andrea; Soror, Tamer; Valentini, Vincenzo

2016-08-01

Aim of the COBRA (Consortium for Brachytherapy Data Analysis) project is to create a multicenter group (consortium) and a web-based system for standardized data collection. GEC-ESTRO (Groupe Européen de Curiethérapie - European Society for Radiotherapy & Oncology) Head and Neck (H&N) Working Group participated in the project and in the implementation of the consortium agreement, the ontology (data-set) and the necessary COBRA software services as well as the peer reviewing of the general anatomic site-specific COBRA protocol. The ontology was defined by a multicenter task-group. Eleven centers from 6 countries signed an agreement and the consortium approved the ontology. We identified 3 tiers for the data set: Registry (epidemiology analysis), Procedures (prediction models and DSS), and Research (radiomics). The COBRA-Storage System (C-SS) is not time-consuming as, thanks to the use of "brokers", data can be extracted directly from the single center's storage systems through a connection with "structured query language database" (SQL-DB), Microsoft Access(®), FileMaker Pro(®), or Microsoft Excel(®). The system is also structured to perform automatic archiving directly from the treatment planning system or afterloading machine. The architecture is based on the concept of "on-purpose data projection". The C-SS architecture is privacy protecting because it will never make visible data that could identify an individual patient. This C-SS can also benefit from the so called "distributed learning" approaches, in which data never leave the collecting institution, while learning algorithms and proposed predictive models are commonly shared. Setting up a consortium is a feasible and practicable tool in the creation of an international and multi-system data sharing system. COBRA C-SS seems to be well accepted by all involved parties, primarily because it does not influence the center's own data storing technologies, procedures, and habits. Furthermore, the method preserves the privacy of all patients.

Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium.

PubMed

Ellis, Matthew J; Gillette, Michael; Carr, Steven A; Paulovich, Amanda G; Smith, Richard D; Rodland, Karin K; Townsend, R Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel C

2013-10-01

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verification using targeted mass spectrometry methods. ©2013 AACR.

National Institutes of Health-Sponsored Clinical Islet Transplantation Consortium Phase 3 Trial: Manufacture of a Complex Cellular Product at Eight Processing Facilities.

PubMed

Ricordi, Camillo; Goldstein, Julia S; Balamurugan, A N; Szot, Gregory L; Kin, Tatsuya; Liu, Chengyang; Czarniecki, Christine W; Barbaro, Barbara; Bridges, Nancy D; Cano, Jose; Clarke, William R; Eggerman, Thomas L; Hunsicker, Lawrence G; Kaufman, Dixon B; Khan, Aisha; Lafontant, David-Erick; Linetsky, Elina; Luo, Xunrong; Markmann, James F; Naji, Ali; Korsgren, Olle; Oberholzer, Jose; Turgeon, Nicole A; Brandhorst, Daniel; Chen, Xiaojuan; Friberg, Andrew S; Lei, Ji; Wang, Ling-Jia; Wilhelm, Joshua J; Willits, Jamie; Zhang, Xiaomin; Hering, Bernhard J; Posselt, Andrew M; Stock, Peter G; Shapiro, A M James; Chen, Xiaojuan

2016-11-01

Eight manufacturing facilities participating in the National Institutes of Health-sponsored Clinical Islet Transplantation (CIT) Consortium jointly developed and implemented a harmonized process for the manufacture of allogeneic purified human pancreatic islet (PHPI) product evaluated in a phase 3 trial in subjects with type 1 diabetes. Manufacturing was controlled by a common master production batch record, standard operating procedures that included acceptance criteria for deceased donor organ pancreata and critical raw materials, PHPI product specifications, certificate of analysis, and test methods. The process was compliant with Current Good Manufacturing Practices and Current Good Tissue Practices. This report describes the manufacturing process for 75 PHPI clinical lots and summarizes the results, including lot release. The results demonstrate the feasibility of implementing a harmonized process at multiple facilities for the manufacture of a complex cellular product. The quality systems and regulatory and operational strategies developed by the CIT Consortium yielded product lots that met the prespecified characteristics of safety, purity, potency, and identity and were successfully transplanted into 48 subjects. No adverse events attributable to the product and no cases of primary nonfunction were observed. © 2016 by the American Diabetes Association.

National Institutes of Health–Sponsored Clinical Islet Transplantation Consortium Phase 3 Trial: Manufacture of a Complex Cellular Product at Eight Processing Facilities

PubMed Central

Balamurugan, A.N.; Szot, Gregory L.; Kin, Tatsuya; Liu, Chengyang; Czarniecki, Christine W.; Barbaro, Barbara; Bridges, Nancy D.; Cano, Jose; Clarke, William R.; Eggerman, Thomas L.; Hunsicker, Lawrence G.; Kaufman, Dixon B.; Khan, Aisha; Lafontant, David-Erick; Linetsky, Elina; Luo, Xunrong; Markmann, James F.; Naji, Ali; Korsgren, Olle; Oberholzer, Jose; Turgeon, Nicole A.; Brandhorst, Daniel; Chen, Xiaojuan; Friberg, Andrew S.; Lei, Ji; Wang, Ling-jia; Wilhelm, Joshua J.; Willits, Jamie; Zhang, Xiaomin; Hering, Bernhard J.; Posselt, Andrew M.; Stock, Peter G.; Shapiro, A.M. James

2016-01-01

Eight manufacturing facilities participating in the National Institutes of Health–sponsored Clinical Islet Transplantation (CIT) Consortium jointly developed and implemented a harmonized process for the manufacture of allogeneic purified human pancreatic islet (PHPI) product evaluated in a phase 3 trial in subjects with type 1 diabetes. Manufacturing was controlled by a common master production batch record, standard operating procedures that included acceptance criteria for deceased donor organ pancreata and critical raw materials, PHPI product specifications, certificate of analysis, and test methods. The process was compliant with Current Good Manufacturing Practices and Current Good Tissue Practices. This report describes the manufacturing process for 75 PHPI clinical lots and summarizes the results, including lot release. The results demonstrate the feasibility of implementing a harmonized process at multiple facilities for the manufacture of a complex cellular product. The quality systems and regulatory and operational strategies developed by the CIT Consortium yielded product lots that met the prespecified characteristics of safety, purity, potency, and identity and were successfully transplanted into 48 subjects. No adverse events attributable to the product and no cases of primary nonfunction were observed. PMID:27465220

Creation of a digital slide and tissue microarray resource from a multi-institutional predictive toxicology study in the rat: an initial report from the PredTox group.

PubMed

Mulrane, Laoighse; Rexhepaj, Elton; Smart, Valerie; Callanan, John J; Orhan, Diclehan; Eldem, Türkan; Mally, Angela; Schroeder, Susanne; Meyer, Kirstin; Wendt, Maria; O'Shea, Donal; Gallagher, William M

2008-08-01

The widespread use of digital slides has only recently come to the fore with the development of high-throughput scanners and high performance viewing software. This development, along with the optimisation of compression standards and image transfer techniques, has allowed the technology to be used in wide reaching applications including integration of images into hospital information systems and histopathological training, as well as the development of automated image analysis algorithms for prediction of histological aberrations and quantification of immunohistochemical stains. Here, the use of this technology in the creation of a comprehensive library of images of preclinical toxicological relevance is demonstrated. The images, acquired using the Aperio ScanScope CS and XT slide acquisition systems, form part of the ongoing EU FP6 Integrated Project, Innovative Medicines for Europe (InnoMed). In more detail, PredTox (abbreviation for Predictive Toxicology) is a subproject of InnoMed and comprises a consortium of 15 industrial (13 large pharma, 1 technology provider and 1 SME) and three academic partners. The primary aim of this consortium is to assess the value of combining data generated from 'omics technologies (proteomics, transcriptomics, metabolomics) with the results from more conventional toxicology methods, to facilitate further informed decision making in preclinical safety evaluation. A library of 1709 scanned images was created of full-face sections of liver and kidney tissue specimens from male Wistar rats treated with 16 proprietary and reference compounds of known toxicity; additional biological materials from these treated animals were separately used to create 'omics data, that will ultimately be used to populate an integrated toxicological database. In respect to assessment of the digital slides, a web-enabled digital slide management system, Digital SlideServer (DSS), was employed to enable integration of the digital slide content into the 'omics database and to facilitate remote viewing by pathologists connected with the project. DSS also facilitated manual annotation of digital slides by the pathologists, specifically in relation to marking particular lesions of interest. Tissue microarrays (TMAs) were constructed from the specimens for the purpose of creating a repository of tissue from animals used in the study with a view to later-stage biomarker assessment. As the PredTox consortium itself aims to identify new biomarkers of toxicity, these TMAs will be a valuable means of validation. In summary, a large repository of histological images was created enabling the subsequent pathological analysis of samples through remote viewing and, along with the utilisation of TMA technology, will allow the validation of biomarkers identified by the PredTox consortium. The population of the PredTox database with these digitised images represents the creation of the first toxicological database integrating 'omics and preclinical data with histological images.

Synthesis of rainfall and runoff data used for Texas Department of Transportation Research Projects 0-4193 and 0-4194

USGS Publications Warehouse

Asquith, William H.; Thompson, David B.; Cleveland, Theodore G.; Fang, Xing

2004-01-01

In the early 2000s, the Texas Department of Transportation funded several research projects to examine the unit hydrograph and rainfall hyetograph techniques for hydrologic design in Texas for the estimation of design flows for stormwater drainage systems. A research consortium comprised of Lamar University, Texas Tech University, the University of Houston, and the U.S. Geological Survey (USGS), was chosen to examine the unit hydrograph and rainfall hyetograph techniques. Rainfall and runoff data collected by the USGS at 91 streamflow-gaging stations in Texas formed a basis for the research. These data were collected as part of USGS small-watershed projects and urban watershed studies that began in the late 1950s and continued through most of the 1970s; a few gages were in operation in the mid-1980s. Selected hydrologic events from these studies were available in the form of over 220 printed reports, which offered the best aggregation of hydrologic data for the research objectives. Digital versions of the data did not exist. Therefore, significant effort was undertaken by the consortium to manually enter the data into a digital database from the printed record. The rainfall and runoff data for over 1,650 storms were entered. To enhance data integrity, considerable quality-control and quality-assurance efforts were conducted as the database was assembled and after assembly to enhance data integrity. This report documents the database and informs interested parties on its usage.

Inroads to predict in vivo toxicology-an introduction to the eTOX Project.

PubMed

Briggs, Katharine; Cases, Montserrat; Heard, David J; Pastor, Manuel; Pognan, François; Sanz, Ferran; Schwab, Christof H; Steger-Hartmann, Thomas; Sutter, Andreas; Watson, David K; Wichard, Jörg D

2012-01-01

There is a widespread awareness that the wealth of preclinical toxicity data that the pharmaceutical industry has generated in recent decades is not exploited as efficiently as it could be. Enhanced data availability for compound comparison ("read-across"), or for data mining to build predictive tools, should lead to a more efficient drug development process and contribute to the reduction of animal use (3Rs principle). In order to achieve these goals, a consortium approach, grouping numbers of relevant partners, is required. The eTOX ("electronic toxicity") consortium represents such a project and is a public-private partnership within the framework of the European Innovative Medicines Initiative (IMI). The project aims at the development of in silico prediction systems for organ and in vivo toxicity. The backbone of the project will be a database consisting of preclinical toxicity data for drug compounds or candidates extracted from previously unpublished, legacy reports from thirteen European and European operation-based pharmaceutical companies. The database will be enhanced by incorporation of publically available, high quality toxicology data. Seven academic institutes and five small-to-medium size enterprises (SMEs) contribute with their expertise in data gathering, database curation, data mining, chemoinformatics and predictive systems development. The outcome of the project will be a predictive system contributing to early potential hazard identification and risk assessment during the drug development process. The concept and strategy of the eTOX project is described here, together with current achievements and future deliverables.

CPTAC Establishes Formal Relationships with Two Academic Institutions in Taiwan | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) has entered into memorandum of understandings (MOUs) with Chang Gung University and Academia Sinica, in Taipei, Taiwan.

eMelanoBase: an online locus-specific variant database for familial melanoma.

PubMed

Fung, David C Y; Holland, Elizabeth A; Becker, Therese M; Hayward, Nicholas K; Bressac-de Paillerets, Brigitte; Mann, Graham J

2003-01-01

A proportion of melanoma-prone individuals in both familial and non-familial contexts has been shown to carry inactivating mutations in either CDKN2A or, rarely, CDK4. CDKN2A is a complex locus that encodes two unrelated proteins from alternately spliced transcripts that are read in different frames. The alpha transcript (exons 1alpha, 2, and 3) produces the p16INK4A cyclin-dependent kinase inhibitor, while the beta transcript (exons 1beta and 2) is translated as p14ARF, a stabilizing factor of p53 levels through binding to MDM2. Mutations in exon 2 can impair both polypeptides and insertions and deletions in exons 1alpha, 1beta, and 2, which can theoretically generate p16INK4A-p14ARF fusion proteins. No online database currently takes into account all the consequences of these genotypes, a situation compounded by some problematic previous annotations of CDKN2A-related sequences and descriptions of their mutations. As an initiative of the international Melanoma Genetics Consortium, we have therefore established a database of germline variants observed in all loci implicated in familial melanoma susceptibility. Such a comprehensive, publicly accessible database is an essential foundation for research on melanoma susceptibility and its clinical application. Our database serves two types of data as defined by HUGO. The core dataset includes the nucleotide variants on the genomic and transcript levels, amino acid variants, and citation. The ancillary dataset includes keyword description of events at the transcription and translation levels and epidemiological data. The application that handles users' queries was designed in the model-view-controller architecture and was implemented in Java. The object-relational database schema was deduced using functional dependency analysis. We hereby present our first functional prototype of eMelanoBase. The service is accessible via the URL www.wmi.usyd.edu.au:8080/melanoma.html. Copyright 2002 Wiley-Liss, Inc.

Using a relational database to improve mortality and length of stay for a department of surgery: a comparative review of 5200 patients.

PubMed

Ang, Darwin N; Behrns, Kevin E

2013-07-01

The emphasis on high-quality care has spawned the development of quality programs, most of which focus on broad outcome measures across a diverse group of providers. Our aim was to investigate the clinical outcomes for a department of surgery with multiple service lines of patient care using a relational database. Mortality, length of stay (LOS), patient safety indicators (PSIs), and hospital-acquired conditions were examined for each service line. Expected values for mortality and LOS were derived from University HealthSystem Consortium regression models, whereas expected values for PSIs were derived from Agency for Healthcare Research and Quality regression models. Overall, 5200 patients were evaluated from the months of January through May of both 2011 (n = 2550) and 2012 (n = 2650). The overall observed-to-expected (O/E) ratio of mortality improved from 1.03 to 0.92. The overall O/E ratio for LOS improved from 0.92 to 0.89. PSIs that predicted mortality included postoperative sepsis (O/E:1.89), postoperative respiratory failure (O/E:1.83), postoperative metabolic derangement (O/E:1.81), and postoperative deep vein thrombosis or pulmonary embolus (O/E:1.8). Mortality and LOS can be improved by using a relational database with outcomes reported to specific service lines. Service line quality can be influenced by distribution of frequent reports, group meetings, and service line-directed interventions.

IDOMAL: an ontology for malaria.

PubMed

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.

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

PubMed Central

Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

2015-01-01

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

The National Land Cover Database

USGS Publications Warehouse

Homer, Collin G.; Fry, Joyce A.; Barnes, Christopher A.

2012-01-01

The National Land Cover Database (NLCD) serves as the definitive Landsat-based, 30-meter resolution, land cover database for the Nation. NLCD provides spatial reference and descriptive data for characteristics of the land surface such as thematic class (for example, urban, agriculture, and forest), percent impervious surface, and percent tree canopy cover. NLCD supports a wide variety of Federal, State, local, and nongovernmental applications that seek to assess ecosystem status and health, understand the spatial patterns of biodiversity, predict effects of climate change, and develop land management policy. NLCD products are created by the Multi-Resolution Land Characteristics (MRLC) Consortium, a partnership of Federal agencies led by the U.S. Geological Survey. All NLCD data products are available for download at no charge to the public from the MRLC Web site: http://www.mrlc.gov.

The Relationship between SAT® Scores and Retention to the Fourth Year: 2006 SAT Validity Sample. Statistical Report 2011-6

ERIC Educational Resources Information Center

Mattern, Krista D.; Patterson, Brian F.

2011-01-01

The College Board formed a research consortium with four-year colleges and universities to build a national higher education database with the primary goal of validating the SAT® for use in college admission. The first sample included first-time, first-year students entering college in fall 2006, with 110 institutions providing students'…

Validity of the SAT® for Predicting Fourth-Year Grades: 2006 SAT Validity Sample. Statistical Report 2011-7

ERIC Educational Resources Information Center

Mattern, Krista D.; Patterson, Brian F.

2006-01-01

The College Board formed a research consortium with four-year colleges and universities to build a national higher education database with the primary goal of validating the SAT®, which is used in college admission and consists of three sections: critical reading (SAT-CR), mathematics (SAT-M) and writing (SAT-W). This report builds on a body of…

The Relationship between SAT® Scores and Retention to the Second Year: 2008 SAT Validity Sample. Statistical Report 2012-1

ERIC Educational Resources Information Center

Mattern, Krista D.; Patterson, Brian F.

2012-01-01

The College Board formed a research consortium with four-year colleges and universities to build a national higher education database with the primary goal of validating the revised SAT®, which consists of three sections: critical reading (SAT-CR), mathematics (SAT-M), and writing (SAT-W), for use in college admission. A study by Mattern and…

CPTAC | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics.

Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies

DTIC Science & Technology

2016-10-01

2016 4 . TITLE AND SUBTITLE 5a. CONTRACT NUMBER Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies 5b. GRANT NUMBER 5c...new biomarker driven trials directly to patients W81XWH-14-2-0159 None listed 20 Table of Contents Page 1. Introduction…………………………………………………………. 4 2...Keywords……………………………………………………………. 4 3. Accomplishments ..……..…………………………………………... 4 4 . Impact…………………………...…………………………………… 8 5. Changes/Problems

Proposed Standardized Neurological Endpoints for Cardiovascular Clinical Trials: An Academic Research Consortium Initiative.

PubMed

Lansky, Alexandra J; Messé, Steven R; Brickman, Adam M; Dwyer, Michael; Bart van der Worp, H; Lazar, Ronald M; Pietras, Cody G; Abrams, Kevin J; McFadden, Eugene; Petersen, Nils H; Browndyke, Jeffrey; Prendergast, Bernard; Ng, Vivian G; Cutlip, Donald E; Kapadia, Samir; Krucoff, Mitchell W; Linke, Axel; Scala Moy, Claudia; Schofer, Joachim; van Es, Gerrit-Anne; Virmani, Renu; Popma, Jeffrey; Parides, Michael K; Kodali, Susheel; Bilello, Michel; Zivadinov, Robert; Akar, Joseph; Furie, Karen L; Gress, Daryl; Voros, Szilard; Moses, Jeffrey; Greer, David; Forrest, John K; Holmes, David; Kappetein, Arie P; Mack, Michael; Baumbach, Andreas

2018-05-14

Surgical and catheter-based cardiovascular procedures and adjunctive pharmacology have an inherent risk of neurological complications. The current diversity of neurological endpoint definitions and ascertainment methods in clinical trials has led to uncertainties in the neurological risk attributable to cardiovascular procedures and inconsistent evaluation of therapies intended to prevent or mitigate neurological injury. Benefit-risk assessment of such procedures should be on the basis of an evaluation of well-defined neurological outcomes that are ascertained with consistent methods and capture the full spectrum of neurovascular injury and its clinical effect. The Neurologic Academic Research Consortium is an international collaboration intended to establish consensus on the definition, classification, and assessment of neurological endpoints applicable to clinical trials of a broad range of cardiovascular interventions. Systematic application of the proposed definitions and assessments will improve our ability to evaluate the risks of cardiovascular procedures and the safety and effectiveness of preventive therapies.

Can non‐clinical repolarization assays predict the results of clinical thorough QT studies? Results from a research consortium

PubMed Central

Park, Eunjung; Gintant, Gary A; Bi, Daoqin; Kozeli, Devi; Pettit, Syril D; Skinner, Matthew; Willard, James; Wisialowski, Todd; Koerner, John; Valentin, Jean‐Pierre

2018-01-01

Background and Purpose Translation of non‐clinical markers of delayed ventricular repolarization to clinical prolongation of the QT interval corrected for heart rate (QTc) (a biomarker for torsades de pointes proarrhythmia) remains an issue in drug discovery and regulatory evaluations. We retrospectively analysed 150 drug applications in a US Food and Drug Administration database to determine the utility of established non‐clinical in vitro IKr current human ether‐à‐go‐go‐related gene (hERG), action potential duration (APD) and in vivo (QTc) repolarization assays to detect and predict clinical QTc prolongation. Experimental Approach The predictive performance of three non‐clinical assays was compared with clinical thorough QT study outcomes based on free clinical plasma drug concentrations using sensitivity and specificity, receiver operating characteristic (ROC) curves, positive (PPVs) and negative predictive values (NPVs) and likelihood ratios (LRs). Key Results Non‐clinical assays demonstrated robust specificity (high true negative rate) but poor sensitivity (low true positive rate) for clinical QTc prolongation at low‐intermediate (1×–30×) clinical exposure multiples. The QTc assay provided the most robust PPVs and NPVs (ability to predict clinical QTc prolongation). ROC curves (overall test accuracy) and LRs (ability to influence post‐test probabilities) demonstrated overall marginal performance for hERG and QTc assays (best at 30× exposures), while the APD assay demonstrated minimal value. Conclusions and Implications The predictive value of hERG, APD and QTc assays varies, with drug concentrations strongly affecting translational performance. While useful in guiding preclinical candidates without clinical QT prolongation, hERG and QTc repolarization assays provide greater value compared with the APD assay. PMID:29181850

Patient-Reported Outcome (PRO) Consortium translation process: consensus development of updated best practices.

PubMed

Eremenco, Sonya; Pease, Sheryl; Mann, Sarah; Berry, Pamela

2017-01-01

This paper describes the rationale and goals of the Patient-Reported Outcome (PRO) Consortium's instrument translation process. The PRO Consortium has developed a number of novel PRO measures which are in the process of qualification by the U.S. Food and Drug Administration (FDA) for use in clinical trials where endpoints based on these measures would support product labeling claims. Given the importance of FDA qualification of these measures, the PRO Consortium's Process Subcommittee determined that a detailed linguistic validation (LV) process was necessary to ensure that all translations of Consortium-developed PRO measures are performed using a standardized approach with the rigor required to meet regulatory and pharmaceutical industry expectations, as well as having a clearly defined instrument translation process that the translation industry can support. The consensus process involved gathering information about current best practices from 13 translation companies with expertise in LV, consolidating the findings to generate a proposed process, and obtaining iterative feedback from the translation companies and PRO Consortium member firms on the proposed process in two rounds of review in order to update existing principles of good practice in LV and to provide sufficient detail for the translation process to ensure consistency across PRO Consortium measures, sponsors, and translation companies. The consensus development resulted in a 12-step process that outlines universal and country-specific new translation approaches, as well as country-specific adaptations of existing translations. The PRO Consortium translation process will play an important role in maintaining the validity of the data generated through these measures by ensuring that they are translated by qualified linguists following a standardized and rigorous process that reflects best practice.

A Preclinical Consortium Approach for Assessing the Efficacy of Combined Anti-CD3 Plus IL-1 Blockade in Reversing New-Onset Autoimmune Diabetes in NOD Mice

PubMed Central

Gill, Ronald G.; Pagni, Philippe P.; Kupfer, Tinalyn; Wasserfall, Clive H.; Deng, Songyan; Posgai, Amanda; Manenkova, Yulia; Bel Hani, Amira; Straub, Laura; Bernstein, Philip; Atkinson, Mark A.; Herold, Kevan C.; von Herrath, Matthias; Staeva, Teodora; Ehlers, Mario R.; Nepom, Gerald T.

2016-01-01

There is an ongoing need to develop strategic combinations of therapeutic agents to prevent type 1 diabetes (T1D) or to preserve islet β-cell mass in new-onset disease. Although clinical trials using candidate therapeutics are commonly based on preclinical studies, concern is growing regarding the reproducibility as well as the potential clinical translation of reported results using animal models of human disorders. In response, the National Institutes of Health Immune Tolerance Network and JDRF established a multicenter consortium of academic institutions designed to assess the efficacy and intergroup reproducibility of clinically applicable immunotherapies for reversing new-onset disease in the NOD mouse model of T1D. Predicated on prior studies, this consortium conducted coordinated, prospective studies, using joint standard operating procedures, fixed criteria for study entry, and common reagents, to optimize combined anti-CD3 treatment plus interleukin-1 (IL-1) blockade to reverse new-onset disease in NOD mice. We did not find that IL-1 blockade with anti–IL-1β monoclonal antibody or IL-1trap provided additional benefit for reversing new-onset disease compared with anti-CD3 treatment alone. These results demonstrate the value of larger, multicenter preclinical studies for vetting and prioritizing therapeutics for future clinical use. PMID:26718498

A Web-based Alternative Non-animal Method Database for Safety Cosmetic Evaluations

PubMed Central

Kim, Seung Won; Kim, Bae-Hwan

2016-01-01

Animal testing was used traditionally in the cosmetics industry to confirm product safety, but has begun to be banned; alternative methods to replace animal experiments are either in development, or are being validated, worldwide. Research data related to test substances are critical for developing novel alternative tests. Moreover, safety information on cosmetic materials has neither been collected in a database nor shared among researchers. Therefore, it is imperative to build and share a database of safety information on toxicological mechanisms and pathways collected through in vivo, in vitro, and in silico methods. We developed the CAMSEC database (named after the research team; the Consortium of Alternative Methods for Safety Evaluation of Cosmetics) to fulfill this purpose. On the same website, our aim is to provide updates on current alternative research methods in Korea. The database will not be used directly to conduct safety evaluations, but researchers or regulatory individuals can use it to facilitate their work in formulating safety evaluations for cosmetic materials. We hope this database will help establish new alternative research methods to conduct efficient safety evaluations of cosmetic materials. PMID:27437094

A Web-based Alternative Non-animal Method Database for Safety Cosmetic Evaluations.

PubMed

Kim, Seung Won; Kim, Bae-Hwan

2016-07-01

Animal testing was used traditionally in the cosmetics industry to confirm product safety, but has begun to be banned; alternative methods to replace animal experiments are either in development, or are being validated, worldwide. Research data related to test substances are critical for developing novel alternative tests. Moreover, safety information on cosmetic materials has neither been collected in a database nor shared among researchers. Therefore, it is imperative to build and share a database of safety information on toxicological mechanisms and pathways collected through in vivo, in vitro, and in silico methods. We developed the CAMSEC database (named after the research team; the Consortium of Alternative Methods for Safety Evaluation of Cosmetics) to fulfill this purpose. On the same website, our aim is to provide updates on current alternative research methods in Korea. The database will not be used directly to conduct safety evaluations, but researchers or regulatory individuals can use it to facilitate their work in formulating safety evaluations for cosmetic materials. We hope this database will help establish new alternative research methods to conduct efficient safety evaluations of cosmetic materials.

Genetics Home Reference: eosinophil peroxidase deficiency

MedlinePlus

... an Eosinophil? International Eosinophil Society, Inc.: Patient Support Groups Rare Disease Clinical Research Network: Consortium of Eosinophil Gastrointestinal Disease Researchers Scientific Articles ...

Searching for religion and mental health studies required health, social science, and grey literature databases.

PubMed

Wright, Judy M; Cottrell, David J; Mir, Ghazala

2014-07-01

To determine the optimal databases to search for studies of faith-sensitive interventions for treating depression. We examined 23 health, social science, religious, and grey literature databases searched for an evidence synthesis. Databases were prioritized by yield of (1) search results, (2) potentially relevant references identified during screening, (3) included references contained in the synthesis, and (4) included references that were available in the database. We assessed the impact of databases beyond MEDLINE, EMBASE, and PsycINFO by their ability to supply studies identifying new themes and issues. We identified pragmatic workload factors that influence database selection. PsycINFO was the best performing database within all priority lists. ArabPsyNet, CINAHL, Dissertations and Theses, EMBASE, Global Health, Health Management Information Consortium, MEDLINE, PsycINFO, and Sociological Abstracts were essential for our searches to retrieve the included references. Citation tracking activities and the personal library of one of the research teams made significant contributions of unique, relevant references. Religion studies databases (Am Theo Lib Assoc, FRANCIS) did not provide unique, relevant references. Literature searches for reviews and evidence syntheses of religion and health studies should include social science, grey literature, non-Western databases, personal libraries, and citation tracking activities. Copyright © 2014 Elsevier Inc. All rights reserved.

Illuminating the Depths of the MagIC (Magnetics Information Consortium) Database

NASA Astrophysics Data System (ADS)

Koppers, A. A. P.; Minnett, R.; Jarboe, N.; Jonestrask, L.; Tauxe, L.; Constable, C.

2015-12-01

The Magnetics Information Consortium (http://earthref.org/MagIC/) is a grass-roots cyberinfrastructure effort envisioned by the paleo-, geo-, and rock magnetic scientific community. Its mission is to archive their wealth of peer-reviewed raw data and interpretations from magnetics studies on natural and synthetic samples. Many of these valuable data are legacy datasets that were never published in their entirety, some resided in other databases that are no longer maintained, and others were never digitized from the field notebooks and lab work. Due to the volume of data collected, most studies, modern and legacy, only publish the interpreted results and, occasionally, a subset of the raw data. MagIC is making an extraordinary effort to archive these data in a single data model, including the raw instrument measurements if possible. This facilitates the reproducibility of the interpretations, the re-interpretation of the raw data as the community introduces new techniques, and the compilation of heterogeneous datasets that are otherwise distributed across multiple formats and physical locations. MagIC has developed tools to assist the scientific community in many stages of their workflow. Contributors easily share studies (in a private mode if so desired) in the MagIC Database with colleagues and reviewers prior to publication, publish the data online after the study is peer reviewed, and visualize their data in the context of the rest of the contributions to the MagIC Database. From organizing their data in the MagIC Data Model with an online editable spreadsheet, to validating the integrity of the dataset with automated plots and statistics, MagIC is continually lowering the barriers to transforming dark data into transparent and reproducible datasets. Additionally, this web application generalizes to other databases in MagIC's umbrella website (EarthRef.org) so that the Geochemical Earth Reference Model (http://earthref.org/GERM/) portal, Seamount Biogeosciences Network (http://earthref.org/SBN/), EarthRef Digital Archive (http://earthref.org/ERDA/) and EarthRef Reference Database (http://earthref.org/ERR/) benefit from its development.

Standardizing terms for clinical pharmacogenetic test results: consensus terms from the Clinical Pharmacogenetics Implementation Consortium (CPIC).

PubMed

Caudle, Kelly E; Dunnenberger, Henry M; Freimuth, Robert R; Peterson, Josh F; Burlison, Jonathan D; Whirl-Carrillo, Michelle; Scott, Stuart A; Rehm, Heidi L; Williams, Marc S; Klein, Teri E; Relling, Mary V; Hoffman, James M

2017-02-01

Reporting and sharing pharmacogenetic test results across clinical laboratories and electronic health records is a crucial step toward the implementation of clinical pharmacogenetics, but allele function and phenotype terms are not standardized. Our goal was to develop terms that can be broadly applied to characterize pharmacogenetic allele function and inferred phenotypes. Terms currently used by genetic testing laboratories and in the literature were identified. The Clinical Pharmacogenetics Implementation Consortium (CPIC) used the Delphi method to obtain a consensus and agree on uniform terms among pharmacogenetic experts. Experts with diverse involvement in at least one area of pharmacogenetics (clinicians, researchers, genetic testing laboratorians, pharmacogenetics implementers, and clinical informaticians; n = 58) participated. After completion of five surveys, a consensus (>70%) was reached with 90% of experts agreeing to the final sets of pharmacogenetic terms. The proposed standardized pharmacogenetic terms will improve the understanding and interpretation of pharmacogenetic tests and reduce confusion by maintaining consistent nomenclature. These standard terms can also facilitate pharmacogenetic data sharing across diverse electronic health care record systems with clinical decision support.Genet Med 19 2, 215-223.

Traditional Chinese medicine research in the post-genomic era: good practice, priorities, challenges and opportunities.

PubMed

Uzuner, Halil; Bauer, Rudolf; Fan, Tai-Ping; Guo, De-An; Dias, Alberto; El-Nezami, Hani; Efferth, Thomas; Williamson, Elizabeth M; Heinrich, Michael; Robinson, Nicola; Hylands, Peter J; Hendry, Bruce M; Cheng, Yung-Chi; Xu, Qihe

2012-04-10

GP-TCM is the 1st EU-funded Coordination Action consortium dedicated to traditional Chinese medicine (TCM) research. This paper aims to summarise the objectives, structure and activities of the consortium and introduces the position of the consortium regarding good practice, priorities, challenges and opportunities in TCM research. Serving as the introductory paper for the GP-TCM Journal of Ethnopharmacology special issue, this paper describes the roadmap of this special issue and reports how the main outputs of the ten GP-TCM work packages are integrated, and have led to consortium-wide conclusions. Literature studies, opinion polls and discussions among consortium members and stakeholders. By January 2012, through 3 years of team building, the GP-TCM consortium had grown into a large collaborative network involving ∼200 scientists from 24 countries and 107 institutions. Consortium members had worked closely to address good practice issues related to various aspects of Chinese herbal medicine (CHM) and acupuncture research, the focus of this Journal of Ethnopharmacology special issue, leading to state-of-the-art reports, guidelines and consensus on the application of omics technologies in TCM research. In addition, through an online survey open to GP-TCM members and non-members, we polled opinions on grand priorities, challenges and opportunities in TCM research. Based on the poll, although consortium members and non-members had diverse opinions on the major challenges in the field, both groups agreed that high-quality efficacy/effectiveness and mechanistic studies are grand priorities and that the TCM legacy in general and its management of chronic diseases in particular represent grand opportunities. Consortium members cast their votes of confidence in omics and systems biology approaches to TCM research and believed that quality and pharmacovigilance of TCM products are not only grand priorities, but also grand challenges. Non-members, however, gave priority to integrative medicine, concerned on the impact of regulation of TCM practitioners and emphasised intersectoral collaborations in funding TCM research, especially clinical trials. The GP-TCM consortium made great efforts to address some fundamental issues in TCM research, including developing guidelines, as well as identifying priorities, challenges and opportunities. These consortium guidelines and consensus will need dissemination, validation and further development through continued interregional, interdisciplinary and intersectoral collaborations. To promote this, a new consortium, known as the GP-TCM Research Association, is being established to succeed the 3-year fixed term FP7 GP-TCM consortium and will be officially launched at the Final GP-TCM Congress in Leiden, the Netherlands, in April 2012. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

A Project to Computerize Performance Objectives and Criterion-Referenced Measures in Occupational Education for Research and Determination of Applicability to Handicapped Learners. Final Report.

ERIC Educational Resources Information Center

Lee, Connie W.; Hinson, Tony M.

This publication is the final report of a 21-month project designed to (1) expand and refine the computer capabilities of the Vocational-Technical Education Consortium of States (V-TECS) to ensure rapid data access for generating routine and special occupational data-based reports; (2) develop and implement a computer storage and retrieval system…

Northeast Artificial Intelligence Consortium Annual Report for 1987. Volume 4. Research in Automated Photointerpretation

DTIC Science & Technology

1989-03-01

KOWLEDGE INFERENCE IMAGE DAAAEENGINE DATABASE Automated Photointerpretation Testbed. 4.1.7 Fig. .1.1-2 An Initial Segmentation of an Image / zx...MRF) theory provide a powerful alternative texture model and have resulted in intensive research activity in MRF model- based texture analysis...interpretation process. 5. Additional, and perhaps more powerful , features have to be incorporated into the image segmentation procedure. 6. Object detection

NLCD tree canopy cover (TCC) maps of the contiguous United States and coastal Alaska

Treesearch

Robert Benton; Bonnie Ruefenacht; Vicky Johnson; Tanushree Biswas; Craig Baker; Mark Finco; Kevin Megown; John Coulston; Ken Winterberger; Mark Riley

2015-01-01

A tree canopy cover (TCC) map is one of three elements in the National Land Cover Database (NLCD) 2011 suite of nationwide geospatial data layers. In 2010, the USDA Forest Service (USFS) committed to creating the TCC layer as a member of the Multi-Resolution Land Cover (MRLC) consortium. A general methodology for creating the TCC layer was reported at the 2012 FIA...

The Relationship between SAT® Scores and Retention to the Second Year: Replication with the 2010 SAT Validity Sample. Statistical Report 2013-1

ERIC Educational Resources Information Center

Mattern, Krista D.; Patterson, Brian F.

2013-01-01

The College Board formed a research consortium with four-year colleges and universities to build a national higher education database with the primary goal of validating the revised SAT for use in college admission. A study by Mattern and Patterson (2009) examined the relationship between SAT scores and retention to the second year. The sample…

The Relationship between SAT Scores and Retention to the Second Year: Replication with 2009 SAT Validity Sample. Statistical Report 2011-3

ERIC Educational Resources Information Center

Mattern, Krista D.; Patterson, Brian F.

2012-01-01

The College Board formed a research consortium with four-year colleges and universities to build a national higher education database with the primary goal of validating the revised SAT for use in college admission. A study by Mattern and Patterson (2009) examined the relationship between SAT scores and retention to the second year of college. The…

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.

PubMed

Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Schneider, Michel; Bansal, Parit; Bridge, Alan J; Poux, Sylvain; Bougueleret, Lydie; Xenarios, Ioannis

2016-01-01

The Universal Protein Resource (UniProt, http://www.uniprot.org ) consortium is an initiative of the SIB Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB), updated every 4 weeks, and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc).The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms. Plant protein entries are produced in the frame of the Plant Proteome Annotation Program (PPAP), with an emphasis on characterized proteins of Arabidopsis thaliana and Oryza sativa. High level annotations provided by UniProtKB/Swiss-Prot are widely used to predict annotation of newly available proteins through automatic pipelines.The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry. We will also present some of the tools and databases that are linked to each entry.

Cohort Profile Update: the TRacking Adolescents' Individual Lives Survey (TRAILS).

PubMed

Oldehinkel, Albertine J; Rosmalen, Judith Gm; Buitelaar, Jan K; Hoek, Hans W; Ormel, Johan; Raven, Dennis; Reijneveld, Sijmen A; Veenstra, René; Verhulst, Frank C; Vollebergh, Wilma Am; Hartman, Catharina A

2015-02-01

TRAILS consists of a population cohort (N=2230) and a clinical cohort (N=543), both of which were followed from about age 11 years onwards. To date, the population cohort has been assessed five times over a period of 11 years, with retention rates ranging between 80% and 96%. The clinical cohort has been assessed four times over a period of 8 years, with retention rates ranging between 77% and 85%. Since the IJE published a cohort profile on the TRAILS in 2008, the participants have matured from adolescents into young adults. The focus shifted from parents and school to entry into the labour market and family formation, including offspring. Furthermore, psychiatric diagnostic interviews were administered, the database was linked to a Psychiatric Case Registry, and the availability of genome-wide SNP variations opened the door to genome-wide association studies regarding a wide range of (endo)phenotypes. With some delay, TRAILS data are available to researchers outside the TRAILS consortium without costs; access can be obtained by submitting a publication proposal (see www.trails.nl). © The Author 2014; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.

The importance of international collaboration for rare diseases research: a European perspective

PubMed Central

Julkowska, D; Austin, C P; Cutillo, C M; Gancberg, D; Hager, C; Halftermeyer, J; Jonker, A H; Lau, L P L; Norstedt, I; Rath, A; Schuster, R; Simelyte, E; van Weely, S

2017-01-01

Over the last two decades, important contributions were made at national, European and international levels to foster collaboration into rare diseases research. The European Union (EU) has put much effort into funding rare diseases research, encouraging national funding organizations to collaborate together in the E-Rare program, setting up European Reference Networks for rare diseases and complex conditions, and initiating the International Rare Diseases Research Consortium (IRDiRC) together with the National Institutes of Health in the USA. Co-ordination of the activities of funding agencies, academic researchers, companies, regulatory bodies, and patient advocacy organizations and partnerships with, for example, the European Research Infrastructures maximizes the collective impact of global investments in rare diseases research. This contributes to accelerating progress, for example, in faster diagnosis through enhanced discovery of causative genes, better understanding of natural history of rare diseases through creation of common registries and databases and boosting of innovative therapeutic approaches. Several examples of funded pre-clinical and clinical gene therapy projects show that integration of multinational and multidisciplinary expertize generates new knowledge and can result in multicentre gene therapy trials. International collaboration in rare diseases research is key to improve the life of people living with a rare disease. PMID:28440796

The importance of international collaboration for rare diseases research: a European perspective.

PubMed

Julkowska, D; Austin, C P; Cutillo, C M; Gancberg, D; Hager, C; Halftermeyer, J; Jonker, A H; Lau, L P L; Norstedt, I; Rath, A; Schuster, R; Simelyte, E; van Weely, S

2017-09-01

Over the last two decades, important contributions were made at national, European and international levels to foster collaboration into rare diseases research. The European Union (EU) has put much effort into funding rare diseases research, encouraging national funding organizations to collaborate together in the E-Rare program, setting up European Reference Networks for rare diseases and complex conditions, and initiating the International Rare Diseases Research Consortium (IRDiRC) together with the National Institutes of Health in the USA. Co-ordination of the activities of funding agencies, academic researchers, companies, regulatory bodies, and patient advocacy organizations and partnerships with, for example, the European Research Infrastructures maximizes the collective impact of global investments in rare diseases research. This contributes to accelerating progress, for example, in faster diagnosis through enhanced discovery of causative genes, better understanding of natural history of rare diseases through creation of common registries and databases and boosting of innovative therapeutic approaches. Several examples of funded pre-clinical and clinical gene therapy projects show that integration of multinational and multidisciplinary expertize generates new knowledge and can result in multicentre gene therapy trials. International collaboration in rare diseases research is key to improve the life of people living with a rare disease.

Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways.

PubMed

Becnel, Lauren B; Darlington, Yolanda F; Ochsner, Scott A; Easton-Marks, Jeremy R; Watkins, Christopher M; McOwiti, Apollo; Kankanamge, Wasula H; Wise, Michael W; DeHart, Michael; Margolis, Ronald N; McKenna, Neil J

2015-01-01

Signaling pathways involving nuclear receptors (NRs), their ligands and coregulators, regulate tissue-specific transcriptomes in diverse processes, including development, metabolism, reproduction, the immune response and neuronal function, as well as in their associated pathologies. The Nuclear Receptor Signaling Atlas (NURSA) is a Consortium focused around a Hub website (www.nursa.org) that annotates and integrates diverse 'omics datasets originating from the published literature and NURSA-funded Data Source Projects (NDSPs). These datasets are then exposed to the scientific community on an Open Access basis through user-friendly data browsing and search interfaces. Here, we describe the redesign of the Hub, version 3.0, to deploy "Web 2.0" technologies and add richer, more diverse content. The Molecule Pages, which aggregate information relevant to NR signaling pathways from myriad external databases, have been enhanced to include resources for basic scientists, such as post-translational modification sites and targeting miRNAs, and for clinicians, such as clinical trials. A portal to NURSA's Open Access, PubMed-indexed journal Nuclear Receptor Signaling has been added to facilitate manuscript submissions. Datasets and information on reagents generated by NDSPs are available, as is information concerning periodic new NDSP funding solicitations. Finally, the new website integrates the Transcriptomine analysis tool, which allows for mining of millions of richly annotated public transcriptomic data points in the field, providing an environment for dataset re-use and citation, bench data validation and hypothesis generation. We anticipate that this new release of the NURSA database will have tangible, long term benefits for both basic and clinical research in this field.

A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research

PubMed Central

Amin, Waqas; Singh, Harpreet; Pople, Andre K.; Winters, Sharon; Dhir, Rajiv; Parwani, Anil V.; Becich, Michael J.

2010-01-01

Context: Tissue banking informatics deals with standardized annotation, collection and storage of biospecimens that can further be shared by researchers. Over the last decade, the Department of Biomedical Informatics (DBMI) at the University of Pittsburgh has developed various tissue banking informatics tools to expedite translational medicine research. In this review, we describe the technical approach and capabilities of these models. Design: Clinical annotation of biospecimens requires data retrieval from various clinical information systems and the de-identification of the data by an honest broker. Based upon these requirements, DBMI, with its collaborators, has developed both Oracle-based organ-specific data marts and a more generic, model-driven architecture for biorepositories. The organ-specific models are developed utilizing Oracle 9.2.0.1 server tools and software applications and the model-driven architecture is implemented in a J2EE framework. Result: The organ-specific biorepositories implemented by DBMI include the Cooperative Prostate Cancer Tissue Resource (http://www.cpctr.info/), Pennsylvania Cancer Alliance Bioinformatics Consortium (http://pcabc.upmc.edu/main.cfm), EDRN Colorectal and Pancreatic Neoplasm Database (http://edrn.nci.nih.gov/) and Specialized Programs of Research Excellence (SPORE) Head and Neck Neoplasm Database (http://spores.nci.nih.gov/current/hn/index.htm). The model-based architecture is represented by the National Mesothelioma Virtual Bank (http://mesotissue.org/). These biorepositories provide thousands of well annotated biospecimens for the researchers that are searchable through query interfaces available via the Internet. Conclusion: These systems, developed and supported by our institute, serve to form a common platform for cancer research to accelerate progress in clinical and translational research. In addition, they provide a tangible infrastructure and resource for exposing research resources and biospecimen services in collaboration with the clinical anatomic pathology laboratory information system (APLIS) and the cancer registry information systems. PMID:20922029

A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research.

PubMed

Amin, Waqas; Singh, Harpreet; Pople, Andre K; Winters, Sharon; Dhir, Rajiv; Parwani, Anil V; Becich, Michael J

2010-08-10

Tissue banking informatics deals with standardized annotation, collection and storage of biospecimens that can further be shared by researchers. Over the last decade, the Department of Biomedical Informatics (DBMI) at the University of Pittsburgh has developed various tissue banking informatics tools to expedite translational medicine research. In this review, we describe the technical approach and capabilities of these models. Clinical annotation of biospecimens requires data retrieval from various clinical information systems and the de-identification of the data by an honest broker. Based upon these requirements, DBMI, with its collaborators, has developed both Oracle-based organ-specific data marts and a more generic, model-driven architecture for biorepositories. The organ-specific models are developed utilizing Oracle 9.2.0.1 server tools and software applications and the model-driven architecture is implemented in a J2EE framework. The organ-specific biorepositories implemented by DBMI include the Cooperative Prostate Cancer Tissue Resource (http://www.cpctr.info/), Pennsylvania Cancer Alliance Bioinformatics Consortium (http://pcabc.upmc.edu/main.cfm), EDRN Colorectal and Pancreatic Neoplasm Database (http://edrn.nci.nih.gov/) and Specialized Programs of Research Excellence (SPORE) Head and Neck Neoplasm Database (http://spores.nci.nih.gov/current/hn/index.htm). The model-based architecture is represented by the National Mesothelioma Virtual Bank (http://mesotissue.org/). These biorepositories provide thousands of well annotated biospecimens for the researchers that are searchable through query interfaces available via the Internet. These systems, developed and supported by our institute, serve to form a common platform for cancer research to accelerate progress in clinical and translational research. In addition, they provide a tangible infrastructure and resource for exposing research resources and biospecimen services in collaboration with the clinical anatomic pathology laboratory information system (APLIS) and the cancer registry information systems.

The Genetics of Endophenotypes of Neurofunction to Understand Schizophrenia (GENUS) consortium: A collaborative cognitive and neuroimaging genetics project.

PubMed

Blokland, Gabriëlla A M; Del Re, Elisabetta C; Mesholam-Gately, Raquelle I; Jovicich, Jorge; Trampush, Joey W; Keshavan, Matcheri S; DeLisi, Lynn E; Walters, James T R; Turner, Jessica A; Malhotra, Anil K; Lencz, Todd; Shenton, Martha E; Voineskos, Aristotle N; Rujescu, Dan; Giegling, Ina; Kahn, René S; Roffman, Joshua L; Holt, Daphne J; Ehrlich, Stefan; Kikinis, Zora; Dazzan, Paola; Murray, Robin M; Di Forti, Marta; Lee, Jimmy; Sim, Kang; Lam, Max; Wolthusen, Rick P F; de Zwarte, Sonja M C; Walton, Esther; Cosgrove, Donna; Kelly, Sinead; Maleki, Nasim; Osiecki, Lisa; Picchioni, Marco M; Bramon, Elvira; Russo, Manuela; David, Anthony S; Mondelli, Valeria; Reinders, Antje A T S; Falcone, M Aurora; Hartmann, Annette M; Konte, Bettina; Morris, Derek W; Gill, Michael; Corvin, Aiden P; Cahn, Wiepke; Ho, New Fei; Liu, Jian Jun; Keefe, Richard S E; Gollub, Randy L; Manoach, Dara S; Calhoun, Vince D; Schulz, S Charles; Sponheim, Scott R; Goff, Donald C; Buka, Stephen L; Cherkerzian, Sara; Thermenos, Heidi W; Kubicki, Marek; Nestor, Paul G; Dickie, Erin W; Vassos, Evangelos; Ciufolini, Simone; Reis Marques, Tiago; Crossley, Nicolas A; Purcell, Shaun M; Smoller, Jordan W; van Haren, Neeltje E M; Toulopoulou, Timothea; Donohoe, Gary; Goldstein, Jill M; Seidman, Larry J; McCarley, Robert W; Petryshen, Tracey L

2018-05-01

Schizophrenia has a large genetic component, and the pathways from genes to illness manifestation are beginning to be identified. The Genetics of Endophenotypes of Neurofunction to Understand Schizophrenia (GENUS) Consortium aims to clarify the role of genetic variation in brain abnormalities underlying schizophrenia. This article describes the GENUS Consortium sample collection. We identified existing samples collected for schizophrenia studies consisting of patients, controls, and/or individuals at familial high-risk (FHR) for schizophrenia. Samples had single nucleotide polymorphism (SNP) array data or genomic DNA, clinical and demographic data, and neuropsychological and/or brain magnetic resonance imaging (MRI) data. Data were subjected to quality control procedures at a central site. Sixteen research groups contributed data from 5199 psychosis patients, 4877 controls, and 725 FHR individuals. All participants have relevant demographic data and all patients have relevant clinical data. The sex ratio is 56.5% male and 43.5% female. Significant differences exist between diagnostic groups for premorbid and current IQ (both p<1×10 -10 ). Data from a diversity of neuropsychological tests are available for 92% of participants, and 30% have structural MRI scans (half also have diffusion-weighted MRI scans). SNP data are available for 76% of participants. The ancestry composition is 70% European, 20% East Asian, 7% African, and 3% other. The Consortium is investigating the genetic contribution to brain phenotypes in a schizophrenia sample collection of >10,000 participants. The breadth of data across clinical, genetic, neuropsychological, and MRI modalities provides an important opportunity for elucidating the genetic basis of neural processes underlying schizophrenia. Copyright © 2017 Elsevier B.V. All rights reserved.

Genetics Home Reference: cerebrotendinous xanthomatosis

MedlinePlus

... links) National Institute of Neurological Disorders and Stroke: Lipid Storage Diseases Information Page Rare Diseases Clinical Research Network: Sterol & Isopernoid Research Consortium Educational Resources (5 ...

Emergency Medicine Resources within the Clinical Translational Science Institutes: A Cross-Sectional Study

PubMed Central

Meurer, William J.; Quinn, James; Lindsell, Christopher; Schneider, Sandra; Newgard, Craig D.

2016-01-01

Background The Clinical and Translational Science Award (CTSA) program aims to strengthen and support translational research by accelerating the process of translating laboratory discoveries into treatments for patients, training a new generation of clinical and translational researchers, and engaging communities in clinical research efforts. Yet, little is known about how emergency care researchers have interacted with and utilized the resources of academic institutions with CTSAs. Objective The purpose of this survey was to describe how emergency care researchers use local CTSA resources, to ascertain what proportion of CTSA consortium members have active emergency care research programs, and to solicit participation in a national CTSA-associated emergency care translational research network. Methods Survey of all emergency departments affiliated with a CTSA. Results Of the 65 CTSA consortium members, three had no emergency care research program and we obtained responses from 46 of the remaining 62 (74% response rate). The interactions with and resources used by emergency care researchers varied widely. Methodology and biostatistics support was most frequently accessed (77%), followed closely by education and training programs (60%). Several emergency care research programs (76%) had submitted for funding through CTSAs, with 71% receiving awards. Most CTSA consortium members had an active emergency care research infrastructure: 21 (46%) had 24/7 availability to recruit and screen for research, 21 (46%) had less than 24/7 research recruitment. A number of emergency care research programs participated in NIH research networks with the Neurological Emergencies Treatment Trials network most highly represented with 23 (59%) sites. Most emergency care research programs (96%) were interested in participating in a CTSA-based emergency care translational research network. Conclusions Despite little initial involvement in development of the CTSA program, there has been moderate interaction between CTSAs and emergency care. There is considerable interest in participating in a CTSA consortium based emergency care translational research network. PMID:26826059

Emergency Medicine Resources Within the Clinical Translational Science Institutes: A Cross-sectional Study.

PubMed

Meurer, William J; Quinn, James; Lindsell, Christopher; Schneider, Sandra; Newgard, Craig D

2016-06-01

The Clinical and Translational Science Award (CTSA) program aims to strengthen and support translational research by accelerating the process of translating laboratory discoveries into treatments for patients, training a new generation of clinical and translational researchers, and engaging communities in clinical research efforts. Yet, little is known about how emergency care researchers have interacted with and utilized the resources of academic institutions with CTSAs. The purpose of this survey was to describe how emergency care researchers use local CTSA resources, to ascertain what proportion of CTSA consortium members have active emergency care research (ECR) programs, and to solicit participation in a national CTSA-associated emergency care translational research network. This study was a survey of all emergency departments affiliated with a CTSA. Of the 65 CTSA consortium members, three had no ECR program and we obtained responses from 46 of the remaining 62 (74% response rate). The interactions with and resources used by emergency care researchers varied widely. Methodology and biostatistics support was most frequently accessed (77%), followed closely by education and training programs (60%). Several ECR programs (76%) had submitted for funding through CTSAs, with 71% receiving awards. Most CTSA consortium members had an active ECR infrastructure: 21 (46%) had 24/7 availability to recruit and screen for research, and 21 (46%) had less than 24/7 research recruitment. A number of emergency care research programs participated in National Institutes of Health research networks with the Neurological Emergencies Treatment Trials network most highly represented with 23 (59%) sites. Most ECR programs (96%) were interested in participating in a CTSA-based emergency care translational research network. Despite little initial involvement in development of the CTSA program, there has been moderate interaction between CTSAs and emergency care. There is considerable interest in participating in a CTSA consortium-based emergency care translational research network. © 2016 by the Society for Academic Emergency Medicine.

Novel LOVD databases for hereditary breast cancer and colorectal cancer genes in the Chinese population.

PubMed

Pan, Min; Cong, Peikuan; Wang, Yue; Lin, Changsong; Yuan, Ying; Dong, Jian; Banerjee, Santasree; Zhang, Tao; Chen, Yanling; Zhang, Ting; Chen, Mingqing; Hu, Peter; Zheng, Shu; Zhang, Jin; Qi, Ming

2011-12-01

The Human Variome Project (HVP) is an international consortium of clinicians, geneticists, and researchers from over 30 countries, aiming to facilitate the establishment and maintenance of standards, systems, and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The HVP-China Node will build new and supplement existing databases of genetic diseases. As the first effort, we have created a novel variant database of BRCA1 and BRCA2, mismatch repair genes (MMR), and APC genes for breast cancer, Lynch syndrome, and familial adenomatous polyposis (FAP), respectively, in the Chinese population using the Leiden Open Variation Database (LOVD) format. We searched PubMed and some Chinese search engines to collect all the variants of these genes in the Chinese population that have already been detected and reported. There are some differences in the gene variants between the Chinese population and that of other ethnicities. The database is available online at http://www.genomed.org/LOVD/. Our database will appear to users who survey other LOVD databases (e.g., by Google search, or by NCBI GeneTests search). Remote submissions are accepted, and the information is updated monthly. © 2011 Wiley Periodicals, Inc.

The IntAct molecular interaction database in 2012

PubMed Central

Kerrien, Samuel; Aranda, Bruno; Breuza, Lionel; Bridge, Alan; Broackes-Carter, Fiona; Chen, Carol; Duesbury, Margaret; Dumousseau, Marine; Feuermann, Marc; Hinz, Ursula; Jandrasits, Christine; Jimenez, Rafael C.; Khadake, Jyoti; Mahadevan, Usha; Masson, Patrick; Pedruzzi, Ivo; Pfeiffenberger, Eric; Porras, Pablo; Raghunath, Arathi; Roechert, Bernd; Orchard, Sandra; Hermjakob, Henning

2012-01-01

IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275 000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact. PMID:22121220

Family history in primary care: understanding GPs' resistance to clinical genetics--qualitative study.

PubMed

Mathers, Jonathan; Greenfield, Sheila; Metcalfe, Alison; Cole, Trevor; Flanagan, Sarah; Wilson, Sue

2010-05-01

National and local evaluations of clinical genetics service pilots have experienced difficulty in engaging with GPs. To understand GPs' reluctance to engage with clinical genetics service developments, via an examination of the role of family history in general practice. Qualitative study using semi-structured one-to-one interviews. The West Midlands, UK. Interviews with 21 GPs working in 15 practices, based on a stratified random sample from the Midlands Research Practices Consortium database. Thematic analysis proceeded alongside data generation. Framework grids were constructed for comparative analytical questioning. Interpretation was framed by two explanatory models: a knowledge deficit model, and practice and professional identity model. There is a clear distinction between the routine use and function of family history in GPs' clinical decision making, and contrasting conceptualisations of genetics and 'genetic conditions'. Although genetics is clearly a part of current GP practice, with acknowledgement of genetic components to multifactorial disease, this is distinguished from 'genetic conditions' which are seen as rare, complex single-gene disorders. Importantly, family history takes its place within a broader notion of the 'family doctor' that interviewees identified as a key aspect of their role. In contrast, clinical genetics was not identified as a core component of generalist practice. The likely effectiveness of educational policy interventions aimed at GPs that focus solely on knowledge deficit models, is questionable. There is a need to acknowledge how appropriate practice is constructed by GPs, within the context of accepted generalist roles and related identities.

HER2 mutations in lung adenocarcinomas: A report from the Lung Cancer Mutation Consortium.

PubMed

Pillai, Rathi N; Behera, Madhusmita; Berry, Lynne D; Rossi, Mike R; Kris, Mark G; Johnson, Bruce E; Bunn, Paul A; Ramalingam, Suresh S; Khuri, Fadlo R

2017-11-01

Human epidermal growth factor receptor 2 (HER2) mutations have been reported in lung adenocarcinomas. Herein, the authors describe the prevalence, clinical features, and outcomes associated with HER2 mutations in 1007 patients in the Lung Cancer Mutation Consortium (LCMC). Patients with advanced-stage lung adenocarcinomas were enrolled to the LCMC. Tumor specimens were assessed for diagnosis and adequacy; multiplexed genotyping was performed in Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories to examine 10 oncogenic drivers. The LCMC database was queried for patients with HER2 mutations to access demographic data, treatment history, and vital status. An exploratory analysis was performed to evaluate the survival of patients with HER2 mutations who were treated with HER2-directed therapies. A total of 920 patients were tested for HER2 mutations; 24 patients (3%) harbored exon 20 insertion mutations (95% confidence interval, 2%-4%). One patient had a concurrent mesenchymal-epithelial transition factor (MET) amplification. The median age of the patients was 62 years, with a slight predominance of females over males (14 females vs 10 males). The majority of the patients were never-smokers (71%) and presented with advanced disease at the time of diagnosis. The median survival for patients who received HER2-targeted therapies (12 patients) was 2.1 years compared with 1.4 years for those who did not (12 patients) (P = .48). Patients with HER2 mutations were found to have inferior survival compared with the rest of the LCMC cohort with other mutations: the median survival was 3.5 years in the LCMC population receiving targeted therapy and 2.4 years for patients not receiving targeted therapy. HER2 mutations were detected in 3% of patients with lung adenocarcinoma in the LCMC. HER2-directed therapies should be investigated in this subgroup of patients. Cancer 2017;123:4099-4105. © 2017 American Cancer Society. © 2017 American Cancer Society.

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

PubMed Central

Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Ruiz, Manuel; Rouard, Mathieu; Hazekamp, Tom; Takeya, Masaru; Doi, Koji; Satoh, Kouji; Costa, Marcos; Simon, Reinhard; Balaji, Jayashree; Akintunde, Akinnola; Mauleon, Ramil; Wanchana, Samart; Shah, Trushar; Anacleto, Mylah; Portugal, Arllet; Ulat, Victor Jun; Thongjuea, Supat; Braak, Kyle; Ritter, Sebastian; Dereeper, Alexis; Skofic, Milko; Rojas, Edwin; Martins, Natalia; Pappas, Georgios; Alamban, Ryan; Almodiel, Roque; Barboza, Lord Hendrix; Detras, Jeffrey; Manansala, Kevin; Mendoza, Michael Jonathan; Morales, Jeffrey; Peralta, Barry; Valerio, Rowena; Zhang, Yi; Gregorio, Sergio; Hermocilla, Joseph; Echavez, Michael; Yap, Jan Michael; Farmer, Andrew; Schiltz, Gary; Lee, Jennifer; Casstevens, Terry; Jaiswal, Pankaj; Meintjes, Ayton; Wilkinson, Mark; Good, Benjamin; Wagner, James; Morris, Jane; Marshall, David; Collins, Anthony; Kikuchi, Shoshi; Metz, Thomas; McLaren, Graham; van Hintum, Theo

2008-01-01

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. PMID:18483570

Proceedings -- US Russian workshop on fuel cell technologies (in English;Russian)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, B.; Sylwester, A.

1996-04-01

On September 26--28, 1995, Sandia National Laboratories sponsored the first Joint US/Russian Workshop on Fuel Cell Technology at the Marriott Hotel in Albuquerque, New Mexico. This workshop brought together the US and Russian fuel cell communities as represented by users, producers, R and D establishments and government agencies. Customer needs and potential markets in both countries were discussed to establish a customer focus for the workshop. Parallel technical sessions defined research needs and opportunities for collaboration to advance fuel cell technology. A desired outcome of the workshop was the formation of a Russian/American Fuel Cell Consortium to advance fuel cellmore » technology for application in emerging markets in both countries. This consortium is envisioned to involve industry and national labs in both countries. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.« less

LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system

PubMed Central

Bannasch, Detlev; Mehrle, Alexander; Glatting, Karl-Heinz; Pepperkok, Rainer; Poustka, Annemarie; Wiemann, Stefan

2004-01-01

We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on the encoded proteins produced in functional genomics and proteomics approaches. The database also serves as a sample-tracking system to manage the process from cDNA to experimental read-out and data interpretation. A web interface enables the scientific community to explore and visualize features of the annotated cDNAs and ORFs combined with experimental results, and thus helps to unravel new features of proteins with as yet unknown functions. PMID:14681468

76 FR 66932 - The National Cancer Institute (NCI) Announces the Initiation of a Public Private Industry...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-28

...The Alliance for Nanotechnology in Cancer of the National Cancer Institute (NCI) is initiating a public private industry partnership called TONIC (Translation Of Nanotechnology In Cancer) to promote translational research and development opportunities of nanotechnology-based cancer solutions. An immediate consequence of this effort will be the formation of a consortium involving government and pharmaceutical, and biotechnology companies. This consortium will evaluate promising nanotechnology platforms and facilitate their successful translation from academic research to clinical environment, resulting in safe, timely, effective and novel diagnosis and treatment options for cancer patients. The purpose of this notice is to inform the community about the Alliance for Nanotechnology in Cancer of NCI's intention to form the consortium and to invite eligible companies (as defined in last paragraph) to participate.

Perceived job insecurity as a risk factor for incident coronary heart disease: systematic review and meta-analysis.

PubMed

Virtanen, Marianna; Nyberg, Solja T; Batty, G David; Jokela, Markus; Heikkilä, Katriina; Fransson, Eleonor I; Alfredsson, Lars; Bjorner, Jakob B; Borritz, Marianne; Burr, Hermann; Casini, Annalisa; Clays, Els; De Bacquer, Dirk; Dragano, Nico; Elovainio, Marko; Erbel, Raimund; Ferrie, Jane E; Hamer, Mark; Jöckel, Karl-Heinz; Kittel, France; Knutsson, Anders; Koskenvuo, Markku; Koskinen, Aki; Lunau, Thorsten; Madsen, Ida E H; Nielsen, Martin L; Nordin, Maria; Oksanen, Tuula; Pahkin, Krista; Pejtersen, Jan H; Pentti, Jaana; Rugulies, Reiner; Salo, Paula; Shipley, Martin J; Siegrist, Johannes; Steptoe, Andrew; Suominen, Sakari B; Theorell, Töres; Toppinen-Tanner, Salla; Väänänen, Ari; Vahtera, Jussi; Westerholm, Peter J M; Westerlund, Hugo; Slopen, Natalie; Kawachi, Ichiro; Singh-Manoux, Archana; Kivimäki, Mika

2013-08-08

To determine the association between self reported job insecurity and incident coronary heart disease. A meta-analysis combining individual level data from a collaborative consortium and published studies identified by a systematic review. We obtained individual level data from 13 cohort studies participating in the Individual-Participant-Data Meta-analysis in Working Populations Consortium. Four published prospective cohort studies were identified by searches of Medline (to August 2012) and Embase databases (to October 2012), supplemented by manual searches. Prospective cohort studies that reported risk estimates for clinically verified incident coronary heart disease by the level of self reported job insecurity. Two independent reviewers extracted published data. Summary estimates of association were obtained using random effects models. The literature search yielded four cohort studies. Together with 13 cohort studies with individual participant data, the meta-analysis comprised up to 174,438 participants with a mean follow-up of 9.7 years and 1892 incident cases of coronary heart disease. Age adjusted relative risk of high versus low job insecurity was 1.32 (95% confidence interval 1.09 to 1.59). The relative risk of job insecurity adjusted for sociodemographic and risk factors was 1.19 (1.00 to 1.42). There was no evidence of significant differences in this association by sex, age (<50 v ≥ 50 years), national unemployment rate, welfare regime, or job insecurity measure. The modest association between perceived job insecurity and incident coronary heart disease is partly attributable to poorer socioeconomic circumstances and less favourable risk factor profiles among people with job insecurity.

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.

PubMed

Irinyi, Laszlo; Serena, Carolina; Garcia-Hermoso, Dea; Arabatzis, Michael; Desnos-Ollivier, Marie; Vu, Duong; Cardinali, Gianluigi; Arthur, Ian; Normand, Anne-Cécile; Giraldo, Alejandra; da Cunha, Keith Cassia; Sandoval-Denis, Marcelo; Hendrickx, Marijke; Nishikaku, Angela Satie; de Azevedo Melo, Analy Salles; Merseguel, Karina Bellinghausen; Khan, Aziza; Parente Rocha, Juliana Alves; Sampaio, Paula; da Silva Briones, Marcelo Ribeiro; e Ferreira, Renata Carmona; de Medeiros Muniz, Mauro; Castañón-Olivares, Laura Rosio; Estrada-Barcenas, Daniel; Cassagne, Carole; Mary, Charles; Duan, Shu Yao; Kong, Fanrong; Sun, Annie Ying; Zeng, Xianyu; Zhao, Zuotao; Gantois, Nausicaa; Botterel, Françoise; Robbertse, Barbara; Schoch, Conrad; Gams, Walter; Ellis, David; Halliday, Catriona; Chen, Sharon; Sorrell, Tania C; Piarroux, Renaud; Colombo, Arnaldo L; Pais, Célia; de Hoog, Sybren; Zancopé-Oliveira, Rosely Maria; Taylor, Maria Lucia; Toriello, Conchita; de Almeida Soares, Célia Maria; Delhaes, Laurence; Stubbe, Dirk; Dromer, Françoise; Ranque, Stéphane; Guarro, Josep; Cano-Lira, Jose F; Robert, Vincent; Velegraki, Aristea; Meyer, Wieland

2015-05-01

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens. © The Author 2015. 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.

Illustrative case studies in the return of exome and genome sequencing results

PubMed Central

Amendola, Laura M; Lautenbach, Denise; Scollon, Sarah; Bernhardt, Barbara; Biswas, Sawona; East, Kelly; Everett, Jessica; Gilmore, Marian J; Himes, Patricia; Raymond, Victoria M; Wynn, Julia; Hart, Ragan; Jarvik, Gail P

2015-01-01

Whole genome and exome sequencing tests are increasingly being ordered in clinical practice, creating a need for research exploring the return of results from these tests. A goal of the Clinical Sequencing and Exploratory Research (CSER) consortium is to gain experience with this process to develop best practice recommendations for offering exome and genome testing and returning results. Genetic counselors in the CSER consortium have an integral role in the return of results from these genomic sequencing tests and have gained valuable insight. We present seven emerging themes related to return of exome and genome sequencing results accompanied by case descriptions illustrating important lessons learned, counseling challenges specific to these tests and considerations for future research and practice. PMID:26478737

Validation of the International Metastatic Renal-Cell Carcinoma Database Consortium (IMDC) prognostic model for first-line pazopanib in metastatic renal carcinoma: the Spanish Oncologic Genitourinary Group (SOGUG) SPAZO study.

PubMed

Pérez-Valderrama, B; Arranz Arija, J A; Rodríguez Sánchez, A; Pinto Marín, A; Borrega García, P; Castellano Gaunas, D E; Rubio Romero, G; Maximiano Alonso, C; Villa Guzmán, J C; Puertas Álvarez, J L; Chirivella González, I; Méndez Vidal, M J; Juan Fita, M J; León-Mateos, L; Lázaro Quintela, M; García Domínguez, R; Jurado García, J M; Vélez de Mendizábal, E; Lambea Sorrosal, J J; García Carbonero, I; González del Alba, A; Suárez Rodríguez, C; Jiménez Gallego, P; Meana García, J A; García Marrero, R D; Gajate Borau, P; Santander Lobera, C; Molins Palau, C; López Brea, M; Fernández Parra, E M; Reig Torras, O; Basterretxea Badiola, L; Vázquez Estévez, S; González Larriba, J L

2016-04-01

Patients with metastatic renal carcinoma (mRCC) treated with first-line pazopanib were not included in the International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) prognostic model. SPAZO (NCT02282579) was a nation-wide retrospective observational study designed to assess the effectiveness and validate the IMDC prognostic model in patients treated with first-line pazopanib in clinical practice. Data of 278 patients, treated with first-line pazopanib for mRCC in 34 centres in Spain, were locally recorded and externally validated. Mean age was 66 years, there were 68.3% male, 93.5% clear-cell type, 74.8% nephrectomized, and 81.3% had ECOG 0-1. Metastatic sites were: lung 70.9%, lymph node 43.9%, bone 26.3%, soft tissue/skin 20.1%, liver 15.1%, CNS 7.2%, adrenal gland 6.5%, pleura/peritoneum 5.8%, pancreas 5%, and kidney 2.2%. After median follow-up of 23 months, 76.4% had discontinued pazopanib (57.2% due to progression), 47.9% had received second-line targeted therapy, and 48.9% had died. According to IMDC prognostic model, 19.4% had favourable risk (FR), 57.2% intermediate risk (IR), and 23.4% poor risk (PR). No unexpected toxicities were recorded. Response rate was 30.3% (FR: 44%, IR: 30% PR: 17.3%). Median progression-free survival (whole population) was 11 months (32 in FR, 11 in IR, 4 in PR). Median and 2-year overall survival (whole population) were 22 months and 48.1%, respectively (FR: not reached and 81.6%, IR: 22 and 48.7%, PR: 7 and 18.8%). These estimations and their 95% confidence intervals are fully consistent with the outcomes predicted by the IMDC prognostic model. Our results validate the IMDC model for first-line pazopanib in mRCC and confirm the effectiveness and safety of this treatment. © The Author 2015. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Tumor Cold Ischemia | Office of Cancer Clinical Proteomics Research

Cancer.gov

In a recently published manuscript in the journal of Molecular and Cellular Proteomics, researchers from the National Cancer Institutes (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigated the effect of cold ischemia on the proteome of fresh frozen tumors.

Retinal Disease in Marfan Syndrome: From the Marfan Eye Consortium of Chicago.

PubMed

Rahmani, Safa; Lyon, Alice T; Fawzi, Amani A; Maumenee, Irene H; Mets, Marilyn B

2015-10-01

To study the prevalence of peripheral retinal disease in patients with Marfan Syndrome (MFS). In this observational, cross-sectional case series, patients with MFS were recruited by the Marfan Eye Consortium of Chicago during the National Marfan Foundation's annual conference. Patients underwent a fully dilated exam by vitreoretinal specialists in addition to ultra-widefield fundus photography using a scanning laser ophthalmoscope (Optos 200Tx; Optos PLC, Dunfermline, Scotland, United Kingdom). Clinical examination revealed posterior segment pathology in 18% of eyes with increased incidence to 70% in patients with a subluxed lens. In six out of 10 subjects in whom the clinical exam was suboptimal (young age, small pupil, and limited cooperation), the Optos provided a superior view of the peripheral retina compared to clinical exam alone. Clinical exam of MFS patients revealed similar posterior segment pathology as noted in previous literature, with improved detection of peripheral retinal disease with the use of ultra-widefield imaging. Copyright 2015, SLACK Incorporated.

Proposed Standardized Neurological Endpoints for Cardiovascular Clinical Trials: An Academic Research Consortium Initiative.

PubMed

Lansky, Alexandra J; Messé, Steven R; Brickman, Adam M; Dwyer, Michael; van der Worp, H Bart; Lazar, Ronald M; Pietras, Cody G; Abrams, Kevin J; McFadden, Eugene; Petersen, Nils H; Browndyke, Jeffrey; Prendergast, Bernard; Ng, Vivian G; Cutlip, Donald E; Kapadia, Samir; Krucoff, Mitchell W; Linke, Axel; Moy, Claudia Scala; Schofer, Joachim; van Es, Gerrit-Anne; Virmani, Renu; Popma, Jeffrey; Parides, Michael K; Kodali, Susheel; Bilello, Michel; Zivadinov, Robert; Akar, Joseph; Furie, Karen L; Gress, Daryl; Voros, Szilard; Moses, Jeffrey; Greer, David; Forrest, John K; Holmes, David; Kappetein, Arie P; Mack, Michael; Baumbach, Andreas

2017-02-14

Surgical and catheter-based cardiovascular procedures and adjunctive pharmacology have an inherent risk of neurological complications. The current diversity of neurological endpoint definitions and ascertainment methods in clinical trials has led to uncertainties in the neurological risk attributable to cardiovascular procedures and inconsistent evaluation of therapies intended to prevent or mitigate neurological injury. Benefit-risk assessment of such procedures should be on the basis of an evaluation of well-defined neurological outcomes that are ascertained with consistent methods and capture the full spectrum of neurovascular injury and its clinical effect. The Neurologic Academic Research Consortium is an international collaboration intended to establish consensus on the definition, classification, and assessment of neurological endpoints applicable to clinical trials of a broad range of cardiovascular interventions. Systematic application of the proposed definitions and assessments will improve our ability to evaluate the risks of cardiovascular procedures and the safety and effectiveness of preventive therapies. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Standardizing the nomenclature of Martian impact crater ejecta morphologies

USGS Publications Warehouse

Barlow, Nadine G.; Boyce, Joseph M.; Costard, Francois M.; Craddock, Robert A.; Garvin, James B.; Sakimoto, Susan E.H.; Kuzmin, Ruslan O.; Roddy, David J.; Soderblom, Laurence A.

2000-01-01

The Mars Crater Morphology Consortium recommends the use of a standardized nomenclature system when discussing Martian impact crater ejecta morphologies. The system utilizes nongenetic descriptors to identify the various ejecta morphologies seen on Mars. This system is designed to facilitate communication and collaboration between researchers. Crater morphology databases will be archived through the U.S. Geological Survey in Flagstaff, where a comprehensive catalog of Martian crater morphologic information will be maintained.

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, Tatiparthi B. K.; Thomas, Alex D.; Stamatis, Dimitri

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencingmore » projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.« less

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

PubMed Central

Orchard, Sandra; Ammari, Mais; Aranda, Bruno; Breuza, Lionel; Briganti, Leonardo; Broackes-Carter, Fiona; Campbell, Nancy H.; Chavali, Gayatri; Chen, Carol; del-Toro, Noemi; Duesbury, Margaret; Dumousseau, Marine; Galeota, Eugenia; Hinz, Ursula; Iannuccelli, Marta; Jagannathan, Sruthi; Jimenez, Rafael; Khadake, Jyoti; Lagreid, Astrid; Licata, Luana; Lovering, Ruth C.; Meldal, Birgit; Melidoni, Anna N.; Milagros, Mila; Peluso, Daniele; Perfetto, Livia; Porras, Pablo; Raghunath, Arathi; Ricard-Blum, Sylvie; Roechert, Bernd; Stutz, Andre; Tognolli, Michael; van Roey, Kim; Cesareni, Gianni; Hermjakob, Henning

2014-01-01

IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org). PMID:24234451

LMSD: LIPID MAPS structure database

PubMed Central

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Brown, Alex; Dennis, Edward A.; Glass, Christopher K.; Merrill, Alfred H.; Murphy, Robert C.; Raetz, Christian R. H.; Russell, David W.; Subramaniam, Shankar

2007-01-01

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available at PMID:17098933

Medical Physics Residency Consortium: collaborative endeavors to meet the ABR 2014 certification requirements.

PubMed

Parker, Brent C; Duhon, John; Yang, Claus C; Wu, H Terry; Hogstrom, Kenneth R; Gibbons, John P

2014-03-06

In 2009, Mary Bird Perkins Cancer Center (MBPCC) established a Radiation Oncology Physics Residency Program to provide opportunities for medical physics residency training to MS and PhD graduates of the CAMPEP-accredited Louisiana State University (LSU)-MBPCC Medical Physics Graduate Program. The LSU-MBPCC Program graduates approximately six students yearly, which equates to a need for up to twelve residency positions in a two-year program. To address this need for residency positions, MBPCC has expanded its Program by developing a Consortium consisting of partnerships with medical physics groups located at other nearby clinical institutions. The consortium model offers the residents exposure to a broader range of procedures, technology, and faculty than available at the individual institutions. The Consortium institutions have shown a great deal of support from their medical physics groups and administrations in developing these partnerships. Details of these partnerships are specified within affiliation agreements between MBPCC and each participating institution. All partner sites began resident training in 2011. The Consortium is a network of for-profit, nonprofit, academic, community, and private entities. We feel that these types of collaborative endeavors will be required nationally to reach the number of residency positions needed to meet the 2014 ABR certification requirements and to maintain graduate medical physics training programs.

Standardizing terms for clinical pharmacogenetic test results: consensus terms from the Clinical Pharmacogenetics Implementation Consortium (CPIC)

PubMed Central

Caudle, Kelly E.; Dunnenberger, Henry M.; Freimuth, Robert R.; Peterson, Josh F.; Burlison, Jonathan D.; Whirl-Carrillo, Michelle; Scott, Stuart A.; Rehm, Heidi L.; Williams, Marc S.; Klein, Teri E.; Relling, Mary V.; Hoffman, James M.

2017-01-01

Introduction: Reporting and sharing pharmacogenetic test results across clinical laboratories and electronic health records is a crucial step toward the implementation of clinical pharmacogenetics, but allele function and phenotype terms are not standardized. Our goal was to develop terms that can be broadly applied to characterize pharmacogenetic allele function and inferred phenotypes. Materials and methods: Terms currently used by genetic testing laboratories and in the literature were identified. The Clinical Pharmacogenetics Implementation Consortium (CPIC) used the Delphi method to obtain a consensus and agree on uniform terms among pharmacogenetic experts. Results: Experts with diverse involvement in at least one area of pharmacogenetics (clinicians, researchers, genetic testing laboratorians, pharmacogenetics implementers, and clinical informaticians; n = 58) participated. After completion of five surveys, a consensus (>70%) was reached with 90% of experts agreeing to the final sets of pharmacogenetic terms. Discussion: The proposed standardized pharmacogenetic terms will improve the understanding and interpretation of pharmacogenetic tests and reduce confusion by maintaining consistent nomenclature. These standard terms can also facilitate pharmacogenetic data sharing across diverse electronic health care record systems with clinical decision support. Genet Med 19 2, 215–223. PMID:27441996

Processing of CT images for analysis of diffuse lung disease in the lung tissue research consortium

NASA Astrophysics Data System (ADS)

Karwoski, Ronald A.; Bartholmai, Brian; Zavaletta, Vanessa A.; Holmes, David; Robb, Richard A.

2008-03-01

The goal of Lung Tissue Resource Consortium (LTRC) is to improve the management of diffuse lung diseases through a better understanding of the biology of Chronic Obstructive Pulmonary Disease (COPD) and fibrotic interstitial lung disease (ILD) including Idiopathic Pulmonary Fibrosis (IPF). Participants are subjected to a battery of tests including tissue biopsies, physiologic testing, clinical history reporting, and CT scanning of the chest. The LTRC is a repository from which investigators can request tissue specimens and test results as well as semi-quantitative radiology reports, pathology reports, and automated quantitative image analysis results from the CT scan data performed by the LTRC core laboratories. The LTRC Radiology Core Laboratory (RCL), in conjunction with the Biomedical Imaging Resource (BIR), has developed novel processing methods for comprehensive characterization of pulmonary processes on volumetric high-resolution CT scans to quantify how these diseases manifest in radiographic images. Specifically, the RCL has implemented a semi-automated method for segmenting the anatomical regions of the lungs and airways. In these anatomic regions, automated quantification of pathologic features of disease including emphysema volumes and tissue classification are performed using both threshold techniques and advanced texture measures to determine the extent and location of emphysema, ground glass opacities, "honeycombing" (HC) and "irregular linear" or "reticular" pulmonary infiltrates and normal lung. Wall thickness measurements of the trachea, and its branches to the 3 rd and limited 4 th order are also computed. The methods for processing, segmentation and quantification are described. The results are reviewed and verified by an expert radiologist following processing and stored in the public LTRC database for use by pulmonary researchers. To date, over 1200 CT scans have been processed by the RCL and the LTRC project is on target for recruitment of the 2200 patients with 1800 CT scans in the repository for the 5-year effort. Ongoing analysis of the results in the LTRC database by the LTRC participating institutions and outside investigators are underway to look at the clinical and physiological significance of the imaging features of these diseases and correlate these findings with quality of life and other important prognostic indicators of severity. In the future, the quantitative measures of disease may have greater utility by showing correlation with prognosis, disease severity and other physiological parameters. These imaging features may provide non-invasive alternative endpoints or surrogate markers to alleviate the need for tissue biopsy or provide an accurate means to monitor rate of disease progression or response to therapy.

Social and behavioral research in genomic sequencing: approaches from the Clinical Sequencing Exploratory Research Consortium Outcomes and Measures Working Group.

PubMed

Gray, Stacy W; Martins, Yolanda; Feuerman, Lindsay Z; Bernhardt, Barbara A; Biesecker, Barbara B; Christensen, Kurt D; Joffe, Steven; Rini, Christine; Veenstra, David; McGuire, Amy L

2014-10-01

The routine use of genomic sequencing in clinical medicine has the potential to dramatically alter patient care and medical outcomes. To fully understand the psychosocial and behavioral impact of sequencing integration into clinical practice, it is imperative that we identify the factors that influence sequencing-related decision making and patient outcomes. In an effort to develop a collaborative and conceptually grounded approach to studying sequencing adoption, members of the National Human Genome Research Institute's Clinical Sequencing Exploratory Research Consortium formed the Outcomes and Measures Working Group. Here we highlight the priority areas of investigation and psychosocial and behavioral outcomes identified by the Working Group. We also review some of the anticipated challenges to measurement in social and behavioral research related to genomic sequencing; opportunities for instrument development; and the importance of qualitative, quantitative, and mixed-method approaches. This work represents the early, shared efforts of multiple research teams as we strive to understand individuals' experiences with genomic sequencing. The resulting body of knowledge will guide recommendations for the optimal use of sequencing in clinical practice.

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

European Society of Cardiology-Recommended Coronary Artery Disease Consortium Pretest Probability Scores More Accurately Predict Obstructive Coronary Disease and Cardiovascular Events Than the Diamond and Forrester Score: The Partners Registry.

PubMed

Bittencourt, Marcio Sommer; Hulten, Edward; Polonsky, Tamar S; Hoffman, Udo; Nasir, Khurram; Abbara, Suhny; Di Carli, Marcelo; Blankstein, Ron

2016-07-19

The most appropriate score for evaluating the pretest probability of obstructive coronary artery disease (CAD) is unknown. We sought to compare the Diamond-Forrester (DF) score with the 2 CAD consortium scores recently recommended by the European Society of Cardiology. We included 2274 consecutive patients (age, 56±13 years; 57% male) without prior CAD referred for coronary computed tomographic angiography. Computed tomographic angiography findings were used to determine the presence or absence of obstructive CAD (≥50% stenosis). We compared the DF score with the 2 CAD consortium scores with respect to their ability to predict obstructive CAD and the potential implications of these scores on the downstream use of testing for CAD, as recommended by current guidelines. The DF score did not satisfactorily fit the data and resulted in a significant overestimation of the prevalence of obstructive CAD (P<0.001); the CAD consortium basic score had no significant lack of fitness; and the CAD consortium clinical provided adequate goodness of fit (P=0.39). The DF score had a lower discrimination for obstructive CAD, with an area under the receiver-operating characteristics curve of 0.713 versus 0.752 and 0.791 for the CAD consortium models (P<0.001 for both). Consequently, the use of the DF score was associated with fewer individuals being categorized as requiring no additional testing (8.3%) compared with the CAD consortium models (24.6% and 30.0%; P<0.001). The proportion of individuals with a high pretest probability was 18% with the DF and only 1.1% with the CAD consortium scores (P<0.001) CONCLUSIONS: Among contemporary patients referred for noninvasive testing, the DF risk score overestimates the risk of obstructive CAD. On the other hand, the CAD consortium scores offered improved goodness of fit and discrimination; thus, their use could decrease the need for noninvasive or invasive testing while increasing the yield of such tests. © 2016 American Heart Association, Inc.

Predicting OptimaL cAncer RehabIlitation and Supportive care (POLARIS): rationale and design for meta-analyses of individual patient data of randomized controlled trials that evaluate the effect of physical activity and psychosocial interventions on health-related quality of life in cancer survivors

PubMed Central

2013-01-01

Background Effective interventions to improve quality of life of cancer survivors are essential. Numerous randomized controlled trials have evaluated the effects of physical activity or psychosocial interventions on health-related quality of life of cancer survivors, with generally small sample sizes and modest effects. Better targeted interventions may result in larger effects. To realize such targeted interventions, we must determine which interventions that are presently available work for which patients, and what the underlying mechanisms are (that is, the moderators and mediators of physical activity and psychosocial interventions). Individual patient data meta-analysis has been described as the ‘gold standard’ of systematic review methodology. Instead of extracting aggregate data from study reports or from authors, the original research data are sought directly from the investigators. Individual patient data meta-analyses allow for adequate statistical analysis of intervention effects and moderators of such effects. Here, we report the rationale and design of the Predicting OptimaL cAncer RehabIlitation and Supportive care (POLARIS) Consortium. The primary aim of POLARIS is 1) to conduct meta-analyses based on individual patient data to evaluate the effect of physical activity and psychosocial interventions on the health-related quality of life of cancer survivors; 2) to identify important demographic, clinical, personal, or intervention-related moderators of the effect; and 3) to build and validate clinical prediction models identifying the most relevant predictors of intervention success. Methods/Design We will invite investigators of randomized controlled trials that evaluate the effects of physical activity and/or psychosocial interventions on health-related quality of life compared with a wait-list, usual care or attention control group among adult cancer survivors to join the POLARIS consortium and share their data for use in pooled analyses that will address the proposed aims. We are in the process of identifying eligible randomized controlled trials through literature searches in four databases. To date, we have identified 132 eligible and unique trials. Discussion The POLARIS consortium will conduct the first individual patient data meta-analyses in order to generate evidence essential to targeting physical activity and psychosocial programs to the individual survivor’s characteristics, capabilities, and preferences. Registration PROSPERO: International prospective register of systematic reviews, CRD42013003805 PMID:24034173

Automatic lung nodule graph cuts segmentation with deep learning false positive reduction

NASA Astrophysics Data System (ADS)

Sun, Wenqing; Huang, Xia; Tseng, Tzu-Liang Bill; Qian, Wei

2017-03-01

To automatic detect lung nodules from CT images, we designed a two stage computer aided detection (CAD) system. The first stage is graph cuts segmentation to identify and segment the nodule candidates, and the second stage is convolutional neural network for false positive reduction. The dataset contains 595 CT cases randomly selected from Lung Image Database Consortium and Image Database Resource Initiative (LIDC/IDRI) and the 305 pulmonary nodules achieved diagnosis consensus by all four experienced radiologists were our detection targets. Consider each slice as an individual sample, 2844 nodules were included in our database. The graph cuts segmentation was conducted in a two-dimension manner, 2733 lung nodule ROIs are successfully identified and segmented. With a false positive reduction by a seven-layer convolutional neural network, 2535 nodules remain detected while the false positive dropped to 31.6%. The average F-measure of segmented lung nodule tissue is 0.8501.

Dictionary learning-based CT detection of pulmonary nodules

NASA Astrophysics Data System (ADS)

Wu, Panpan; Xia, Kewen; Zhang, Yanbo; Qian, Xiaohua; Wang, Ge; Yu, Hengyong

2016-10-01

Segmentation of lung features is one of the most important steps for computer-aided detection (CAD) of pulmonary nodules with computed tomography (CT). However, irregular shapes, complicated anatomical background and poor pulmonary nodule contrast make CAD a very challenging problem. Here, we propose a novel scheme for feature extraction and classification of pulmonary nodules through dictionary learning from training CT images, which does not require accurately segmented pulmonary nodules. Specifically, two classification-oriented dictionaries and one background dictionary are learnt to solve a two-category problem. In terms of the classification-oriented dictionaries, we calculate sparse coefficient matrices to extract intrinsic features for pulmonary nodule classification. The support vector machine (SVM) classifier is then designed to optimize the performance. Our proposed methodology is evaluated with the lung image database consortium and image database resource initiative (LIDC-IDRI) database, and the results demonstrate that the proposed strategy is promising.

Sleep atlas and multimedia database.

PubMed

Penzel, T; Kesper, K; Mayer, G; Zulley, J; Peter, J H

2000-01-01

The ENN sleep atlas and database was set up on a dedicated server connected to the internet thus providing all services such as WWW, ftp and telnet access. The database serves as a platform to promote the goals of the European Neurological Network, to exchange patient cases for second opinion between experts and to create a case-oriented multimedia sleep atlas with descriptive text, images and video-clips of all known sleep disorders. The sleep atlas consists of a small public and a large private part for members of the consortium. 20 patient cases were collected and presented with educational information similar to published case reports. Case reports are complemented with images, video-clips and biosignal recordings. A Java based viewer for biosignals provided in EDF format was installed in order to move free within the sleep recordings without the need to download the full recording on the client.

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

PubMed Central

Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.; Unni, Deepak R.; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

2016-01-01

We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

Proteome Characterization Centers - TCGA

Cancer.gov

The centers, a component of NCI’s Clinical Proteomic Tumor Analysis Consortium, will analyze a subset of TCGA samples to define proteins translated from cancer genomes and their related biological processes.

CASMI TSCC Launch Event, Paris, France, July 2013: An Assessment of the Key Barriers to the Commercialization and Clinical Adoption of Pluripotent Stem Cell Therapies*

PubMed Central

Bure, Kim; Brindley, David A.

2014-01-01

Abstract The high incidence of unmet medical needs in combination with the rising burden of chronic diseases, linked to an increasingly aging population, necessitates new approaches to therapeutic intervention. One potential class of health care innovation that may offer an alternative approach to addressing current shortfalls is stem cell therapies. The CASMI Translational Stem Cell Consortium (CTSCC) was formed to elucidate the key hurdles to the commercialization and clinical adoption of stem cell technologies, with a particular focus on pluripotent stem cell (PSC) technologies. As a global pre-competitive academic–industry consortium, the CTSCC unites thought leaders from a range of sectors and technical specialties in defining and discovering solutions to roadblocks that will impede the field. Targeted toward stakeholder requirements at the delivery end of the translational spectrum, the CTSCC aims to provide mechanisms for multidirectional dialogue and to produce academically rigorous and commercially practicable research outputs to accelerate industry progress. On the 30th and 31st of July, 2013, the CASMI Translational Stem Cell Consortium (CTSCC) held a launch event at the Saint James Club, Paris, France. PMID:24392658

Advances in the Diagnosis and Management of Cystic Fibrosis in the Genomic Era.

PubMed

Wiencek, Joesph R; Lo, Stanley F

2018-06-01

Cystic fibrosis (CF) is a complex autosomal recessive disease that continues to present unique diagnostic challenges. Because CF was first described in 1938, there has been a substantial growth of genetic and phenotypic information about the disorder. During the past few years, as more evidence has become available, a consortium of international experts determined that the 2008 guidelines from the CF Foundation needed to be reviewed and updated. The goal of this review is to highlight the latest advances in CF multidisciplinary care, together with the recent updates to the 2017 CF Foundation diagnostic guidelines. Data from newborn screening programs, patient registries, clinical databases, and functional research have led to a better understanding of the CF transmembrane conductance regulator ( CFTR ) gene. Recent consensus guidelines have provided recommendations for clinicians and laboratorians to better assist with interpretation of disease status and related CF mutations. The highly recommended Clinical and Functional Translation of CFTR project should be the first resource in the evaluation of disease severity for CF mutations. Screen-positive newborns and patients with high clinical suspicion for CF are always recommended to undergo confirmatory sweat chloride testing with interpretations based on updated reference intervals. Every patient diagnosed with CF should receive genotyping, as novel molecular therapies are becoming standard of practice. The future of CF management must consider healthcare system disparities as CF transitions from a historically childhood disease to a predominantly adult epidemic. © 2018 American Association for Clinical Chemistry.

Evaluating Various Areas of Process Improvement in an Effort to Improve Clinical Research: Discussions from the 2012 Clinical Translational Science Award (CTSA) Clinical Research Management Workshop

PubMed Central

Cola, Philip A.; Rosenblum, Daniel

2013-01-01

Abstract Emphasis has been placed on assessing the efficiency of clinical and translational research as part of the National Institutes of Health (NIH) goal to “improve human health.” Improvements identified and implemented by individual organizations cannot address the research infrastructure needs of all clinical and translational research conducted. NIH's National Center for Advancing Translational Sciences (NCATS) has brought together 61 Clinical and Translational Science Award (CTSA) sites creating a virtual national laboratory that reflects the diversity and breadth of academic medical centers to collectively improve clinical and translational science. The annual Clinical Research Management workshop is organized by the CTSA consortium with participation from CTSA awardees, NIH, and others with an interest in clinical research management. The primary objective of the workshop is to disseminate information that improves clinical research management although the specific objectives of each workshop evolve within the consortium. The fifth annual workshop entitled “Learning by doing; applying evidence‐based tools to re‐engineer clinical research management” took place in June 2012. The primary objective of the 2012 workshop was to utilize data to evaluate, modify, and improve clinical research management. This report provides a brief summary of the workshop proceedings and the major themes discussed among the participants. PMID:23919369

Evaluating various areas of process improvement in an effort to improve clinical research: discussions from the 2012 Clinical Translational Science Award (CTSA) Clinical Research Management workshop.

PubMed

Strasser, Jane E; Cola, Philip A; Rosenblum, Daniel

2013-08-01

Emphasis has been placed on assessing the efficiency of clinical and translational research as part of the National Institutes of Health (NIH) goal to "improve human health." Improvements identified and implemented by individual organizations cannot address the research infrastructure needs of all clinical and translational research conducted. NIH's National Center for Advancing Translational Sciences (NCATS) has brought together 61 Clinical and Translational Science Award (CTSA) sites creating a virtual national laboratory that reflects the diversity and breadth of academic medical centers to collectively improve clinical and translational science. The annual Clinical Research Management workshop is organized by the CTSA consortium with participation from CTSA awardees, NIH, and others with an interest in clinical research management. The primary objective of the workshop is to disseminate information that improves clinical research management although the specific objectives of each workshop evolve within the consortium. The fifth annual workshop entitled "Learning by doing; applying evidence-based tools to re-engineer clinical research management" took place in June 2012. The primary objective of the 2012 workshop was to utilize data to evaluate, modify, and improve clinical research management. This report provides a brief summary of the workshop proceedings and the major themes discussed among the participants. © 2013 Wiley Periodicals, Inc.

Comparison between SLC3A1 and SLC7A9 cystinuria patients and carriers: a need for a new classification.

PubMed

Dello Strologo, Luca; Pras, Elon; Pontesilli, Claudia; Beccia, Ercole; Ricci-Barbini, Vittorino; de Sanctis, Luisa; Ponzone, Alberto; Gallucci, Michele; Bisceglia, Luigi; Zelante, Leopoldo; Jimenez-Vidal, Maite; Font, Mariona; Zorzano, Antonio; Rousaud, Ferran; Nunes, Virginia; Gasparini, Paolo; Palacín, Manuel; Rizzoni, Gianfranco

2002-10-01

Recent developments in the genetics and physiology of cystinuria do not support the traditional classification, which is based on the excretion of cystine and dibasic amino acids in obligate heterozygotes. Mutations of only two genes (SLC3A1 and SLC7A9), identified by the International Cystinuria Consortium (ICC), have been found to be responsible for all three types of the disease. The ICC set up a multinational database and collected genetic and clinical data from 224 patients affected by cystinuria, 125 with full genotype definition. Amino acid urinary excretion patterns of 189 heterozygotes with genetic definition and of 83 healthy controls were also included. All SLC3A1 carriers and 14% of SLC7A9 carriers showed a normal amino acid urinary pattern (i.e., type I phenotype). The rest of the SLC7A9 carriers showed phenotype non-I (type III, 80.5%; type II, 5.5%). This makes the traditional classification imprecise. A new classification is needed: type A, due to two mutations of SLC3A1 (rBAT) on chromosome 2 (45.2% in our database); type B, due to two mutations of SLC7A9 on chromosome 19 (53.2% in this series); and a possible third type, AB (1.6%), with one mutation on each of the above-mentioned genes. Clinical data show that cystinuria is more severe in males than in females. The two types of cystinuria (A and B) had a similar outcome in this retrospective study, but the effect of the treatment could not be analyzed. Stone events do not correlate with amino acid urinary excretion. Renal function was clearly impaired in 17% of the patients.

Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways

PubMed Central

Becnel, Lauren B.; Darlington, Yolanda F.; Ochsner, Scott A.; Easton-Marks, Jeremy R.; Watkins, Christopher M.; McOwiti, Apollo; Kankanamge, Wasula H.; Wise, Michael W.; DeHart, Michael; Margolis, Ronald N.; McKenna, Neil J.

2015-01-01

Signaling pathways involving nuclear receptors (NRs), their ligands and coregulators, regulate tissue-specific transcriptomes in diverse processes, including development, metabolism, reproduction, the immune response and neuronal function, as well as in their associated pathologies. The Nuclear Receptor Signaling Atlas (NURSA) is a Consortium focused around a Hub website (www.nursa.org) that annotates and integrates diverse ‘omics datasets originating from the published literature and NURSA-funded Data Source Projects (NDSPs). These datasets are then exposed to the scientific community on an Open Access basis through user-friendly data browsing and search interfaces. Here, we describe the redesign of the Hub, version 3.0, to deploy “Web 2.0” technologies and add richer, more diverse content. The Molecule Pages, which aggregate information relevant to NR signaling pathways from myriad external databases, have been enhanced to include resources for basic scientists, such as post-translational modification sites and targeting miRNAs, and for clinicians, such as clinical trials. A portal to NURSA’s Open Access, PubMed-indexed journal Nuclear Receptor Signaling has been added to facilitate manuscript submissions. Datasets and information on reagents generated by NDSPs are available, as is information concerning periodic new NDSP funding solicitations. Finally, the new website integrates the Transcriptomine analysis tool, which allows for mining of millions of richly annotated public transcriptomic data points in the field, providing an environment for dataset re-use and citation, bench data validation and hypothesis generation. We anticipate that this new release of the NURSA database will have tangible, long term benefits for both basic and clinical research in this field. PMID:26325041

Comparison of Survival Outcomes Among Cancer Patients Treated In and Out of Clinical Trials

PubMed Central

2014-01-01

Background Clinical trials test the efficacy of a treatment in a select patient population. We examined whether cancer clinical trial patients were similar to nontrial, “real-world” patients with respect to presenting characteristics and survival. Methods We reviewed the SWOG national clinical trials consortium database to identify candidate trials. Demographic factors, stage, and overall survival for patients in the standard arms were compared with nontrial control subjects selected from the Surveillance, Epidemiology, and End Results program. Multivariable survival analyses using Cox regression were conducted. The survival functions from aggregate data across all studies were compared separately by prognosis (≥50% vs <50% average 2-year survival). All statistical tests were two-sided. Results We analyzed 21 SWOG studies (11 good prognosis and 10 poor prognosis) comprising 5190 patients enrolled from 1987 to 2007. Trial patients were younger than nontrial patients (P < .001). In multivariable analysis, trial participation was not associated with improved overall survival for all 11 good-prognosis studies but was associated with better survival for nine of 10 poor-prognosis studies (P < .001). The impact of trial participation on overall survival endured for only 1 year. Conclusions Trial participation was associated with better survival in the first year after diagnosis, likely because of eligibility criteria that excluded higher comorbidity patients from trials. Similar survival patterns between trial and nontrial patients after the first year suggest that trial standard arm outcomes are generalizable over the long term and may improve confidence that trial treatment effects will translate to the real-world setting. Reducing eligibility criteria would improve access to clinical trials. PMID:24627276

Bladder Cancer Advocacy Network

MedlinePlus

... Event No Repeat Daily Weekly Monthly Yearly Repeat gap Repeat by day SU MO TU WE TH ... is Bladder Cancer? Newly Diagnosed Treatments Clinical Trials Research Research Grants Think Tank Research Network Genomics Consortium ...

Medical Physics Residency Consortium: collaborative endeavors to meet the ABR 2014 certification requirements

PubMed Central

Parker, Brent C.; Duhon, John; Yang, Claus C.; Wu, H. Terry; Hogstrom, Kenneth R.

2014-01-01

In 2009, Mary Bird Perkins Cancer Center (MBPCC) established a Radiation Oncology Physics Residency Program to provide opportunities for medical physics residency training to MS and PhD graduates of the CAMPEP‐accredited Louisiana State University (LSU)‐MBPCC Medical Physics Graduate Program. The LSU‐MBPCC Program graduates approximately six students yearly, which equates to a need for up to twelve residency positions in a two‐year program. To address this need for residency positions, MBPCC has expanded its Program by developing a Consortium consisting of partnerships with medical physics groups located at other nearby clinical institutions. The consortium model offers the residents exposure to a broader range of procedures, technology, and faculty than available at the individual institutions. The Consortium institutions have shown a great deal of support from their medical physics groups and administrations in developing these partnerships. Details of these partnerships are specified within affiliation agreements between MBPCC and each participating institution. All partner sites began resident training in 2011. The Consortium is a network of for‐profit, nonprofit, academic, community, and private entities. We feel that these types of collaborative endeavors will be required nationally to reach the number of residency positions needed to meet the 2014 ABR certification requirements and to maintain graduate medical physics training programs. PACS numbers: 01.40.Fk, 01.40.gb PMID:24710434

The Magnetics Information Consortium (MagIC) Online Database: Uploading, Searching and Visualizing Paleomagnetic and Rock Magnetic Data

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A.; Tauxe, L.; Constable, C.; Pisarevsky, S. A.; Jackson, M.; Solheid, P.; Banerjee, S.; Johnson, C.

2006-12-01

The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by both rock and paleomagnetic data. The goal of MagIC is to archive all measurements and the derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual map interface to browse and select locations. The query result set is displayed in a digestible tabular format allowing the user to descend through hierarchical levels such as from locations to sites, samples, specimens, and measurements. At each stage, the result set can be saved and, if supported by the data, can be visualized by plotting global location maps, equal area plots, or typical Zijderveld, hysteresis, and various magnetization and remanence diagrams. User contributions to the MagIC database are critical to achieving a useful research tool. We have developed a standard data and metadata template (Version 2.1) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate population of these templates within Microsoft Excel. These tools allow for the import/export of text files and provide advanced functionality to manage and edit the data, and to perform various internal checks to maintain data integrity and prepare for uploading. The MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm executes the upload and takes only a few minutes to process several thousand data records. The standardized MagIC template files are stored in the digital archives of EarthRef.org where they remain available for download by the public (in both text and Excel format). Finally, the contents of these template files are automatically parsed into the online relational database, making the data available for online searches in the paleomagnetic and rock magnetic search nodes. The MagIC database contains all data transferred from the IAGA paleomagnetic poles database (GPMDB), the lava flow paleosecular variation database (PSVRL), lake sediment database (SECVR) and the PINT database. Additionally, a substantial number of data compiled under the Time Averaged Field Investigations project is now included plus a significant fraction of the data collected at SIO and the IRM. Ongoing additions of legacy data include over 40 papers from studies on the Hawaiian Islands and Mexico, data compilations from archeomagnetic studies and updates to the lake sediment dataset.

Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)*

PubMed Central

Renard, Bernhard Y.; Xu, Buote; Kirchner, Marc; Zickmann, Franziska; Winter, Dominic; Korten, Simone; Brattig, Norbert W.; Tzur, Amit; Hamprecht, Fred A.; Steen, Hanno

2012-01-01

Currently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without reliable, fully annotated reference genomes required for proteomic analyses. Standard database search algorithms fail to identify peptides that are not exactly contained in a protein database. De novo searches are generally hindered by their restricted reliability, and current error-tolerant search strategies are limited by global, heuristic tradeoffs between database and spectral information. We propose a Bayesian information criterion-driven error-tolerant peptide search (BICEPS) and offer an open source implementation based on this statistical criterion to automatically balance the information of each single spectrum and the database, while limiting the run time. We show that BICEPS performs as well as current database search algorithms when such algorithms are applied to sequenced organisms, whereas BICEPS only uses a remotely related organism database. For instance, we use a chicken instead of a human database corresponding to an evolutionary distance of more than 300 million years (International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716). We demonstrate the successful application to cross-species proteomics with a 33% increase in the number of identified proteins for a filarial nematode sample of Litomosoides sigmodontis. PMID:22493179

Genome databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Courteau, J.

1991-10-11

Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts inmore » the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.« less

NCI's Proteome Characterization Centers Announced | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute (NCI), part of the National Institutes of Health, announces the launch of a Clinical Proteomic Tumor Analysis Consortium (CPTAC). CPTAC is a comprehensive, coordinated team effort to accelerate the understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows.

CPTAC Releases Largest-Ever Breast Cancer Proteome Dataset from Previously Genome Characterized Tumors | Office of Cancer Clinical Proteomics Research

Cancer.gov

National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have released a dataset of proteins and  phosphopeptides identified through deep proteomic and phosphoproteomic analysis of breast tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).

Recommended Implementation of Arterial Spin Labeled Perfusion MRI for Clinical Applications: A consensus of the ISMRM Perfusion Study Group and the European Consortium for ASL in Dementia

PubMed Central

Alsop, David C.; Detre, John A.; Golay, Xavier; Günther, Matthias; Hendrikse, Jeroen; Hernandez-Garcia, Luis; Lu, Hanzhang; MacIntosh, Bradley J.; Parkes, Laura M.; Smits, Marion; van Osch, Matthias J. P.; Wang, Danny JJ; Wong, Eric C.; Zaharchuk, Greg

2014-01-01

This article provides a summary statement of recommended implementations of arterial spin labeling (ASL) for clinical applications. It is a consensus of the ISMRM Perfusion Study Group and the European ‘ASL in Dementia’ consortium, both of whom met to reach this consensus in October 2012 in Amsterdam. Although ASL continues to undergo rapid technical development, we believe that current ASL methods are robust and ready to provide useful clinical information, and that a consensus statement on recommended implementations will help the clinical community to adopt a standardized approach. In this article we describe the major considerations and tradeoffs in implementing an ASL protocol, and provide specific recommendations for a standard approach. Our conclusions are that, as an optimal default implementation we recommend: pseudo-continuous labeling, background suppression, a segmented 3D readout without vascular crushing gradients, and calculation and presentation of both label/control difference images and cerebral blood flow in absolute units using a simplified model. PMID:24715426

Perceived job insecurity as a risk factor for incident coronary heart disease: systematic review and meta-analysis

PubMed Central

Nyberg, Solja T; Batty, G David; Jokela, Markus; Heikkilä, Katriina; Fransson, Eleonor I; Alfredsson, Lars; Bjorner, Jakob B; Borritz, Marianne; Burr, Hermann; Casini, Annalisa; Clays, Els; De Bacquer, Dirk; Dragano, Nico; Elovainio, Marko; Erbel, Raimund; Ferrie, Jane E; Hamer, Mark; Jöckel, Karl-Heinz; Kittel, France; Knutsson, Anders; Koskenvuo, Markku; Koskinen, Aki; Lunau, Thorsten; Madsen, Ida E H; Nielsen, Martin L; Nordin, Maria; Oksanen, Tuula; Pahkin, Krista; Pejtersen, Jan H; Pentti, Jaana; Rugulies, Reiner; Salo, Paula; Shipley, Martin J; Siegrist, Johannes; Steptoe, Andrew; Suominen, Sakari B; Theorell, Töres; Toppinen-Tanner, Salla; Väänänen, Ari; Vahtera, Jussi; Westerholm, Peter J M; Westerlund, Hugo; Slopen, Natalie; Kawachi, Ichiro; Singh-Manoux, Archana; Kivimäki, Mika

2013-01-01

Objective To determine the association between self reported job insecurity and incident coronary heart disease. Design A meta-analysis combining individual level data from a collaborative consortium and published studies identified by a systematic review. Data sources We obtained individual level data from 13 cohort studies participating in the Individual-Participant-Data Meta-analysis in Working Populations Consortium. Four published prospective cohort studies were identified by searches of Medline (to August 2012) and Embase databases (to October 2012), supplemented by manual searches. Review methods Prospective cohort studies that reported risk estimates for clinically verified incident coronary heart disease by the level of self reported job insecurity. Two independent reviewers extracted published data. Summary estimates of association were obtained using random effects models. Results The literature search yielded four cohort studies. Together with 13 cohort studies with individual participant data, the meta-analysis comprised up to 174 438 participants with a mean follow-up of 9.7 years and 1892 incident cases of coronary heart disease. Age adjusted relative risk of high versus low job insecurity was 1.32 (95% confidence interval 1.09 to 1.59). The relative risk of job insecurity adjusted for sociodemographic and risk factors was 1.19 (1.00 to 1.42). There was no evidence of significant differences in this association by sex, age (<50 v ≥50 years), national unemployment rate, welfare regime, or job insecurity measure. Conclusions The modest association between perceived job insecurity and incident coronary heart disease is partly attributable to poorer socioeconomic circumstances and less favourable risk factor profiles among people with job insecurity. PMID:23929894

Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for rasburicase therapy in the context of G6PD deficiency genotype.

PubMed

Relling, M V; McDonagh, E M; Chang, T; Caudle, K E; McLeod, H L; Haidar, C E; Klein, T; Luzzatto, L

2014-08-01

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is associated with development of acute hemolytic anemia (AHA) induced by a number of drugs. We provide guidance as to which G6PD genotypes are associated with G6PD deficiency in males and females. Rasburicase is contraindicated in G6PD-deficient patients due to the risk of AHA and possibly methemoglobinemia. Unless preemptive genotyping has established a positive diagnosis of G6PD deficiency, quantitative enzyme assay remains the mainstay of screening prior to rasburicase use. The purpose of this article is to help interpret the results of clinical G6PD genotype tests so that they can guide the use of rasburicase. Detailed guidelines on other aspects of the use of rasburicase, including analyses of cost-effectiveness, are beyond the scope of this document. Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines are published and updated periodically on https://www.pharmgkb.org/page/cpic to reflect new developments in the field.

Northeast Artificial Intelligence Consortium Annual Report - 1988. Volume 12. Computer Architectures for Very Large Knowledge Bases

DTIC Science & Technology

1989-10-01

Vol. 18, No. 5, 1975, pp. 253-263. [CAR84] D.B. Carlin, J.P. Bednarz, CJ. Kaiser, J.C. Connolly, M.G. Harvey , "Multichannel optical recording using... Kellog [31] takes a similar approach as ILEX in the sense that it uses existing systems rather than developing specialized hardwares (the Xerox 1100...parallel complexity. In Proceedings of the International Conference on Database Theory, pages 1-30, September 1986. [31] C. Kellog . From data management to

Genegis: Computational Tools for Spatial Analyses of DNA Profiles with Associated Photo-Identification and Telemetry Records of Marine Mammals

DTIC Science & Technology

2013-09-30

profiles of right whales Eubalaena glacialis from the North Atlantic Right Whale Consortium; 2) DNA profiles of sperm whales Physeter macrocephalus...of other cetacean databases in Wildbook format (e.g., North Atlantic right whales, sperm whales and Hector’s dolphins); 8) Supported continuing...of sperm whales, using samples collected during the 5-year Voyage of the Odyssey; and 3) DNA profiles of Hector’s dolphins from Cloudy Bay, New

CFD Aerothermodynamic Characterization Of The IXV Hypersonic Vehicle

NASA Astrophysics Data System (ADS)

Roncioni, P.; Ranuzzi, G.; Marini, M.; Battista, F.; Rufolo, G. C.

2011-05-01

In this paper, and in the framework of the ESA technical assistance activities for IXV project, the numerical activities carried out by ASI/CIRA to support the development of Aerodynamic and Aerothermodynamic databases, independent from the ones developed by the IXV Industrial consortium, are reported. A general characterization of the IXV aerothermodynamic environment has been also provided for cross checking and verification purposes. The work deals with the first year activities of Technical Assistance Contract agreed between the Italian Space Agency/CIRA and ESA.

75 FR 21005 - National Institute of Allergy and Infectious Diseases; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-22

... Infectious Diseases Special Emphasis Panel; ``Inner City Asthma Consortium: Statistical and Clinical..., Microbiology and Infectious Diseases Research, National Institutes of Health, HHS) Dated: April 15, 2010...

Federating clinical data from six pediatric hospitals: process and initial results for microbiology from the PHIS+ consortium.

PubMed

Gouripeddi, Ramkiran; Warner, Phillip B; Mo, Peter; Levin, James E; Srivastava, Rajendu; Shah, Samir S; de Regt, David; Kirkendall, Eric; Bickel, Jonathan; Korgenski, E Kent; Precourt, Michelle; Stepanek, Richard L; Mitchell, Joyce A; Narus, Scott P; Keren, Ron

2012-01-01

Microbiology study results are necessary for conducting many comparative effectiveness research studies. Unlike core laboratory test results, microbiology results have a complex structure. Federating and integrating microbiology data from six disparate electronic medical record systems is challenging and requires a team of varied skills. The PHIS+ consortium which is partnership between members of the Pediatric Research in Inpatient Settings (PRIS) network, the Children's Hospital Association and the University of Utah, have used "FURTHeR' for federating laboratory data. We present our process and initial results for federating microbiology data from six pediatric hospitals.

Recommendations From the International Consortium on Professional Nursing Practice in Long-Term Care Homes.

PubMed

McGilton, Katherine S; Bowers, Barbara J; Heath, Hazel; Shannon, Kay; Dellefield, Mary Ellen; Prentice, Dawn; Siegel, Elena O; Meyer, Julienne; Chu, Charlene H; Ploeg, Jenny; Boscart, Veronique M; Corazzini, Kirsten N; Anderson, Ruth A; Mueller, Christine A

2016-02-01

In response to the International Association of Gerontology and Geriatrics' global agenda for clinical research and quality of care in long-term care homes (LTCHs), the International Consortium on Professional Nursing Practice in Long Term Care Homes (the Consortium) was formed to develop nursing leadership capacity and address the concerns regarding the current state of professional nursing practice in LTCHs. At its invitational, 2-day inaugural meeting, the Consortium brought together international nurse experts to explore the potential of registered nurses (RNs) who work as supervisors or charge nurses within the LTCHs and the value of their contribution in nursing homes, consider what RN competencies might be needed, discuss effective educational (curriculum and practice) experiences, health care policy, and human resources planning requirements, and to identify what sustainable nurse leadership strategies and models might enhance the effectiveness of RNs in improving resident, family, and staff outcomes. The Consortium made recommendations about the following priority issues for action: (1) define the competencies of RNs required to care for older adults in LTCHs; (2) create an LTCH environment in which the RN role is differentiated from other team members and RNs can practice to their full scope; and (3) prepare RN leaders to operate effectively in person-centered care LTCH environments. In addition to clear recommendations for practice, the Consortium identified several areas in which further research is needed. The Consortium advocated for a research agenda that emphasizes an international coordination of research efforts to explore similar issues, the pursuit of examining the impact of nursing and organizational models, and the showcasing of excellence in nursing practice in care homes, so that others might learn from what works. Several studies already under way are also described. Copyright © 2016 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies.

PubMed

Abugessaisa, Imad; Noguchi, Shuhei; Hasegawa, Akira; Harshbarger, Jayson; Kondo, Atsushi; Lizio, Marina; Severin, Jessica; Carninci, Piero; Kawaji, Hideya; Kasukawa, Takeya

2017-08-29

The FANTOM5 consortium described the promoter-level expression atlas of human and mouse by using CAGE (Cap Analysis of Gene Expression) with single molecule sequencing. In the original publications, GRCh37/hg19 and NCBI37/mm9 assemblies were used as the reference genomes of human and mouse respectively; later, the Genome Reference Consortium released newer genome assemblies GRCh38/hg38 and GRCm38/mm10. To increase the utility of the atlas in forthcoming researches, we reprocessed the data to make them available on the recent genome assemblies. The data include observed frequencies of transcription starting sites (TSSs) based on the realignment of CAGE reads, and TSS peaks that are converted from those based on the previous reference. Annotations of the peak names were also updated based on the latest public databases. The reprocessed results enable us to examine frequencies of transcription initiations on the recent genome assemblies and to refer promoters with updated information across the genome assemblies consistently.

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes.

PubMed

Treu, Laura; Kougias, Panagiotis G; Campanaro, Stefano; Bassani, Ilaria; Angelidaki, Irini

2016-09-01

This research aimed to better characterize the biogas microbiome by means of high throughput metagenomic sequencing and to elucidate the core microbial consortium existing in biogas reactors independently from the operational conditions. Assembly of shotgun reads followed by an established binning strategy resulted in the highest, up to now, extraction of microbial genomes involved in biogas producing systems. From the 236 extracted genome bins, it was remarkably found that the vast majority of them could only be characterized at high taxonomic levels. This result confirms that the biogas microbiome is comprised by a consortium of unknown species. A comparative analysis between the genome bins of the current study and those extracted from a previous metagenomic assembly demonstrated a similar phylogenetic distribution of the main taxa. Finally, this analysis led to the identification of a subset of common microbes that could be considered as the core essential group in biogas production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assembly: a resource for assembled genomes at NCBI

PubMed Central

Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G.; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D.; Pruitt, Kim D.; Kimchi, Avi

2016-01-01

The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

The Multi-Resolution Land Characteristics (MRLC) Consortium: 20 years of development and integration of USA national land cover data

USGS Publications Warehouse

Wickham, James D.; Homer, Collin G.; Vogelmann, James E.; McKerrow, Alexa; Mueller, Rick; Herold, Nate; Coluston, John

2014-01-01

The Multi-Resolution Land Characteristics (MRLC) Consortium demonstrates the national benefits of USA Federal collaboration. Starting in the mid-1990s as a small group with the straightforward goal of compiling a comprehensive national Landsat dataset that could be used to meet agencies’ needs, MRLC has grown into a group of 10 USA Federal Agencies that coordinate the production of five different products, including the National Land Cover Database (NLCD), the Coastal Change Analysis Program (C-CAP), the Cropland Data Layer (CDL), the Gap Analysis Program (GAP), and the Landscape Fire and Resource Management Planning Tools (LANDFIRE). As a set, the products include almost every aspect of land cover from impervious surface to detailed crop and vegetation types to fire fuel classes. Some products can be used for land cover change assessments because they cover multiple time periods. The MRLC Consortium has become a collaborative forum, where members share research, methodological approaches, and data to produce products using established protocols, and we believe it is a model for the production of integrated land cover products at national to continental scales. We provide a brief overview of each of the main products produced by MRLC and examples of how each product has been used. We follow that with a discussion of the impact of the MRLC program and a brief overview of future plans.

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

Large scale validation of the M5L lung CAD on heterogeneous CT datasets.

PubMed

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.

Comparison of two commonly used clinical cognitive screening tests to diagnose mild cognitive impairment in heart failure with the golden standard European Consortium Criteria.

PubMed

Alagiakrishnan, Kannayiram; Mah, Darren; Dyck, Jason R B; Senthilselvan, Ambikaipakan; Ezekowitz, Justin

2017-02-01

This study on mild cognitive impairment (MCI) in heart failure (HF) compares the utility of Montreal Cognitive Assessment (MoCA) to the Mini-Mental Status Exam (MMSE) for diagnosing MCI in a HF population when compared to the golden standard European Consortium Criteria (ECC). Participants were recruited from the Alberta HEART study at the Mazankowski Alberta Heart Institute in Edmonton and St. Mary's hospital in Camrose. This study enrolled 53 community adults aged>50years: 33 HF and 20 controls. Participants were assessed using both the MMSE and MoCA for MCI. MCI was diagnosed using the golden standard, European Consortium Criteria. Sensitivity and specificity analysis, positive and negative predictive values, likelihood ratios and kappa statistic were calculated. The mean age was 72.8years (SD 8.4), 60.4% were females and 34% had underlying ischemic heart disease. Overall, two thirds of patients (22/33, 66%) with HF had MCI. In comparison to European Consortium Criteria, the sensitivity and specificity of MoCA were 82% and 91% in identifying individuals with MCI, and MMSE were 9% and 91%, respectively. The positive and negative predictive values for MoCA were 95% and 71%, and for MMSE were 67% and 33%, respectively. Kappa statistics showed good agreement between MoCA and consortium criteria (kappa=0.68) and a low agreement between MMSE and consortium criteria (kappa=0.07). Cognitive dysfunction is common in patients with HF. Overall, the MoCA seems to be a better screening tool than MMSE for MCI in HF patients. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.

PubMed

Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L; Zhang, Jingyu; Packer, Nicolle H; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P

2016-08-05

Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. Copyright © 2016 Elsevier Ltd. All rights reserved.

Variability in Standard Outcomes of Posterior Lumbar Fusion Determined by National Databases.

PubMed

Joseph, Jacob R; Smith, Brandon W; Park, Paul

2017-01-01

National databases are used with increasing frequency in spine surgery literature to evaluate patient outcomes. The differences between individual databases in relationship to outcomes of lumbar fusion are not known. We evaluated the variability in standard outcomes of posterior lumbar fusion between the University HealthSystem Consortium (UHC) database and the Healthcare Cost and Utilization Project National Inpatient Sample (NIS). NIS and UHC databases were queried for all posterior lumbar fusions (International Classification of Diseases, Ninth Revision code 81.07) performed in 2012. Patient demographics, comorbidities (including obesity), length of stay (LOS), in-hospital mortality, and complications such as urinary tract infection, deep venous thrombosis, pulmonary embolism, myocardial infarction, durotomy, and surgical site infection were collected using specific International Classification of Diseases, Ninth Revision codes. Analysis included 21,470 patients from the NIS database and 14,898 patients from the UHC database. Demographic data were not significantly different between databases. Obesity was more prevalent in UHC (P = 0.001). Mean LOS was 3.8 days in NIS and 4.55 in UHC (P < 0.0001). Complications were significantly higher in UHC, including urinary tract infection, deep venous thrombosis, pulmonary embolism, myocardial infarction, surgical site infection, and durotomy. In-hospital mortality was similar between databases. NIS and UHC databases had similar demographic patient populations undergoing posterior lumbar fusion. However, the UHC database reported significantly higher complication rate and longer LOS. This difference may reflect academic institutions treating higher-risk patients; however, a definitive reason for the variability between databases is unknown. The inability to precisely determine the basis of the variability between databases highlights the limitations of using administrative databases for spinal outcome analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

Brain Tumor Epidemiology – A Hub within Multidisciplinary Neuro-oncology. Report on the 15th Brain Tumor Epidemiology Consortium (BTEC) Annual Meeting, Vienna, 2014

PubMed Central

Woehrer, Adelheid; Lau, Ching C.; Prayer, Daniela; Bauchet, Luc; Rosenfeld, Myrna; Capper, David; Fisher, Paul G.; Kool, Marcel; Müller, Martin; Kros, Johan M.; Kruchko, Carol; Wiemels, Joseph; Wrensch, Margaret; Danysh, Heather E.; Zouaoui, Sonia; Heck, Julia E.; Johnson, Kimberly J.; Qi, Xiaoyang; O’Neill, Brian P.; Afzal, Samina; Scheurer, Michael E.; Bainbridge, Matthew N.; Nousome, Darryl; El Bahassi, Mustapha; Hainfellner, Johannes A.; Barnholtz-Sloan, Jill S.

2015-01-01

The Brain Tumor Epidemiology Consortium (BTEC) is an open scientific forum, which fosters the development of multi-center, international and inter-disciplinary collaborations. BTEC aims to develop a better understanding of the etiology, outcomes, and prevention of brain tumors (http://epi.grants.cancer.gov/btec/). The 15th annual Brain Tumor Epidemiology Consortium Meeting, hosted by the Austrian Societies of Neuropathology and Neuro-oncology, was held on September 9 – 11, 2014 in Vienna, Austria. The meeting focused on the central role of brain tumor epidemiology within multidisciplinary neuro-oncology. Knowledge of disease incidence, outcomes, as well as risk factors is fundamental to all fields involved in research and treatment of patients with brain tumors; thus, epidemiology constitutes an important link between disciplines, indeed the very hub. This was reflected by the scientific program, which included various sessions linking brain tumor epidemiology with clinical neuro-oncology, tissue-based research, and cancer registration. Renowned experts from Europe and the United States contributed their personal perspectives stimulating further group discussions. Several concrete action plans evolved for the group to move forward until next year’s meeting, which will be held at the Mayo Clinic at Rochester, MN, USA. PMID:25518914

The Magnetics Information Consortium (MagIC)

NASA Astrophysics Data System (ADS)

Johnson, C.; Constable, C.; Tauxe, L.; Koppers, A.; Banerjee, S.; Jackson, M.; Solheid, P.

2003-12-01

The Magnetics Information Consortium (MagIC) is a multi-user facility to establish and maintain a state-of-the-art relational database and digital archive for rock and paleomagnetic data. The goal of MagIC is to make such data generally available and to provide an information technology infrastructure for these and other research-oriented databases run by the international community. As its name implies, MagIC will not be restricted to paleomagnetic or rock magnetic data only, although MagIC will focus on these kinds of information during its setup phase. MagIC will be hosted under EarthRef.org at http://earthref.org/MAGIC/ where two "integrated" web portals will be developed, one for paleomagnetism (currently functional as a prototype that can be explored via the http://earthref.org/databases/PMAG/ link) and one for rock magnetism. The MagIC database will store all measurements and their derived properties for studies of paleomagnetic directions (inclination, declination) and their intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). Ultimately, this database will allow researchers to study "on the internet" and to download important data sets that display paleo-secular variations in the intensity of the Earth's magnetic field over geological time, or that display magnetic data in typical Zijderveld, hysteresis/FORC and various magnetization/remanence diagrams. The MagIC database is completely integrated in the EarthRef.org relational database structure and thus benefits significantly from already-existing common database components, such as the EarthRef Reference Database (ERR) and Address Book (ERAB). The ERR allows researchers to find complete sets of literature resources as used in GERM (Geochemical Earth Reference Model), REM (Reference Earth Model) and MagIC. The ERAB contains addresses for all contributors to the EarthRef.org databases, and also for those who participated in data collection, archiving and analysis in the magnetic studies. Integration with these existing components will guarantee direct traceability to the original sources of the MagIC data and metadata. The MagIC database design focuses around the general workflow that results in the determination of typical paleomagnetic and rock magnetic analyses. This ensures that individual data points can be traced between the actual measurements and their associated specimen, sample, site, rock formation and locality. This permits a distinction between original and derived data, where the actual measurements are performed at the specimen level, and data at the sample level and higher are then derived products in the database. These relations will also allow recalculation of derived properties, such as site means, when new data becomes available for a specific locality. Data contribution to the MagIC database is critical in achieving a useful research tool. We have developed a standard data and metadata template that can be used to provide all data at the same time as publication. Software tools are provided to facilitate easy population of these templates. The tools allow for the import/export of data files in a delimited text format, and they provide some advanced functionality to validate data and to check internal coherence of the data in the template. During and after publication these standardized MagIC templates will be stored in the ERR database of EarthRef.org from where they can be downloaded at all times. Finally, the contents of these template files will be automatically parsed into the online relational database.

The Challenge of Human Spermatozoa Proteome: A Systematic Review.

PubMed

Gilany, Kambiz; Minai-Tehrani, Arash; Amini, Mehdi; Agharezaee, Niloofar; Arjmand, Babak

2017-01-01

Currently, there are 20,197 human protein-coding genes in the most expertly curated database (UniProtKB/Swiss-Pro). Big efforts have been made by the international consortium, the Chromosome-Centric Human Proteome Project (C-HPP) and independent researchers, to map human proteome. In brief, anno 2017 the human proteome was outlined. The male factor contributes to 50% of infertility in couples. However, there are limited human spermatozoa proteomic studies. Firstly, the development of the mapping of the human spermatozoa was analyzed. The human spermatozoa have been used as a model for missing proteins. It has been shown that human spermatozoa are excellent sources for finding missing proteins. Y chromosome proteome mapping is led by Iran. However, it seems that it is extremely challenging to map the human spermatozoa Y chromosome proteins based on current mass spectrometry-based proteomics technology. Post-translation modifications (PTMs) of human spermatozoa proteome are the most unexplored area and currently the exact role of PTMs in male infertility is unknown. Additionally, the clinical human spermatozoa proteomic analysis, anno 2017 was done in this study.

Peginterferon beta-1a versus other self-injectable disease-modifying therapies in the treatment of relapsing-remitting multiple sclerosis in Scotland: a cost-effectiveness analysis.

PubMed

Hernandez, Luis; Guo, Shien; Toro-Diaz, Hector; Carroll, Stuart; Syed Farooq, Syed Feisal

2017-03-01

Peginterferon beta-1a 125 mcg administered subcutaneously every 2 weeks, a new disease-modifying therapy (DMT) for relapsing-remitting multiple sclerosis (RRMS), was approved in January 2015 by the Scottish Medicines Consortium. This study assesses long-term clinical and economic outcomes of peginterferon beta-1a compared with other self-injectable DMTs (interferon beta-1a [22 mcg, 30 mcg, and 44 mcg], interferon beta-1b, and glatiramer acetate 20 mg) in the treatment of RRMS, from the National Health Service and Personal Social Services perspective in Scotland. A previously published, validated Markov cohort model was adapted for this analysis. The model estimates changes in patient disability, occurrence of relapses, and other adverse events, and translates them into quality-adjusted life years and costs. Natural history data came from the ADVANCE trial of peginterferon beta-1a, the London Ontario (Canada) database, and a large population-based MS survey in the UK. The comparative efficacy of each DMT vs placebo was obtained from a network meta-analysis. Costs (2015 British Pounds) were obtained from public databases and literature. Clinical and economic outcomes were projected over 30 years and discounted at 3.5% per year. Over 30 years, peginterferon beta-1a was dominant compared with interferon beta-1a (22, 30, and 44 mcg), and interferon beta-1b, and cost-effective compared with glatiramer acetate 20 mg. Results were most sensitive to variations in each DMT's efficacy and acquisition costs. Deterministic and probabilistic sensitivity analyses confirmed the robustness of the results. The impact of improved adherence with peginterferon beta-1a on clinical and economic outcomes and the impact of subsequent DMTs after treatment discontinuation were not considered. Oral and infused DMTs were not included as comparators. Conclusion Long-term treatment with peginterferon beta-1a improves clinical outcomes, while its cost profile makes it either dominant or cost-effective compared with other self-injectable DMTs for the treatment of RRMS in Scotland.

Notice of Changes to RFA-CA-15-022 and Pre-Application Webinar | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute will hold a public Pre-Application webinar on Wednesday, January 13, 2016 at 12:00 p.m. (EST) for the Funding Opportunity Announcement (FOA) RFA-CA-15-022 entitled “Proteogenomic Translational Research Centers for Clinical Proteomic Tumor Analysis Consortium (U01).”

CPTAC Contributes to Healthdata.gov | Office of Cancer Clinical Proteomics Research

Cancer.gov

Recently, proteomic data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) funded by National Cancer Institute (NCI) was highlighted to the wider research community at Healthdata.gov. Healthdata.gov aims to make health data more accessible to entrepreneurs, researchers, and policy makers in the hopes of improving health outcomes f

Leaderboard Now Open: CPTAC’s DREAM Proteogenomics Computational Challenge | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is pleased to announce the opening of the leaderboard to its Proteogenomics Computational DREAM Challenge. The leadership board remains open for submissions during September 25, 2017 through October 8, 2017, with the Challenge expected to run until November 17, 2017.

Core Clinical Data Elements for Cancer Genomic Repositories: A Multi-stakeholder Consensus.

PubMed

Conley, Robert B; Dickson, Dane; Zenklusen, Jean Claude; Al Naber, Jennifer; Messner, Donna A; Atasoy, Ajlan; Chaihorsky, Lena; Collyar, Deborah; Compton, Carolyn; Ferguson, Martin; Khozin, Sean; Klein, Roger D; Kotte, Sri; Kurzrock, Razelle; Lin, C Jimmy; Liu, Frank; Marino, Ingrid; McDonough, Robert; McNeal, Amy; Miller, Vincent; Schilsky, Richard L; Wang, Lisa I

2017-11-16

The Center for Medical Technology Policy and the Molecular Evidence Development Consortium gathered a diverse group of more than 50 stakeholders to develop consensus on a core set of data elements and values essential to understanding the clinical utility of molecularly targeted therapies in oncology. Copyright © 2017 Elsevier Inc. All rights reserved.

Improved Infrastucture for Cdms and JPL Molecular Spectroscopy Catalogues

NASA Astrophysics Data System (ADS)

Endres, Christian; Schlemmer, Stephan; Drouin, Brian; Pearson, John; Müller, Holger S. P.; Schilke, P.; Stutzki, Jürgen

2014-06-01

Over the past years a new infrastructure for atomic and molecular databases has been developed within the framework of the Virtual Atomic and Molecular Data Centre (VAMDC). Standards for the representation of atomic and molecular data as well as a set of protocols have been established which allow now to retrieve data from various databases through one portal and to combine the data easily. Apart from spectroscopic databases such as the Cologne Database for Molecular Spectroscopy (CDMS), the Jet Propulsion Laboratory microwave, millimeter and submillimeter spectral line catalogue (JPL) and the HITRAN database, various databases on molecular collisions (BASECOL, KIDA) and reactions (UMIST) are connected. Together with other groups within the VAMDC consortium we are working on common user tools to simplify the access for new customers and to tailor data requests for users with specified needs. This comprises in particular tools to support the analysis of complex observational data obtained with the ALMA telescope. In this presentation requests to CDMS and JPL will be used to explain the basic concepts and the tools which are provided by VAMDC. In addition a new portal to CDMS will be presented which has a number of new features, in particular meaningful quantum numbers, references linked to data points, access to state energies and improved documentation. Fit files are accessible for download and queries to other databases are possible.

CPTAC Biospecimen Collection Solicitation | Office of Cancer Clinical Proteomics Research

Cancer.gov

A funding opportunity in support of the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) seeks to prospectively procure tumor samples, collected for proteomics investigation. The scope of work under this Statement of Work encompasses the activities needed to prospectively procure high quality, clinically annotated human tumor samples, blood and plasma, and when feasible, normal tissue from volunteer patients suffering from colon, ovarian, and breast cancer.

Brain Immune Interactions as the Basis of Gulf War Illness: Gulf War Illness Consortium (GWIC)

DTIC Science & Technology

2015-10-01

August to train all clinical staff and to ensure proper quality control measures are in place for the clinical studies. This has been followed up by...clinical and preclinical studies Training for researchers and clinical staff was completed at in-person meeting in Boston in August 2014 and continued to...Catechol-O- methyl transferase ( COMT ). COMT is associated with synaptic catecholamine neurotransmitters. COMT helps regulate cortical dopamine in the

Screening and management of mental health and substance use disorders in HIV treatment settings in low- and middle-income countries within the global IeDEA consortium.

PubMed

Parcesepe, Angela M; Mugglin, Catrina; Nalugoda, Fred; Bernard, Charlotte; Yunihastuti, Evy; Althoff, Keri; Jaquet, Antoine; Haas, Andreas D; Duda, Stephany N; Wester, C William; Nash, Denis

2018-03-01

Integration of services to screen and manage mental health and substance use disorders (MSDs) into HIV care settings has been identified as a promising strategy to improve mental health and HIV treatment outcomes among people living with HIV/AIDS (PLWHA) in low- and middle-income countries (LMICs). Data on the extent to which HIV treatment sites in LMICs screen and manage MSDs are limited. The objective of this study was to assess practices for screening and treatment of MSDs at HIV clinics in LMICs participating in the International epidemiology Databases to Evaluate AIDS (IeDEA) consortium. We surveyed a stratified random sample of 95 HIV clinics in 29 LMICs in the Caribbean, Central and South America, Asia-Pacific and sub-Saharan Africa. The survey captured information onsite characteristics and screening and treatment practices for depression, post-traumatic stress disorder (PTSD), substance use disorders (SUDs) and other mental health disorders. Most sites (n = 76, 80%) were in urban areas. Mental health screening varied by disorder: 57% of sites surveyed screened for depression, 19% for PTSD, 55% for SUDs and 29% for other mental health disorders. Depression, PTSD, SUDs and other mental health disorders were reported as managed on site (having services provided at the HIV clinic or same health facility) at 70%, 51%, 41% and 47% of sites respectively. Combined availability of screening and on-site management of depression, PTSD, and SUDs, and other mental health disorders was reported by 42%, 14%, 26% and 19% of sites, respectively. On-site management of depression and PTSD was reported significantly less often in rural as compared to urban settings (depression: 33% and 78% respectively; PTSD: 24% and 58% respectively). Screening for depression and SUDs was least commonly reported by HIV programmes that treated only children as compared to HIV programmes that treated only adults or treated both adults and children. Significant gaps exist in the management of MSDs in HIV care settings in LMICs, particularly in rural settings. Identification and evaluation of optimal implementation strategies to scale and sustain integrated MSDs and HIV care is needed. © 2018 The Authors. Journal of the International AIDS Society published by John Wiley & sons Ltd on behalf of the International AIDS Society.

GlycomeDB – integration of open-access carbohydrate structure databases

PubMed Central

Ranzinger, René; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

2008-01-01

Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource. PMID:18803830

Predictive capabilities of statistical learning methods for lung nodule malignancy classification using diagnostic image features: an investigation using the Lung Image Database Consortium dataset

NASA Astrophysics Data System (ADS)

Hancock, Matthew C.; Magnan, Jerry F.

2017-03-01

To determine the potential usefulness of quantified diagnostic image features as inputs to a CAD system, we investigate the predictive capabilities of statistical learning methods for classifying nodule malignancy, utilizing the Lung Image Database Consortium (LIDC) dataset, and only employ the radiologist-assigned diagnostic feature values for the lung nodules therein, as well as our derived estimates of the diameter and volume of the nodules from the radiologists' annotations. We calculate theoretical upper bounds on the classification accuracy that is achievable by an ideal classifier that only uses the radiologist-assigned feature values, and we obtain an accuracy of 85.74 (+/-1.14)% which is, on average, 4.43% below the theoretical maximum of 90.17%. The corresponding area-under-the-curve (AUC) score is 0.932 (+/-0.012), which increases to 0.949 (+/-0.007) when diameter and volume features are included, along with the accuracy to 88.08 (+/-1.11)%. Our results are comparable to those in the literature that use algorithmically-derived image-based features, which supports our hypothesis that lung nodules can be classified as malignant or benign using only quantified, diagnostic image features, and indicates the competitiveness of this approach. We also analyze how the classification accuracy depends on specific features, and feature subsets, and we rank the features according to their predictive power, statistically demonstrating the top four to be spiculation, lobulation, subtlety, and calcification.

Remote sensing and GIS technology in the Global Land Ice Measurements from Space (GLIMS) Project

USGS Publications Warehouse

Raup, B.; Kääb, Andreas; Kargel, J.S.; Bishop, M.P.; Hamilton, G.; Lee, E.; Paul, F.; Rau, F.; Soltesz, D.; Khalsa, S.J.S.; Beedle, M.; Helm, C.

2007-01-01

Global Land Ice Measurements from Space (GLIMS) is an international consortium established to acquire satellite images of the world's glaciers, analyze them for glacier extent and changes, and to assess these change data in terms of forcings. The consortium is organized into a system of Regional Centers, each of which is responsible for glaciers in their region of expertise. Specialized needs for mapping glaciers in a distributed analysis environment require considerable work developing software tools: terrain classification emphasizing snow, ice, water, and admixtures of ice with rock debris; change detection and analysis; visualization of images and derived data; interpretation and archival of derived data; and analysis to ensure consistency of results from different Regional Centers. A global glacier database has been designed and implemented at the National Snow and Ice Data Center (Boulder, CO); parameters have been expanded from those of the World Glacier Inventory (WGI), and the database has been structured to be compatible with (and to incorporate) WGI data. The project as a whole was originated, and has been coordinated by, the US Geological Survey (Flagstaff, AZ), which has also led the development of an interactive tool for automated analysis and manual editing of glacier images and derived data (GLIMSView). This article addresses remote sensing and Geographic Information Science techniques developed within the framework of GLIMS in order to fulfill the goals of this distributed project. Sample applications illustrating the developed techniques are also shown. ?? 2006 Elsevier Ltd. All rights reserved.

Photovoltaic Manufacturing Consortium (PVMC) – Enabling America’s Solar Revolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metacarpa, David

The U.S. Photovoltaic Manufacturing Consortium (US-PVMC) is an industry-led consortium which was created with the mission to accelerate the research, development, manufacturing, field testing, commercialization, and deployment of next-generation solar photovoltaic technologies. Formed as part of the U.S. Department of Energy's (DOE) SunShot initiative, and headquartered in New York State, PVMC is managed by the State University of New York Polytechnic Institute (SUNY Poly) at the Colleges of Nanoscale Science and Engineering. PVMC is a hybrid of industry-led consortium and manufacturing development facility, with capabilities for collaborative and proprietary industry engagement. Through its technology development programs, advanced manufacturing development facilities,more » system demonstrations, and reliability and testing capabilities, PVMC has demonstrated itself to be a recognized proving ground for innovative solar technologies and system designs. PVMC comprises multiple locations, with the core manufacturing and deployment support activities conducted at the Solar Energy Development Center (SEDC), and the core Si wafering and metrology technologies being headed out of the University of Central Florida. The SEDC provides a pilot line for proof-of-concept prototyping, offering critical opportunities to demonstrate emerging concepts in PV manufacturing, such as evaluations of innovative materials, system components, and PV system designs. The facility, located in Halfmoon NY, encompasses 40,000 square feet of dedicated PV development space. The infrastructure and capabilities housed at PVMC includes PV system level testing at the Prototype Demonstration Facility (PDF), manufacturing scale cell & module fabrication at the Manufacturing Development Facility (MDF), cell and module testing, reliability equipment on its PV pilot line, all integrated with a PV performance database and analytical characterizations for PVMC and its partners test and commercial arrays. Additional development and deployment support are also housed at the SEDC, such as cost modeling and cost model based development activities for PV and thin film modules, components, and system level designs for reduced LCOE through lower installation hardware costs, labor reductions, soft costs and reduced operations and maintenance costs. The progression of the consortium activities started with infrastructure and capabilities build out focused on CIGS thin film photovoltaics, with a particular focus on flexible cell and module production. As marketplace changes and partners objectives shifted, the consortium shifted heavily towards deployment and market pull activities including Balance of System, cost modeling, and installation cost reduction efforts along with impacts to performance and DER operational costs. The consortium consisted of a wide array of PV supply chain companies from equipment and component suppliers through national developers and installers with a particular focus on commercial scale deployments (typically 25 to 2MW installations). With DOE funding ending after the fifth budget period, the advantages and disadvantages of such a consortium is detailed along with potential avenues for self-sustainability is reviewed.« less

NLCD 2011 database

EPA Pesticide Factsheets

National Land Cover Database 2011 (NLCD 2011) is the most recent national land cover product created by the Multi-Resolution Land Characteristics (MRLC) Consortium. NLCD 2011 provides - for the first time - the capability to assess wall-to-wall, spatially explicit, national land cover changes and trends across the United States from 2001 to 2011. As with two previous NLCD land cover products NLCD 2011 keeps the same 16-class land cover classification scheme that has been applied consistently across the United States at a spatial resolution of 30 meters. NLCD 2011 is based primarily on a decision-tree classification of circa 2011 Landsat satellite data. This dataset is associated with the following publication:Homer, C., J. Dewitz, L. Yang, S. Jin, P. Danielson, G. Xian, J. Coulston, N. Herold, J. Wickham , and K. Megown. Completion of the 2011 National Land Cover Database for the Conterminous United States – Representing a Decade of Land Cover Change Information. PHOTOGRAMMETRIC ENGINEERING AND REMOTE SENSING. American Society for Photogrammetry and Remote Sensing, Bethesda, MD, USA, 81(0): 345-354, (2015).

Significance of genome-wide association studies in molecular anthropology.

PubMed

Gupta, Vipin; Khadgawat, Rajesh; Sachdeva, Mohinder Pal

2009-12-01

The successful advent of a genome-wide approach in association studies raises the hopes of human geneticists for solving a genetic maze of complex traits especially the disorders. This approach, which is replete with the application of cutting-edge technology and supported by big science projects (like Human Genome Project; and even more importantly the International HapMap Project) and various important databases (SNP database, CNV database, etc.), has had unprecedented success in rapidly uncovering many of the genetic determinants of complex disorders. The magnitude of this approach in the genetics of classical anthropological variables like height, skin color, eye color, and other genome diversity projects has certainly expanded the horizons of molecular anthropology. Therefore, in this article we have proposed a genome-wide association approach in molecular anthropological studies by providing lessons from the exemplary study of the Wellcome Trust Case Control Consortium. We have also highlighted the importance and uniqueness of Indian population groups in facilitating the design and finding optimum solutions for other genome-wide association-related challenges.

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

PubMed

Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

2016-01-04

We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Equine Clinical Genomics: A Clinician’s Primer

PubMed Central

Brosnahan, Margaret Mary; Brooks, Samantha A.; Antczak, Douglas F.

2012-01-01

Summary The objective of this review is to introduce equine clinicians to the rapidly evolving field of clinical genomics with a vision of improving the health and welfare of the domestic horse. For fifteen years a consortium of veterinary geneticists and clinicians has worked together under the umbrella of The Horse Genome Project. This group, encompassing 22 laboratories in 12 countries, has made rapid progress, developing several iterations of linkage, physical and comparative gene maps of the horse with increasing levels of detail. In early 2006, the research was greatly facilitated when the U.S. National Human Genome Research Institute of the National Institutes of Health added the horse to the list of mammalian species scheduled for whole genome sequencing. The genome of the domestic horse has now been sequenced and is available to researchers worldwide in publicly accessible databases. This achievement creates the potential for transformative change within the horse industry, particularly in the fields of internal medicine, sports medicine and reproduction. The genome sequence has enabled the development of new genome-wide tools and resources for studying inherited diseases of the horse. To date, researchers have identified eleven mutations causing ten clinical syndromes in the horse. Testing is commercially available for all but one of these diseases. Future research will probably identify the genetic bases for other equine diseases, produce new diagnostic tests and generate novel therapeutics for some of these conditions. This will enable equine clinicians to play a critical role in ensuring the thoughtful and appropriate application of this knowledge as they assist clients with breeding and clinical decision-making. PMID:20840582

Future Directions in Oncofertility and Fertility Preservation: A Report from the 2011 Oncofertility Consortium Conference

PubMed Central

Waimey, Kate E.; Duncan, Francesca E.; Su, H. Irene; Smith, Kristin; Wallach, Harlan; Jona, Kemi; Coutifaris, Christos; Gracia, Clarisa R.; Shea, Lonnie D.; Brannigan, Robert E.; Chang, R. Jeffrey; Zelinski, Mary B.; Stouffer, Richard L.; Taylor, Robert L.

2013-01-01

Fertility impairment and loss due to cancer or its treatment is a significant survivorship consideration for many pediatric, adolescent, and young adult cancer survivors. Chemotherapeutics, radiation, and surgery can impact the future fertility of men, women, and children with cancer. The field of oncofertility, founded to ensure the reproductive future of cancer survivors, gained momentum with 5 years of funding through a 2007 National Institutes of Health Roadmap Grant for Biomedical Research. This report from working group meetings at the fifth annual Oncofertility Consortium Conference speaks to the present state of oncofertility research and clinical care, existing gaps, and future directions for the field. This summary from conference participants and leaders in the field addresses the science, clinical specialties, and academic scholarship that can guide the field as the Roadmap Grant funding comes to a close. PMID:23610740

Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and VKORC1 Genotypes and Warfarin Dosing

PubMed Central

Johnson, JA; Gong, L; Whirl-Carrillo, M; Gage, BF; Scott, SA; Stein, CM; Anderson, JL; Kimmel, SE; Lee, MTM; Pirmohamed, M; Wadelius, M; Klein, TE; Altman, RB

2011-01-01

Warfarin is a widely used anticoagulant with a narrow therapeutic index and large interpatient variability in the dose required to achieve target anticoagulation. Common genetic variants in the cytochrome P450-2C9 (CYP2C9) and vitamin K–epoxide reductase complex (VKORC1) enzymes, in addition to known nongenetic factors, account for ~50% of warfarin dose variability. The purpose of this article is to assist in the interpretation and use of CYP2C9 and VKORC1 geno-type data for estimating therapeutic warfarin dose to achieve an INR of 2–3, should genotype results be available to the clinician. The Clinical Pharmacogenetics Implementation Consortium (CPIC) of the National Institutes of Health Pharmacogenomics Research Network develops peer-reviewed gene–drug guidelines that are published and updated periodically on http://www.pharmgkb.org based on new developments in the field.1 PMID:21900891

Filmless PACS in a multiple facility environment

NASA Astrophysics Data System (ADS)

Wilson, Dennis L.; Glicksman, Robert A.; Prior, Fred W.; Siu, Kai-Yeung; Goldburgh, Mitchell M.

1996-05-01

A Picture Archiving and Communication System centered on a shared image file server can support a filmless hospital. Systems based on this architecture have proven themselves in over four years of clinical operation. Changes in healthcare delivery are causing radiology groups to support multiple facilities for remote clinic support and consolidation of services. There will be a corresponding need for communicating over a standardized wide area network (WAN). Interactive workflow, a natural extension to the single facility case, requires a means to work effectively and seamlessly across moderate to low speed communication networks. Several schemes for supporting a consortium of medical treatment facilities over a WAN are explored. Both centralized and distributed database approaches are evaluated against several WAN scenarios. Likewise, several architectures for distributing image file servers or buffers over a WAN are explored, along with the caching and distribution strategies that support them. An open system implementation is critical to the success of a wide area system. The role of the Digital Imaging and Communications in Medicine (DICOM) standard in supporting multi- facility and multi-vendor open systems is also addressed. An open system can be achieved by using a DICOM server to provide a view of the system-wide distributed database. The DICOM server interface to a local version of the global database lets a local workstation treat the multiple, distributed data servers as though they were one local server for purposes of examination queries. The query will recover information about the examination that will permit retrieval over the network from the server on which the examination resides. For efficiency reasons, the ability to build cross-facility radiologist worklists and clinician-oriented patient folders is essential. The technologies of the World-Wide-Web can be used to generate worklists and patient folders across facilities. A reliable broadcast protocol may be a convenient way to notify many different users and many image servers about new activities in the network of image servers. In addition to ensuring reliability of message delivery and global serialization of each broadcast message in the network, the broadcast protocol should not introduce significant communication overhead.

Systematic review of systemic sclerosis-specific instruments for the EULAR Outcome Measures Library: An evolutional database model of validated patient-reported outcomes.

PubMed

Ingegnoli, Francesca; Carmona, Loreto; Castrejon, Isabel

2017-04-01

The EULAR Outcome Measures Library (OML) is a freely available database of validated patient-reported outcomes (PROs). The aim of this study was to provide a comprehensive review of validated PROs specifically developed for systemic sclerosis (SSc) to feed the EULAR OML. A sensitive search was developed in Medline and Embase to identify all validation studies, cohort studies, reviews, or meta-analyses in which the objective were the development or validation of specific PROs evaluating organ involvement, disease activity or damage in SSc. A reviewer screened title and abstracts, selected the studies, and collected data concerning validation using ad hoc forms based on the COSMIN checklist. From 13,140 articles captured, 74 met the predefined criteria. After excluding two instruments as they were unavailable in English the selected 23 studies provided information on seven SSc-specific PROs on different SSc domains: burden of illness (symptom burden index), functional status (Scleroderma Assessment Questionnaire), functional ability (scleroderma Functional Score), Raynaud's phenomenon (Raynaud's condition score), mouth involvement (Mouth Handicap in SSc), gastro-intestinal involvement (University of California Los Angeles-Scleroderma Clinical Trial Consortium Gastro-Intestinal tract 2.0), and skin involvement (skin self-assessment). Each of them is partially validated and has different psychometric requirements. Seven SSc-specific PROs have a minimum validation and were included in the EULAR OML. Further development in the area of disease-specific PROs in SSc is warranted. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparison of rat and rabbit embryo-fetal developmental ...

EPA Pesticide Factsheets

Regulatory non-clinical safety testing of human pharmaceutical compounds typically requires embryo fetal developmental toxicity (EFDT) testing in two species, (one rodent and one non-rodent, usually the rat and the rabbit). The question has been raised whether under some conditions EFDT testing could be limited to one species, or whether the need for testing in a second species could be decided on a case by case basis. As part of an RIVM/CBG-MEB/HESI/US EPA consortium initiative, we built and queried a database of 379 EFDT studies conducted for marketed and non-marketed pharmaceutical compounds. The animal models (rat and rabbit) were assessed for their potential for adverse developmental and maternal outcomes. The database was analyzed for the prevalence of EFDT incidence and the nature and severity of adverse findings in the two species. Some manifestation of EFDT in either one or both species (rat and rabbit) was demonstrated for 282 compounds (74%), and EFDT was detected in only one species (rat or rabbit) in almost a third (31%, 118 compounds), with approximately 58% rat and 42% rabbit studies identifying an EFDT signal among the 379 compounds tested. For 24 compounds (6%), fetal malformations were observed in one species (rat or rabbit) in the absence of any EFDT in the second species. In general, growth retardation, fetal variations, and malformations were more prominent in the rat, whereas embryo-fetal death was observed more often in the rabbit. Discor

No clinical utility of KRAS variant rs61764370 for ovarian or breast cancer.

PubMed

Hollestelle, Antoinette; van der Baan, Frederieke H; Berchuck, Andrew; Johnatty, Sharon E; Aben, Katja K; Agnarsson, Bjarni A; Aittomäki, Kristiina; Alducci, Elisa; Andrulis, Irene L; Anton-Culver, Hoda; Antonenkova, Natalia N; Antoniou, Antonis C; Apicella, Carmel; Arndt, Volker; Arnold, Norbert; Arun, Banu K; Arver, Brita; Ashworth, Alan; Baglietto, Laura; Balleine, Rosemary; Bandera, Elisa V; Barrowdale, Daniel; Bean, Yukie T; Beckmann, Lars; Beckmann, Matthias W; Benitez, Javier; Berger, Andreas; Berger, Raanan; Beuselinck, Benoit; Bisogna, Maria; Bjorge, Line; Blomqvist, Carl; Bogdanova, Natalia V; Bojesen, Anders; Bojesen, Stig E; Bolla, Manjeet K; Bonanni, Bernardo; Brand, Judith S; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Brooks-Wilson, Angela; Bruinsma, Fiona; Brunet, Joan; Brüning, Thomas; Budzilowska, Agnieszka; Bunker, Clareann H; Burwinkel, Barbara; Butzow, Ralf; Buys, Saundra S; Caligo, Maria A; Campbell, Ian; Carter, Jonathan; Chang-Claude, Jenny; Chanock, Stephen J; Claes, Kathleen B M; Collée, J Margriet; Cook, Linda S; Couch, Fergus J; Cox, Angela; Cramer, Daniel; Cross, Simon S; Cunningham, Julie M; Cybulski, Cezary; Czene, Kamila; Damiola, Francesca; Dansonka-Mieszkowska, Agnieszka; Darabi, Hatef; de la Hoya, Miguel; deFazio, Anna; Dennis, Joseph; Devilee, Peter; Dicks, Ed M; Diez, Orland; Doherty, Jennifer A; Domchek, Susan M; Dorfling, Cecilia M; Dörk, Thilo; Silva, Isabel Dos Santos; du Bois, Andreas; Dumont, Martine; Dunning, Alison M; Duran, Mercedes; Easton, Douglas F; Eccles, Diana; Edwards, Robert P; Ehrencrona, Hans; Ejlertsen, Bent; Ekici, Arif B; Ellis, Steve D; Engel, Christoph; Eriksson, Mikael; Fasching, Peter A; Feliubadalo, Lidia; Figueroa, Jonine; Flesch-Janys, Dieter; Fletcher, Olivia; Fontaine, Annette; Fortuzzi, Stefano; Fostira, Florentia; Fridley, Brooke L; Friebel, Tara; Friedman, Eitan; Friel, Grace; Frost, Debra; Garber, Judy; García-Closas, Montserrat; Gayther, Simon A; Gentry-Maharaj, Aleksandra; Gerdes, Anne-Marie; Giles, Graham G; Glasspool, Rosalind; Glendon, Gord; Godwin, Andrew K; Goodman, Marc T; Gore, Martin; Greene, Mark H; Grip, Mervi; Gronwald, Jacek; Gschwantler Kaulich, Daphne; Guénel, Pascal; Guzman, Starr R; Haeberle, Lothar; Haiman, Christopher A; Hall, Per; Halverson, Sandra L; Hamann, Ute; Hansen, Thomas V O; Harter, Philipp; Hartikainen, Jaana M; Healey, Sue; Hein, Alexander; Heitz, Florian; Henderson, Brian E; Herzog, Josef; T Hildebrandt, Michelle A; Høgdall, Claus K; Høgdall, Estrid; Hogervorst, Frans B L; Hopper, John L; Humphreys, Keith; Huzarski, Tomasz; Imyanitov, Evgeny N; Isaacs, Claudine; Jakubowska, Anna; Janavicius, Ramunas; Jaworska, Katarzyna; Jensen, Allan; Jensen, Uffe Birk; Johnson, Nichola; Jukkola-Vuorinen, Arja; Kabisch, Maria; Karlan, Beth Y; Kataja, Vesa; Kauff, Noah; Kelemen, Linda E; Kerin, Michael J; Kiemeney, Lambertus A; Kjaer, Susanne K; Knight, Julia A; Knol-Bout, Jacoba P; Konstantopoulou, Irene; Kosma, Veli-Matti; Krakstad, Camilla; Kristensen, Vessela; Kuchenbaecker, Karoline B; Kupryjanczyk, Jolanta; Laitman, Yael; Lambrechts, Diether; Lambrechts, Sandrina; Larson, Melissa C; Lasa, Adriana; Laurent-Puig, Pierre; Lazaro, Conxi; Le, Nhu D; Le Marchand, Loic; Leminen, Arto; Lester, Jenny; Levine, Douglas A; Li, Jingmei; Liang, Dong; Lindblom, Annika; Lindor, Noralane; Lissowska, Jolanta; Long, Jirong; Lu, Karen H; Lubinski, Jan; Lundvall, Lene; Lurie, Galina; Mai, Phuong L; Mannermaa, Arto; Margolin, Sara; Mariette, Frederique; Marme, Frederik; Martens, John W M; Massuger, Leon F A G; Maugard, Christine; Mazoyer, Sylvie; McGuffog, Lesley; McGuire, Valerie; McLean, Catriona; McNeish, Iain; Meindl, Alfons; Menegaux, Florence; Menéndez, Primitiva; Menkiszak, Janusz; Menon, Usha; Mensenkamp, Arjen R; Miller, Nicola; Milne, Roger L; Modugno, Francesmary; Montagna, Marco; Moysich, Kirsten B; Müller, Heiko; Mulligan, Anna Marie; Muranen, Taru A; Narod, Steven A; Nathanson, Katherine L; Ness, Roberta B; Neuhausen, Susan L; Nevanlinna, Heli; Neven, Patrick; Nielsen, Finn C; Nielsen, Sune F; Nordestgaard, Børge G; Nussbaum, Robert L; Odunsi, Kunle; Offit, Kenneth; Olah, Edith; Olopade, Olufunmilayo I; Olson, Janet E; Olson, Sara H; Oosterwijk, Jan C; Orlow, Irene; Orr, Nick; Orsulic, Sandra; Osorio, Ana; Ottini, Laura; Paul, James; Pearce, Celeste L; Pedersen, Inge Sokilde; Peissel, Bernard; Pejovic, Tanja; Pelttari, Liisa M; Perkins, Jo; Permuth-Wey, Jenny; Peterlongo, Paolo; Peto, Julian; Phelan, Catherine M; Phillips, Kelly-Anne; Piedmonte, Marion; Pike, Malcolm C; Platte, Radka; Plisiecka-Halasa, Joanna; Poole, Elizabeth M; Poppe, Bruce; Pylkäs, Katri; Radice, Paolo; Ramus, Susan J; Rebbeck, Timothy R; Reed, Malcolm W R; Rennert, Gad; Risch, Harvey A; Robson, Mark; Rodriguez, Gustavo C; Romero, Atocha; Rossing, Mary Anne; Rothstein, Joseph H; Rudolph, Anja; Runnebaum, Ingo; Salani, Ritu; Salvesen, Helga B; Sawyer, Elinor J; Schildkraut, Joellen M; Schmidt, Marjanka K; Schmutzler, Rita K; Schneeweiss, Andreas; Schoemaker, Minouk J; Schrauder, Michael G; Schumacher, Fredrick; Schwaab, Ira; Scuvera, Giulietta; Sellers, Thomas A; Severi, Gianluca; Seynaeve, Caroline M; Shah, Mitul; Shrubsole, Martha; Siddiqui, Nadeem; Sieh, Weiva; Simard, Jacques; Singer, Christian F; Sinilnikova, Olga M; Smeets, Dominiek; Sohn, Christof; Soller, Maria; Song, Honglin; Soucy, Penny; Southey, Melissa C; Stegmaier, Christa; Stoppa-Lyonnet, Dominique; Sucheston, Lara; Swerdlow, Anthony; Tangen, Ingvild L; Tea, Muy-Kheng; Teixeira, Manuel R; Terry, Kathryn L; Terry, Mary Beth; Thomassen, Mads; Thompson, Pamela J; Tihomirova, Laima; Tischkowitz, Marc; Toland, Amanda Ewart; Tollenaar, Rob A E M; Tomlinson, Ian; Torres, Diana; Truong, Thérèse; Tsimiklis, Helen; Tung, Nadine; Tworoger, Shelley S; Tyrer, Jonathan P; Vachon, Celine M; Van 't Veer, Laura J; van Altena, Anne M; Van Asperen, C J; van den Berg, David; van den Ouweland, Ans M W; van Doorn, Helena C; Van Nieuwenhuysen, Els; van Rensburg, Elizabeth J; Vergote, Ignace; Verhoef, Senno; Vierkant, Robert A; Vijai, Joseph; Vitonis, Allison F; von Wachenfeldt, Anna; Walsh, Christine; Wang, Qin; Wang-Gohrke, Shan; Wappenschmidt, Barbara; Weischer, Maren; Weitzel, Jeffrey N; Weltens, Caroline; Wentzensen, Nicolas; Whittemore, Alice S; Wilkens, Lynne R; Winqvist, Robert; Wu, Anna H; Wu, Xifeng; Yang, Hannah P; Zaffaroni, Daniela; Pilar Zamora, M; Zheng, Wei; Ziogas, Argyrios; Chenevix-Trench, Georgia; Pharoah, Paul D P; Rookus, Matti A; Hooning, Maartje J; Goode, Ellen L

2016-05-01

Clinical genetic testing is commercially available for rs61764370, an inherited variant residing in a KRAS 3' UTR microRNA binding site, based on suggested associations with increased ovarian and breast cancer risk as well as with survival time. However, prior studies, emphasizing particular subgroups, were relatively small. Therefore, we comprehensively evaluated ovarian and breast cancer risks as well as clinical outcome associated with rs61764370. Centralized genotyping and analysis were performed for 140,012 women enrolled in the Ovarian Cancer Association Consortium (15,357 ovarian cancer patients; 30,816 controls), the Breast Cancer Association Consortium (33,530 breast cancer patients; 37,640 controls), and the Consortium of Modifiers of BRCA1 and BRCA2 (14,765 BRCA1 and 7904 BRCA2 mutation carriers). We found no association with risk of ovarian cancer (OR=0.99, 95% CI 0.94-1.04, p=0.74) or breast cancer (OR=0.98, 95% CI 0.94-1.01, p=0.19) and results were consistent among mutation carriers (BRCA1, ovarian cancer HR=1.09, 95% CI 0.97-1.23, p=0.14, breast cancer HR=1.04, 95% CI 0.97-1.12, p=0.27; BRCA2, ovarian cancer HR=0.89, 95% CI 0.71-1.13, p=0.34, breast cancer HR=1.06, 95% CI 0.94-1.19, p=0.35). Null results were also obtained for associations with overall survival following ovarian cancer (HR=0.94, 95% CI 0.83-1.07, p=0.38), breast cancer (HR=0.96, 95% CI 0.87-1.06, p=0.38), and all other previously-reported associations. rs61764370 is not associated with risk of ovarian or breast cancer nor with clinical outcome for patients with these cancers. Therefore, genotyping this variant has no clinical utility related to the prediction or management of these cancers. Copyright © 2015 Elsevier Inc. All rights reserved.

No clinical utility of KRAS variant rs61764370 for ovarian or breast cancer

PubMed Central

Hollestelle, Antoinette; van der Baan, Frederieke H.; Berchuck, Andrew; Johnatty, Sharon E.; Aben, Katja K.; Agnarsson, Bjarni A.; Aittomäki, Kristiina; Alducci, Elisa; Andrulis, Irene L.; Anton-Culver, Hoda; Antonenkova, Natalia N.; Antoniou, Antonis C.; Apicella, Carmel; Arndt, Volker; Arnold, Norbert; Arun, Banu K.; Arver, Brita; Ashworth, Alan; Baglietto, Laura; Balleine, Rosemary; Bandera, Elisa V.; Barrowdale, Daniel; Bean, Yukie T.; Beckmann, Lars; Beckmann, Matthias W.; Benitez, Javier; Berger, Andreas; Berger, Raanan; Beuselinck, Benoit; Bisogna, Maria; Bjorge, Line; Blomqvist, Carl; Bogdanova, Natalia V.; Bojesen, Anders; Bojesen, Stig E.; Bolla, Manjeet K.; Bonanni, Bernardo; Brand, Judith S.; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Brooks-Wilson, Angela; Bruinsma, Fiona; Brunet, Joan; Brüning, Thomas; Budzilowska, Agnieszka; Bunker, Clareann H.; Burwinkel, Barbara; Butzow, Ralf; Buys, Saundra S.; Caligo, Maria A.; Campbell, Ian; Carter, Jonathan; Chang-Claude, Jenny; Chanock, Stephen J.; Claes, Kathleen B.M.; Collée, J. Margriet; Cook, Linda S.; Couch, Fergus J.; Cox, Angela; Cramer, Daniel; Cross, Simon S.; Cunningham, Julie M.; Cybulski, Cezary; Czene, Kamila; Damiola, Francesca; Dansonka-Mieszkowska, Agnieszka; Darabi, Hatef; de la Hoya, Miguel; deFazio, Anna; Dennis, Joseph; Devilee, Peter; Dicks, Ed M.; Diez, Orland; Doherty, Jennifer A.; Domchek, Susan M.; Dorfling, Cecilia M.; Dörk, Thilo; Santos Silva, Isabel Dos; du Bois, Andreas; Dumont, Martine; Dunning, Alison M.; Duran, Mercedes; Easton, Douglas F.; Eccles, Diana; Edwards, Robert P.; Ehrencrona, Hans; Ejlertsen, Bent; Ekici, Arif B.; Ellis, Steve D.; Engel, Christoph; Eriksson, Mikael; Fasching, Peter A.; Feliubadalo, Lidia; Figueroa, Jonine; Flesch-Janys, Dieter; Fletcher, Olivia; Fontaine, Annette; Fortuzzi, Stefano; Fostira, Florentia; Fridley, Brooke L.; Friebel, Tara; Friedman, Eitan; Friel, Grace; Frost, Debra; Garber, Judy; García-Closas, Montserrat; Gayther, Simon A.; Gentry-Maharaj, Aleksandra; Gerdes, Anne-Marie; Giles, Graham G.; Glasspool, Rosalind; Glendon, Gord; Godwin, Andrew K.; Goodman, Marc T.; Gore, Martin; Greene, Mark H.; Grip, Mervi; Gronwald, Jacek; Kaulich, Daphne Gschwantler; Guénel, Pascal; Guzman, Starr R.; Haeberle, Lothar; Haiman, Christopher A.; Hall, Per; Halverson, Sandra L.; Hamann, Ute; Hansen, Thomas V.O.; Harter, Philipp; Hartikainen, Jaana M.; Healey, Sue; Hein, Alexander; Heitz, Florian; Henderson, Brian E.; Herzog, Josef; Hildebrandt, Michelle A. T.; Høgdall, Claus K.; Høgdall, Estrid; Hogervorst, Frans B.L.; Hopper, John L.; Humphreys, Keith; Huzarski, Tomasz; Imyanitov, Evgeny N.; Isaacs, Claudine; Jakubowska, Anna; Janavicius, Ramunas; Jaworska, Katarzyna; Jensen, Allan; Jensen, Uffe Birk; Johnson, Nichola; Jukkola-Vuorinen, Arja; Kabisch, Maria; Karlan, Beth Y.; Kataja, Vesa; Kauff, Noah; Kelemen, Linda E.; Kerin, Michael J.; Kiemeney, Lambertus A.; Kjaer, Susanne K.; Knight, Julia A.; Knol-Bout, Jacoba P.; Konstantopoulou, Irene; Kosma, Veli-Matti; Krakstad, Camilla; Kristensen, Vessela; Kuchenbaecker, Karoline B.; Kupryjanczyk, Jolanta; Laitman, Yael; Lambrechts, Diether; Lambrechts, Sandrina; Larson, Melissa C.; Lasa, Aadriana; Laurent-Puig, Pierre; Lazaro, Conxi; Le, Nhu D.; Le Marchand, Loic; Leminen, Arto; Lester, Jenny; Levine, Douglas A.; Li, Jingmei; Liang, Dong; Lindblom, Annika; Lindor, Noralane; Lissowska, Jolanta; Long, Jirong; Lu, Karen H.; Lubinski, Jan; Lundvall, Lene; Lurie, Galina; Mai, Phuong L.; Mannermaa, Arto; Margolin, Sara; Mariette, Frederique; Marme, Frederik; Martens, John W.M.; Massuger, Leon F.A.G.; Maugard, Christine; Mazoyer, Sylvie; McGuffog, Lesley; McGuire, Valerie; McLean, Catriona; McNeish, Iain; Meindl, Alfons; Menegaux, Florence; Menéndez, Primitiva; Menkiszak, Janusz; Menon, Usha; Mensenkamp, Arjen R.; Miller, Nicola; Milne, Roger L.; Modugno, Francesmary; Montagna, Marco; Moysich, Kirsten B.; Müller, Heiko; Mulligan, Anna Marie; Muranen, Taru A.; Narod, Steven A.; Nathanson, Katherine L.; Ness, Roberta B.; Neuhausen, Susan L.; Nevanlinna, Heli; Neven, Patrick; Nielsen, Finn C.; Nielsen, Sune F.; Nordestgaard, Børge G.; Nussbaum, Robert L.; Odunsi, Kunle; Offit, Kenneth; Olah, Edith; Olopade, Olufunmilayo I.; Olson, Janet E.; Olson, Sara H.; Oosterwijk, Jan C.; Orlow, Irene; Orr, Nick; Orsulic, Sandra; Osorio, Ana; Ottini, Laura; Paul, James; Pearce, Celeste L.; Pedersen, Inge Sokilde; Peissel, Bernard; Pejovic, Tanja; Pelttari, Liisa M.; Perkins, Jo; Permuth-Wey, Jenny; Peterlongo, Paolo; Peto, Julian; Phelan, Catherine M.; Phillips, Kelly-Anne; Piedmonte, Marion; Pike, Malcolm C.; Platte, Radka; Plisiecka-Halasa, Joanna; Poole, Elizabeth M.; Poppe, Bruce; Pylkäs, Katri; Radice, Paolo; Ramus, Susan J.; Rebbeck, Timothy R.; Reed, Malcolm W.R.; Rennert, Gad; Risch, Harvey A.; Robson, Mark; Rodriguez, Gustavo C.; Romero, Atocha; Rossing, Mary Anne; Rothstein, Joseph H.; Rudolph, Anja; Runnebaum, Ingo; Salani, Ritu; Salvesen, Helga B.; Sawyer, Elinor J.; Schildkraut, Joellen M.; Schmidt, Marjanka K.; Schmutzler, Rita K.; Schneeweiss, Andreas; Schoemaker, Minouk J.; Schrauder, Michael G.; Schumacher, Fredrick; Schwaab, Ira; Scuvera, Giulietta; Sellers, Thomas A.; Severi, Gianluca; Seynaeve, Caroline M.; Shah, Mitul; Shrubsole, Martha; Siddiqui, Nadeem; Sieh, Weiva; Simard, Jacques; Singer, Christian F.; Sinilnikova, Olga M.; Smeets, Dominiek; Sohn, Christof; Soller, Maria; Song, Honglin; Soucy, Penny; Southey, Melissa C.; Stegmaier, Christa; Stoppa-Lyonnet, Dominique; Sucheston, Lara; Swerdlow, Anthony; Tangen, Ingvild L.; Tea, Muy-Kheng; Teixeira, Manuel R.; Terry, Kathryn L.; Terry, Mary Beth; Thomassen, Madas; Thompson, Pamela J.; Tihomirova, Laima; Tischkowitz, Marc; Toland, Amanda Ewart; Tollenaar, Rob A.E.M.; Tomlinson, Ian; Torres, Diana; Truong, Thérèse; Tsimiklis, Helen; Tung, Nadine; Tworoger, Shelley S.; Tyrer, Jonathan P.; Vachon, Celine M.; Van 't Veer, Laura J.; van Altena, Anne M.; Van Asperen, C.J.; van den Berg, David; van den Ouweland, Ans M.W.; van Doorn, Helena C.; Van Nieuwenhuysen, Els; van Rensburg, Elizabeth J.; Vergote, Ignace; Verhoef, Senno; Vierkant, Robert A.; Vijai, Joseph; Vitonis, Allison F.; von Wachenfeldt, Anna; Walsh, Christine; Wang, Qin; Wang-Gohrke, Shan; Wappenschmidt, Barbara; Weischer, Maren; Weitzel, Jeffrey N.; Weltens, Caroline; Wentzensen, Nicolas; Whittemore, Alice S.; Wilkens, Lynne R.; Winqvist, Robert; Wu, Anna H.; Wu, Xifeng; Yang, Hannah P.; Zaffaroni, Daniela; Zamora, M. Pilar; Zheng, Wei; Ziogas, Argyrios; Chenevix-Trench, Georgia; Pharoah, Paul D.P.; Rookus, Matti A.; Hooning, Maartje J.; Goode, Ellen L.

2015-01-01

Objective Clinical genetic testing is commercially available for rs61764370, an inherited variant residing in a KRAS 3′ UTR microRNA binding site, based on suggested associations with increased ovarian and breast cancer risk as well as with survival time. However, prior studies, emphasizing particular subgroups, were relatively small. Therefore, we comprehensively evaluated ovarian and breast cancer risks as well as clinical outcome associated with rs61764370. Methods Centralized genotyping and analysis were performed for 140,012 women enrolled in the Ovarian Cancer Association Consortium (15,357 ovarian cancer patients; 30,816 controls), the Breast Cancer Association Consortium (33,530 breast cancer patients; 37,640 controls), and the Consortium of Modifiers of BRCA1 and BRCA2 (14,765 BRCA1 and 7904 BRCA2 mutation carriers). Results We found no association with risk of ovarian cancer (OR= 0.99, 95% CI 0.94–1.04,p = 0.74) or breast cancer (OR = 0.98, 95% CI 0.94–1.01, p = 0.19) and results were consistent among mutation carriers (BRCA1, ovarian cancer HR = 1.09, 95% CI 0.97–1.23, p = 0.14, breast cancer HR = 1.04, 95% CI 0.97–1.12, p = 0.27; BRCA2, ovarian cancer HR = 0.89, 95% CI 0.71–1.13, p = 0.34, breast cancer HR = 1.06, 95% CI 0.94–1.19, p = 0.35). Null results were also obtained for associations with overall survival following ovarian cancer (HR = 0.94, 95% CI 0.83–1.07, p = 0.38), breast cancer (HR = 0.96, 95% CI 0.87–1.06, p = 0.38), and all other previously-reported associations. Conclusions rs61764370 is not associated with risk of ovarian or breast cancer nor with clinical outcome for patients with these cancers. Therefore, genotyping this variant has no clinical utility related to the prediction or management of these cancers. PMID:25940428

CRC Clinical Trials Management System (CTMS): An Integrated Information Management Solution for Collaborative Clinical Research

PubMed Central

Payne, Philip R.O.; Greaves, Andrew W.; Kipps, Thomas J.

2003-01-01

The Chronic Lymphocytic Leukemia (CLL) Research Consortium (CRC) consists of 9 geographically distributed sites conducting a program of research including both basic science and clinical components. To enable the CRC’s clinical research efforts, a system providing for real-time collaboration was required. CTMS provides such functionality, and demonstrates that the use of novel data modeling, web-application platforms, and management strategies provides for the deployment of an extensible, cost effective solution in such an environment. PMID:14728471

Federating Clinical Data from Six Pediatric Hospitals: Process and Initial Results for Microbiology from the PHIS+ Consortium

PubMed Central

Gouripeddi, Ramkiran; Warner, Phillip B.; Mo, Peter; Levin, James E.; Srivastava, Rajendu; Shah, Samir S.; de Regt, David; Kirkendall, Eric; Bickel, Jonathan; Korgenski, E. Kent; Precourt, Michelle; Stepanek, Richard L.; Mitchell, Joyce A.; Narus, Scott P.; Keren, Ron

2012-01-01

Microbiology study results are necessary for conducting many comparative effectiveness research studies. Unlike core laboratory test results, microbiology results have a complex structure. Federating and integrating microbiology data from six disparate electronic medical record systems is challenging and requires a team of varied skills. The PHIS+ consortium which is partnership between members of the Pediatric Research in Inpatient Settings (PRIS) network, the Children’s Hospital Association and the University of Utah, have used “FURTHeR’ for federating laboratory data. We present our process and initial results for federating microbiology data from six pediatric hospitals. PMID:23304298

Accelerating target discovery using pre-competitive open science-patients need faster innovation more than anyone else.

PubMed

Low, Eric; Bountra, Chas; Lee, Wen Hwa

2016-01-01

We are experiencing a new era enabled by unencumbered access to high quality data through the emergence of open science initiatives in the historically challenging area of early stage drug discovery. At the same time, many patient-centric organisations are taking matters into their own hands by participating in, enabling and funding research. Here we present the rationale behind the innovative partnership between the Structural Genomics Consortium (SGC)-an open, pre-competitive pre-clinical research consortium and the research-focused patient organisation Myeloma UK to create a new, comprehensive platform to accelerate the discovery and development of new treatments for multiple myeloma.

Xenotransplantation of porcine islet cells as a potential option for the treatment of type 1 diabetes in the future.

PubMed

Reichart, B; Niemann, H; Chavakis, T; Denner, J; Jaeckel, E; Ludwig, B; Marckmann, G; Schnieke, A; Schwinzer, R; Seissler, J; Tönjes, R R; Klymiuk, N; Wolf, E; Bornstein, S R

2015-01-01

Solid organ and cell transplantation, including pancreatic islets constitute the treatment of choice for chronic terminal diseases. However, the clinical use of allogeneic transplantation is limited by the growing shortage of human organs. This has prompted us to initiate a unique multi-center and multi-team effort to promote translational research in xenotransplantation to bring xenotransplantation to the clinical setting. Supported by the German Research Foundation, an interdisciplinary group of surgeons, internal medicine doctors, diabetologists, material sciences experts, immunologists, cell biologists, virologists, veterinarians, and geneticists have established a collaborative research center (CRC) focusing on the biology of xenogeneic cell, tissue, and organ transplantation. A major strength of this consortium is the inclusion of members of the regulatory bodies, including the Paul-Ehrlich Institute (PEI), infection specialists from the Robert Koch Institute and PEI, veterinarians from the German Primate Center, and representatives of influential ethical and religious institutions. A major goal of this consortium is to promote islet xenotransplantation, based on the extensive expertise and experience of the existing clinical islet transplantation program. Besides comprehensive approaches to understand and prevent inflammation-mediated islet xenotransplant dysfunction [immediate blood-mediated inflammatory reaction (IBMIR)], we also take advantage of the availability of and experience with islet macroencapsulation, with the goal to improve graft survival and function. This consortium harbors a unique group of scientists with complementary expertise under a cohesive program aiming at developing new therapeutic approaches for islet replacement and solid organ xenotransplantation. © Georg Thieme Verlag KG Stuttgart · New York.

Developing the Safety of Atrial Fibrillation Ablation Registry Initiative (SAFARI) as a collaborative pan-stakeholder critical path registry model: a Cardiac Safety Research Consortium "Incubator" Think Tank.

PubMed

Al-Khatib, Sana M; Calkins, Hugh; Eloff, Benjamin C; Kowey, Peter; Hammill, Stephen C; Ellenbogen, Kenneth A; Marinac-Dabic, Danica; Waldo, Albert L; Brindis, Ralph G; Wilbur, David J; Jackman, Warren M; Yaross, Marcia S; Russo, Andrea M; Prystowsky, Eric; Varosy, Paul D; Gross, Thomas; Pinnow, Ellen; Turakhia, Mintu P; Krucoff, Mitchell W

2010-10-01

Although several randomized clinical trials have demonstrated the safety and efficacy of catheter ablation of atrial fibrillation (AF) in experienced centers, the outcomes of this procedure in routine clinical practice and in patients with persistent and long-standing persistent AF remain uncertain. Brisk adoption of this therapy by physicians with diverse training and experience highlights potential concerns regarding the safety and effectiveness of this procedure. Some of these concerns could be addressed by a national registry of AF ablation procedures such as the Safety of Atrial Fibrillation Ablation Registry Initiative that was initially proposed at a Cardiac Safety Research Consortium Think Tank meeting in April 2009. In January 2010, the Cardiac Safety Research Consortium, in collaboration with the Duke Clinical Research Institute, the US Food and Drug Administration, the American College of Cardiology, and the Heart Rhythm Society, held a follow-up meeting of experts in the field to review the construct and progress to date. Other participants included the National Heart, Lung, and Blood Institute; the Centers for Medicare and Medicaid Services; the Agency for Healthcare Research and Quality; the AdvaMed AF working group; and additional industry representatives. This article summarizes the discussions that occurred at the meeting of the state of the Safety of Atrial Fibrillation Ablation Registry Initiative, the identification of a clear pathway for its implementation, and the exploration of solutions to potential issues in the execution of this registry. Copyright © 2010 Mosby, Inc. All rights reserved.

The Magnetics Information Consortium (MagIC) Online Database: Uploading, Searching and Visualizing Paleomagnetic and Rock Magnetic Data

NASA Astrophysics Data System (ADS)

Koppers, A.; Tauxe, L.; Constable, C.; Pisarevsky, S.; Jackson, M.; Solheid, P.; Banerjee, S.; Johnson, C.; Genevey, A.; Delaney, R.; Baker, P.; Sbarbori, E.

2005-12-01

The Magnetics Information Consortium (MagIC) operates an online relational database including both rock and paleomagnetic data. The goal of MagIC is to store all measurements and their derived properties for studies of paleomagnetic directions (inclination, declination) and their intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). MagIC is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. These nodes provide basic search capabilities based on location, reference, methods applied, material type and geological age, while allowing the user to drill down from sites all the way to the measurements. At each stage, the data can be saved and, if the available data supports it, the data can be visualized by plotting equal area plots, VGP location maps or typical Zijderveld, hysteresis, FORC, and various magnetization and remanence diagrams. All plots are made in SVG (scalable vector graphics) and thus can be saved and easily read into the user's favorite graphics programs without loss of resolution. User contributions to the MagIC database are critical to achieve a useful research tool. We have developed a standard data and metadata template (version 1.6) that can be used to format and upload all data at the time of publication in Earth Science journals. Software tools are provided to facilitate easy population of these templates within Microsoft Excel. These tools allow for the import/export of text files and they provide advanced functionality to manage/edit the data, and to perform various internal checks to high grade the data and to make them ready for uploading. The uploading is all done online by using the MagIC Contribution Wizard at http://earthref.org/MAGIC/upload.htm that takes only a few minutes to process a contribution of approximately 5,000 data records. After uploading these standardized MagIC template files will be stored in the digital archives of EarthRef.org from where they can be downloaded at all times. Finally, the contents of these template files will be automatically parsed into the online relational database, making the data available for online searches in the paleomagnetic and rock magnetic search nodes. The MagIC database contains all data transferred from the IAGA paleomagnetic poles database (GPMDB), the lava flow paleosecular variation database (PSVRL), lake sediment database (SECVR) and the PINT database. In addition to that a substantial number of data compiled under the Time Averaged Field Investigations project is now included plus a significant fraction of the data collected at SIO and the IRM. Ongoing additions of legacy data include ~40 papers from studies on the Hawaiian Islands, data compilations from archeomagnetic studies and updates to the lake sediment dataset.

CPTAC Releases Cancer Proteome Confirmatory Ovarian Study Data | Office of Cancer Clinical Proteomics Research

Cancer.gov

A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying diagnostics and therapies that will improve patients’ lives. Because a comprehensive molecular view of cancer is important for ultimately guiding treatment, the National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) has released the cancer proteome confirmatory ovarian study data sets.

Computational Omics Funding Opportunity | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the NVIDIA Foundation are pleased to announce funding opportunities in the fight against cancer. Each organization has launched a request for proposals (RFP) that will collectively fund up to $2 million to help to develop a new generation of data-intensive scientific tools to find new ways to treat cancer.

Evaluation Guidelines for the Clinical and Translational Science Awards (CTSAs)

PubMed Central

Rubio, Doris M.; Thomas, Veronica G.

2013-01-01

Abstract The National Center for Advancing Translational Sciences (NCATS), a part of the National Institutes of Health, currently funds the Clinical and Translational Science Awards (CTSAs), a national consortium of 61 medical research institutions in 30 states and the District of Columbia. The program seeks to transform the way biomedical research is conducted, speed the translation of laboratory discoveries into treatments for patients, engage communities in clinical research efforts, and train a new generation of clinical and translational researchers. An endeavor as ambitious and complex as the CTSA program requires high‐quality evaluations in order to show that the program is well implemented, efficiently managed, and demonstrably effective. In this paper, the Evaluation Key Function Committee of the CTSA Consortium presents an overall framework for evaluating the CTSA program and offers policies to guide the evaluation work. The guidelines set forth are designed to serve as a tool for education within the CTSA community by illuminating key issues and practices that should be considered during evaluation planning, implementation, and utilization. Additionally, these guidelines can provide a basis for ongoing discussions about how the principles articulated in this paper can most effectively be translated into operational reality. PMID:23919366

CDISC Terminology

Cancer.gov

Clinical Data Interchange Standards Consortium (CDISC) is an international, non-profit organization that develops and supports global data standards for medical research. CDISC is working actively with EVS to develop and support controlled terminology in several areas, notably CDISC's Study Data Tabulation Model (SDTM).

Selection criteria for patients with chronic ankle instability in controlled research: a position statement of the International Ankle Consortium.

PubMed

Gribble, Phillip A; Delahunt, Eamonn; Bleakley, Chris; Caulfield, Brian; Docherty, Carrie L; Fourchet, François; Fong, Daniel; Hertel, Jay; Hiller, Claire; Kaminski, Thomas W; McKeon, Patrick O; Refshauge, Kathryn M; van der Wees, Philip; Vicenzino, Bill; Wikstrom, Erik A

2013-08-01

The International Ankle Consortium is an international community of researchers and clinicians whose primary scholastic purpose is to promote scholarship and dissemination of research-informed knowledge related to pathologies of the ankle complex. The constituents of the International Ankle Consortium and other similar organizations have yet to properly define the clinical phenomenon known as chronic ankle instability (CAI) and its related characteristics for consistent patient recruitment and advancement of research in this area. Although research on CAI and awareness of its impact on society and healthcare systems have grown substantially in the last 2 decades, the inconsistency in participant/patient selection criteria across studies presents a potential obstacle to addressing the problem properly. This major gap within the literature limits the ability to generalize this evidence to the target patient population. Therefore, there is a need to provide standards for patient/participant selection criteria in research focused on CAI, with justifications using the best available evidence.

Primary Immune Deficiency Treatment Consortium (PIDTC) report.

PubMed

Griffith, Linda M; Cowan, Morton J; Notarangelo, Luigi D; Kohn, Donald B; Puck, Jennifer M; Pai, Sung-Yun; Ballard, Barbara; Bauer, Sarah C; Bleesing, Jack J H; Boyle, Marcia; Brower, Amy; Buckley, Rebecca H; van der Burg, Mirjam; Burroughs, Lauri M; Candotti, Fabio; Cant, Andrew J; Chatila, Talal; Cunningham-Rundles, Charlotte; Dinauer, Mary C; Dvorak, Christopher C; Filipovich, Alexandra H; Fleisher, Thomas A; Bobby Gaspar, Hubert; Gungor, Tayfun; Haddad, Elie; Hovermale, Emily; Huang, Faith; Hurley, Alan; Hurley, Mary; Iyengar, Sumathi; Kang, Elizabeth M; Logan, Brent R; Long-Boyle, Janel R; Malech, Harry L; McGhee, Sean A; Modell, Fred; Modell, Vicki; Ochs, Hans D; O'Reilly, Richard J; Parkman, Robertson; Rawlings, David J; Routes, John M; Shearer, William T; Small, Trudy N; Smith, Heather; Sullivan, Kathleen E; Szabolcs, Paul; Thrasher, Adrian; Torgerson, Troy R; Veys, Paul; Weinberg, Kenneth; Zuniga-Pflucker, Juan Carlos

2014-02-01

The Primary Immune Deficiency Treatment Consortium (PIDTC) is a network of 33 centers in North America that study the treatment of rare and severe primary immunodeficiency diseases. Current protocols address the natural history of patients treated for severe combined immunodeficiency (SCID), Wiskott-Aldrich syndrome, and chronic granulomatous disease through retrospective, prospective, and cross-sectional studies. The PIDTC additionally seeks to encourage training of junior investigators, establish partnerships with European and other International colleagues, work with patient advocacy groups to promote community awareness, and conduct pilot demonstration projects. Future goals include the conduct of prospective treatment studies to determine optimal therapies for primary immunodeficiency diseases. To date, the PIDTC has funded 2 pilot projects: newborn screening for SCID in Navajo Native Americans and B-cell reconstitution in patients with SCID after hematopoietic stem cell transplantation. Ten junior investigators have received grant awards. The PIDTC Annual Scientific Workshop has brought together consortium members, outside speakers, patient advocacy groups, and young investigators and trainees to report progress of the protocols and discuss common interests and goals, including new scientific developments and future directions of clinical research. Here we report the progress of the PIDTC to date, highlights of the first 2 PIDTC workshops, and consideration of future consortium objectives. Published by Mosby, Inc.

The RECONS 25 Parsec Database: Who Are the Stars? Where Are the Planets?

NASA Astrophysics Data System (ADS)

Henry, Todd J.; Dieterich, S.; Hosey, A. D.; Ianna, P. A.; Jao, W.; Koerner, D. W.; Riedel, A. R.; Slatten, K. J.; Subasavage, J.; Winters, J. G.; RECONS

2013-01-01

Since 1994, RECONS (www.recons.org, REsearch Consortium On Nearby Stars) has been discovering and characterizing the Sun's neighbors. Nearby stars provide increased fluxes, larger astrometric perturbations, and higher probabilities for eventual resolution and detailed study of planets than similar stars at larger distances. Examination of the nearby stellar sample will reveal the prevalence and structure of solar systems, as well as the balance of Jovian and terrestrial worlds. These are the stars and planets that will ultimately be key in our search for life elsewhere. Here we outline what we know ... and what we don't know ... about the population of the nearest stars. We have expanded the original RECONS 10 pc horizon to 25 pc and are constructing a database that currently includes 2124 systems. By using the CTIO 0.9m telescope --- now operated by RECONS as part of the SMARTS Consortium --- we have published the first accurate parallaxes for 149 systems within 25 pc and currently have an additional 213 unpublished systems to add. Still, we predict that roughly two-thirds of the systems within 25 pc do not yet have accurate distance measurements. In addition to revealing the Sun's stellar neighbors, we have been using astrometric techniques to search for massive planets orbiting roughly 200 of the nearest red dwarfs. Unlike radial velocity searches, our astrometric effort is most sensitive to Jovian planets in Jovian orbits, i.e. those that span decades. We have now been monitoring stars for up to 13 years with positional accuracies of a few milliarcseconds per night. We have detected stellar and brown dwarf companions, as well as enigmatic, unseen secondaries, but have yet to reveal a single super-Jupiter ... a somewhat surprising result. In total, only 3% of stars within 25 pc are known to possess planets. It seems clear that we have a great deal of work to do to map out the stars, planets, and perhaps life in the solar neighborhood. This effort is supported by the NSF through grant AST-0908402 and via observations made possible by the SMARTS Consortium.

Evaluating Patient-Centered Outcomes in Clinical Trials of Procedural Sedation, Part 2 Safety: Sedation Consortium on Endpoints and Procedures for Treatment, Education, and Research Recommendations.

PubMed

Ward, Denham S; Williams, Mark R; Berkenbosch, John W; Bhatt, Maala; Carlson, Douglas; Chappell, Phillip; Clark, Randall M; Constant, Isabelle; Conway, Aaron; Cravero, Joseph; Dahan, Albert; Dexter, Franklin; Dionne, Raymond; Dworkin, Robert H; Gan, Tong J; Gozal, David; Green, Steven; Irwin, Michael G; Karan, Suzanne; Kochman, Michael; Lerman, Jerrold; Lightdale, Jenifer R; Litman, Ronald S; Mason, Keira P; Miner, James; O'Connor, Robert E; Pandharipande, Pratik; Riker, Richard R; Roback, Mark G; Sessler, Daniel I; Sexton, Anne; Tobin, Joseph R; Turk, Dennis C; Twersky, Rebecca S; Urman, Richard D; Weiss, Mark; Wunsch, Hannah; Zhao-Wong, Anna

2018-05-17

The Sedation Consortium on Endpoints and Procedures for Treatment, Education, and Research, established by the Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks, a public-private partnership with the US Food and Drug Administration, convened a second meeting of sedation experts from a variety of clinical specialties and research backgrounds to develop recommendations for procedural sedation research. The previous meeting addressed efficacy and patient- and/or family-centered outcomes. This meeting addressed issues of safety, which was defined as "the avoidance of physical or psychological harm." A literature review identified 133 articles addressing safety measures in procedural sedation clinical trials. After basic reporting of vital signs, the most commonly measured safety parameter was oxygen saturation. Adverse events were inconsistently defined throughout the studies. Only 6 of the 133 studies used a previously validated measure of safety. The meeting identified methodological problems associated with measuring infrequent adverse events. With a consensus discussion, a set of core and supplemental measures were recommended to code for safety in future procedural clinical trials. When adopted, these measures should improve the integration of safety data across studies and facilitate comparisons in systematic reviews and meta-analyses.

Accrediting osteopathic postdoctoral training institutions.

PubMed

Duffy, Thomas

2011-04-01

All postdoctoral training programs approved by the American Osteopathic Association are required to be part of an Osteopathic Postdoctoral Training Institution (OPTI) consortium. The author reviews recent activities related to OPTI operations, including the transfer the OPTI Annual Report to an electronic database, revisions to the OPTI Accreditation Handbook, training at the 2010 OPTI Workshop, and new requirements of the American Osteopathic Association Commission on Osteopathic College Accreditation. The author also reviews the OPTI accreditation process, cites common commendations and deficiencies for reviews completed from 2008 to 2010, and provides an overview of plans for future improvements.

Cloud-Based NoSQL Open Database of Pulmonary Nodules for Computer-Aided Lung Cancer Diagnosis and Reproducible Research.

PubMed

Ferreira Junior, José Raniery; Oliveira, Marcelo Costa; de Azevedo-Marques, Paulo Mazzoncini

2016-12-01

Lung cancer is the leading cause of cancer-related deaths in the world, and its main manifestation is pulmonary nodules. Detection and classification of pulmonary nodules are challenging tasks that must be done by qualified specialists, but image interpretation errors make those tasks difficult. In order to aid radiologists on those hard tasks, it is important to integrate the computer-based tools with the lesion detection, pathology diagnosis, and image interpretation processes. However, computer-aided diagnosis research faces the problem of not having enough shared medical reference data for the development, testing, and evaluation of computational methods for diagnosis. In order to minimize this problem, this paper presents a public nonrelational document-oriented cloud-based database of pulmonary nodules characterized by 3D texture attributes, identified by experienced radiologists and classified in nine different subjective characteristics by the same specialists. Our goal with the development of this database is to improve computer-aided lung cancer diagnosis and pulmonary nodule detection and classification research through the deployment of this database in a cloud Database as a Service framework. Pulmonary nodule data was provided by the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), image descriptors were acquired by a volumetric texture analysis, and database schema was developed using a document-oriented Not only Structured Query Language (NoSQL) approach. The proposed database is now with 379 exams, 838 nodules, and 8237 images, 4029 of them are CT scans and 4208 manually segmented nodules, and it is allocated in a MongoDB instance on a cloud infrastructure.

Meeting report of the International Consortium of Stem Cell Networks' Workshop Towards Clinical Trials Using Stem Cells for Amyotrophic Lateral Sclerosis/Motor Neuron Disease.

PubMed

Chaddah, Maya R; Dickie, Brian G; Lyall, Drew; Marshall, Caroline J; Sykes, J Ben; Bruijn, Lucie I

2011-09-01

The International Consortium of Stem Cell Networks' (ICSCN) Workshop Towards Clinical Trials Using Stem Cells for Amyotrophic Lateral Sclerosis (ALS)/Motor Neuron Disease (MND) was held on 24-25 January 2011. Twenty scientific talks addressed aspects of cell derivation and characterization; preclinical research and phased clinical trials involving stem cells; latest developments in induced pluripotent (iPS) cell technology; industry involvement and investment. Three moderated panel discussions focused on unregulated ALS/MND treatments, and the state of the art and barriers to future progress in using stem cells for ALS/MND. This review highlights the major insights that emanated from the workshop around the lessons learned and barriers to progress for using stem cells for understanding disease mechanism, drug discovery, and as therapy for ALS/MND. The full meeting report is only available in the online version of the journal. Please find this material with the following direct link to the article: http://www.informahealthcare.com/als/doi/10.3109/17482968.2011.590992 .

The road map towards providing a robust Raman spectroscopy-based cancer diagnostic platform and integration into clinic

NASA Astrophysics Data System (ADS)

Lau, Katherine; Isabelle, Martin; Lloyd, Gavin R.; Old, Oliver; Shepherd, Neil; Bell, Ian M.; Dorney, Jennifer; Lewis, Aaran; Gaifulina, Riana; Rodriguez-Justo, Manuel; Kendall, Catherine; Stone, Nicolas; Thomas, Geraint; Reece, David

2016-03-01

Despite the demonstrated potential as an accurate cancer diagnostic tool, Raman spectroscopy (RS) is yet to be adopted by the clinic for histopathology reviews. The Stratified Medicine through Advanced Raman Technologies (SMART) consortium has begun to address some of the hurdles in its adoption for cancer diagnosis. These hurdles include awareness and acceptance of the technology, practicality of integration into the histopathology workflow, data reproducibility and availability of transferrable models. We have formed a consortium, in joint efforts, to develop optimised protocols for tissue sample preparation, data collection and analysis. These protocols will be supported by provision of suitable hardware and software tools to allow statistically sound classification models to be built and transferred for use on different systems. In addition, we are building a validated gastrointestinal (GI) cancers model, which can be trialled as part of the histopathology workflow at hospitals, and a classification tool. At the end of the project, we aim to deliver a robust Raman based diagnostic platform to enable clinical researchers to stage cancer, define tumour margin, build cancer diagnostic models and discover novel disease bio markers.

An integrated photogrammetric and spatial database management system for producing fully structured data using aerial and remote sensing images.

PubMed

Ahmadi, Farshid Farnood; Ebadi, Hamid

2009-01-01

3D spatial data acquired from aerial and remote sensing images by photogrammetric techniques is one of the most accurate and economic data sources for GIS, map production, and spatial data updating. However, there are still many problems concerning storage, structuring and appropriate management of spatial data obtained using these techniques. According to the capabilities of spatial database management systems (SDBMSs); direct integration of photogrammetric and spatial database management systems can save time and cost of producing and updating digital maps. This integration is accomplished by replacing digital maps with a single spatial database. Applying spatial databases overcomes the problem of managing spatial and attributes data in a coupled approach. This management approach is one of the main problems in GISs for using map products of photogrammetric workstations. Also by the means of these integrated systems, providing structured spatial data, based on OGC (Open GIS Consortium) standards and topological relations between different feature classes, is possible at the time of feature digitizing process. In this paper, the integration of photogrammetric systems and SDBMSs is evaluated. Then, different levels of integration are described. Finally design, implementation and test of a software package called Integrated Photogrammetric and Oracle Spatial Systems (IPOSS) is presented.

MODBASE, a database of annotated comparative protein structure models

PubMed Central

Pieper, Ursula; Eswar, Narayanan; Stuart, Ashley C.; Ilyin, Valentin A.; Sali, Andrej

2002-01-01

MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server. PMID:11752309

Pulmonary Nodule Classification with Deep Convolutional Neural Networks on Computed Tomography Images.

PubMed

Li, Wei; Cao, Peng; Zhao, Dazhe; Wang, Junbo

2016-01-01

Computer aided detection (CAD) systems can assist radiologists by offering a second opinion on early diagnosis of lung cancer. Classification and feature representation play critical roles in false-positive reduction (FPR) in lung nodule CAD. We design a deep convolutional neural networks method for nodule classification, which has an advantage of autolearning representation and strong generalization ability. A specified network structure for nodule images is proposed to solve the recognition of three types of nodules, that is, solid, semisolid, and ground glass opacity (GGO). Deep convolutional neural networks are trained by 62,492 regions-of-interest (ROIs) samples including 40,772 nodules and 21,720 nonnodules from the Lung Image Database Consortium (LIDC) database. Experimental results demonstrate the effectiveness of the proposed method in terms of sensitivity and overall accuracy and that it consistently outperforms the competing methods.

Classification of pulmonary nodules in lung CT images using shape and texture features

NASA Astrophysics Data System (ADS)

Dhara, Ashis Kumar; Mukhopadhyay, Sudipta; Dutta, Anirvan; Garg, Mandeep; Khandelwal, Niranjan; Kumar, Prafulla

2016-03-01

Differentiation of malignant and benign pulmonary nodules is important for prognosis of lung cancer. In this paper, benign and malignant nodules are classified using support vector machine. Several shape-based and texture-based features are used to represent the pulmonary nodules in the feature space. A semi-automated technique is used for nodule segmentation. Relevant features are selected for efficient representation of nodules in the feature space. The proposed scheme and the competing technique are evaluated on a data set of 542 nodules of Lung Image Database Consortium and Image Database Resource Initiative. The nodules with composite rank of malignancy "1","2" are considered as benign and "4","5" are considered as malignant. Area under the receiver operating characteristics curve is 0:9465 for the proposed method. The proposed method outperforms the competing technique.

Enhancing AFLOW Visualization using Jmol

NASA Astrophysics Data System (ADS)

Lanasa, Jacob; New, Elizabeth; Stefek, Patrik; Honaker, Brigette; Hanson, Robert; Aflow Collaboration

The AFLOW library is a database of theoretical solid-state structures and calculated properties created using high-throughput ab initio calculations. Jmol is a Java-based program capable of visualizing and analyzing complex molecular structures and energy landscapes. In collaboration with the AFLOW consortium, our goal is the enhancement of the AFLOWLIB database through the extension of Jmol's capabilities in the area of materials science. Modifications made to Jmol include the ability to read and visualize AFLOW binary alloy data files, the ability to extract from these files information using Jmol scripting macros that can be utilized in the creation of interactive web-based convex hull graphs, the capability to identify and classify local atomic environments by symmetry, and the ability to search one or more related crystal structures for atomic environments using a novel extension of inorganic polyhedron-based SMILES strings

Construction of databases: advances and significance in clinical research.

PubMed

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.

The Afya Bora Fellowship: An Innovative Program Focused on Creating an Interprofessional Network of Leaders in Global Health.

PubMed

Green, Wendy M; Farquhar, Carey; Mashalla, Yohana

2017-09-01

Most current health professions education programs are focused on the development of clinical skills. As a result, they may not address the complex and interconnected nature of global health. Trainees require relevant clinical, programmatic, and leadership skills to meet the challenges of practicing in an increasingly globalized environment. To develop health care leaders within sub-Saharan Africa, the Afya Bora Consortium developed a one-year fellowship for medical doctors and nurses. Fellows from nine institutions in the United States and sub-Saharan Africa participate in 12 learning modules focused on leadership development and program management. Classroom-based training is augmented with an experiential apprenticeship component. Since 2011, 100 fellows have graduated from the program. During their apprenticeships, fellows developed projects beneficial to their development and to host organizations. The program has developed fellows' skills in leadership, lent expertise to local organizations, and built knowledge in local contexts. Most fellows have returned to their countries of origin, thus building local capacity. U.S.-based fellows examine global health challenges from regional perspectives and learn from sub-Saharan African experts and peers. The Consortium provides ongoing support to alumni through career development awards and alumni network engagement with current and past fellow cohorts. The Consortium expanded from its initial network of five countries to six and continues to seek opportunities for geographical and institutional expansion.

Making the MagIC (Magnetics Information Consortium) Web Application Accessible to New Users and Useful to Experts

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A.; Jarboe, N.; Tauxe, L.; Constable, C.; Jonestrask, L.

2017-12-01

Challenges are faced by both new and experienced users interested in contributing their data to community repositories, in data discovery, or engaged in potentially transformative science. The Magnetics Information Consortium (https://earthref.org/MagIC) has recently simplified its data model and developed a new containerized web application to reduce the friction in contributing, exploring, and combining valuable and complex datasets for the paleo-, geo-, and rock magnetic scientific community. The new data model more closely reflects the hierarchical workflow in paleomagnetic experiments to enable adequate annotation of scientific results and ensure reproducibility. The new open-source (https://github.com/earthref/MagIC) application includes an upload tool that is integrated with the data model to provide early data validation feedback and ease the friction of contributing and updating datasets. The search interface provides a powerful full text search of contributions indexed by ElasticSearch and a wide array of filters, including specific geographic and geological timescale filtering, to support both novice users exploring the database and experts interested in compiling new datasets with specific criteria across thousands of studies and millions of measurements. The datasets are not large, but they are complex, with many results from evolving experimental and analytical approaches. These data are also extremely valuable due to the cost in collecting or creating physical samples and the, often, destructive nature of the experiments. MagIC is heavily invested in encouraging young scientists as well as established labs to cultivate workflows that facilitate contributing their data in a consistent format. This eLightning presentation includes a live demonstration of the MagIC web application, developed as a configurable container hosting an isomorphic Meteor JavaScript application, MongoDB database, and ElasticSearch search engine. Visitors can explore the MagIC Database through maps and image or plot galleries or search and filter the raw measurements and their derived hierarchy of analytical interpretations.

SU-F-P-35: A Multi-Institutional Plan Quality Checking Tool Built On Oncospace: A Shared Radiation Oncology Database System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowers, M; Robertson, S; Moore, J

Purpose: Late toxicity from radiation to critical structures limits the possible dose in Radiation Therapy. Perfectly conformal treatment of a target is not realizable, so the clinician must accept a certain level of collateral radiation to nearby OARs. But how much? General guidelines exist for healthy tissue sparing which guide RT treatment planning, but are these guidelines good enough to create the optimal plan given the individualized patient anatomy? We propose a means to evaluate the planned dose level to an OAR using a multi-institutional data-store of previously treated patients, so a clinician might reconsider planning objectives. Methods: The toolmore » is built on Oncospace, a federated data-store system, which consists of planning data import, web based analysis tools, and a database containing:1) DVHs: dose by percent volume delivered to each ROI for each patient previously treated and included in the database.2) Overlap Volume Histograms (OVHs): Anatomical measure defined as the percent volume of an ROI within a given distance to target structures.Clinicians know what OARs are important to spare. For any ROI, Oncospace knows for which patients’ anatomy that ROI was harder to plan in the past (the OVH is less). The planned dose should be close to the least dose of previous patients. The tool displays the dose those OARs were subjected to, and the clinician can make a determination about the planning objectives used.Multiple institutions contribute to the Oncospace Consortium, and their DVH and OVH data are combined and color coded in the output. Results: The Oncospace website provides a plan quality display tool which identifies harder to treat patients, and graphically displays the dose delivered to them for comparison with the proposed plan. Conclusion: The Oncospace Consortium manages a data-store of previously treated patients which can be used for quality checking new plans. Grant funding by Elekta.« less

The extent of intestinal failure-associated liver disease in patients referred for intestinal rehabilitation is associated with increased mortality: an analysis of the pediatric intestinal failure consortium database.

PubMed

Javid, Patrick J; Oron, Assaf P; Duggan, Christopher; Squires, Robert H; Horslen, Simon P

2017-09-05

The advent of regional multidisciplinary intestinal rehabilitation programs has been associated with improved survival in pediatric intestinal failure. Yet, the optimal timing of referral for intestinal rehabilitation remains unknown. We hypothesized that the degree of intestinal failure-associated liver disease (IFALD) at initiation of intestinal rehabilitation would be associated with overall outcome. The multicenter, retrospective Pediatric Intestinal Failure Consortium (PIFCon) database was used to identify all subjects with baseline bilirubin data. Conjugated bilirubin (CBili) was used as a marker for IFALD, and we stratified baseline bilirubin values as CBili<2 mg/dL, CBili 2-4 mg/dL, and CBili>4 mg/dL. The association between baseline CBili and mortality was examined using Cox proportional hazards regression. Of 272 subjects in the database, 191 (70%) children had baseline bilirubin data collected. 38% and 28% of patients had CBili >4 mg/dL and CBili <2 mg/dL, respectively, at baseline. All-cause mortality was 23%. On univariate analysis, mortality was associated with CBili 2-4 mg/dL, CBili >4 mg/dL, prematurity, race, and small bowel atresia. On regression analysis controlling for age, prematurity, and diagnosis, the risk of mortality was increased by 3-fold for baseline CBili 2-4 mg/dL (HR 3.25 [1.07-9.92], p=0.04) and 4-fold for baseline CBili >4 mg/dL (HR 4.24 [1.51-11.92], p=0.006). On secondary analysis, CBili >4 mg/dL at baseline was associated with a lower chance of attaining enteral autonomy. In children with intestinal failure treated at intestinal rehabilitation programs, more advanced IFALD at referral is associated with increased mortality and decreased prospect of attaining enteral autonomy. Early referral of children with intestinal failure to intestinal rehabilitation programs should be strongly encouraged. Treatment Study, Level III. Copyright © 2017 Elsevier Inc. All rights reserved.

Clinical translation and regulatory aspects of CAR/TCR-based adoptive cell therapies-the German Cancer Consortium approach.

PubMed

Krackhardt, Angela M; Anliker, Brigitte; Hildebrandt, Martin; Bachmann, Michael; Eichmüller, Stefan B; Nettelbeck, Dirk M; Renner, Matthias; Uharek, Lutz; Willimsky, Gerald; Schmitt, Michael; Wels, Winfried S; Schüssler-Lenz, Martina

2018-04-01

Adoptive transfer of T cells genetically modified by TCRs or CARs represents a highly attractive novel therapeutic strategy to treat malignant diseases. Various approaches for the development of such gene therapy medicinal products (GTMPs) have been initiated by scientists in recent years. To date, however, the number of clinical trials commenced in Germany and Europe is still low. Several hurdles may contribute to the delay in clinical translation of these therapeutic innovations including the significant complexity of manufacture and non-clinical testing of these novel medicinal products, the limited knowledge about the intricate regulatory requirements of the academic developers as well as limitations of funds for clinical testing. A suitable good manufacturing practice (GMP) environment is a key prerequisite and platform for the development, validation, and manufacture of such cell-based therapies, but may also represent a bottleneck for clinical translation. The German Cancer Consortium (DKTK) and the Paul-Ehrlich-Institut (PEI) have initiated joint efforts of researchers and regulators to facilitate and advance early phase, academia-driven clinical trials. Starting with a workshop held in 2016, stakeholders from academia and regulatory authorities in Germany have entered into continuing discussions on a diversity of scientific, manufacturing, and regulatory aspects, as well as the benefits and risks of clinical application of CAR/TCR-based cell therapies. This review summarizes the current state of discussions of this cooperative approach providing a basis for further policy-making and suitable modification of processes.

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

PubMed Central

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. PMID:25158685

NCI's Clinical Proteomic Tumor Analysis Consortium 1st Annual Scientific Symposium | Office of Cancer Clinical Proteomics Research

Cancer.gov

On behalf of the National Cancer Institute and the Office of Cancer Clinical Proteomics Research, you are invited to the First Annual CPTAC Scientific Symposium on Wednesday, November 13, 2013. The purpose of this symposium, which consists of plenary and poster sessions, is for investigators from CPTAC community and beyond to share and discuss novel biological discoveries, analytical methods, and translational approaches using CPTAC data.

The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis.

PubMed

Rosenthal, Alex; Gabrielian, Andrei; Engle, Eric; Hurt, Darrell E; Alexandru, Sofia; Crudu, Valeriu; Sergueev, Eugene; Kirichenko, Valery; Lapitskii, Vladzimir; Snezhko, Eduard; Kovalev, Vassili; Astrovko, Andrei; Skrahina, Alena; Taaffe, Jessica; Harris, Michael; Long, Alyssa; Wollenberg, Kurt; Akhundova, Irada; Ismayilova, Sharafat; Skrahin, Aliaksandr; Mammadbayov, Elcan; Gadirova, Hagigat; Abuzarov, Rafik; Seyfaddinova, Mehriban; Avaliani, Zaza; Strambu, Irina; Zaharia, Dragos; Muntean, Alexandru; Ghita, Eugenia; Bogdan, Miron; Mindru, Roxana; Spinu, Victor; Sora, Alexandra; Ene, Catalina; Vashakidze, Sergo; Shubladze, Natalia; Nanava, Ucha; Tuzikov, Alexander; Tartakovsky, Michael

2017-11-01

The TB Portals program is an international consortium of physicians, radiologists, and microbiologists from countries with a heavy burden of drug-resistant tuberculosis working with data scientists and information technology professionals. Together, we have built the TB Portals, a repository of socioeconomic/geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis backed by shareable, physical samples. Currently, there are 1,299 total cases from five country sites (Azerbaijan, Belarus, Moldova, Georgia, and Romania), 976 (75.1%) of which are multidrug or extensively drug resistant and 38.2%, 51.9%, and 36.3% of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. The top Mycobacterium tuberculosis lineages represented among collected samples are Beijing, T1, and H3, and single nucleotide polymorphisms (SNPs) that confer resistance to isoniazid, rifampin, ofloxacin, and moxifloxacin occur the most frequently. These data and samples have promoted drug discovery efforts and research into genomics and quantitative image analysis to improve diagnostics while also serving as a valuable resource for researchers and clinical providers. The TB Portals database and associated projects are continually growing, and we invite new partners and collaborations to our initiative. The TB Portals data and their associated analytical and statistical tools are freely available at https://tbportals.niaid.nih.gov/.

The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis

PubMed Central

Gabrielian, Andrei; Engle, Eric; Hurt, Darrell E.; Alexandru, Sofia; Crudu, Valeriu; Sergueev, Eugene; Kirichenko, Valery; Lapitskii, Vladzimir; Snezhko, Eduard; Kovalev, Vassili; Astrovko, Andrei; Skrahina, Alena; Harris, Michael; Long, Alyssa; Wollenberg, Kurt; Akhundova, Irada; Ismayilova, Sharafat; Skrahin, Aliaksandr; Mammadbayov, Elcan; Gadirova, Hagigat; Abuzarov, Rafik; Seyfaddinova, Mehriban; Avaliani, Zaza; Strambu, Irina; Zaharia, Dragos; Muntean, Alexandru; Ghita, Eugenia; Bogdan, Miron; Mindru, Roxana; Spinu, Victor; Sora, Alexandra; Ene, Catalina; Vashakidze, Sergo; Shubladze, Natalia; Nanava, Ucha; Tuzikov, Alexander; Tartakovsky, Michael

2017-01-01

ABSTRACT The TB Portals program is an international consortium of physicians, radiologists, and microbiologists from countries with a heavy burden of drug-resistant tuberculosis working with data scientists and information technology professionals. Together, we have built the TB Portals, a repository of socioeconomic/geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis backed by shareable, physical samples. Currently, there are 1,299 total cases from five country sites (Azerbaijan, Belarus, Moldova, Georgia, and Romania), 976 (75.1%) of which are multidrug or extensively drug resistant and 38.2%, 51.9%, and 36.3% of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. The top Mycobacterium tuberculosis lineages represented among collected samples are Beijing, T1, and H3, and single nucleotide polymorphisms (SNPs) that confer resistance to isoniazid, rifampin, ofloxacin, and moxifloxacin occur the most frequently. These data and samples have promoted drug discovery efforts and research into genomics and quantitative image analysis to improve diagnostics while also serving as a valuable resource for researchers and clinical providers. The TB Portals database and associated projects are continually growing, and we invite new partners and collaborations to our initiative. The TB Portals data and their associated analytical and statistical tools are freely available at https://tbportals.niaid.nih.gov/. PMID:28904183

Comparative Effectiveness Research Through a Collaborative Electronic Reporting Consortium.

PubMed

Fiks, Alexander G; Grundmeier, Robert W; Steffes, Jennifer; Adams, William G; Kaelber, David C; Pace, Wilson D; Wasserman, Richard C

2015-07-01

The United States lacks a system to use routinely collected electronic health record (EHR) clinical data to conduct comparative effectiveness research (CER) on pediatric drug therapeutics and other child health topics. This Special Article describes the creation and details of a network of EHR networks devised to use clinical data in EHRs for conducting CER, led by the American Academy of Pediatrics Pediatric Research in Office Settings (PROS). To achieve this goal, PROS has linked data from its own EHR-based "ePROS" network with data from independent practices and health systems across the United States. Beginning with 4 of proof-of-concept retrospective CER studies on psychotropic and asthma medication use and side effects with a planned full-scale prospective CER study on treatment of pediatric hypertension, the Comparative Effectiveness Research Through Collaborative Electronic Reporting (CER(2)) collaborators are developing a platform to advance the methodology of pediatric pharmacoepidemiology. CER(2) will provide a resource for future CER studies in pediatric drug therapeutics and other child health topics. This article outlines the vision for and present composition of this network, governance, and challenges and opportunities for using the network to advance child health and health care. The goal of this network is to engage child health researchers from around the United States in participating in collaborative research using the CER(2) database. Copyright © 2015 by the American Academy of Pediatrics.

The German national registry for primary immunodeficiencies (PID)

PubMed Central

Gathmann, B; Goldacker, S; Klima, M; Belohradsky, B H; Notheis, G; Ehl, S; Ritterbusch, H; Baumann, U; Meyer-Bahlburg, A; Witte, T; Schmidt, R; Borte, M; Borte, S; Linde, R; Schubert, R; Bienemann, K; Laws, H-J; Dueckers, G; Roesler, J; Rothoeft, T; Krüger, R; Scharbatke, E C; Masjosthusmann, K; Wasmuth, J-C; Moser, O; Kaiser, P; Groß-Wieltsch, U; Classen, C F; Horneff, G; Reiser, V; Binder, N; El-Helou, S M; Klein, C; Grimbacher, B; Kindle, G

2013-01-01

In 2009, a federally funded clinical and research consortium (PID–NET, http://www.pid-net.org) established the first national registry for primary immunodeficiencies (PID) in Germany. The registry contains clinical and genetic information on PID patients and is set up within the framework of the existing European Database for Primary Immunodeficiencies, run by the European Society for Primary Immunodeficiencies. Following the example of other national registries, a central data entry clerk has been employed to support data entry at the participating centres. Regulations for ethics approvals have presented a major challenge for participation of individual centres and have led to a delay in data entry in some cases. Data on 630 patients, entered into the European registry between 2004 and 2009, were incorporated into the national registry. From April 2009 to March 2012, the number of contributing centres increased from seven to 21 and 738 additional patients were reported, leading to a total number of 1368 patients, of whom 1232 were alive. The age distribution of living patients differs significantly by gender, with twice as many males than females among children, but 15% more women than men in the age group 30 years and older. The diagnostic delay between onset of symptoms and diagnosis has decreased for some PID over the past 20 years, but remains particularly high at a median of 4 years in common variable immunodeficiency (CVID), the most prevalent PID. PMID:23607573

CPTAC Releases Cancer Proteome Confirmatory Colon Study Data | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) announces the release of the cancer proteome confirmatory colon study data. The goal of the study is to analyze the proteomes of approximately 100 confirmatory colon tumor patients, which includes tumor and adjacent normal samples, with liquid chromatography-tandem mass spectrometry (LC-MS/MS) global proteomic and phosphoproteomic profiling.

CPTAC Accelerates Precision Proteomics Biomedical Research | Office of Cancer Clinical Proteomics Research

Cancer.gov

The accurate quantitation of proteins or peptides using Mass Spectrometry (MS) is gaining prominence in the biomedical research community as an alternative method for analyte measurement. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigators have been at the forefront in the promotion of reproducible MS techniques, through the development and application of standardized proteomic methods for protein quantitation on biologically relevant samples.

Human Cancer Models Initiative | Office of Cancer Genomics

Cancer.gov

The Human Cancer Models Initiative (HCMI) is an international consortium that is generating novel human tumor-derived culture models, which are annotated with genomic and clinical data. In an effort to advance cancer research and more fully understand how in vitro findings are related to clinical biology, HCMI-developed models and related data will be available as a community resource for cancer and other research.

Human Cancer Models Initiative | Office of Cancer Genomics

Cancer.gov

The Human Cancer Models Initiative (HCMI) is an international consortium that is generating novel human tumor-derived culture models, which are annotated with genomic and clinical data. In an effort to advance cancer research and more fully understand how in vitro findings are related to clinical biology, HCMI-developed models and related data will be available as a community resource for cancer research.

Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard

PubMed Central

Duhaime, Melissa Beth; Kottmann, Renzo; Field, Dawn; Glöckner, Frank Oliver

2011-01-01

In any sequencing project, the possible depth of comparative analysis is determined largely by the amount and quality of the accompanying contextual data. The structure, content, and storage of this contextual data should be standardized to ensure consistent coverage of all sequenced entities and facilitate comparisons. The Genomic Standards Consortium (GSC) has developed the “Minimum Information about Genome/Metagenome Sequences (MIGS/MIMS)” checklist for the description of genomes and here we annotate all 30 publicly available marine bacteriophage sequences to the MIGS standard. These annotations build on existing International Nucleotide Sequence Database Collaboration (INSDC) records, and confirm, as expected that current submissions lack most MIGS fields. MIGS fields were manually curated from the literature and placed in XML format as specified by the Genomic Contextual Data Markup Language (GCDML). These “machine-readable” reports were then analyzed to highlight patterns describing this collection of genomes. Completed reports are provided in GCDML. This work represents one step towards the annotation of our complete collection of genome sequences and shows the utility of capturing richer metadata along with raw sequences. PMID:21677864

A Molecular Framework for Understanding DCIS

DTIC Science & Technology

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].

PubMed

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.

Report of the tenth annual International Pachyonychia Congenita Consortium meeting

PubMed Central

van Steensel, Maurice A.M.; Coulombe, Pierre A.; Kaspar, Roger L.; Milstone, Leonard M.; McLean, W.H. Irwin; Roop, Dennis R.; Smith, Frances J.D.; Sprecher, Eli; Schwartz, Mary E.

2013-01-01

The International Pachyonychia Congenita Consortium (IPCC) was founded in 2004 in Park City, Utah, USA. Its goal is to find a cure for pachyonychia congenita, a rare keratinizing disorder. From February 14th–17th, 2013, the group convened in Park City for their tenth annual meeting. The 2013 meeting focused on how to best move forward with clinical trials and on learning from work in other scientific areas, with an emphasis on understanding mechanisms of pain and hyperkeratosis. Considerable time was spent on discussing the best way to move forward with development of new treatments and how to obtain or develop tools that can measure treatment outcomes in PC. PMID:24518109

An electronic infrastructure for research and treatment of the thalassemias and other hemoglobinopathies: the Euro-mediterranean ITHANET project.

PubMed

Lederer, Carsten W; Basak, A Nazli; Aydinok, Yesim; Christou, Soteroula; El-Beshlawy, Amal; Eleftheriou, Androulla; Fattoum, Slaheddine; Felice, Alex E; Fibach, Eitan; Galanello, Renzo; Gambari, Roberto; Gavrila, Lucian; Giordano, Piero C; Grosveld, Frank; Hassapopoulou, Helen; Hladka, Eva; Kanavakis, Emmanuel; Locatelli, Franco; Old, John; Patrinos, George P; Romeo, Giovanni; Taher, Ali; Traeger-Synodinos, Joanne; Vassiliou, Panayiotis; Villegas, Ana; Voskaridou, Ersi; Wajcman, Henri; Zafeiropoulos, Anastasios; Kleanthous, Marina

2009-01-01

Hemoglobin (Hb) disorders are common, potentially lethal monogenic diseases, posing a global health challenge. With worldwide migration and intermixing of carriers, demanding flexible health planning and patient care, hemoglobinopathies may serve as a paradigm for the use of electronic infrastructure tools in the collection of data, the dissemination of knowledge, the harmonization of treatment, and the coordination of research and preventive programs. ITHANET, a network covering thalassemias and other hemoglobinopathies, comprises 26 organizations from 16 countries, including non-European countries of origin for these diseases (Egypt, Israel, Lebanon, Tunisia and Turkey). Using electronic infrastructure tools, ITHANET aims to strengthen cross-border communication and data transfer, cooperative research and treatment of thalassemia, and to improve support and information of those affected by hemoglobinopathies. Moreover, the consortium has established the ITHANET Portal, a novel web-based instrument for the dissemination of information on hemoglobinopathies to researchers, clinicians and patients. The ITHANET Portal is a growing public resource, providing forums for discussion and research coordination, and giving access to courses and databases organized by ITHANET partners. Already a popular repository for diagnostic protocols and news related to hemoglobinopathies, the ITHANET Portal also provides a searchable, extendable database of thalassemia mutations and associated background information. The experience of ITHANET is exemplary for a consortium bringing together disparate organizations from heterogeneous partner countries to face a common health challenge. The ITHANET Portal as a web-based tool born out of this experience amends some of the problems encountered and facilitates education and international exchange of data and expertise for hemoglobinopathies.

Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.

PubMed

Falk, Marni J; Shen, Lishuang; Gonzalez, Michael; Leipzig, Jeremy; Lott, Marie T; Stassen, Alphons P M; Diroma, Maria Angela; Navarro-Gomez, Daniel; Yeske, Philip; Bai, Renkui; Boles, Richard G; Brilhante, Virginia; Ralph, David; DaRe, Jeana T; Shelton, Robert; Terry, Sharon F; Zhang, Zhe; Copeland, William C; van Oven, Mannis; Prokisch, Holger; Wallace, Douglas C; Attimonelli, Marcella; Krotoski, Danuta; Zuchner, Stephan; Gai, Xiaowu

2015-03-01

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial diseases. Copyright © 2014 Elsevier Inc. All rights reserved.

Gender differences in adverse outcomes after contemporary percutaneous coronary intervention: an analysis from the Blue Cross Blue Shield of Michigan Cardiovascular Consortium (BMC2) percutaneous coronary intervention registry.

PubMed

Duvernoy, Claire S; Smith, Dean E; Manohar, Prerana; Schaefer, Ann; Kline-Rogers, Eva; Share, David; McNamara, Richard; Gurm, Hitinder S; Moscucci, Mauro

2010-04-01

Prior studies have shown a relationship between female gender and adverse outcomes after percutaneous coronary interventions (PCIs). Whether this relationship still exists with contemporary PCI remains to be determined. We evaluated gender differences in clinical outcomes in a large registry of contemporary PCI. Data were prospectively collected from 22,725 consecutive PCIs in a multicenter regional consortium (Blue Cross Blue Shield of Michigan Cardiovascular Consortium) between January 2002 and December 2003. The primary end point was in-hospital all-cause mortality; other clinical outcomes evaluated included in-hospital death, vascular complications, transfusion, postprocedure myocardial infarction, stroke, and a combined major cardiovascular adverse event (MACE) end point including myocardial infarction, death, stroke, emergency coronary artery bypass grafting, and repeated PCI at the same site. Independent predictors of adverse outcomes were identified using multivariate logistic regression analysis. Compared with men, women were older, had a higher prevalence of comorbidities, and had a significantly higher frequency of adverse outcomes after PCI. After adjustment for baseline demographics, comorbidities, clinical presentation, and lesion characteristics, female gender was associated with an increased risk of in-hospital death, vascular complication, blood transfusion, stroke, and MACE. The relationship between female gender and increased risk of death and MACE was no longer present after further adjustment for kidney function and low body surface area. Differences in mortality rates between men and women no longer exist after PCI. However, our data suggest that technological advancements have not completely offset the relationship between gender and adverse outcomes after PCI. Copyright 2010 Mosby, Inc. All rights reserved.

BRCA1 and BRCA2 genetic testing—pitfalls and recommendations for managing variants of uncertain clinical significance

PubMed Central

Eccles, D. M.; Mitchell, G.; Monteiro, A. N. A.; Schmutzler, R.; Couch, F. J.; Spurdle, A. B.; Gómez-García, E. B.

2015-01-01

Background Increasing use of BRCA1/2 testing for tailoring cancer treatment and extension of testing to tumour tissue for somatic mutation is moving BRCA1/2 mutation screening from a primarily prevention arena delivered by specialist genetic services into mainstream oncology practice. A considerable number of gene tests will identify rare variants where clinical significance cannot be inferred from sequence information alone. The proportion of variants of uncertain clinical significance (VUS) is likely to grow with lower thresholds for testing and laboratory providers with less experience of BRCA. Most VUS will not be associated with a high risk of cancer but a misinterpreted VUS has the potential to lead to mismanagement of both the patient and their relatives. Design Members of the Clinical Working Group of ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) global consortium (www.enigmaconsortium.org) observed wide variation in practices in reporting, disclosure and clinical management of patients with a VUS. Examples from current clinical practice are presented and discussed to illustrate potential pitfalls, explore factors contributing to misinterpretation, and propose approaches to improving clarity. Results and conclusion Clinicians, patients and their relatives would all benefit from an improved level of genetic literacy. Genetic laboratories working with clinical geneticists need to agree on a clinically clear and uniform format for reporting BRCA test results to non-geneticists. An international consortium of experts, collecting and integrating all available lines of evidence and classifying variants according to an internationally recognized system, will facilitate reclassification of variants for clinical use. PMID:26153499

Database on veterinary clinical research in homeopathy.

PubMed

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.

The opportunities and obstacles in developing a vascular birthmark database for clinical and research use.

PubMed

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.

Common variant rs356182 near SNCA defines a Parkinson's disease endophenotype.

PubMed

Cooper, Christine A; Jain, Nimansha; Gallagher, Michael D; Weintraub, Daniel; Xie, Sharon X; Berlyand, Yosef; Espay, Alberto J; Quinn, Joseph; Edwards, Karen L; Montine, Thomas; Van Deerlin, Vivianna M; Trojanowski, John; Zabetian, Cyrus P; Chen-Plotkin, Alice S

2017-01-01

Parkinson's disease (PD) presents clinically with several motor subtypes that exhibit variable treatment response and prognosis. Here, we investigated genetic variants for their potential association with PD motor phenotype and progression. We screened 10 SNPs, previously associated with PD risk, for association with tremor-dominant (TD) versus postural-instability gait disorder (PIGD) motor subtypes. SNPs that correlated with the TD/PIGD ratio in a discovery cohort of 251 PD patients were then evaluated in a multi-site replication cohort of 559 PD patients. SNPs associated with motor phenotype in both cross-sectional cohorts were next evaluated for association with (1) rates of motor progression in a longitudinal subgroup of 230 PD patients and (2) brain alpha-synuclein ( SNCA ) expression in the GTEx (Genotype-Tissue Expression project) consortium database. Genotype at rs356182, near SNCA , correlated with the TD/PIGD ratio in both the discovery (Bonferroni-corrected P = 0.04) and replication cohorts ( P = 0.02). The rs356182 GG genotype was associated with a more tremor-predominant phenotype and predicted a slower rate of motor progression (1-point difference in annual rate of UPDRS-III motor score change, P = 0.01). The rs356182 genotype was associated with SNCA expression in the cerebellum ( P = 0.005). Our study demonstrates that the GG genotype at rs356182 provides molecular definition for a clinically important endophenotype associated with (1) more tremor-predominant motor phenomenology, (2) slower rates of motor progression, and (3) decreased brain expression of SNCA . Such molecularly defined endophenotyping in PD may benefit both clinical trial design and tailoring of clinical care as we enter the era of precision medicine.

1000 Norms Project: protocol of a cross-sectional study cataloging human variation.

PubMed

McKay, Marnee J; Baldwin, Jennifer N; Ferreira, Paulo; Simic, Milena; Vanicek, Natalie; Hiller, Claire E; Nightingale, Elizabeth J; Moloney, Niamh A; Quinlan, Kate G; Pourkazemi, Fereshteh; Sman, Amy D; Nicholson, Leslie L; Mousavi, Seyed J; Rose, Kristy; Raymond, Jacqueline; Mackey, Martin G; Chard, Angus; Hübscher, Markus; Wegener, Caleb; Fong Yan, Alycia; Refshauge, Kathryn M; Burns, Joshua

2016-03-01

Clinical decision-making regarding diagnosis and management largely depends on comparison with healthy or 'normal' values. Physiotherapists and researchers therefore need access to robust patient-centred outcome measures and appropriate reference values. However there is a lack of high-quality reference data for many clinical measures. The aim of the 1000 Norms Project is to generate a freely accessible database of musculoskeletal and neurological reference values representative of the healthy population across the lifespan. In 2012 the 1000 Norms Project Consortium defined the concept of 'normal', established a sampling strategy and selected measures based on clinical significance, psychometric properties and the need for reference data. Musculoskeletal and neurological items tapping the constructs of dexterity, balance, ambulation, joint range of motion, strength and power, endurance and motor planning will be collected in this cross-sectional study. Standardised questionnaires will evaluate quality of life, physical activity, and musculoskeletal health. Saliva DNA will be analysed for the ACTN3 genotype ('gene for speed'). A volunteer cohort of 1000 participants aged 3 to 100 years will be recruited according to a set of self-reported health criteria. Descriptive statistics will be generated, creating tables of mean values and standard deviations stratified for age and gender. Quantile regression equations will be used to generate age charts and age-specific centile values. This project will be a powerful resource to assist physiotherapists and clinicians across all areas of healthcare to diagnose pathology, track disease progression and evaluate treatment response. This reference dataset will also contribute to the development of robust patient-centred clinical trial outcome measures. Copyright © 2015 Chartered Society of Physiotherapy. Published by Elsevier Ltd. All rights reserved.

Proceedings of the Strategy Meeting for the Development of an International Consortium for Chinese Medicine and Cancer

PubMed Central

White, Jeffrey D.; Lin, Hongsheng; Wu, Roy S.; Lam, Stephen; Li, Jie; Dou, Jinhui; Kumar, Nagi; Lin, Lizhu; Lao, Lixing

2017-01-01

On November 3, 2014, in Bethesda, MD, the Office of Cancer Complementary and Alternative Medicine of the National Cancer Institute held a meeting to examine the potential utility and feasibility of establishing an international consortium for Chinese medicine and cancer. There is significant interest in the West in using components of Chinese medicine (CM) —such as botanicals and herbal medicines, acupuncture and acupressure, and qigong—in the field of oncology, as potential anticancer agents, for symptom management, and to improve quality of life. The proposal for a consortium on CM came from the Chinese Academy of Chinese Medical Sciences, with the aims of improving scientific communications and collaborations and modernizing the studies of CM for cancer. The US National Cancer Institute’s Office of Cancer Complementary and Alternative Medicine agreed to work with Chinese Academy of Chinese Medical Sciences to explore the feasibility of establishing an international consortium for Chinese medicine and cancer. At the meeting, participants from the United States, China, Canada, Australia, and Korea discussed issues in CM and cancer research, treatment, and management, including potential mechanisms of action, proof of efficacy, adverse effects, regulatory issues, and the need for improving the quality of randomized clinical trials of CM treatments and supportive care interventions. Presented in these proceedings are some of the main issues and opportunities discussed by workshop participants. PMID:29244995

Progress in the capture, manipulation, and delivery of medical media and its impact on education, clinical care, and research.

PubMed

Bernardo, Theresa M; Malinowski, Robert P

2005-01-01

In this article, advances in the application of medical media to education, clinical care, and research are explored and illustrated with examples, and their future potential is discussed. Impact is framed in terms of the Sloan Consortium's five pillars of quality education: access; student and faculty satisfaction; learning effectiveness; and cost effectiveness. (Hiltz SR, Zhang Y, Turoff M. Studies of effectiveness of learning networks. In Bourne J, Moore J, ed. Elements of Quality Online Education. Needham, MA: Sloan-Consortium, 2002:15-45). The alternatives for converting analog media (text, photos, graphics, sound, video, animations, radiographs) to digital media and direct digital capture are covered, as are options for storing, manipulating, retrieving, and sharing digital collections. Diagnostic imaging is given particular attention, clarifying the difference between computerized radiography and digital radiography and explaining the accepted standard (DICOM) and the advantages of Web PACS. Some novel research applications of medical media are presented.

Highlights of the Global HIV-1 CSF Escape Consortium Meeting, 9 June 2016, Bethesda, MD, USA.

PubMed

Joseph, Jeymohan; Cinque, Paola; Colosi, Deborah; Dravid, Ameet; Ene, Luminita; Fox, Howard; Gabuzda, Dana; Gisslen, Magnus; Beth Joseph, Sarah; Letendre, Scott; Mukerji, Shibani S; Nath, Avindra; Perez-Valero, Ignacio; Persaud, Deborah; Price, Richard W; Rao, Vasudev R; Sacktor, Ned; Swanstrom, Ronald; Winston, Alan; Wojna, Valerie; Wright, Edwina; Spudich, Serena

2016-10-05

CSF HIV escape is a recently recognised phenomenon that suggests that despite suppressive treatment, HIV RNA may be detected in the CNS compartment in some individuals. In rare cases this is associated with clinical neurological disease, while in most cases, neurological consequences are not apparent. Attempts at characterising the biological substrates of CSF escape and further investigating the neurological consequences need to be made to better understand the implications of this condition for the HIV cure agenda as well as for clinical outcomes. The Global CSF HIV-1 Escape Consortium meeting, convened by the US National Institute of Mental Health, was a first step to gather investigators from diverse sites to discuss opportunities for future collaborative work on this emerging issue. To better understand CSF HIV escape and allow cross-site data reconciliation, it will be useful to reach a consensus set of definitions of the distinct forms of CSF escape, without which concerted cross-site efforts are difficult.

CERAD (Consortium to Establish a Registry for Alzheimer’s Disease) The first 20 years

PubMed Central

Fillenbaum, Gerda G.; van Belle, Gerald; Morris, John C.; Mohs, Richard C.; Mirra, Suzanne S.; Davis, Patricia C.; Tariot, Pierre N.; Silverman, Jeremy M.; Clark, Christopher M.; Welsh-Bohmer, Kathleen A.; Heyman, Albert

2009-01-01

The Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) was funded by the National Institute on Aging in 1986 to develop standardized, validated measures for the assessment of Alzheimer’s disease (AD). The present report describes the measures that CERAD developed during its first decade, and their continued use in their original and translated forms. These measures include clinical, neuropsychological, neuropathological and behavioral assessments of AD, and also assessment of family history and parkinsonism in AD. An approach to evaluating neuroimages did not meet the standards desired. Further evaluations which could not be completed because of lack of funding (but where some materials are available), include evaluation of very severe AD, and of service use and need by patient and caregiver. The information that was developed in the U.S. and abroad permits standardized assessment of AD in clinical practice, facilitates epidemiological studies, and provides information valuable for individual and public health planning. CERAD materials and data remain available for those wishing to use them. PMID:18631955

Soft computing approach to 3D lung nodule segmentation in CT.

PubMed

Badura, P; Pietka, E

2014-10-01

This paper presents a novel, multilevel approach to the segmentation of various types of pulmonary nodules in computed tomography studies. It is based on two branches of computational intelligence: the fuzzy connectedness (FC) and the evolutionary computation. First, the image and auxiliary data are prepared for the 3D FC analysis during the first stage of an algorithm - the masks generation. Its main goal is to process some specific types of nodules connected to the pleura or vessels. It consists of some basic image processing operations as well as dedicated routines for the specific cases of nodules. The evolutionary computation is performed on the image and seed points in order to shorten the FC analysis and improve its accuracy. After the FC application, the remaining vessels are removed during the postprocessing stage. The method has been validated using the first dataset of studies acquired and described by the Lung Image Database Consortium (LIDC) and by its latest release - the LIDC-IDRI (Image Database Resource Initiative) database. Copyright © 2014 Elsevier Ltd. All rights reserved.

Investigating the Potential Impacts of Energy Production in the Marcellus Shale Region Using the Shale Network Database and CUAHSI-Supported Data Tools

NASA Astrophysics Data System (ADS)

Brazil, L.

2017-12-01

The Shale Network's extensive database of water quality observations enables educational experiences about the potential impacts of resource extraction with real data. Through open source tools that are developed and maintained by the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI), researchers, educators, and citizens can access and analyze the very same data that the Shale Network team has used in peer-reviewed publications about the potential impacts of hydraulic fracturing on water. The development of the Shale Network database has been made possible through collection efforts led by an academic team and involving numerous individuals from government agencies, citizen science organizations, and private industry. Thus far, CUAHSI-supported data tools have been used to engage high school students, university undergraduate and graduate students, as well as citizens so that all can discover how energy production impacts the Marcellus Shale region, which includes Pennsylvania and other nearby states. This presentation will describe these data tools, how the Shale Network has used them in developing educational material, and the resources available to learn more.

MetaboLights: towards a new COSMOS of metabolomics data management.

PubMed

Steinbeck, Christoph; Conesa, Pablo; Haug, Kenneth; Mahendraker, Tejasvi; Williams, Mark; Maguire, Eamonn; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Salek, Reza M; Griffin, Julian L

2012-10-01

Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.

Alternatives to relational database: comparison of NoSQL and XML approaches for clinical data storage.

PubMed

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.

CPTAC Proteomics Data on UCSC Genome Browser | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data via the UCSC Genome Browser. This effort extends accessibility of the CPTAC data to more researchers and provides an additional level of analysis to assist the cancer biology community.

Computational Omics Pre-Awardees | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) is pleased to announce the pre-awardees of the Computational Omics solicitation. Working with NVIDIA Foundation's Compute the Cure initiative and Leidos Biomedical Research Inc., the NCI, through this solicitation, seeks to leverage computational efforts to provide tools for the mining and interpretation of large-scale publicly available ‘omics’ datasets.

Back Complaints in the Elders (BACE); design of cohort studies in primary care: an international consortium

PubMed Central

2011-01-01

Background Although back complaints are common among older people, limited information is available in the literature about the clinical course of back pain in older people and the identification of older persons at risk for the transition from acute back complaints to chronic back pain. The aim of this study is to assess the course of back complaints and identify prognostic factors for the transition from acute back complaints to chronic back complaints in older people who visit a primary health care physician. Methods/design The design is a prospective cohort study with one-year follow-up. There will be no interference with usual care. Patients older than 55 years who consult a primary health care physician with a new episode of back complaints will be included in this study. Data will be collected using a questionnaire, physical examination and X-ray at baseline, and follow-up questionnaires after 6 weeks and 3, 6, 9 and 12 months. The study 'Back Complaints in the Elders' (BACE) will take place in different countries: starting in the Netherlands, Brazil and Australia. The research groups collaborate in the BACE consortium. The design and basic objectives of the study will be the same across the studies. Discussion This consortium is a collaboration between different research groups, aiming to provide insight into the course of back complaints in older people and to identify prognostic factors for the transition from acute back complaints to chronic back complaints in older persons. The BACE consortium allows to investigate differences between older people with back complaints and the health care systems in the different countries and to increase the statistical power by enabling meta-analyses using the individual patient data. Additional research groups worldwide are invited to join the BACE consortium. PMID:21854620

Acute porphyrias in the USA: features of 108 subjects from porphyrias consortium.

PubMed

Bonkovsky, Herbert L; Maddukuri, Vinaya C; Yazici, Cemal; Anderson, Karl E; Bissell, D Montgomery; Bloomer, Joseph R; Phillips, John D; Naik, Hetanshi; Peter, Inga; Baillargeon, Gwen; Bossi, Krista; Gandolfo, Laura; Light, Carrie; Bishop, David; Desnick, Robert J

2014-12-01

Recent descriptions of the clinical and laboratory features of subjects with acute porphyrias in the US are lacking. Our aim was to describe clinical, biochemical, and genetic features of 108 subjects. Between September 2010 and December 2012, 108 subjects with acute porphyrias (90 acute intermittent porphyrias, 9 hereditary coproporphyrias, 9 variegate porphyrias) were enrolled into an observational study. Genetic testing was performed at a central genetic testing laboratory and clinical information entered into a central database. Selected features were compared with data for adults in the US. Most subjects (88/108, 81%) were female, with self-reported onset of symptoms in the second through fourth decades of life. The most common symptom was abdominal pain. Appendectomies and cholecystectomies were common before a diagnosis of porphyria. The diagnosis was delayed by a mean of 15 years. Anxiety and depression were common, and 18% complained of chronic symptoms, especially neuropathic and other pains. The incidences of systemic arterial hypertension, chronic kidney disease, seizure disorders, and psychiatric conditions were markedly increased. Mutations of the known causative genes were found in 102/105 of those tested, with novel mutations being found in 37, including in 7/8 subjects with hereditary coproporphyria. Therapy with intravenous hematin was the most effective therapy both for treatment of acute attacks and for prevention of recurrent attacks. Acute porphyrias often remain undiagnosed for more than a decade after first symptoms develop. Intravenous hematin is the treatment of choice, both for treatment of acute attacks and for prevention of recurrent attacks. Copyright © 2014 Elsevier Inc. All rights reserved.

Biomedical science journals in the Arab world.

PubMed

Tadmouri, Ghazi O

2004-10-01

Medieval Arab scientists established the basis of medical practice and gave important attention to the publication of scientific results. At present, modern scientific publishing in the Arab world is in its developmental stage. Arab biomedical journals are less than 300, most of which are published in Egypt, Lebanon, and the Kingdom of Saudi Arabia. Yet, many of these journals do not have on-line access or are indexed in major bibliographic databases. The majority of indexed journals, however, do not have a stable presence in the popular PubMed database and their indexes are discontinued since 2001. The exposure of Arab biomedical journals in international indices undoubtedly plays an important role in improving the scientific quality of these journals. The successful examples discussed in this review encourage us to call for the formation of a consortium of Arab biomedical journal publishers to assist in redressing the balance of the region from biomedical data consumption to data production.

Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

PubMed Central

Vizcaíno, Juan Antonio; Foster, Joseph M.; Martens, Lennart

2010-01-01

Despite the fact that data deposition is not a generalised fact yet in the field of proteomics, several mass spectrometry (MS) based proteomics repositories are publicly available for the scientific community. The main existing resources are: the Global Proteome Machine Database (GPMDB), PeptideAtlas, the PRoteomics IDEntifications database (PRIDE), Tranche, and NCBI Peptidome. In this review the capabilities of each of these will be described, paying special attention to four key properties: data types stored, applicable data submission strategies, supported formats, and available data mining and visualization tools. Additionally, the data contents from model organisms will be enumerated for each resource. There are other valuable smaller and/or more specialized repositories but they will not be covered in this review. Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced. PMID:20615486

Mining Connected Data

NASA Astrophysics Data System (ADS)

Michel, L.; Motch, C.; Pineau, F. X.

2009-05-01

As members of the Survey Science Consortium of the XMM-Newton mission the Strasbourg Observatory is in charge of the real-time cross-correlations of X-ray data with archival catalogs. We also are committed to provide a specific tools to handle these cross-correlations and propose identifications at other wavelengths. In order to do so, we developed a database generator (Saada) managing persitent links and supporting heterogeneous input datasets. This system allows to easily build an archive containing numerous and complex links between individual items [1]. It also offers a powerfull query engine able to select sources on the basis of the properties (existence, distance, colours) of the X-ray-archival associations. We present such a database in operation for the 2XMMi catalogue. This system is flexible enough to provide both a public data interface and a servicing interface which could be used in the framework of the Simbol-X ground segment.

Placenta previa: an outcome-based cohort study in a contemporary obstetric population.

PubMed

Lal, Ann K; Hibbard, Judith U

2015-08-01

The objective of the study is to characterize the maternal and neonatal morbidities of women with placenta previa. This retrospective group study used the Consortium on Safe Labor electronic database, including 12 clinical centers, and 19 hospitals. Patients with placenta previa noted at the time of delivery were included. Maternal and neonatal variables were compared to a control group of women undergoing cesarean delivery with no previa. Logistic regression and general linear regression were used for the analysis, with p < 0.05 significance. There were 19,069 patients in the study: 452 in the placenta previa group and 18,617 in the control group. Neonates born to mothers with placenta previa had lower gestational ages and birth weights. In univariate analysis only, these neonates were at increased risk of lower 5 min Apgar scores, neonatal intensive care unit admission, anemia, respiratory distress syndrome, mechanical ventilation, and intraventricular hemorrhage. There was no association of placenta previa with small for gestational age infants, congenital anomalies or death. As previously shown, women with placenta previa have significantly more maternal morbidities. Increased maternal morbidity was noted; however, only those neonatal morbidities associated with preterm delivery occurred in the placenta previa group.

A European multi-language initiative to make the general population aware of independent clinical research: the European Communication on Research Awareness Need project.

PubMed

Mosconi, Paola; Antes, Gerd; Barbareschi, Giorgio; Burls, Amanda; Demotes-Mainard, Jacques; Chalmers, Iain; Colombo, Cinzia; Garattini, Silvio; Gluud, Christian; Gyte, Gill; Mcllwain, Catherine; Penfold, Matt; Post, Nils; Satolli, Roberto; Valetto, Maria Rosa; West, Brian; Wolff, Stephanie

2016-01-12

The ECRAN (European Communication on Research Awareness Needs) project was initiated in 2012, with support from the European Commission, to improve public knowledge about the importance of independent, multinational, clinical trials in Europe. Participants in the ECRAN consortium included clinicians and methodologists directly involved in clinical trials; researchers working in partnership with the public and patients; representatives of patients; and experts in science communication. We searched for, and evaluated, relevant existing materials and developed additional materials and tools, making them freely available under a Creative Commons licence. The principal communication materials developed were: 1. A website ( http://ecranproject.eu ) in six languages, including a Media centre section to help journalists to disseminate information about the ECRAN project 2. An animated film about clinical trials, dubbed in the 23 official languages of the European Community, and an interactive tutorial 3. An inventory of resources, available in 23 languages, searchable by topic, author, and media type 4. Two educational games for young people, developed in six languages 5. Testing Treatments interactive in a dozen languages, including five official European Community languages 6. An interactive tutorial slide presentation testing viewers' knowledge about clinical trials Over a 2-year project, our multidisciplinary and multinational consortium was able to produce, and make freely available in many languages, new materials to promote public knowledge about the importance of independent and international clinical trials. Sustained funding for the ECRAN information platform could help to promote successful recruitment to independent clinical trials supported through the European Clinical Research Infrastructure Network.

Applying the archetype approach to the database of a biobank information management system.

PubMed

Späth, Melanie Bettina; Grimson, Jane

2011-03-01

The purpose of this study is to investigate the feasibility of applying the openEHR archetype approach to modelling the data in the database of an existing proprietary biobank information management system. A biobank information management system stores the clinical/phenotypic data of the sample donor and sample related information. The clinical/phenotypic data is potentially sourced from the donor's electronic health record (EHR). The study evaluates the reuse of openEHR archetypes that have been developed for the creation of an interoperable EHR in the context of biobanking, and proposes a new set of archetypes specifically for biobanks. The ultimate goal of the research is the development of an interoperable electronic biomedical research record (eBMRR) to support biomedical knowledge discovery. The database of the prostate cancer biobank of the Irish Prostate Cancer Research Consortium (PCRC), which supports the identification of novel biomarkers for prostate cancer, was taken as the basis for the modelling effort. First the database schema of the biobank was analyzed and reorganized into archetype-friendly concepts. Then, archetype repositories were searched for matching archetypes. Some existing archetypes were reused without change, some were modified or specialized, and new archetypes were developed where needed. The fields of the biobank database schema were then mapped to the elements in the archetypes. Finally, the archetypes were arranged into templates specifically to meet the requirements of the PCRC biobank. A set of 47 archetypes was found to cover all the concepts used in the biobank. Of these, 29 (62%) were reused without change, 6 were modified and/or extended, 1 was specialized, and 11 were newly defined. These archetypes were arranged into 8 templates specifically required for this biobank. A number of issues were encountered in this research. Some arose from the immaturity of the archetype approach, such as immature modelling support tools, difficulties in defining high-quality archetypes and the problem of overlapping archetypes. In addition, the identification of suitable existing archetypes was time-consuming and many semantic conflicts were encountered during the process of mapping the PCRC BIMS database to existing archetypes. These include differences in the granularity of documentation, in metadata-level versus data-level modelling, in terminologies and vocabularies used, and in the amount of structure imposed on the information to be recorded. Furthermore, the current way of modelling the sample entity was found to be cumbersome in the sample-centric activity of biobanking. The archetype approach is a promising approach to create a shareable eBMRR based on the study participant/donor for biobanks. Many archetypes originally developed for the EHR domain can be reused to model the clinical/phenotypic and sample information in the biobank context, which validates the genericity of these archetypes and their potential for reuse in the context of biomedical research. However, finding suitable archetypes in the repositories and establishing an exact mapping between the fields in the PCRC BIMS database and the elements of existing archetypes that have been designed for clinical practice can be challenging and time-consuming and involves resolving many common system integration conflicts. These may be attributable to differences in the requirements for information documentation between clinical practice and biobanking. This research also recognized the need for better support tools, modelling guidelines and best practice rules and reconfirmed the need for better domain knowledge governance. Furthermore, the authors propose that the establishment of an independent sample record with the sample as record subject should be investigated. The research presented in this paper is limited by the fact that the new archetypes developed during this research are based on a single biobank instance. These new archetypes may not be complete, representing only those subsets of items required by this particular database. Nevertheless, this exercise exposes some of the gaps that exist in the archetype modelling landscape and highlights the concepts that need to be modelled with archetypes to enable the development of an eBMRR. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Practice databases and their uses in clinical research.

PubMed

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.

Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and HLA‐B Genotypes and Phenytoin Dosing

PubMed Central

Rettie, A E; Whirl‐Carrillo, M; Smith, L H; Mintzer, S; Lee, M T M; Klein, T E; Callaghan, J T

2014-01-01

Phenytoin is a widely used antiepileptic drug with a narrow therapeutic index and large interpatient variability, partly due to genetic variations in the gene encoding cytochrome P450 (CYP)2C9 (CYP2C9). Furthermore, the variant allele HLA‐B*15:02, encoding human leukocyte antigen, is associated with an increased risk of Stevens–Johnson syndrome and toxic epidermal necrolysis in response to phenytoin treatment. We summarize evidence from the published literature supporting these associations and provide recommendations for the use of phenytoin based on CYP2C9 and/or HLA‐B genotype (also available on PharmGKB: http://www.pharmgkb.org). The purpose of this guideline is to provide information for the interpretation of HLA‐B and/or CYP2C9 genotype tests so that the results can guide dosing and/or use of phenytoin. Detailed guidelines for the use of phenytoin as well as analyses of cost‐effectiveness are out of scope. Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines are periodically updated at http://www.pharmgkb.org. Clinical Pharmacology & Therapeutics (2014); 96 5, 542–548. doi:10.1038/clpt.2014.159 PMID:25099164

The new collaborative path in medical device development: the medical device innovation consortium.

PubMed

Kampfrath, Thomas; Cotten, Steven W

2013-10-01

The United States medical device market is the world's largest with over $100 billion in sales in 2011. Despite robust industry growth, the efficiency of the FDA approval process for moderate-risk (Class II) and high-risk devices (Class III) requiring 510(k) submission or pre-market approval (PMA) has been criticized. Recently, the FDA's Center for Devices and Radiological Health (CDRH) announced the creation of a Medical Device Innovation Consortium (MDIC), a public-private partnership (PPP) to share knowledge in regulatory science. Overarching goals include creating a forum for the exchange of ideas among the FDA, industry, and non-profit entities; providing monetary investments for project proposals prioritized by key working groups; and developing tools that support cost effective innovation, data-driven methodology, and implementation strategies. Clinical chemists and clinical laboratory scientists have several unique opportunities to contribute to the MDIC. These laboratory professionals have invaluable experience with the real-life performance of a variety of medical devices and their expertise can recognize unmet needs and contribute towards the acceleration of device development. Copyright © 2013 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Consortium for Imaging and Biomarkers (CIB) | Division of Cancer Prevention

Cancer.gov

Overdiagnosis and false positives present significant clinical problems in the prevention, detection and treatment of | 8 lead investigators combining imaging methods for the visualization of lesions with biomarkers to improve the accuracy of screening, early cancer detection, and the diagnosis of early stage cancers.

Governing Body Committees | Office of Cancer Clinical Proteomics Research

Cancer.gov

OCCPR relies on governing body committees to provide objective and expert advice on the coordination and future direction of the CPTAC Program. The Steering Committee (SC) consists of awardees and OCCPR leadership, who formulate, coordinate, and oversee strategic decisions and policies regarding consortium-wide activities.

Medical students' clinical performance of dealing with patients in the context of domestic violence.

PubMed

Kong, Hyun-Hee; Im, Sunju; Seo, Ji-Hyun; Kim, Do-Kyong; Roh, HyeRin

2018-03-01

The aim of this study was to inquire about the clinical performance and determine the performance pattern of medical students in standardized patient (SP) based examinations of domestic violence (DV). The clinical performance sores in DV station with SP of third-year (n=111, in 2014) and 4th-year (n=143, in 2016) medical students of five universities in the Busan-Gyeongnam Clinical Skills Examination Consortium were subjected in this study. The scenarios and checklists of DV cases were developed by the case development committee of the consortium. The students' performance was compared with other stations encountered in SP. The items of the checklists were categorized to determine the performance pattern of students investigating DV into six domains: disclosure strategy (D), DV related history taking (H), checking the perpetrator's psychosocial state (P), checking the victim's condition (V), negotiating and persuading the interviewee (N), and providing information about DV (I). Medical students showed poorer performance in DV stations than in the other stations with SP in the same examination. Most students did confirm the perpetrator and commented on confidentiality but ignored the perpetrator's state and patient's physical and psychological condition. The students performed well in the domains of D, H, and I but performed poorly in domains P, V, and N. Medical students showed poor clinical performance in the DV station. They performed an 'event oriented interview' rather than 'patient centered' communication. An integrated educational program of DV should be set to improve students' clinical performance.

A review of the use of bromelain in cardiovascular diseases.

PubMed

Ley, Chit Moy; Tsiami, Amalia; Ni, Qing; Robinson, Nicola

2011-07-01

In 2004 an estimated 17.1 million people died from cardiovascular diseases (CVDs) worldwide, representing 29% of all global deaths. According to the American Heart Association, heart disease and stroke are the main cause of death and disability among people with type 2 diabetes. Additional safe and effective approaches are needed for the prevention and management of CVDs which may include nutritional supplements. To identify the potential of bromelain (a food supplement) on the risk factors associated with CVDs. An electronic and manual search was conducted during November 2009 to March 2010. The databases searched included: Ovid MEDLINE; All EBM Reviews-Cochrane Database of Systematic Reviews (Cochrane DSR), American College of Physicians (ACP) Journal Club, Database of Abstracts of Reviews of Effects (DARE), Cochrane Central Register of Controlled Trials (CCTR), Cochrane Methodology Register (CMR), Health Technology Assessment (HTA) and National Health Service Economic Evaluation Database (NHSEED); Allied and Complementary Medicine (AMED); British Nursing Index and Archive; EMBASE; Health Management Information Consortium (HMIC); Science Direct and Electronic Thesis Online Services (ETHOS). Only papers in the English language were included. Randomised controlled trials (RCTs), human studies, animal studies and experimental studies related to bromelain for CVDs. The quality assessment of all the selected studies was conducted by the authors. Data from 3 animal trials and 3 human trials were included in the review. Data collected included: type of trial, drug dosage, duration, outcome measures, characteristics of bromelain used, significance of results and conclusion. Out of 223 papers retrieved, 6 papers met the inclusion criteria and could be included in the review. These comprised of 3 animal and 3 human trials, each of which investigated the use of bromelain for CVDs. Results suggested that bromelain could be used for treating acute thrombophlebitis, as it decreases aggregation of blood platelets, has a cardio-protective effect, ameliorates rejection-induced arterial wall remodelling, prevents thrombin-induced human platelet aggregation as well as reduces thrombus formation. No substantive study of bromelain and clinical CVDs has been carried out in human populations. Only a few studies on bromelain and CVDs were published from 1948 to 2010. This may be an area worthy to be explored in future CVDs research.

Clinical Databases for Chest Physicians.

PubMed

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.

LungMAP: The Molecular Atlas of Lung Development Program

PubMed Central

Ardini-Poleske, Maryanne E.; Ansong, Charles; Carson, James P.; Corley, Richard A.; Deutsch, Gail H.; Hagood, James S.; Kaminski, Naftali; Mariani, Thomas J.; Potter, Steven S.; Pryhuber, Gloria S.; Warburton, David; Whitsett, Jeffrey A.; Palmer, Scott M.; Ambalavanan, Namasivayam

2017-01-01

The National Heart, Lung, and Blood Institute is funding an effort to create a molecular atlas of the developing lung (LungMAP) to serve as a research resource and public education tool. The lung is a complex organ with lengthy development time driven by interactive gene networks and dynamic cross talk among multiple cell types to control and coordinate lineage specification, cell proliferation, differentiation, migration, morphogenesis, and injury repair. A better understanding of the processes that regulate lung development, particularly alveologenesis, will have a significant impact on survival rates for premature infants born with incomplete lung development and will facilitate lung injury repair and regeneration in adults. A consortium of four research centers, a data coordinating center, and a human tissue repository provides high-quality molecular data of developing human and mouse lungs. LungMAP includes mouse and human data for cross correlation of developmental processes across species. LungMAP is generating foundational data and analysis, creating a web portal for presentation of results and public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology that incorporates the latest findings of the consortium. The LungMAP website (www.lungmap.net) currently contains more than 6,000 high-resolution lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers for young audiences. This paper presents a brief description of research conducted by the consortium, database, and portal development and upcoming features that will enhance the LungMAP experience for a community of users. PMID:28798251

Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of “Unknown Function”

PubMed Central

Quanbeck, Stephanie M.; Brachova, Libuse; Campbell, Alexis A.; Guan, Xin; Perera, Ann; He, Kun; Rhee, Seung Y.; Bais, Preeti; Dickerson, Julie A.; Dixon, Philip; Wohlgemuth, Gert; Fiehn, Oliver; Barkan, Lenore; Lange, Iris; Lange, B. Markus; Lee, Insuk; Cortes, Diego; Salazar, Carolina; Shuman, Joel; Shulaev, Vladimir; Huhman, David V.; Sumner, Lloyd W.; Roth, Mary R.; Welti, Ruth; Ilarslan, Hilal; Wurtele, Eve S.; Nikolau, Basil J.

2012-01-01

Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and transcriptomics. This paper describes the analysis of Arabidopsis metabolomics data sets acquired by a consortium that includes five analytical laboratories, bioinformaticists, and biostatisticians, which aims to develop and validate metabolomics as a hypothesis-generating functional genomics tool. The consortium is determining the metabolomes of Arabidopsis T-DNA mutant stocks, grown in standardized controlled environment optimized to minimize environmental impacts on the metabolomes. Metabolomics data were generated with seven analytical platforms, and the combined data is being provided to the research community to formulate initial hypotheses about genes of unknown function (GUFs). A public database (www.PlantMetabolomics.org) has been developed to provide the scientific community with access to the data along with tools to allow for its interactive analysis. Exemplary datasets are discussed to validate the approach, which illustrate how initial hypotheses can be generated from the consortium-produced metabolomics data, integrated with prior knowledge to provide a testable hypothesis concerning the functionality of GUFs. PMID:22645570

Magnitude of Anemia at Discharge Increases 30-Day Hospital Readmissions.

PubMed

Koch, Colleen G; Li, Liang; Sun, Zhiyuan; Hixson, Eric D; Tang, Anne; Chagin, Kevin; Kattan, Michael; Phillips, Shannon C; Blackstone, Eugene H; Henderson, J Michael

2017-12-01

Anemia during hospitalization is associated with poor health outcomes. Does anemia at discharge place patients at risk for hospital readmission within 30 days of discharge? Our objectives were to examine the prevalence and magnitude of anemia at hospital discharge and determine whether anemia at discharge was associated with 30-day readmissions among a cohort of hospitalizations in a single health care system. From January 1, 2009, to August 31, 2011, there were 152,757 eligible hospitalizations within a single health care system. The endpoint was any hospitalization within 30 days of discharge. The University HealthSystem Consortium's clinical database was used for demographics and comorbidities; hemoglobin values are from the hospitals' electronic medical records, and readmission status was obtained from the University HealthSystem Consortium administrative data systems. Mild anemia was defined as hemoglobin of greater than 11 to less than 12 g/dl in women and greater than 11 to less than 13 g/dl in men; moderate, greater than 9 to less than or equal to 11 g/dl; and severe, less than or equal to 9 g/dl. Logistic regression was used to assess the association of anemia and 30-day readmissions adjusted for demographics, comorbidity, and hospitalization type. Among 152,757 hospitalizations, 72% of patients were discharged with anemia: 31,903 (21%), mild; 52,971 (35%), moderate; and 25,522 (17%), severe. Discharge anemia was associated with severity-dependent increased odds for 30-day hospital readmission compared with those without anemia: for mild anemia, 1.74 (1.65-1.82); moderate anemia, 2.76 (2.64-2.89); and severe anemia, 3.47 (3.30-3.65), P < 0.001. Anemia at discharge is associated with a severity-dependent increased risk for 30-day readmission. A strategy focusing on anemia treatment care paths during index hospitalization offers an opportunity to influence subsequent readmissions.

The implementation of isoniazid preventive therapy in HIV clinics: the experience from the TB/HIV in Rio (THRio) study.

PubMed

Durovni, Betina; Cavalcante, Solange C; Saraceni, Valeria; Vellozo, Vitoria; Israel, Giselle; King, Bonnie S; Cohn, Silvia; Efron, Anne; Pacheco, Antonio G; Moulton, Lawrence H; Chaisson, Richard E; Golub, Jonathan E

2010-11-01

The TB/HIV in Rio (THRio) study was launched in September 2005 to assess the impact of integrated tuberculosis (TB) and HIV treatment strategies in 29 HIV clinics in Rio de Janeiro, Brazil. THRio is a cluster-randomized trial (CRT) to determine whether routine screening for and treatment of latent TB in HIV clinic patients with access to antiretroviral therapy will reduce TB incidence at the clinic level. THRio is part of the Consortium to Respond Effectively to AIDS/TB Epidemic that is implementing research studies to assess the impact of bold, new public health paradigms for controlling the AIDS/TB epidemic. Twenty-nine public primary HIV clinics were randomly assigned a date to begin implementing TB screening procedures and provision of isoniazid preventive therapy (IPT) for TB/HIV coinfected patients. Final analysis of the CRT is expected in 2011. Starting at date of tuberculin skin test (TST)/IPT implementation at each clinic through August 2010, 1670 HIV-infected patients initiated IPT, of which 215 are still receiving treatment. Of the remaining 1455 patients, 1230 (85%) completed therapy and only 20 (1.2%) patients initiating IPT reported adverse reactions leading to discontinuation of therapy. IPT completion was higher among HIV-infected patients receiving HAART (87%) than those not yet receiving HAART (79%, P < 0.01). Times to TST and IPT have markedly decreased postintervention, but remain considerably long. The richness of the THRio database has resulted in several analyses of this expansive cohort of HIV-infected patients that are reviewed here. The national implementation of TST and IPT for HIV-positive patients in Brazil has been invigorated partly due to THRio's baseline results. Expanded use of IPT in HIV patients in Rio de Janeiro is achievable with high adherence and low adverse events, although this effort requires a package of activities including training, advocacy and reorganization of services.

WE-E-BRB-11: Riview a Web-Based Viewer for Radiotherapy.

PubMed

Apte, A; Wang, Y; Deasy, J

2012-06-01

Collaborations involving radiotherapy data collection, such as the recently proposed international radiogenomics consortium, require robust, web-based tools to facilitate reviewing treatment planning information. We present the architecture and prototype characteristics for a web-based radiotherapy viewer. The web-based environment developed in this work consists of the following components: 1) Import of DICOM/RTOG data: CERR was leveraged to import DICOM/RTOG data and to convert to database friendly RT objects. 2) Extraction and Storage of RT objects: The scan and dose distributions were stored as .png files per slice and view plane. The file locations were written to the MySQL database. Structure contours and DVH curves were written to the database as numeric data. 3) Web interfaces to query, retrieve and visualize the RT objects: The Web application was developed using HTML 5 and Ruby on Rails (RoR) technology following the MVC philosophy. The open source ImageMagick library was utilized to overlay scan, dose and structures. The application allows users to (i) QA the treatment plans associated with a study, (ii) Query and Retrieve patients matching anonymized ID and study, (iii) Review up to 4 plans simultaneously in 4 window panes (iv) Plot DVH curves for the selected structures and dose distributions. A subset of data for lung cancer patients was used to prototype the system. Five user accounts were created to have access to this study. The scans, doses, structures and DVHs for 10 patients were made available via the web application. A web-based system to facilitate QA, and support Query, Retrieve and the Visualization of RT data was prototyped. The RIVIEW system was developed using open source and free technology like MySQL and RoR. We plan to extend the RIVIEW system further to be useful in clinical trial data collection, outcomes research, cohort plan review and evaluation. © 2012 American Association of Physicists in Medicine.

Malnutrition Diagnosis during Adult Inpatient Hospitalizations: Analysis of a Multi-Institutional Collaborative Database of Academic Medical Centers.

PubMed

Tobert, Conrad M; Mott, Sarah L; Nepple, Kenneth G

2018-01-01

Malnutrition is a significant problem for hospitalized patients. However, the true prevalence of reported malnutrition diagnosis in real-world clinical practice is largely unknown. Using a large collaborative multi-institutional database, the rate of malnutrition diagnosis was assessed and used to assess institutional variables associated with higher rates of malnutrition diagnosis. The aim of this study was to define the prevalence of malnutrition diagnosis reported among inpatient hospitalizations. The University Health System Consortium (Vizient) database was retrospectively reviewed for reported rates of malnutrition diagnosis. All adult inpatient hospitalization at 105 member institutions during fiscal years 2014 and 2015 were evaluated. Malnutrition diagnosis based on the presence of an International Classification of Diseases-Ninth Revision diagnosis code. Hospital volume and publicly available hospital rankings and patient satisfaction scores were obtained. Multiple regression analysis was performed to assess the association between these variables and reported rates of malnutrition. A total of 5,896,792 hospitalizations were identified from 105 institutions during the 2-year period. It was found that 292,754 patients (5.0%) had a malnutrition diagnosis during their hospital stay. By institution, median rate of malnutrition diagnosis during hospitalization was 4.0%, whereas the rate of severe malnutrition diagnosis was 0.9%. There was a statistically significant increase in malnutrition diagnosis from 4.0% to 4.9% between 2014 and 2015 (P<0.01). Institutional factors associated with increased diagnosis of malnutrition were higher hospital volume, hospital ranking, and patient satisfaction scores (P<0.01). Missing a malnutrition diagnosis appears to be a universal issue because the rate of malnutrition diagnosis was consistently low across academic medical centers. Institutional variables were associated with the prevalence of malnutrition diagnosis, which suggests that institutional culture influences malnutrition diagnosis. Quality improvement efforts aimed at improved structure and process appear to be needed to improve the identification of malnutrition. Copyright © 2018 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Standards for Clinical Grade Genomic Databases.

PubMed

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.

NCI Launches Proteomics Assay Portal | Office of Cancer Clinical Proteomics Research

Cancer.gov

In a paper recently published by the journal Nature Methods, Investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) announced the launch of a proteomics Assay Portal for multiple reaction monitoring-mass spectrometry (MRM-MS) assays.  This community web-based repository for well-characterized quantitative proteomic assays currently consists of 456 unique peptide assays to 282 unique proteins and ser

Brain Immune Interactions as the Basis of Gulf War Illness: Gulf War Illness Consortium (GWIC)

DTIC Science & Technology

2016-10-01

between the immune system and the brain. The GWIC includes both clinical ( human ) and preclinical (animal and cell) studies and researchers in the 10...47 pesticides , DFP, sarin 16. Price Code (Leave Bl k) 17. Security Classification of Report Unclassified 18. Security Classification of this...stronger and longer proinflammatory signaling effects between the immune system and the brain. The GWIC includes both clinical ( human ) and

CPTAC Releases Largest-Ever Colorectal Cancer Proteome Dataset from Previously Genome Characterized Tumors | Office of Cancer Clinical Proteomics Research

Cancer.gov

On September 4, 2013, NCI’s Clinical Proteomics Tumor Analysis Consortium (CPTAC) publicly released proteomic data produced from colorectal tumor samples previously analyzed by The Cancer Genome Atlas (TCGA).  This is the initial release of proteomic tumor data designed to complement genomic data on the same tumors. The data is publicly available at the CPTAC data portal.

CPTAC Releases Largest-Ever Ovarian Cancer Proteome Dataset from Previously Genome Characterized Tumors | Office of Cancer Clinical Proteomics Research

Cancer.gov

National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have just released a comprehensive dataset of the proteomic analysis of high grade serous ovarian tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).  This is one of the largest public datasets covering the proteome, phosphoproteome and glycoproteome with complementary deep genomic sequencing data on the same tumor.

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

PubMed

Kılıç, Sefa; Sagitova, Dinara M; Wolfish, Shoshannah; Bely, Benoit; Courtot, Mélanie; Ciufo, Stacy; Tatusova, Tatiana; O'Donovan, Claire; Chibucos, Marcus C; Martin, Maria J; Erill, Ivan

2016-01-01

Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/. © The Author(s) 2016. Published by Oxford University Press.

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

PubMed

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-03-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modernizing the MagIC Paleomagnetic and Rock Magnetic Database Technology Stack to Encourage Code Reuse and Reproducible Science

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A. A. P.; Jarboe, N.; Jonestrask, L.; Tauxe, L.; Constable, C.

2016-12-01

The Magnetics Information Consortium (https://earthref.org/MagIC/) develops and maintains a database and web application for supporting the paleo-, geo-, and rock magnetic scientific community. Historically, this objective has been met with an Oracle database and a Perl web application at the San Diego Supercomputer Center (SDSC). The Oracle Enterprise Cluster at SDSC, however, was decommissioned in July of 2016 and the cost for MagIC to continue using Oracle became prohibitive. This provided MagIC with a unique opportunity to reexamine the entire technology stack and data model. MagIC has developed an open-source web application using the Meteor (http://meteor.com) framework and a MongoDB database. The simplicity of the open-source full-stack framework that Meteor provides has improved MagIC's development pace and the increased flexibility of the data schema in MongoDB encouraged the reorganization of the MagIC Data Model. As a result of incorporating actively developed open-source projects into the technology stack, MagIC has benefited from their vibrant software development communities. This has translated into a more modern web application that has significantly improved the user experience for the paleo-, geo-, and rock magnetic scientific community.

Assessment of Variation in Microbial Community Amplicon Sequencing by the Microbiome Quality Control (MBQC) Project Consortium

EPA Science Inventory

Precision medicine has been made possible by the translation of ‘omics to the clinic, and human microbiome studies must likewise transition to applications in public health. This will require especially robust measurements and assimilation of data from multiple population-scale c...

Korea University Joins the International Efforts in Clinical Proteogenomics Cancer Research | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute's (NCI) Office of Cancer Clinical Proteomics Research, part of the National Institutes of Health, and Korea University (KU) located in The Republic of Korea have signed a Memorandum of Understanding (MOU) in clinical proteogenomics cancer research. The MOU between NCI and KU represents the twenty-ninth institution and eleventh country to join the continued effort of the International Cancer Proteogenome Consortium (ICPC), an effort catalyzed through the vision of the 47th Vice President of the United States Joseph R. Biden, Jr. and the Cancer Moonshot.

Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium.

PubMed

Grossman, R L; Abel, B; Angiuoli, S; Barrett, J C; Bassett, D; Bramlett, K; Blumenthal, G M; Carlsson, A; Cortese, R; DiGiovanna, J; Davis-Dusenbery, B; Dittamore, R; Eberhard, D A; Febbo, P; Fitzsimons, M; Flamig, Z; Godsey, J; Goswami, J; Gruen, A; Ortuño, F; Han, J; Hayes, D; Hicks, J; Holloway, D; Hovelson, D; Johnson, J; Juhl, H; Kalamegham, R; Kamal, R; Kang, Q; Kelloff, G J; Klozenbuecher, M; Kolatkar, A; Kuhn, P; Langone, K; Leary, R; Loverso, P; Manmathan, H; Martin, A-M; Martini, J; Miller, D; Mitchell, M; Morgan, T; Mulpuri, R; Nguyen, T; Otto, G; Pathak, A; Peters, E; Philip, R; Posadas, E; Reese, D; Reese, M G; Robinson, D; Dei Rossi, A; Sakul, H; Schageman, J; Singh, S; Scher, H I; Schmitt, K; Silvestro, A; Simmons, J; Simmons, T; Sislow, J; Talasaz, A; Tang, P; Tewari, M; Tomlins, S; Toukhy, H; Tseng, H R; Tuck, M; Tzou, A; Vinson, J; Wang, Y; Wells, W; Welsh, A; Wilbanks, J; Wolf, J; Young, L; Lee, Jsh; Leiman, L C

2017-05-01

The cancer community understands the value of blood profiling measurements in assessing and monitoring cancer. We describe an effort among academic, government, biotechnology, diagnostic, and pharmaceutical companies called the Blood Profiling Atlas in Cancer (BloodPAC) Project. BloodPAC will aggregate, make freely available, and harmonize for further analyses, raw datasets, relevant associated clinical data (e.g., clinical diagnosis, treatment history, and outcomes), and sample preparation and handling protocols to accelerate the development of blood profiling assays. © 2017 Authors Clinical Pharmacology & Therapeutics published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

BRCA1 and BRCA2 genetic testing-pitfalls and recommendations for managing variants of uncertain clinical significance.

PubMed

Eccles, D M; Mitchell, G; Monteiro, A N A; Schmutzler, R; Couch, F J; Spurdle, A B; Gómez-García, E B

2015-10-01

Increasing use of BRCA1/2 testing for tailoring cancer treatment and extension of testing to tumour tissue for somatic mutation is moving BRCA1/2 mutation screening from a primarily prevention arena delivered by specialist genetic services into mainstream oncology practice. A considerable number of gene tests will identify rare variants where clinical significance cannot be inferred from sequence information alone. The proportion of variants of uncertain clinical significance (VUS) is likely to grow with lower thresholds for testing and laboratory providers with less experience of BRCA. Most VUS will not be associated with a high risk of cancer but a misinterpreted VUS has the potential to lead to mismanagement of both the patient and their relatives. Members of the Clinical Working Group of ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) global consortium (www.enigmaconsortium.org) observed wide variation in practices in reporting, disclosure and clinical management of patients with a VUS. Examples from current clinical practice are presented and discussed to illustrate potential pitfalls, explore factors contributing to misinterpretation, and propose approaches to improving clarity. Clinicians, patients and their relatives would all benefit from an improved level of genetic literacy. Genetic laboratories working with clinical geneticists need to agree on a clinically clear and uniform format for reporting BRCA test results to non-geneticists. An international consortium of experts, collecting and integrating all available lines of evidence and classifying variants according to an internationally recognized system, will facilitate reclassification of variants for clinical use. © The Author 2015. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

[The future of clinical laboratory database management system].

PubMed

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.

Advances in clinical NK cell studies: Donor selection, manufacturing and quality control

PubMed Central

Koehl, U.; Kalberer, C.; Spanholtz, J.; Lee, D. A.; Miller, J. S.; Cooley, S.; Lowdell, M.; Uharek, L.; Klingemann, H.; Curti, A.; Leung, W.; Alici, E.

2016-01-01

ABSTRACT Natural killer (NK) cells are increasingly used in clinical studies in order to treat patients with various malignancies. The following review summarizes platform lectures and 2013–2015 consortium meetings on manufacturing and clinical use of NK cells in Europe and United States. A broad overview of recent pre-clinical and clinical results in NK cell therapies is provided based on unstimulated, cytokine-activated, as well as genetically engineered NK cells using chimeric antigen receptors (CAR). Differences in donor selection, manufacturing and quality control of NK cells for cancer immunotherapies are described and basic recommendations are outlined for harmonization in future NK cell studies. PMID:27141397

25 CFR 1000.73 - Once a Tribe/Consortium has been awarded a grant, may the Tribe/Consortium obtain information...

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 2 2013-04-01 2013-04-01 false Once a Tribe/Consortium has been awarded a grant, may the Tribe/Consortium obtain information from a non-BIA bureau? 1000.73 Section 1000.73 Indians OFFICE OF THE... § 1000.73 Once a Tribe/Consortium has been awarded a grant, may the Tribe/Consortium obtain information...

CPTAC Evaluates Long-Term Reproducibility of Quantitative Proteomics Using Breast Cancer Xenografts | Office of Cancer Clinical Proteomics Research

Cancer.gov

Liquid chromatography tandem-mass spectrometry (LC-MS/MS)- based methods such as isobaric tags for relative and absolute quantification (iTRAQ) and tandem mass tags (TMT) have been shown to provide overall better quantification accuracy and reproducibility over other LC-MS/MS techniques. However, large scale projects like the Clinical Proteomic Tumor Analysis Consortium (CPTAC) require comparisons across many genomically characterized clinical specimens in a single study and often exceed the capability of traditional iTRAQ-based quantification.

Engineering Ligninolytic Consortium for Bioconversion of Lignocelluloses to Ethanol and Chemicals.

PubMed

Bilal, Muhammad; Nawaz, Muhammad Zohaib; Iqbal, Hafiz M N; Hou, Jialin; Mahboob, Shahid; Al-Ghanim, Khalid A; Cheng, Hairong

2018-01-01

Rising environmental concerns and recent global scenario of cleaner production and consumption are leading to the design of green industrial processes to produce alternative fuels and chemicals. Although bioethanol is one of the most promising and eco-friendly alternatives to fossil fuels yet its production from food and feed has received much negative criticism. The main objective of this study was to present the noteworthy potentialities of lignocellulosic biomass as an enormous and renewable biological resource. The particular focus was also given on engineering ligninolytic consortium for bioconversion of lignocelluloses to ethanol and chemicals on sustainable and environmentally basis. Herein, an effort has been made to extensively review, analyze and compile salient information related to the topic of interest. Several authentic bibliographic databases including PubMed, Scopus, Elsevier, Springer, Bentham Science and other scientific databases were searched with utmost care, and inclusion/ exclusion criterion was adopted to appraise the quality of retrieved peer-reviewed research literature. Bioethanol production from lignocellulosic biomass can largely satisfy the possible inconsistency of first-generation ethanol since it utilizes inedible lignocellulosic feedstocks, primarily sourced from agriculture and forestry wastes. Two major polysaccharides in lignocellulosic biomass namely, cellulose and hemicellulose constitute a complex lignocellulosic network by connecting with lignin, which is highly recalcitrant to depolymerization. Several attempts have been made to reduce the cost involved in the process through improving the pretreatment process. While, the ligninolytic enzymes of white rot fungi (WRF) including laccase, lignin peroxidase (LiP), and manganese peroxidase (MnP) have appeared as versatile biocatalysts for delignification of several lignocellulosic residues. The first part of the review is mainly focused on engineering ligninolytic consortium. In the second part, WRF and its unique ligninolytic enzyme-based bio-delignification of lignocellulosic biomass, enzymatic hydrolysis, and fermentation of hydrolyzed feedstock are discussed. The metabolic engineering, enzymatic engineering, synthetic biology aspects for ethanol production and platform chemicals production are comprehensively reviewed in the third part. Towards the end information is also given on futuristic viewpoints. In conclusion, given the present unpredicted scenario of energy and fuel crisis accompanied by global warming, lignocellulosic bioethanol holds great promise as an alternative to petroleum. Apart from bioethanol, the simultaneous production of other value-added products may improve the economics of lignocellulosic bioethanol bioconversion process. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The learning curve of robot-assisted radical cystectomy: results from the International Robotic Cystectomy Consortium.

PubMed

Hayn, Matthew H; Hussain, Abid; Mansour, Ahmed M; Andrews, Paul E; Carpentier, Paul; Castle, Erik; Dasgupta, Prokar; Rimington, Peter; Thomas, Raju; Khan, Shamim; Kibel, Adam; Kim, Hyung; Manoharan, Murugesan; Menon, Mani; Mottrie, Alex; Ornstein, David; Peabody, James; Pruthi, Raj; Palou Redorta, Joan; Richstone, Lee; Schanne, Francis; Stricker, Hans; Wiklund, Peter; Chandrasekhar, Rameela; Wilding, Greg E; Guru, Khurshid A

2010-08-01

Robot-assisted radical cystectomy (RARC) has evolved as a minimally invasive alternative to open radical cystectomy for patients with invasive bladder cancer. We sought to define the learning curve for RARC by evaluating results from a multicenter, contemporary, consecutive series of patients who underwent this procedure. Utilizing the International Robotic Cystectomy Consortium database, a prospectively maintained and institutional review board-approved database, we identified 496 patients who underwent RARC by 21 surgeons at 14 institutions from 2003 to 2009. Cut-off points for operative time, lymph node yield (LNY), estimated blood loss (EBL), and margin positivity were identified. Using specifically designed statistical mixed models, we were able to inversely predict the number of patients required for an institution to reach the predetermined cut-off points. Mean operative time was 386 min, mean EBL was 408 ml, and mean LNY was 18. Overall, 34 of 482 patients (7%) had a positive surgical margin (PSM). Using statistical models, it was estimated that 21 patients were required for operative time to reach 6.5h and 8, 20, and 30 patients were required to reach an LNY of 12, 16, and 20, respectively. For all patients, PSM rates of <5% were achieved after 30 patients. For patients with pathologic stage higher than T2, PSM rates of <15% were achieved after 24 patients. RARC is a challenging procedure but is a technique that is reproducible throughout multiple centers. This report helps to define the learning curve for RARC and demonstrates an acceptable level of proficiency by the 30th case for proxy measures of RARC quality. Copyright (c) 2010 European Association of Urology. Published by Elsevier B.V. All rights reserved.

National Land Cover Database 2001 (NLCD01)

USGS Publications Warehouse

LaMotte, Andrew E.

2016-01-01

This 30-meter data set represents land use and land cover for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System (see http://water.usgs.gov/GIS/browse/nlcd01-partition.jpg). The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (http://www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004), (see: http://www.mrlc.gov/mrlc2k.asp). The NLCD 2001 was created by partitioning the United States into mapping zones. A total of 68 mapping zones (see http://water.usgs.gov/GIS/browse/nlcd01-mappingzones.jpg), were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov.

National Land Cover Database 2001 (NLCD01) Imperviousness Layer Tile 1, Northwest United States: IMPV01_1

USGS Publications Warehouse

LaMotte, Andrew E.; Wieczorek, Michael

2010-01-01

This 30-meter resolution data set represents the imperviousness layer for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System, browse graphic: nlcd01-partition. The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004) and http://www.mrlc.gov/mrlc2k.asp.. The NLCD 2001 was created by partitioning the United States into mapping-zones. A total of 68 mapping-zones browse graphic: nlcd01-mappingzones.jpg were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping-zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov.

National Land Cover Database 2001 (NLCD01) Tree Canopy Layer Tile 2, Northeast United States: CNPY01_2

USGS Publications Warehouse

LaMotte, Andrew E.; Wieczorek, Michael

2010-01-01

This 30-meter resolution data set represents the tree canopy layer for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System, browse graphic: nlcd01-partition.jpg The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004) and http://www.mrlc.gov/mrlc2k.asp. The NLCD 2001 was created by partitioning the United States into mapping-zones. A total of 68 mapping-zones browse graphic: nlcd01-mappingzones.jpg were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping-zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov.

National Land Cover Database 2001 (NLCD01) Imperviousness Layer Tile 4, Southeast United States: IMPV01_4

USGS Publications Warehouse

Wieczorek, Michael; LaMotte, Andrew E.

2010-01-01

This 30-meter resolution data set represents the imperviousness layer for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System, browse graphic: nlcd01-partition. The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004) and http://www.mrlc.gov/mrlc2k.asp.. The NLCD 2001 was created by partitioning the United States into mapping-zones. A total of 68 mapping-zones browse graphic: nlcd01-mappingzones.jpg were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping-zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov.

National Land Cover Database 2001 (NLCD01) Tree Canopy Layer Tile 1, Northwest United States: CNPY01_1

USGS Publications Warehouse

LaMotte, Andrew E.; Wieczorek, Michael

2010-01-01

This 30-meter resolution data set represents the tree canopy layer for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System, browse graphic: nlcd01-partition.jpg. The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004) and http://www.mrlc.gov/mrlc2k.asp. The NLCD 2001 was created by partitioning the United States into mapping-zones. A total of 68 mapping-zones browse graphic: nlcd01-mappingzones.jpg were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping-zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov

National Land Cover Database 2001 (NLCD01) Imperviousness Layer Tile 2, Northeast United States: IMPV01_2

USGS Publications Warehouse

LaMotte, Andrew E.; Wieczorek, Michael

2010-01-01

This 30-meter resolution data set represents the imperviousness layer for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System, browse graphic: nlcd01-partition. The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004) and http://www.mrlc.gov/mrlc2k.asp.. The NLCD 2001 was created by partitioning the United States into mapping-zones. A total of 68 mapping-zones browse graphic: nlcd01-mappingzones.jpg were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping-zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov.

National Land Cover Database 2001 (NLCD01) Tree Canopy Layer Tile 4, Southeast United States: CNPY01_4

USGS Publications Warehouse

LaMotte, Andrew E.; Wieczorek, Michael

2010-01-01

This 30-meter resolution data set represents the tree canopy layer for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System, browse graphic: nlcd01-partition.jpg The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004) and http://www.mrlc.gov/mrlc2k.asp. The NLCD 2001 was created by partitioning the United States into mapping-zones. A total of 68 mapping-zones browse graphic: nlcd01-mappingzones.jpg were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping-zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov.

National Land Cover Database 2001 (NLCD01) Imperviousness Layer Tile 3, Southwest United States: IMPV01_3

USGS Publications Warehouse

LaMotte, Andrew E.; Wieczorek, Michael

2010-01-01

This 30-meter resolution data set represents the imperviousness layer for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System, browse graphic: nlcd01-partition. The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004) and http://www.mrlc.gov/mrlc2k.asp.. The NLCD 2001 was created by partitioning the United States into mapping-zones. A total of 68 mapping-zones browse graphic: nlcd01-mappingzones.jpg were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping-zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov.

National Land Cover Database 2001 (NLCD01) Tree Canopy Layer Tile 3, Southwest United States: CNPY01_3

USGS Publications Warehouse

LaMotte, Andrew E.; Wieczorek, Michael

2010-01-01

This 30-meter resolution data set represents the tree canopy layer for the conterminous United States for the 2001 time period. The data have been arranged into four tiles to facilitate timely display and manipulation within a Geographic Information System, browse graphic: nlcd01-partition.jpg The National Land Cover Data Set for 2001 was produced through a cooperative project conducted by the Multi-Resolution Land Characteristics (MRLC) Consortium. The MRLC Consortium is a partnership of Federal agencies (www.mrlc.gov), consisting of the U.S. Geological Survey (USGS), the National Oceanic and Atmospheric Administration (NOAA), the U.S. Environmental Protection Agency (USEPA), the U.S. Department of Agriculture (USDA), the U.S. Forest Service (USFS), the National Park Service (NPS), the U.S. Fish and Wildlife Service (USFWS), the Bureau of Land Management (BLM), and the USDA Natural Resources Conservation Service (NRCS). One of the primary goals of the project is to generate a current, consistent, seamless, and accurate National Land Cover Database (NLCD) circa 2001 for the United States at medium spatial resolution. For a detailed definition and discussion on MRLC and the NLCD 2001 products, refer to Homer and others (2004) and http://www.mrlc.gov/mrlc2k.asp. The NLCD 2001 was created by partitioning the United States into mapping-zones. A total of 68 mapping-zones browse graphic: nlcd01-mappingzones.jpg were delineated within the conterminous United States based on ecoregion and geographical characteristics, edge-matching features, and the size requirement of Landsat mosaics. Mapping-zones encompass the whole or parts of several states. Questions about the NLCD mapping zones can be directed to the NLCD 2001 Land Cover Mapping Team at the USGS/EROS, Sioux Falls, SD (605) 594-6151 or mrlc@usgs.gov.

Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials

PubMed Central

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.

PubMed

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.

Are adverse effects incorporated in economic models? An initial review of current practice.

PubMed

Craig, D; McDaid, C; Fonseca, T; Stock, C; Duffy, S; Woolacott, N

2009-12-01

To identify methodological research on the incorporation of adverse effects in economic models and to review current practice. Major electronic databases (Cochrane Methodology Register, Health Economic Evaluations Database, NHS Economic Evaluation Database, EconLit, EMBASE, Health Management Information Consortium, IDEAS, MEDLINE and Science Citation Index) were searched from inception to September 2007. Health technology assessment (HTA) reports commissioned by the National Institute for Health Research (NIHR) HTA programme and published between 2004 and 2007 were also reviewed. The reviews of methodological research on the inclusion of adverse effects in decision models and of current practice were carried out according to standard methods. Data were summarised in a narrative synthesis. Of the 719 potentially relevant references in the methodological research review, five met the inclusion criteria; however, they contained little information of direct relevance to the incorporation of adverse effects in models. Of the 194 HTA monographs published from 2004 to 2007, 80 were reviewed, covering a range of research and therapeutic areas. In total, 85% of the reports included adverse effects in the clinical effectiveness review and 54% of the decision models included adverse effects in the model; 49% included adverse effects in the clinical review and model. The link between adverse effects in the clinical review and model was generally weak; only 3/80 (< 4%) used the results of a meta-analysis from the systematic review of clinical effectiveness and none used only data from the review without further manipulation. Of the models including adverse effects, 67% used a clinical adverse effects parameter, 79% used a cost of adverse effects parameter, 86% used one of these and 60% used both. Most models (83%) used utilities, but only two (2.5%) used solely utilities to incorporate adverse effects and were explicit that the utility captured relevant adverse effects; 53% of those models that included utilities derived them from patients on treatment and could therefore be interpreted as capturing adverse effects. In total, 30% of the models that included adverse effects used withdrawals related to drug toxicity and therefore might be interpreted as using withdrawals to capture adverse effects, but this was explicitly stated in only three reports. Of the 37 models that did not include adverse effects, 18 provided justification for this omission, most commonly lack of data; 19 appeared to make no explicit consideration of adverse effects in the model. There is an implicit assumption within modelling guidance that adverse effects are very important but there is a lack of clarity regarding how they should be dealt with and considered in modelling. In many cases a lack of clear reporting in the HTAs made it extremely difficult to ascertain what had actually been carried out in consideration of adverse effects. The main recommendation is for much clearer and explicit reporting of adverse effects, or their exclusion, in decision models and for explicit recognition in future guidelines that 'all relevant outcomes' should include some consideration of adverse events.

Circulating 25-hydroxyvitamin D and the risk of rarer cancers: Design and methods of the Cohort Consortium Vitamin D Pooling Project of Rarer Cancers.

PubMed

Gallicchio, Lisa; Helzlsouer, Kathy J; Chow, Wong-Ho; Freedman, D Michal; Hankinson, Susan E; Hartge, Patricia; Hartmuller, Virginia; Harvey, Chinonye; Hayes, Richard B; Horst, Ronald L; Koenig, Karen L; Kolonel, Laurence N; Laden, Francine; McCullough, Marjorie L; Parisi, Dominick; Purdue, Mark P; Shu, Xiao-Ou; Snyder, Kirk; Stolzenberg-Solomon, Rachael Z; Tworoger, Shelley S; Varanasi, Arti; Virtamo, Jarmo; Wilkens, Lynne R; Xiang, Yong-Bing; Yu, Kai; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Abnet, Christian C; Albanes, Demetrius; Bertrand, Kimberly; Weinstein, Stephanie J

2010-07-01

The Cohort Consortium Vitamin D Pooling Project of Rarer Cancers (VDPP), a consortium of 10 prospective cohort studies from the United States, Finland, and China, was formed to examine the associations between circulating 25-hydroxyvitamin D (25(OH)D) concentrations and the risk of rarer cancers. Cases (total n = 5,491) included incident primary endometrial (n = 830), kidney (n = 775), ovarian (n = 516), pancreatic (n = 952), and upper gastrointestinal tract (n = 1,065) cancers and non-Hodgkin lymphoma (n = 1,353) diagnosed in the participating cohorts. At least 1 control was matched to each case on age, date of blood collection (1974-2006), sex, and race/ethnicity (n = 6,714). Covariate data were obtained from each cohort in a standardized manner. The majority of the serum or plasma samples were assayed in a central laboratory using a direct, competitive chemiluminescence immunoassay on the DiaSorin LIAISON platform (DiaSorin, Inc., Stillwater, Minnesota). Masked quality control samples included serum standards from the US National Institute of Standards and Technology. Conditional logistic regression analyses were conducted using clinically defined cutpoints, with 50-<75 nmol/L as the reference category. Meta-analyses were also conducted using inverse-variance weights in random-effects models. This consortium approach permits estimation of the association between 25(OH)D and several rarer cancers with high accuracy and precision across a wide range of 25(OH)D concentrations.

Circulating 25-Hydroxyvitamin D and the Risk of Rarer Cancers: Design and Methods of the Cohort Consortium Vitamin D Pooling Project of Rarer Cancers

PubMed Central

Gallicchio, Lisa; Helzlsouer, Kathy J.; Chow, Wong-Ho; Freedman, D. Michal; Hankinson, Susan E.; Hartge, Patricia; Hartmuller, Virginia; Harvey, Chinonye; Hayes, Richard B.; Horst, Ronald L.; Koenig, Karen L.; Kolonel, Laurence N.; Laden, Francine; McCullough, Marjorie L.; Parisi, Dominick; Purdue, Mark P.; Shu, Xiao-Ou; Snyder, Kirk; Stolzenberg-Solomon, Rachael Z.; Tworoger, Shelley S.; Varanasi, Arti; Virtamo, Jarmo; Wilkens, Lynne R.; Xiang, Yong-Bing; Yu, Kai; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Abnet, Christian C.; Albanes, Demetrius; Bertrand, Kimberly; Weinstein, Stephanie J.

2010-01-01

The Cohort Consortium Vitamin D Pooling Project of Rarer Cancers (VDPP), a consortium of 10 prospective cohort studies from the United States, Finland, and China, was formed to examine the associations between circulating 25-hydroxyvitamin D (25(OH)D) concentrations and the risk of rarer cancers. Cases (total n = 5,491) included incident primary endometrial (n = 830), kidney (n = 775), ovarian (n = 516), pancreatic (n = 952), and upper gastrointestinal tract (n = 1,065) cancers and non-Hodgkin lymphoma (n = 1,353) diagnosed in the participating cohorts. At least 1 control was matched to each case on age, date of blood collection (1974–2006), sex, and race/ethnicity (n = 6,714). Covariate data were obtained from each cohort in a standardized manner. The majority of the serum or plasma samples were assayed in a central laboratory using a direct, competitive chemiluminescence immunoassay on the DiaSorin LIAISON platform (DiaSorin, Inc., Stillwater, Minnesota). Masked quality control samples included serum standards from the US National Institute of Standards and Technology. Conditional logistic regression analyses were conducted using clinically defined cutpoints, with 50–<75 nmol/L as the reference category. Meta-analyses were also conducted using inverse-variance weights in random-effects models. This consortium approach permits estimation of the association between 25(OH)D and several rarer cancers with high accuracy and precision across a wide range of 25(OH)D concentrations. PMID:20562188

Infectious precipitants of acute hyperammonemia are associated with indicators of increased morbidity in patients with urea cycle disorders.

PubMed

McGuire, Peter J; Lee, Hye-Seung; Summar, Marshall L

2013-12-01

To prospectively characterize acute hyperammonemic episodes in patients with urea cycle disorders (UCDs) in terms of precipitating factors, treatments, and use of medical resources. This was a prospective, longitudinal observational study of hyperammonemic episodes in patients with UCD enrolled in the National Institutes of Health-sponsored Urea Cycle Disorders Consortium Longitudinal Study. An acute hyperammonemic event was defined as plasma ammonia level >100 μmol/L. Physician-reported data regarding the precipitating event and laboratory and clinical variables were recorded in a central database. In our study population, 128 patients with UCD experienced a total of 413 hyperammonemia events. Most patients experienced between 1 and 3 (65%) or between 4 and 6 (23%) hyperammonemia events since study inception, averaging fewer than 1 event/year. The most common identifiable precipitant was infection (33%), 24% of which were upper/lower respiratory tract infections. Indicators of increased morbidity were seen with infection, including increased hospitalization rates (P = .02), longer hospital stays (+2.0 days; P = .003), and increased use of intravenous ammonia scavengers (+45%-52%; P = .003-.03). Infection is the most common precipitant of acute hyperammonemia in patients with UCD and is associated with indicators of increased morbidity (ie, hospitalization rate, length of stay, and use of intravenous ammonia scavengers). These findings suggest that the catabolic and immune effects of infection may be a target for clinical intervention in inborn errors of metabolism. Published by Mosby, Inc.

The CERAD Neuropsychologic Battery Total Score and the progression of Alzheimer disease.

PubMed

Rossetti, Heidi C; Munro Cullum, C; Hynan, Linda S; Lacritz, Laura H

2010-01-01

To establish the Consortium to Establish a Registry for Alzheimer's Disease (CERAD) neuropsychologic battery as a valid measure of cognitive progression in Alzheimer disease (AD) by deriving annualized CERAD Total Change Scores and corresponding confidence intervals in AD and controls from which to define clinically meaningful change. Subjects included 383 normal control (NC) and 655 AD subjects with serial data from the CERAD registry database. Annualized CERAD Total Change Scores were derived and Reliable Change Indexes (RCIs) calculated to establish statistically reliable change values. CERAD Change Scores were compared with annualized change scores from the Mini-Mental State Examination (MMSE), Clinical Dementia Rating Scale (CDR) Sum of Boxes, and Blessed Dementia Rating Scale (BDRS). For the CERAD Total Score, the AD sample showed significantly greater decline than the NC sample over the 4-year interval, with AD subjects declining an average of 22.2 points compared with the NCs' improving an average 2.8 points from baseline to last visit [Group x Time interaction [F(4,1031)=246.08, P<0.001)]. By Visit 3, the majority of AD subjects (65.2%) showed a degree of cognitive decline that fell outside the RCI. CERAD Change Scores significantly correlated (P<0.001) with MMSE (r=-0.66), CDR (r=-0.42), and BDRS (r=-0.38) change scores. Results support the utility of the CERAD Total Score as a measure of AD progression and provide comparative data for annualized change in CERAD Total Score and other summary measures.

A hierarchical SVG image abstraction layer for medical imaging

NASA Astrophysics Data System (ADS)

Kim, Edward; Huang, Xiaolei; Tan, Gang; Long, L. Rodney; Antani, Sameer

2010-03-01

As medical imaging rapidly expands, there is an increasing need to structure and organize image data for efficient analysis, storage and retrieval. In response, a large fraction of research in the areas of content-based image retrieval (CBIR) and picture archiving and communication systems (PACS) has focused on structuring information to bridge the "semantic gap", a disparity between machine and human image understanding. An additional consideration in medical images is the organization and integration of clinical diagnostic information. As a step towards bridging the semantic gap, we design and implement a hierarchical image abstraction layer using an XML based language, Scalable Vector Graphics (SVG). Our method encodes features from the raw image and clinical information into an extensible "layer" that can be stored in a SVG document and efficiently searched. Any feature extracted from the raw image including, color, texture, orientation, size, neighbor information, etc., can be combined in our abstraction with high level descriptions or classifications. And our representation can natively characterize an image in a hierarchical tree structure to support multiple levels of segmentation. Furthermore, being a world wide web consortium (W3C) standard, SVG is able to be displayed by most web browsers, interacted with by ECMAScript (standardized scripting language, e.g. JavaScript, JScript), and indexed and retrieved by XML databases and XQuery. Using these open source technologies enables straightforward integration into existing systems. From our results, we show that the flexibility and extensibility of our abstraction facilitates effective storage and retrieval of medical images.

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

PubMed

Zhang, Junjun; Baran, Joachim; Cros, A; Guberman, Jonathan M; Haider, Syed; Hsu, Jack; Liang, Yong; Rivkin, Elena; Wang, Jianxin; Whitty, Brett; Wong-Erasmus, Marie; Yao, Long; Kasprzyk, Arek

2011-01-01

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.

75 FR 4827 - Submission for OMB Review; Comment Request Clinical Trials Reporting Program (CTRP) Database (NCI)

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...

North American Clinical Trials Network (NACTN) for Treatment of Spinal Cord Injury: A Consortium of Military, Veterans Administration, and Civilian Hospitals

DTIC Science & Technology

2011-01-31

of the patient on arrival and includes a clinical evaluation, 5 measurement of state of consciousness with the Glasgow Coma Scale (GCS) and of...associated injuries with the Abbreviated Injury Scale . The American Spinal Injury Association impairment scale (AIS) is scored on admission and at key...the AIS Impairment Scale , and where appropriate, the Functional Independence Measure FIM™, the Spinal Cord Independence Measure (SCIM), and the

FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project.

PubMed

Beaulieu, Chandree L; Majewski, Jacek; Schwartzentruber, Jeremy; Samuels, Mark E; Fernandez, Bridget A; Bernier, Francois P; Brudno, Michael; Knoppers, Bartha; Marcadier, Janet; Dyment, David; Adam, Shelin; Bulman, Dennis E; Jones, Steve J M; Avard, Denise; Nguyen, Minh Thu; Rousseau, Francois; Marshall, Christian; Wintle, Richard F; Shen, Yaoqing; Scherer, Stephen W; Friedman, Jan M; Michaud, Jacques L; Boycott, Kym M

2014-06-05

Inherited monogenic disease has an enormous impact on the well-being of children and their families. Over half of the children living with one of these conditions are without a molecular diagnosis because of the rarity of the disease, the marked clinical heterogeneity, and the reality that there are thousands of rare diseases for which causative mutations have yet to be identified. It is in this context that in 2010 a Canadian consortium was formed to rapidly identify mutations causing a wide spectrum of pediatric-onset rare diseases by using whole-exome sequencing. The FORGE (Finding of Rare Disease Genes) Canada Consortium brought together clinicians and scientists from 21 genetics centers and three science and technology innovation centers from across Canada. From nation-wide requests for proposals, 264 disorders were selected for study from the 371 submitted; disease-causing variants (including in 67 genes not previously associated with human disease; 41 of these have been genetically or functionally validated, and 26 are currently under study) were identified for 146 disorders over a 2-year period. Here, we present our experience with four strategies employed for gene discovery and discuss FORGE's impact in a number of realms, from clinical diagnostics to the broadening of the phenotypic spectrum of many diseases to the biological insight gained into both disease states and normal human development. Lastly, on the basis of this experience, we discuss the way forward for rare-disease genetic discovery both in Canada and internationally. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

The Spanish biology/disease initiative within the human proteome project: Application to rheumatic diseases.

PubMed

Ruiz-Romero, Cristina; Calamia, Valentina; Albar, Juan Pablo; Casal, José Ignacio; Corrales, Fernando J; Fernández-Puente, Patricia; Gil, Concha; Mateos, Jesús; Vivanco, Fernando; Blanco, Francisco J

2015-09-08

The Spanish Chromosome 16 consortium is integrated in the global initiative Human Proteome Project, which aims to develop an entire map of the proteins encoded following a gene-centric strategy (C-HPP) in order to make progress in the understanding of human biology in health and disease (B/D-HPP). Chromosome 16 contains many genes encoding proteins involved in the development of a broad range of diseases, which have a significant impact on the health care system. The Spanish HPP consortium has developed a B/D platform with five programs focused on selected medical areas: cancer, obesity, cardiovascular, infectious and rheumatic diseases. Each of these areas has a clinical leader associated to a proteomic investigator with the responsibility to get a comprehensive understanding of the proteins encoded by Chromosome 16 genes. Proteomics strategies have enabled great advances in the area of rheumatic diseases, particularly in osteoarthritis, with studies performed on joint cells, tissues and fluids. In this manuscript we describe how the Spanish HPP-16 consortium has developed a B/D platform with five programs focused on selected medical areas: cancer, obesity, cardiovascular, infectious and rheumatic diseases. Each of these areas has a clinical leader associated to a proteomic investigator with the responsibility to get a comprehensive understanding of the proteins encoded by Chromosome 16 genes. We show how the Proteomic strategy has enabled great advances in the area of rheumatic diseases, particularly in osteoarthritis, with studies performed on joint cells, tissues and fluids. This article is part of a Special Issue entitled: HUPO 2014. Copyright © 2015 Elsevier B.V. All rights reserved.

The Lung Image Database Consortium (LIDC): ensuring the integrity of expert-defined "truth".

PubMed

Armato, Samuel G; Roberts, Rachael Y; McNitt-Gray, Michael F; Meyer, Charles R; Reeves, Anthony P; McLennan, Geoffrey; Engelmann, Roger M; Bland, Peyton H; Aberle, Denise R; Kazerooni, Ella A; MacMahon, Heber; van Beek, Edwin J R; Yankelevitz, David; Croft, Barbara Y; Clarke, Laurence P

2007-12-01

Computer-aided diagnostic (CAD) systems fundamentally require the opinions of expert human observers to establish "truth" for algorithm development, training, and testing. The integrity of this "truth," however, must be established before investigators commit to this "gold standard" as the basis for their research. The purpose of this study was to develop a quality assurance (QA) model as an integral component of the "truth" collection process concerning the location and spatial extent of lung nodules observed on computed tomography (CT) scans to be included in the Lung Image Database Consortium (LIDC) public database. One hundred CT scans were interpreted by four radiologists through a two-phase process. For the first of these reads (the "blinded read phase"), radiologists independently identified and annotated lesions, assigning each to one of three categories: "nodule >or=3 mm," "nodule <3 mm," or "non-nodule >or=3 mm." For the second read (the "unblinded read phase"), the same radiologists independently evaluated the same CT scans, but with all of the annotations from the previously performed blinded reads presented; each radiologist could add to, edit, or delete their own marks; change the lesion category of their own marks; or leave their marks unchanged. The post-unblinded read set of marks was grouped into discrete nodules and subjected to the QA process, which consisted of identification of potential errors introduced during the complete image annotation process and correction of those errors. Seven categories of potential error were defined; any nodule with a mark that satisfied the criterion for one of these categories was referred to the radiologist who assigned that mark for either correction or confirmation that the mark was intentional. A total of 105 QA issues were identified across 45 (45.0%) of the 100 CT scans. Radiologist review resulted in modifications to 101 (96.2%) of these potential errors. Twenty-one lesions erroneously marked as lung nodules after the unblinded reads had this designation removed through the QA process. The establishment of "truth" must incorporate a QA process to guarantee the integrity of the datasets that will provide the basis for the development, training, and testing of CAD systems.

BRIDG: a domain information model for translational and clinical protocol-driven research.

PubMed

Becnel, Lauren B; Hastak, Smita; Ver Hoef, Wendy; Milius, Robert P; Slack, MaryAnn; Wold, Diane; Glickman, Michael L; Brodsky, Boris; Jaffe, Charles; Kush, Rebecca; Helton, Edward

2017-09-01

It is critical to integrate and analyze data from biological, translational, and clinical studies with data from health systems; however, electronic artifacts are stored in thousands of disparate systems that are often unable to readily exchange data. To facilitate meaningful data exchange, a model that presents a common understanding of biomedical research concepts and their relationships with health care semantics is required. The Biomedical Research Integrated Domain Group (BRIDG) domain information model fulfills this need. Software systems created from BRIDG have shared meaning "baked in," enabling interoperability among disparate systems. For nearly 10 years, the Clinical Data Standards Interchange Consortium, the National Cancer Institute, the US Food and Drug Administration, and Health Level 7 International have been key stakeholders in developing BRIDG. BRIDG is an open-source Unified Modeling Language-class model developed through use cases and harmonization with other models. With its 4+ releases, BRIDG includes clinical and now translational research concepts in its Common, Protocol Representation, Study Conduct, Adverse Events, Regulatory, Statistical Analysis, Experiment, Biospecimen, and Molecular Biology subdomains. The model is a Clinical Data Standards Interchange Consortium, Health Level 7 International, and International Standards Organization standard that has been utilized in national and international standards-based software development projects. It will continue to mature and evolve in the areas of clinical imaging, pathology, ontology, and vocabulary support. BRIDG 4.1.1 and prior releases are freely available at https://bridgmodel.nci.nih.gov . © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Alliance of Glycobiologists for Detection of Cancer | Division of Cancer Prevention

Cancer.gov

A consortium of eight Tumor Glycomics Laboratories is working to reveal cancer-related dynamics of complex carbohydrates to develop new, validated clinical biomarkers for early detection. Studying important biologic mechanisms, Alliance investigators focus their efforts on diverse classes of glycan markers that are likely to play important roles in cancer development. | 8

Development of a 2001 National Land Cover Database for the United States

USGS Publications Warehouse

Homer, Collin G.; Huang, Chengquan; Yang, Limin; Wylie, Bruce K.; Coan, Michael

2004-01-01

Multi-Resolution Land Characterization 2001 (MRLC 2001) is a second-generation Federal consortium designed to create an updated pool of nation-wide Landsat 5 and 7 imagery and derive a second-generation National Land Cover Database (NLCD 2001). The objectives of this multi-layer, multi-source database are two fold: first, to provide consistent land cover for all 50 States, and second, to provide a data framework which allows flexibility in developing and applying each independent data component to a wide variety of other applications. Components in the database include the following: (1) normalized imagery for three time periods per path/row, (2) ancillary data, including a 30 m Digital Elevation Model (DEM) derived into slope, aspect and slope position, (3) perpixel estimates of percent imperviousness and percent tree canopy, (4) 29 classes of land cover data derived from the imagery, ancillary data, and derivatives, (5) classification rules, confidence estimates, and metadata from the land cover classification. This database is now being developed using a Mapping Zone approach, with 66 Zones in the continental United States and 23 Zones in Alaska. Results from three initial mapping Zones show single-pixel land cover accuracies ranging from 73 to 77 percent, imperviousness accuracies ranging from 83 to 91 percent, tree canopy accuracies ranging from 78 to 93 percent, and an estimated 50 percent increase in mapping efficiency over previous methods. The database has now entered the production phase and is being created using extensive partnering in the Federal government with planned completion by 2006.

How I do it: a practical database management system to assist clinical research teams with data collection, organization, and reporting.

PubMed

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.

Creation of an NCI comparative brain tumor consortium: informing the translation of new knowledge from canine to human brain tumor patients

PubMed Central

Mazcko, Christina; Brown, Diane E.; Koehler, Jennifer W.; Miller, Andrew D.; Miller, C. Ryan; Bentley, R. Timothy; Packer, Rebecca A.; Breen, Matthew; Boudreau, C. Elizabeth; Levine, Jonathan M.; Simpson, R. Mark; Halsey, Charles; Kisseberth, William; Rossmeisl, John H.; Dickinson, Peter J.; Fan, Timothy M.; Corps, Kara; Aldape, Kenneth; Puduvalli, Vinay; Pluhar, G. Elizabeth; Gilbert, Mark R.

2016-01-01

On September 14–15, 2015, a meeting of clinicians and investigators in the fields of veterinary and human neuro-oncology, clinical trials, neuropathology, and drug development was convened at the National Institutes of Health campus in Bethesda, Maryland. This meeting served as the inaugural event launching a new consortium focused on improving the knowledge, development of, and access to naturally occurring canine brain cancer, specifically glioma, as a model for human disease. Within the meeting, a SWOT (strengths, weaknesses, opportunities, and threats) assessment was undertaken to critically evaluate the role that naturally occurring canine brain tumors could have in advancing this aspect of comparative oncology aimed at improving outcomes for dogs and human beings. A summary of this meeting and subsequent discussion are provided to inform the scientific and clinical community of the potential for this initiative. Canine and human comparisons represent an unprecedented opportunity to complement conventional brain tumor research paradigms, addressing a devastating disease for which innovative diagnostic and treatment strategies are clearly needed. PMID:27179361

Clinical Management of Pediatric Acute-Onset Neuropsychiatric Syndrome: Part I—Psychiatric and Behavioral Interventions

PubMed Central

Murphy, Tanya; Leckman, James; Shaw, Richard; Williams, Kyle; Kapphahn, Cynthia; Frankovich, Jennifer; Geller, Daniel; Bernstein, Gail; Chang, Kiki; Elia, Josephine; Swedo, Susan

2017-01-01

Abstract Objective: This article outlines the consensus guidelines for symptomatic treatment for children with Pediatric Acute-Onset Neuropsychiatric Syndrome (PANS) and Pediatric Autoimmune Neuropsychiatric Syndrome Associated with Streptococcal Infection (PANDAS). Methods: Extant literature on behavioral, psychotherapeutic, and psychopharmacologic treatments for PANS and PANDAS was reviewed. Members of the PANS Research Consortium pooled their clinical experiences to find agreement on treatment of PANS and PANDAS symptoms. Results: Current guidelines result from consensus among the Consortium members. Conclusion: While underlying infectious and inflammatory processes in PANS and PANDAS patients are treated, psychiatric and behavioral symptoms need simultaneous treatment to decrease suffering and improve adherence to therapeutic intervention. Psychological, behavioral, and psychopharmacologic interventions tailored to each child's presentation can provide symptom improvement and improve functioning during both the acute and chronic stages of illness. In general, typical evidence-based interventions are appropriate for the varied symptoms of PANS and PANDAS. Individual differences in expected response to psychotropic medication may require marked reduction of initial treatment dose. Antimicrobials and immunomodulatory therapies may be indicated, as discussed in Parts 2 and 3 of this guideline series. PMID:28722481

Enhancing the development and approval of acute stroke therapies: Stroke Therapy Academic Industry roundtable.

PubMed

Fisher, Marc; Albers, Gregory W; Donnan, Geoffrey A; Furlan, Anthony J; Grotta, James C; Kidwell, Chelsea S; Sacco, Ralph L; Wechsler, Lawrence R

2005-08-01

Previous Stroke Therapy Academic Industry Roundtable (STAIR) meetings focused on preclinical evidence of drug efficacy and enhancing acute stroke trial design and performance. A fourth (STAIR-IV) was held to discuss relevant issues related to acute stroke drug development and regulatory approval. The STAIR-IV meeting had 3 main focus areas. The first topic was novel approaches to statistical design of acute stroke trials and appropriate outcome measures. The second focus was the need for better cooperation among participants in stroke therapy development that may be addressed through a national consortium of stroke trial centers in the United States and elsewhere. Lastly, regulatory issues related to the approval of novel mono and multiple acute stroke therapies were discussed. The development of additional acute stroke therapies represents a large unmet need with many remaining challenges and also opportunities to incorporate novel approaches to clinical trial design that will lead to regulatory approval. The STAIR-IV meeting explored new concepts of trial methodology and data analysis, initiatives for implementing a US clinical trialist consortium, and pertinent regulatory issues to expedite approval of novel therapies.

[Quality management and participation into clinical database].

PubMed

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.

PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome

PubMed Central

Sarika; Arora, Vasu; Iquebal, M. A.; Rai, Anil; Kumar, Dinesh

2013-01-01

Molecular markers play a significant role for crop improvement in desirable characteristics, such as high yield, resistance to disease and others that will benefit the crop in long term. Pigeonpea (Cajanus cajan L.) is the recently sequenced legume by global consortium led by ICRISAT (Hyderabad, India) and been analysed for gene prediction, synteny maps, markers, etc. We present PIgeonPEa Microsatellite DataBase (PIPEMicroDB) with an automated primer designing tool for pigeonpea genome, based on chromosome wise as well as location wise search of primers. Total of 123 387 Short Tandem Repeats (STRs) were extracted from pigeonpea genome, available in public domain using MIcroSAtellite tool (MISA). The database is an online relational database based on ‘three-tier architecture’ that catalogues information of microsatellites in MySQL and user-friendly interface is developed using PHP. Search for STRs may be customized by limiting their location on chromosome as well as number of markers in that range. This is a novel approach and is not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of selected markers with left and right flankings of size up to 500 bp. This will enable researchers to select markers of choice at desired interval over the chromosome. Furthermore, one can use individual STRs of a targeted region over chromosome to narrow down location of gene of interest or linked Quantitative Trait Loci (QTLs). Although it is an in silico approach, markers’ search based on characteristics and location of STRs is expected to be beneficial for researchers. Database URL: http://cabindb.iasri.res.in/pigeonpea/ PMID:23396298

PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome.

PubMed

Sarika; Arora, Vasu; Iquebal, M A; Rai, Anil; Kumar, Dinesh

2013-01-01

Molecular markers play a significant role for crop improvement in desirable characteristics, such as high yield, resistance to disease and others that will benefit the crop in long term. Pigeonpea (Cajanus cajan L.) is the recently sequenced legume by global consortium led by ICRISAT (Hyderabad, India) and been analysed for gene prediction, synteny maps, markers, etc. We present PIgeonPEa Microsatellite DataBase (PIPEMicroDB) with an automated primer designing tool for pigeonpea genome, based on chromosome wise as well as location wise search of primers. Total of 123 387 Short Tandem Repeats (STRs) were extracted from pigeonpea genome, available in public domain using MIcroSAtellite tool (MISA). The database is an online relational database based on 'three-tier architecture' that catalogues information of microsatellites in MySQL and user-friendly interface is developed using PHP. Search for STRs may be customized by limiting their location on chromosome as well as number of markers in that range. This is a novel approach and is not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of selected markers with left and right flankings of size up to 500 bp. This will enable researchers to select markers of choice at desired interval over the chromosome. Furthermore, one can use individual STRs of a targeted region over chromosome to narrow down location of gene of interest or linked Quantitative Trait Loci (QTLs). Although it is an in silico approach, markers' search based on characteristics and location of STRs is expected to be beneficial for researchers. Database URL: http://cabindb.iasri.res.in/pigeonpea/

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

PubMed

Katayama, Toshiaki; Arakawa, Kazuharu; Nakao, Mitsuteru; Ono, Keiichiro; Aoki-Kinoshita, Kiyoko F; Yamamoto, Yasunori; Yamaguchi, Atsuko; Kawashima, Shuichi; Chun, Hong-Woo; Aerts, Jan; Aranda, Bruno; Barboza, Lord Hendrix; Bonnal, Raoul Jp; Bruskiewich, Richard; Bryne, Jan C; Fernández, José M; Funahashi, Akira; Gordon, Paul Mk; Goto, Naohisa; Groscurth, Andreas; Gutteridge, Alex; Holland, Richard; Kano, Yoshinobu; Kawas, Edward A; Kerhornou, Arnaud; Kibukawa, Eri; Kinjo, Akira R; Kuhn, Michael; Lapp, Hilmar; Lehvaslaiho, Heikki; Nakamura, Hiroyuki; Nakamura, Yasukazu; Nishizawa, Tatsuya; Nobata, Chikashi; Noguchi, Tamotsu; Oinn, Thomas M; Okamoto, Shinobu; Owen, Stuart; Pafilis, Evangelos; Pocock, Matthew; Prins, Pjotr; Ranzinger, René; Reisinger, Florian; Salwinski, Lukasz; Schreiber, Mark; Senger, Martin; Shigemoto, Yasumasa; Standley, Daron M; Sugawara, Hideaki; Tashiro, Toshiyuki; Trelles, Oswaldo; Vos, Rutger A; Wilkinson, Mark D; York, William; Zmasek, Christian M; Asai, Kiyoshi; Takagi, Toshihisa

2010-08-21

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

PubMed Central

2010-01-01

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies. PMID:20727200

Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population.

PubMed

Lee, Sangmoon; Seo, Jihae; Park, Jinman; Nam, Jae-Yong; Choi, Ahyoung; Ignatius, Jason S; Bjornson, Robert D; Chae, Jong-Hee; Jang, In-Jin; Lee, Sanghyuk; Park, Woong-Yang; Baek, Daehyun; Choi, Murim

2017-06-27

Despite efforts to interrogate human genome variation through large-scale databases, systematic preference toward populations of Caucasian descendants has resulted in unintended reduction of power in studying non-Caucasians. Here we report a compilation of coding variants from 1,055 healthy Korean individuals (KOVA; Korean Variant Archive). The samples were sequenced to a mean depth of 75x, yielding 101 singleton variants per individual. Population genetics analysis demonstrates that the Korean population is a distinct ethnic group comparable to other discrete ethnic groups in Africa and Europe, providing a rationale for such independent genomic datasets. Indeed, KOVA conferred 22.8% increased variant filtering power in addition to Exome Aggregation Consortium (ExAC) when used on Korean exomes. Functional assessment of nonsynonymous variant supported the presence of purifying selection in Koreans. Analysis of copy number variants detected 5.2 deletions and 10.3 amplifications per individual with an increased fraction of novel variants among smaller and rarer copy number variable segments. We also report a list of germline variants that are associated with increased tumor susceptibility. This catalog can function as a critical addition to the pre-existing variant databases in pursuing genetic studies of Korean individuals.

Earth science big data at users' fingertips: the EarthServer Science Gateway Mobile

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Fargetta, Marco; Pappalardo, Marco; Rundo, Francesco

2014-05-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. In this contribution we will report on the EarthServer Science Gateway Mobile, an app for both iOS and Android-based devices that allows users to seamlessly access some of the EarthServer applications using SAML-based federated authentication and fine-grained authorisation mechanisms.

The "North German Tumor Bank of Colorectal Cancer": status report after the first 2 years of support by the German Cancer Aid Foundation.

PubMed

Oberländer, Martina; Linnebacher, Michael; König, Alexandra; Bogoevska, Valentina; Brodersen, Christiane; Kaatz, Regina; Krohn, Mathias; Hackmann, Michael; Ingenerf, Josef; Christoph, Jan; Mate, Sebastian; Prokosch, Hans-Ulrich; Yekebas, Emre F; Thorns, Christoph; Büning, Jürgen; Prall, Friedrich; Uhlig, Ria; Roblick, Uwe J; Izbicki, Jakob R; Klar, Ernst; Bruch, Hans-Peter; Vollmar, Brigitte; Habermann, Jens K

2013-02-01

Research projects and clinical trials strongly rely on high-quality biospecimens which are provided by biobanks. Since differences in sample processing and storage can strongly affect the outcome of such studies, standardization between biobanks is necessary to guarantee reliable results of large, multicenter studies. The German Cancer Aid Foundation (Deutsche Krebshilfe e.V.) has therefore initiated the priority program "tumor tissue banks" in 2010 by funding four biobank networks focusing on central nervous system tumors, melanomas, breast carcinomas, and colorectal carcinomas. The latter one, the North German Tumor Bank of Colorectal Cancer (ColoNet) is managed by surgeons, pathologists, gastroenterologists, oncologists, scientists, and medical computer scientists. The ColoNet consortium has developed and harmonized standard operating procedures concerning all biobanking aspects. Crucial steps for quality assurance have been implemented and resulted in certification according to DIN EN ISO 9001. A further achievement is the construction of a web-based database for exploring available samples. In addition, common scientific projects have been initiated. Thus, ColoNet's repository will be used for research projects in order to improve early diagnosis, therapy, follow-up, and prognosis of colorectal cancer patients. Apart from the routine sample storage at -170 °C, the tumor banks' unique characteristic is the participation of outpatient clinics and private practices to further expand the sample and clinical data collection. The first 2 years of funding by the German Cancer Aid Foundation have already led to a closer scientific connection between the participating institutions and to a substantial collection of biospecimens obtained under highly standardized conditions.

Genetic predictors of response to serotonergic and noradrenergic antidepressants in major depressive disorder: a genome-wide analysis of individual-level data and a meta-analysis.

PubMed

Tansey, Katherine E; Guipponi, Michel; Perroud, Nader; Bondolfi, Guido; Domenici, Enrico; Evans, David; Hall, Stephanie K; Hauser, Joanna; Henigsberg, Neven; Hu, Xiaolan; Jerman, Borut; Maier, Wolfgang; Mors, Ole; O'Donovan, Michael; Peters, Tim J; Placentino, Anna; Rietschel, Marcella; Souery, Daniel; Aitchison, Katherine J; Craig, Ian; Farmer, Anne; Wendland, Jens R; Malafosse, Alain; Holmans, Peter; Lewis, Glyn; Lewis, Cathryn M; Stensbøl, Tine Bryan; Kapur, Shitij; McGuffin, Peter; Uher, Rudolf

2012-01-01

It has been suggested that outcomes of antidepressant treatment for major depressive disorder could be significantly improved if treatment choice is informed by genetic data. This study aims to test the hypothesis that common genetic variants can predict response to antidepressants in a clinically meaningful way. The NEWMEDS consortium, an academia-industry partnership, assembled a database of over 2,000 European-ancestry individuals with major depressive disorder, prospectively measured treatment outcomes with serotonin reuptake inhibiting or noradrenaline reuptake inhibiting antidepressants and available genetic samples from five studies (three randomized controlled trials, one part-randomized controlled trial, and one treatment cohort study). After quality control, a dataset of 1,790 individuals with high-quality genome-wide genotyping provided adequate power to test the hypotheses that antidepressant response or a clinically significant differential response to the two classes of antidepressants could be predicted from a single common genetic polymorphism. None of the more than half million genetic markers significantly predicted response to antidepressants overall, serotonin reuptake inhibitors, or noradrenaline reuptake inhibitors, or differential response to the two types of antidepressants (genome-wide significance p<5×10(-8)). No biological pathways were significantly overrepresented in the results. No significant associations (genome-wide significance p<5×10(-8)) were detected in a meta-analysis of NEWMEDS and another large sample (STAR*D), with 2,897 individuals in total. Polygenic scoring found no convergence among multiple associations in NEWMEDS and STAR*D. No single common genetic variant was associated with antidepressant response at a clinically relevant level in a European-ancestry cohort. Effects specific to particular antidepressant drugs could not be investigated in the current study. Please see later in the article for the Editors' Summary.

Separate may not be equal: A preliminary investigation of clinical correlates of electronic psychiatric record accessibility in academic medical centers

PubMed Central

Kozubal, Dana E.; Samus, Quincy M.; Bakare, Aishat A.; Trecker, Carrilin C.; Wong, Hei-Wah; Guo, Huiying; Cheng, Jeffrey; Allen, Paul X.; Mayer, Lawrence S.; Jamison, Kay R.; Kaplin, Adam I.

2014-01-01

Objectives Electronic Medical Records (EMR) have the potential to improve the coordination of healthcare in this country, yet the field of psychiatry has lagged behind other medical disciplines in its adoption of EMR. Methods Psychiatrists at 18 of the top US hospitals completed an electronic survey detailing whether their psychiatric records were stored electronically and accessible to non-psychiatric physicians. Electronic hospital records and accessibility statuses were correlated with patient care outcomes obtained from the University Health System Consortium Clinical Database available for 13 of the 18 top US hospitals. Results 44% of hospitals surveyed maintained most or all of their psychiatric records electronically and 28% made psychiatric records accessible to non-psychiatric physicians; only 22% did both. Compared with hospitals where psychiatric records were not stored electronically, the average 7-day readmission rate of psychiatric patients was significantly lower at hospitals with psychiatric EMR (5.1% vs. 7.0%, p = .040). Similarly, the 14 and 30-day readmission rates at hospitals where psychiatric records were accessible to non-psychiatric physicians were lower than those of their counterparts with non-accessible records (5.8% vs. 9.5%, p = .019, 8.6% vs. 13.6%, p = .013, respectively). The 7, 14, and 30-day readmission rates were significantly lower in hospitals where psychiatric records were both stored electronically and made accessible than at hospitals where records were either not electronic or not accessible (4% vs 6.6%, 5.8% vs 9.1%, 8.9 vs 13%, respectively, all with p = 0.045). Conclusions Having psychiatric EMR that were accessible to non-psychiatric physicians correlated with improved clinical care as measured by lower readmission rates specific for psychiatric patients. PMID:23266060

BRCA1/2 missense mutations and the value of in-silico analyses.

PubMed

Sadowski, Carolin E; Kohlstedt, Daniela; Meisel, Cornelia; Keller, Katja; Becker, Kerstin; Mackenroth, Luisa; Rump, Andreas; Schröck, Evelin; Wimberger, Pauline; Kast, Karin

2017-11-01

The clinical implications of genetic variants in BRCA1/2 in healthy and affected individuals are considerable. Variant interpretation, however, is especially challenging for missense variants. The majority of them are classified as variants of unknown clinical significance (VUS). Computational (in-silico) predictive programs are easy to access, but represent only one tool out of a wide range of complemental approaches to classify VUS. With this single-center study, we aimed to evaluate the impact of in-silico analyses in a spectrum of different BRCA1/2 missense variants. We conducted mutation analysis of BRCA1/2 in 523 index patients with suspected hereditary breast and ovarian cancer (HBOC). Classification of the genetic variants was performed according to the German Consortium (GC)-HBOC database. Additionally, all missense variants were classified by the following three in-silico prediction tools: SIFT, Mutation Taster (MT2) and PolyPhen2 (PPH2). Overall 201 different variants, 68 of which constituted missense variants were ranked as pathogenic, neutral, or unknown. The classification of missense variants by in-silico tools resulted in a higher amount of pathogenic mutations (25% vs. 13.2%) compared to the GC-HBOC-classification. Altogether, more than fifty percent (38/68, 55.9%) of missense variants were ranked differently. Sensitivity of in-silico-tools for mutation prediction was 88.9% (PPH2), 100% (SIFT) and 100% (MT2). We found a relevant discrepancy in variant classification by using in-silico prediction tools, resulting in potential overestimation and/or underestimation of cancer risk. More reliable, notably gene-specific, prediction tools and functional tests are needed to improve clinical counseling. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Models of interinstitutional partnerships between research intensive universities and minority serving institutions (MSI) across the Clinical Translational Science Award (CTSA) consortium.

PubMed

Ofili, Elizabeth O; Fair, Alecia; Norris, Keith; Verbalis, Joseph G; Poland, Russell; Bernard, Gordon; Stephens, David S; Dubinett, Steven M; Imperato-McGinley, Julianne; Dottin, Robert P; Pulley, Jill; West, Andrew; Brown, Arleen; Mellman, Thomas A

2013-12-01

Health disparities are an immense challenge to American society. Clinical and Translational Science Awards (CTSAs) housed within the National Center for Advancing Translational Science (NCATS) are designed to accelerate the translation of experimental findings into clinically meaningful practices and bring new therapies to the doorsteps of all patients. Research Centers at Minority Institutions (RCMI) program at the National Institute on Minority Health and Health Disparities (NIMHD) are designed to build capacity for biomedical research and training at minority serving institutions. The CTSA created a mechanism fostering formal collaborations between research intensive universities and minority serving institutions (MSI) supported by the RCMI program. These consortium-level collaborations activate unique translational research approaches to reduce health disparities with credence to each academic institutions history and unique characteristics. Five formal partnerships between research intensive universities and MSI have formed as a result of the CTSA and RCMI programs. These partnerships present a multifocal approach; shifting cultural change and consciousness toward addressing health disparities, and training the next generation of minority scientists. This collaborative model is based on the respective strengths and contributions of the partnering institutions, allowing bidirectional interchange and leveraging NIH and institutional investments providing measurable benchmarks toward the elimination of health disparities. © 2013 Wiley Periodicals, Inc.

The time is now for a new approach to primary ovarian insufficiency

PubMed Central

Cooper, Amber R.; Baker, Valerie L.; Sterling, Evelina W.; Ryan, Mary E.; Woodruff, Teresa K.; Nelson, Lawrence M.

2010-01-01

Objective To articulate the need for a new approach to primary ovarian insufficiency. The condition, also known as premature menopause or premature ovarian failure, is defined by the presence of menopausal-level serum gonad otropins in association with irregular menses in adolescent girls or women younger than 40 years. It can be iatrogenic as related to cancer therapy or may arise spontaneously, either alone or as part of a host of ultrarare syndromes. In a large percentage of spontaneous cases no pathogenic mechanism can be identified. Design Literature review and consensus building at a multidisciplinary scientific workshop. Conclusion(s) There are major gaps in knowledge regarding the etiologic mechanisms, psychosocial effects, natural history, and medical and psychosocial management of primary ovarian insufficiency. An international research consortium and disease registry formed under the guidance of an umbrella organization would provide a pathway to comprehensively increase basic and clinical knowledge about the condition. Such a consortium and patient registry also would provide clinical samples and clinical data with a goal toward defining the specific pathogenic mechanisms. An international collaborative approach that combines the structure of a patient registry with the principles of integrative care and community-based participatory research is needed to advance the field of primary ovarian insufficiency. PMID:20188353

LungMAP: The Molecular Atlas of Lung Development Program.

PubMed

Ardini-Poleske, Maryanne E; Clark, Robert F; Ansong, Charles; Carson, James P; Corley, Richard A; Deutsch, Gail H; Hagood, James S; Kaminski, Naftali; Mariani, Thomas J; Potter, Steven S; Pryhuber, Gloria S; Warburton, David; Whitsett, Jeffrey A; Palmer, Scott M; Ambalavanan, Namasivayam

2017-11-01

The National Heart, Lung, and Blood Institute is funding an effort to create a molecular atlas of the developing lung (LungMAP) to serve as a research resource and public education tool. The lung is a complex organ with lengthy development time driven by interactive gene networks and dynamic cross talk among multiple cell types to control and coordinate lineage specification, cell proliferation, differentiation, migration, morphogenesis, and injury repair. A better understanding of the processes that regulate lung development, particularly alveologenesis, will have a significant impact on survival rates for premature infants born with incomplete lung development and will facilitate lung injury repair and regeneration in adults. A consortium of four research centers, a data coordinating center, and a human tissue repository provides high-quality molecular data of developing human and mouse lungs. LungMAP includes mouse and human data for cross correlation of developmental processes across species. LungMAP is generating foundational data and analysis, creating a web portal for presentation of results and public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology that incorporates the latest findings of the consortium. The LungMAP website (www.lungmap.net) currently contains more than 6,000 high-resolution lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers for young audiences. This paper presents a brief description of research conducted by the consortium, database, and portal development and upcoming features that will enhance the LungMAP experience for a community of users. Copyright © 2017 the American Physiological Society.

"Watching the Detectives" report of the general assembly of the EU project DETECTIVE Brussels, 24-25 November 2015.

PubMed

Fernando, Ruani N; Chaudhari, Umesh; Escher, Sylvia E; Hengstler, Jan G; Hescheler, Jürgen; Jennings, Paul; Keun, Hector C; Kleinjans, Jos C S; Kolde, Raivo; Kollipara, Laxmikanth; Kopp-Schneider, Annette; Limonciel, Alice; Nemade, Harshal; Nguemo, Filomain; Peterson, Hedi; Prieto, Pilar; Rodrigues, Robim M; Sachinidis, Agapios; Schäfer, Christoph; Sickmann, Albert; Spitkovsky, Dimitry; Stöber, Regina; van Breda, Simone G J; van de Water, Bob; Vivier, Manon; Zahedi, René P; Vinken, Mathieu; Rogiers, Vera

2016-06-01

SEURAT-1 is a joint research initiative between the European Commission and Cosmetics Europe aiming to develop in vitro- and in silico-based methods to replace the in vivo repeated dose systemic toxicity test used for the assessment of human safety. As one of the building blocks of SEURAT-1, the DETECTIVE project focused on a key element on which in vitro toxicity testing relies: the development of robust and reliable, sensitive and specific in vitro biomarkers and surrogate endpoints that can be used for safety assessments of chronically acting toxicants, relevant for humans. The work conducted by the DETECTIVE consortium partners has established a screening pipeline of functional and "-omics" technologies, including high-content and high-throughput screening platforms, to develop and investigate human biomarkers for repeated dose toxicity in cellular in vitro models. Identification and statistical selection of highly predictive biomarkers in a pathway- and evidence-based approach constitute a major step in an integrated approach towards the replacement of animal testing in human safety assessment. To discuss the final outcomes and achievements of the consortium, a meeting was organized in Brussels. This meeting brought together data-producing and supporting consortium partners. The presentations focused on the current state of ongoing and concluding projects and the strategies employed to identify new relevant biomarkers of toxicity. The outcomes and deliverables, including the dissemination of results in data-rich "-omics" databases, were discussed as were the future perspectives of the work completed under the DETECTIVE project. Although some projects were still in progress and required continued data analysis, this report summarizes the presentations, discussions and the outcomes of the project.

“Watching the Detectives” Report of the general assembly of the EU project DETECTIVE Brussels, 24-25 November, 2015

PubMed Central

Fernando, Ruani N.; Chaudhari, Umesh; Escher, Sylvia E.; Hengstler, Jan G.; Hescheler, Jürgen; Jennings, Paul; Keun, Hector C.; Kleinjans, Jos C. S.; Kolde, Raivo; Kollipara, Laxmikanth; Kopp-Schneider, Annette; Limonciel, Alice; Nemade, Harshal; Nguemo, Filomain; Peterson, Hedi; Prieto, Pilar; Rodrigues, Robim M.; Sachinidis, Agapios; Schäfer, Christoph; Sickmann, Albert; Spitkovsky, Dimitry; Stöber, Regina; van Breda, Simone G.J.; van de Water, Bob; Vivier, Manon; Zahedi, René P.

2017-01-01

SEURAT-1 is a joint research initiative between the European Commission and Cosmetics Europe aiming to develop in vitro and in silico based methods to replace the in vivo repeated dose systemic toxicity test used for the assessment of human safety. As one of the building blocks of SEURAT-1, the DETECTIVE project focused on a key element on which in vitro toxicity testing relies: the development of robust and reliable, sensitive and specific in vitro biomarkers and surrogate endpoints that can be used for safety assessments of chronically acting toxicants, relevant for humans. The work conducted by the DETECTIVE consortium partners has established a screening pipeline of functional and “-omics” technologies, including high-content and high-throughput screening platforms, to develop and investigate human biomarkers for repeated dose toxicity in cellular in vitro models. Identification and statistical selection of highly predictive biomarkers in a pathway- and evidence-based approach constitutes a major step in an integrated approach towards the replacement of animal testing in human safety assessment. To discuss the final outcomes and achievements of the consortium, a meeting was organized in Brussels. This meeting brought together data-producing and supporting consortium partners. The presentations focused on the current state of ongoing and concluding projects and the strategies employed to identify new relevant biomarkers of toxicity. The outcomes and deliverables, including the dissemination of results in data-rich “-omics” databases, were discussed as were the future perspectives of the work completed under the DETECTIVE project. Although some projects were still in progress and required continued data analysis, this report summarizes the presentations, discussions and the outcomes of the project. PMID:27129694

Clinical decision support tools: performance of personal digital assistant versus online drug information databases.

PubMed

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.

Medical research at the Albert Schweitzer Hospital.

PubMed

Issifou, Saadou; Adegnika, Ayola A; Lell, Bertrand

2010-03-01

Built in 1981, the Medical Research Unit is located at the campus of the Albert Schweitzer Hospital. The main scientific activities of this research unit lie on clinical research focusing on antimalarial drugs and vaccines, and basic studies on pathogenesis of infectious diseases. Since 2002 the Medical Research Unit has experience in organising and hosting high quality training in clinical research in collaboration with the Vienna School of Clinical Research and other partners. For the future, this unit is involved as a key partner in the Central African Network on Tuberculosis, HIV/AIDS and Malaria (CANTAM) consortium playing a central role for the excellence in clinical research in Central Africa.

A systematic review of administrative and clinical databases of infants admitted to neonatal units.

PubMed

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/.

Charting a Roadmap for Heart Failure Biomarker Studies

PubMed Central

Ahmad, Tariq; Fiuzat, Mona; Pencina, Michael J.; Geller, Nancy L.; Zannad, Faiez; Cleland, John G. F.; Snider, James V.; Blankenberg, Stephan; Adams, Kirkwood F.; Redberg, Rita F.; Kim, Jae B.; Mascette, Alice; Mentz, Robert J.; O'Connor, Christopher M.; Felker, G. Michael; Januzzi, James L.

2014-01-01

Heart failure is a syndrome with a pathophysiological basis that can be traced to dysfunction in several interconnected molecular pathways. Identification of biomarkers of heart failure that allow measurement of the disease on a molecular level has resulted in enthusiasm for their use in prognostication and selection of appropriate therapies. However, despite considerable amounts of information available on numerous biomarkers, inconsistent research methodologies and lack of clinical correlations have made bench-to-bedside translations rare and left the literature with countless publications of varied quality. There is a need for a systematic and collaborative approach aimed at definitively studying the clinical benefits of novel biomarkers. In this review, on the basis of input from academia, industry, and governmental agencies, we propose a systematized approach based on adherence to specific quality measures for studies looking to augment current prediction model or use biomarkers to tailor therapeutics. We suggest that study quality, rather than results, should determine publication and propose a system for grading biomarker studies. We outline the need for collaboration between clinical investigators and statisticians to introduce more advanced statistical methodologies into the field of biomarkers that would allow for data from a large number of variables to be distilled into clinically actionable information. Lastly, we propose the creation of a heart failure biomarker consortium that would allow for a comprehensive list of biomarkers to be concomitantly analyzed in a pooled sample of randomized clinical trials and hypotheses to be generated for testing in biomarker-guided trials. Such a consortium could collaborate in sharing samples to identify biomarkers, undertake meta- analyses on completed trials, and spearhead clinical trials to test the clinical utility of new biomarkers. PMID:24929535

Best Performers Announced for the NCI-CPTAC DREAM Proteogenomics Computational Challenge | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) is pleased to announce that teams led by Jaewoo Kang (Korea University), and Yuanfang Guan with Hongyang Li (University of Michigan) as the best performers of the NCI-CPTAC DREAM Proteogenomics Computational Challenge. Over 500 participants from 20 countries registered for the Challenge, which offered $25,000 in cash awards contributed by the NVIDIA Foundation through its Compute the Cure initiative.

CPTAC Team Releases Targeted Proteomic Assays for Ovarian Cancer | Office of Cancer Clinical Proteomics Research

Cancer.gov

Pacific Northwest National Laboratory (PNNL) investigators in the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI), announces the public release of 98 targeted mass spectrometry-based assays for ovarian cancer research studies.  Chosen based on proteogenomic observations from the recently published multi-institutional collaborative project between PNNL and Johns Hopkins University that comprehensively examined the collections of proteins in the tumors of ovarian cancer patients (highlighted in a paper in

CPTAC Collaborates with Molecular & Cellular Proteomics to Address Reproducibility in Targeted Assay Development | Office of Cancer Clinical Proteomics Research

Cancer.gov

The journal Molecular & Cellular Proteomics (MCP), in collaboration with the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI), part of the National Institutes of Health, announce new guidelines and requirements for papers describing the development and application of targeted mass spectrometry measurements of peptides, modified peptides and proteins (Mol Cell Proteomics 2017; PMID: 28183812).  NCI’s participation is part of NIH’s overall effort to address the r

Announcing the Launch of CPTAC’s Proteogenomics DREAM Challenge | Office of Cancer Clinical Proteomics Research

Cancer.gov

This week, we are excited to announce the launch of the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) Proteogenomics Computational DREAM Challenge.  The aim of this Challenge is to encourage the generation of computational methods for extracting information from the cancer proteome and for linking those data to genomic and transcriptomic information.  The specific goals are to predict proteomic and phosphoproteomic data from other multiple data types including transcriptomics and genetics.

International network of cancer genome projects

PubMed Central

2010-01-01

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumors from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of over 25,000 cancer genomes at the genomic, epigenomic, and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically-relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies. PMID:20393554

NCI Releases Video: Proteogenomics Research - On the Frontier of Precision Medicine | Office of Cancer Clinical Proteomics Research

Cancer.gov

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI), part of the National Institutes of Health, announces the release of an educational video titled “Proteogenomics Research: On the Frontier of Precision Medicine."  Launched at the HUPO2017 Global Leadership Gala Dinner, catalyzed in part by the Cancer Moonshot initiative and featuring as keynote speaker the 47th Vice President of the United States of America Joseph R.

CPTAC Releases Cancer Proteome Confirmatory Breast Study Data | Office of Cancer Clinical Proteomics Research

Cancer.gov

An estimated 252,710 new cases of female breast cancer, accounting for 15% of all new cancer cases, occurred in 2017. To better understand proteogenomic abnormalities in breast cancer, the National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) announces the release of the cancer proteome confirmatory breast study data. The goal of the study was to comprehensively characterize the proteome and phosphoproteome on approximately 100 prospectively collected breast tumor and adjacent normal tissues.

CPTAC Investigators Discuss Research Insights and Perspectives as part of ASBMB Journal Club - 12 Nov | Office of Cancer Clinical Proteomics Research

Cancer.gov

On Wednesday, November 12, 2014 from 2:00 PM to 3:00 PM EST, Daniel Liebler, PhD (Vanderbilt University) and Karin Rodland, PhD (Pacific Northwestern National Laboratory) and Ruedi Aebersold, PhD (Swiss Federal Institute of Technology) will share their research insight as part of the ASBMB Journal Club.  Both Doctors Liebler and Rodland are Principal Investigators in the NCI’s Clinical Proteomic Tumor Analysis Consortium.

A dynamic clinical dental relational database.

PubMed

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.

Correlation coefficient based supervised locally linear embedding for pulmonary nodule recognition.

PubMed

Wu, Panpan; Xia, Kewen; Yu, Hengyong

2016-11-01

Dimensionality reduction techniques are developed to suppress the negative effects of high dimensional feature space of lung CT images on classification performance in computer aided detection (CAD) systems for pulmonary nodule detection. An improved supervised locally linear embedding (SLLE) algorithm is proposed based on the concept of correlation coefficient. The Spearman's rank correlation coefficient is introduced to adjust the distance metric in the SLLE algorithm to ensure that more suitable neighborhood points could be identified, and thus to enhance the discriminating power of embedded data. The proposed Spearman's rank correlation coefficient based SLLE (SC(2)SLLE) is implemented and validated in our pilot CAD system using a clinical dataset collected from the publicly available lung image database consortium and image database resource initiative (LICD-IDRI). Particularly, a representative CAD system for solitary pulmonary nodule detection is designed and implemented. After a sequential medical image processing steps, 64 nodules and 140 non-nodules are extracted, and 34 representative features are calculated. The SC(2)SLLE, as well as SLLE and LLE algorithm, are applied to reduce the dimensionality. Several quantitative measurements are also used to evaluate and compare the performances. Using a 5-fold cross-validation methodology, the proposed algorithm achieves 87.65% accuracy, 79.23% sensitivity, 91.43% specificity, and 8.57% false positive rate, on average. Experimental results indicate that the proposed algorithm outperforms the original locally linear embedding and SLLE coupled with the support vector machine (SVM) classifier. Based on the preliminary results from a limited number of nodules in our dataset, this study demonstrates the great potential to improve the performance of a CAD system for nodule detection using the proposed SC(2)SLLE. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships.

PubMed

Kalman, Lisa V; Datta, Vivekananda; Williams, Mickey; Zook, Justin M; Salit, Marc L; Han, Jin Yeong

2016-11-01

Characterized reference materials (RMs) are needed for clinical laboratory test development and validation, quality control procedures, and proficiency testing to assure their quality. In this article, we review the development and characterization of RMs for clinical molecular genetic tests. We describe various types of RMs and how to access and utilize them, especially focusing on the Genetic Testing Reference Materials Coordination Program (Get-RM) and the Genome in a Bottle (GIAB) Consortium. This review also reinforces the need for collaborative efforts in the clinical genetic testing community to develop additional RMs.

Public variant databases: liability?

PubMed

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.

Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

PubMed

de Sousa Costa, Robherson Wector; da Silva, Giovanni Lucca França; de Carvalho Filho, Antonio Oseas; Silva, Aristófanes Corrêa; de Paiva, Anselmo Cardoso; Gattass, Marcelo

2018-05-23

Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

Fuzzy Clustering Applied to ROI Detection in Helical Thoracic CT Scans with a New Proposal and Variants

PubMed Central

Castro, Alfonso; Boveda, Carmen; Arcay, Bernardino; Sanjurjo, Pedro

2016-01-01

The detection of pulmonary nodules is one of the most studied problems in the field of medical image analysis due to the great difficulty in the early detection of such nodules and their social impact. The traditional approach involves the development of a multistage CAD system capable of informing the radiologist of the presence or absence of nodules. One stage in such systems is the detection of ROI (regions of interest) that may be nodules in order to reduce the space of the problem. This paper evaluates fuzzy clustering algorithms that employ different classification strategies to achieve this goal. After characterising these algorithms, the authors propose a new algorithm and different variations to improve the results obtained initially. Finally it is shown as the most recent developments in fuzzy clustering are able to detect regions that may be nodules in CT studies. The algorithms were evaluated using helical thoracic CT scans obtained from the database of the LIDC (Lung Image Database Consortium). PMID:27517049

2016 update of the PRIDE database and its related tools

PubMed Central

Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi; Dianes, José A.; Griss, Johannes; Lavidas, Ilias; Mayer, Gerhard; Perez-Riverol, Yasset; Reisinger, Florian; Ternent, Tobias; Xu, Qing-Wei; Wang, Rui; Hermjakob, Henning

2016-01-01

The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development ‘PRIDE Cluster’ and ‘PRIDE Proteomes’, which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive. PMID:26527722

PanScan, the Pancreatic Cancer Cohort Consortium, and the Pancreatic Cancer Case-Control Consortium

Cancer.gov

The Pancreatic Cancer Cohort Consortium consists of more than a dozen prospective epidemiologic cohort studies within the NCI Cohort Consortium, whose leaders work together to investigate the etiology and natural history of pancreatic cancer.

Development of a relational database to capture and merge clinical history with the quantitative results of radionuclide renography.

PubMed

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.

Relationship between methanogenic archaea and subgingival microbial complexes in human periodontitis.

PubMed

Horz, H P; Robertz, N; Vianna, M E; Henne, K; Conrads, G

2015-10-01

We compared the amounts of methanogenic archaea with ten of the most important periodontal pathogens in 125 clinical samples. Correlation analysis suggests that the support of the periodontitis-associated bacterial consortium by methanogenic archaea may be driven through direct or indirect interactions with Prevotella intermedia. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Johns Hopkins RTR Consortium: A Collaborative Approach to Advance Translational Science and Standardize Clinical Monitoring of Restorative Transplantation

DTIC Science & Technology

2016-10-01

received non-myeloablative conditioning with 50cGy total body and 350cGy thymic irradiation for induction. Aim1: Group I was treated with high-dose...regimen of non-myeloablative irradiation and peritransplant tacrolimus. The long-term graft survival off of immunosuppression for animals treated

Public variant databases: liability?

PubMed Central

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

Northern New Jersey Nursing Education Consortium: a partnership for graduate nursing education.

PubMed

Quinless, F W; Levin, R F

1998-01-01

The purpose of this article is to describe the evolution and implementation of the Northern New Jersey Nursing Education consortium--a consortium of seven member institutions established in 1992. Details regarding the specific functions of the consortium relative to cross-registration of students in graduate courses, financial disbursement of revenue, faculty development activities, student services, library privileges, and institutional research review board mechanisms are described. The authors also review the administrative organizational structure through which the work conducted by the consortium occurs. Both the advantages and disadvantages of such a graduate consortium are explored, and specific examples of recent potential and real conflicts are fully discussed. The authors detail governance and structure of the consortium as a potential model for replication in other environments.

Standardizing Naming Conventions in Radiation Oncology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santanam, Lakshmi; Hurkmans, Coen; Mutic, Sasa

2012-07-15

Purpose: The aim of this study was to report on the development of a standardized target and organ-at-risk naming convention for use in radiation therapy and to present the nomenclature for structure naming for interinstitutional data sharing, clinical trial repositories, integrated multi-institutional collaborative databases, and quality control centers. This taxonomy should also enable improved plan benchmarking between clinical institutions and vendors and facilitation of automated treatment plan quality control. Materials and Methods: The Advanced Technology Consortium, Washington University in St. Louis, Radiation Therapy Oncology Group, Dutch Radiation Oncology Society, and the Clinical Trials RT QA Harmonization Group collaborated in creatingmore » this new naming convention. The International Commission on Radiation Units and Measurements guidelines have been used to create standardized nomenclature for target volumes (clinical target volume, internal target volume, planning target volume, etc.), organs at risk, and planning organ-at-risk volumes in radiation therapy. The nomenclature also includes rules for specifying laterality and margins for various structures. The naming rules distinguish tumor and nodal planning target volumes, with correspondence to their respective tumor/nodal clinical target volumes. It also provides rules for basic structure naming, as well as an option for more detailed names. Names of nonstandard structures used mainly for plan optimization or evaluation (rings, islands of dose avoidance, islands where additional dose is needed [dose painting]) are identified separately. Results: In addition to its use in 16 ongoing Radiation Therapy Oncology Group advanced technology clinical trial protocols and several new European Organization for Research and Treatment of Cancer protocols, a pilot version of this naming convention has been evaluated using patient data sets with varying treatment sites. All structures in these data sets were satisfactorily identified using this nomenclature. Conclusions: Use of standardized naming conventions is important to facilitate comparison of dosimetry across patient datasets. The guidelines presented here will facilitate international acceptance across a wide range of efforts, including groups organizing clinical trials, Radiation Oncology Institute, Dutch Radiation Oncology Society, Integrating the Healthcare Enterprise, Radiation Oncology domain (IHE-RO), and Digital Imaging and Communication in Medicine (DICOM).« less

How can the research potential of the clinical quality databases be maximized? The Danish experience.

PubMed

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.

Reporting discrepancies between the ClinicalTrials.gov results database and peer-reviewed publications.

PubMed

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.

How to catch all those mutations--the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010.

PubMed

Kohonen-Corish, Maija R J; Al-Aama, Jumana Y; Auerbach, Arleen D; Axton, Myles; Barash, Carol Isaacson; Bernstein, Inge; Béroud, Christophe; Burn, John; Cunningham, Fiona; Cutting, Garry R; den Dunnen, Johan T; Greenblatt, Marc S; Kaput, Jim; Katz, Michael; Lindblom, Annika; Macrae, Finlay; Maglott, Donna; Möslein, Gabriela; Povey, Sue; Ramesar, Raj; Richards, Sue; Seminara, Daniela; Sobrido, María-Jesús; Tavtigian, Sean; Taylor, Graham; Vihinen, Mauno; Winship, Ingrid; Cotton, Richard G H

2010-12-01

The third Human Variome Project (HVP) Meeting "Integration and Implementation" was held under UNESCO Patronage in Paris, France, at the UNESCO Headquarters May 10-14, 2010. The major aims of the HVP are the collection, curation, and distribution of all human genetic variation affecting health. The HVP has drawn together disparate groups, by country, gene of interest, and expertise, who are working for the common good with the shared goal of pushing the boundaries of the human variome and collaborating to avoid unnecessary duplication. The meeting addressed the 12 key areas that form the current framework of HVP activities: Ethics; Nomenclature and Standards; Publication, Credit and Incentives; Data Collection from Clinics; Overall Data Integration and Access-Peripheral Systems/Software; Data Collection from Laboratories; Assessment of Pathogenicity; Country Specific Collection; Translation to Healthcare and Personalized Medicine; Data Transfer, Databasing, and Curation; Overall Data Integration and Access-Central Systems; and Funding Mechanisms and Sustainability. In addition, three societies that support the goals and the mission of HVP also held their own Workshops with the view to advance disease-specific variation data collection and utilization: the International Society for Gastrointestinal Hereditary Tumours, the Micronutrient Genomics Project, and the Neurogenetics Consortium. © 2010 Wiley-Liss, Inc.

How to Catch All Those Mutations—The Report of the Third Human Variome Project Meeting, UNESCO Paris, May 2010

PubMed Central

Kohonen-Corish, Maija R.J.; Al-Aama, Jumana Y.; Auerbach, Arleen D.; Axton, Myles; Barash, Carol Isaacson; Bernstein, Inge; Béroud, Christophe; Burn, John; Cunningham, Fiona; Cutting, Garry R.; den Dunnen, Johan T.; Greenblatt, Marc S.; Kaput, Jim; Katz, Michael; Lindblom, Annika; Macrae, Finlay; Maglott, Donna; Möslein, Gabriela; Povey, Sue; Ramesar, Raj; Richards, Sue; Seminara, Daniela; Sobrido, María-Jesús; Tavtigian, Sean; Taylor, Graham; Vihinen, Mauno; Winship, Ingrid; Cotton, Richard G.H.

2011-01-01

The third Human Variome Project (HVP) Meeting “Integration and Implementation” was held under UNESCO Patronage in Paris, France, at the UNESCO Headquarters May 10–14, 2010. The major aims of the HVP are the collection, curation, and distribution of all human genetic variation affecting health. The HVP has drawn together disparate groups, by country, gene of interest, and expertise, who are working for the common good with the shared goal of pushing the boundaries of the human variome and collaborating to avoid unnecessary duplication. The meeting addressed the 12 key areas that form the current framework of HVP activities: Ethics; Nomenclature and Standards; Publication, Credit and Incentives; Data Collection from Clinics; Overall Data Integration and Access—Peripheral Systems/Software; Data Collection from Laboratories; Assessment of Pathogenicity; Country Specific Collection; Translation to Healthcare and Personalized Medicine; Data Transfer, Databasing, and Curation; Overall Data Integration and Access—Central Systems; and Funding Mechanisms and Sustainability. In addition, three societies that support the goals and the mission of HVP also held their own Workshops with the view to advance disease-specific variation data collection and utilization: the International Society for Gastrointestinal Hereditary Tumours, the Micronutrient Genomics Project, and the Neurogenetics Consortium. PMID:20960468

The Relationship Between Length of Stay and Readmissions in Bariatric Surgery Patients

PubMed Central

Lois, Alex W.; Frelich, Matthew J.; Sahr, Natasha A.; Hohmann, Samuel F.; Wang, Tao; Gould, Jon C.

2015-01-01

Background Hospital readmissions are a quality indicator in bariatric surgery. In recent years, length of stay following bariatric surgery has trended down significantly. We hypothesized that a shorter postoperative hospitalization does not increase the likelihood of readmission. Methods The University HealthSystem Consortium (UHC) is an alliance of academic medical centers and affiliated hospitals. The UHC’s clinical database contains information on inpatient stay and returns (readmissions) up to 30 days post-discharge. A multicenter analysis of outcomes was performed using data from the January 2009 to December 2013 for patients 18 years and older. Patients were identified by bariatric procedure ICD-9 codes and restricted by diagnosis codes for morbid obesity. Results A total of 95,294 patients met inclusion criteria. The mean patient age was 45.4 (±0.11) years and 73,941 (77.6%) subjects were female. There were 5,423 (5.7%) readmissions within the study period. Patients with hospitalizations of 3 days and more than 3 days were twice and four times as likely to be readmitted than those with hospitalizations of one day, respectively (p<0.001). Conclusions Patients with longer postoperative hospitalizations were more likely to be readmitted following bariatric surgery. Early discharge does not appear to be associated with increased readmission rates. PMID:26032831

Atopic Dermatitis and Comorbidities: Added Value of Comprehensive Dermatoepidemiology.

PubMed

Nijsten, Tamar

2017-05-01

Atopic dermatitis is common and in its severe form is devastating. This chronic inflammatory dermatosis is part of the atopic syndrome, which includes asthma, food allergies, and hay fever and is known to be associated with mental health disorders. In line with psoriasis, several recent observational studies using national survey and linkage data have suggested a link between atopic dermatitis and cardiovascular disease. The atopic dermatitis field can benefit from the past experiences in psoriasis research and should not follow the same path, but, rather, aim for a more comprehensive approach from the beginning. A recent German consortium studying links between atopic dermatitis and cardiovascular disease first screened a large claims database, followed by analyses of more deeply phenotyped (birth) cohorts with longitudinal data. In addition, genetic and metabolic analyses assessing the predisposition of patients with atopic dermatitis for cardiovascular disease were performed. Overall, the association between atopic dermatitis and cardiovascular disease was at most modest, but in more refined cohorts the cardiovascular risk profile and genetic architecture was comparable. A more integrated approach could create clarity about the clinical relevance of cardiovascular disease in individuals with atopic dermatitis sooner, avoid speculation that affects patient care, and save scientific resources. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

ClinicalTrials.gov

MedlinePlus

... 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 ...

10 CFR 603.515 - Qualification of a consortium.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS TECHNOLOGY INVESTMENT AGREEMENTS Pre-Award Business Evaluation Recipient Qualification § 603.515 Qualification of a consortium. (a) A consortium that... under the agreement. (b) If the prospective recipient of a TIA is a consortium that is not formally...

10 CFR 603.515 - Qualification of a consortium.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS TECHNOLOGY INVESTMENT AGREEMENTS Pre-Award Business Evaluation Recipient Qualification § 603.515 Qualification of a consortium. (a) A consortium that... under the agreement. (b) If the prospective recipient of a TIA is a consortium that is not formally...

10 CFR 603.515 - Qualification of a consortium.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Energy DEPARTMENT OF ENERGY (CONTINUED) ASSISTANCE REGULATIONS TECHNOLOGY INVESTMENT AGREEMENTS Pre-Award Business Evaluation Recipient Qualification § 603.515 Qualification of a consortium. (a) A consortium that... under the agreement. (b) If the prospective recipient of a TIA is a consortium that is not formally...

25 CFR 1000.33 - What amount of funding is to be removed from the Consortium's AFA for the withdrawing Tribe?

Code of Federal Regulations, 2010 CFR

2010-04-01

... Participation in Tribal Self-Governance Withdrawal from A Consortium Annual Funding Agreement § 1000.33 What... the Consortium agreement is reduced if: (1) The Consortium, Tribe, OSG, and bureau agree it is...

City officials planning to promote Norplant.

PubMed

Banisky, S

1992-12-03

The adolescent pregnancy rate in Baltimore, Maryland is 97/1000 15 to 17 years old females and one of the highest rates in the US. In fact, Baltimore has had a chronically high rate. The rate for Maryland is almost 3 times lower (35). Many adolescent mothers do not finish high school and are condemned to poverty. Thus, the Baltimore Health Commissioner has created the Baltimore City Norplant Consortium made up of hospitals, private physicians, and foundation officials. The Commissioner hopes to promote the 6 capsule subdermal implant which steadily releases a contraceptive. Norplant, to teenagers who either use contraceptives inconsistently or do not use them at all. Yet, this group is the hardest group to motivate so the Consortium is facing a real challenge. The Consortium plans on a Norplant advertising campaign and would like family life classes in city schools to discuss Norplant. It is advancing its goals carefully, however, because of possible criticism that it is coercing poor teenagers to accept Norplant. Teenagers have already been requesting Norplant from city clinics. If 5-10% of adolescents who use contraception irregularly would use Norplant, the adolescent pregnancy rate would decline significantly. In 1992, the Abell Foundation dedicated almost $200,000 to buying Norplant for women with no medical insurance to grant theses women the same option as other women, because capsules are expensive and physicians charge a higher fee to insert Norplant. Abell is funding an 11-minute educational videotape featuring women and men from Maryland who explain how Norplant has affected them. The video is to be shown in clinic waiting rooms. Presently 4000-5000 women in Baltimore have accepted Norplant. Nationwide 71% of Norplant users are less than 30 years old. It is important to provide adequate counseling for younger patients including possible side effects, e.g., irregular bleeding.

Association of polygenic risk score with the risk of chronic lymphocytic leukemia and monoclonal B-cell lymphocytosis.

PubMed

Kleinstern, Geffen; Camp, Nicola J; Goldin, Lynn R; Vachon, Celine M; Vajdic, Claire M; de Sanjose, Silvia; Weinberg, J Brice; Benavente, Yolanda; Casabonne, Delphine; Liebow, Mark; Nieters, Alexandra; Hjalgrim, Henrik; Melbye, Mads; Glimelius, Bengt; Adami, Hans-Olov; Boffetta, Paolo; Brennan, Paul; Maynadie, Marc; McKay, James; Cocco, Pier Luigi; Shanafelt, Tait D; Call, Timothy G; Norman, Aaron D; Hanson, Curtis; Robinson, Dennis; Chaffee, Kari G; Brooks-Wilson, Angela R; Monnereau, Alain; Clavel, Jacqueline; Glenn, Martha; Curtin, Karen; Conde, Lucia; Bracci, Paige M; Morton, Lindsay M; Cozen, Wendy; Severson, Richard K; Chanock, Stephen J; Spinelli, John J; Johnston, James B; Rothman, Nathaniel; Skibola, Christine F; Leis, Jose F; Kay, Neil E; Smedby, Karin E; Berndt, Sonja I; Cerhan, James R; Caporaso, Neil; Slager, Susan L

2018-06-07

Inherited loci have been found to be associated with risk of chronic lymphocytic leukemia (CLL). A combined polygenic risk score (PRS) of representative single nucleotide polymorphisms (SNPs) from these loci may improve risk prediction over individual SNPs. Herein, we evaluated the association of a PRS with CLL risk and its precursor, monoclonal B-cell lymphocytosis (MBL). We assessed its validity and discriminative ability in an independent sample and evaluated effect modification and confounding by family history (FH) of hematological cancers. For discovery, we pooled genotype data on 41 representative SNPs from 1499 CLL and 2459 controls from the InterLymph Consortium. For validation, we used data from 1267 controls from Mayo Clinic and 201 CLL, 95 MBL, and 144 controls with a FH of CLL from the Genetic Epidemiology of CLL Consortium. We used odds ratios (ORs) to estimate disease associations with PRS and c-statistics to assess discriminatory accuracy. In InterLymph, the continuous PRS was strongly associated with CLL risk (OR, 2.49; P = 4.4 × 10 -94 ). We replicated these findings in the Genetic Epidemiology of CLL Consortium and Mayo controls (OR, 3.02; P = 7.8 × 10 -30 ) and observed high discrimination (c-statistic = 0.78). When jointly modeled with FH, PRS retained its significance, along with FH status. Finally, we found a highly significant association of the continuous PRS with MBL risk (OR, 2.81; P = 9.8 × 10 -16 ). In conclusion, our validated PRS was strongly associated with CLL risk, adding information beyond FH. The PRS provides a means of identifying those individuals at greater risk for CLL as well as those at increased risk of MBL, a condition that has potential clinical impact beyond CLL.

Public health and clinical impact of increasing emergency department-based HIV testing: perspectives from the 2007 conference of the National Emergency Department HIV Testing Consortium.

PubMed

Kecojevic, Aleksandar; Lindsell, Christopher J; Lyons, Michael S; Holtgrave, David; Torres, Gretchen; Heffelfinger, James; Brown, Jeremy; Couture, Eileen; Jung, Julianna; Connell, Samantha; Rothman, Richard E

2011-07-01

Understanding perceived benefits and disadvantages of HIV testing in emergency departments (EDs) is imperative to overcoming barriers to implementation. We codify those domains of public health and clinical care most affected by implementing HIV testing in EDs, as determined by expert opinion. Opinions were systematically collected from attendees of the 2007 National ED HIV Testing Consortium meeting. Structured evaluation of strengths, weaknesses, opportunities, and threats analysis was conducted to assess the impact of ED-based HIV testing on public health. A modified Delphi method was used to assess the impact of ED-based HIV testing on clinical care from both individual patient and individual provider perspectives. Opinions were provided by 98 experts representing 42 academic and nonacademic institutions. Factors most frequently perceived to affect public health were (strengths) high volume of ED visits and high prevalence of HIV, (weaknesses) undue burden on EDs, (opportunities) reduction of HIV stigma, and (threats) lack of resources in EDs. Diagnostic testing and screening for HIV were considered to have a favorable impact on ED clinical care from both individual patient and individual provider perspectives; however, negative test results were not perceived to have any benefit from the provider's perspective. The need for HIV counseling in the ED was considered to have a negative impact on clinical care from the provider's perspective. Experts in ED-based HIV testing perceived expanded ED HIV testing to have beneficial impacts for both the public health and individual clinical care; however, limited resources were frequently cited as a possible impediment. Many issues must be resolved through further study, education, and policy changes if the full potential of HIV testing in EDs is to be realized. Copyright © 2011. Published by Mosby, Inc.

Acute White-Matter Abnormalities in Sports-Related Concussion: A Diffusion Tensor Imaging Study from the NCAA-DoD CARE Consortium.

PubMed

Mustafi, Sourajit Mitra; Harezlak, Jaroslaw; Koch, Kevin M; Nencka, Andrew S; Meier, Timothy; West, John D; Giza, Christopher C; DiFiori, John; Guskiewicz, Kevin K; Mihalik, Jason; LaConte, Stephen M; Duma, Stefan M; Broglio, Steven P; Saykin, Andrew J; McCrea, Michael; McAllister, Thomas; Wu, Yu-Chien

2017-10-25

Sport-related concussion (SRC) is an important public health issue. While standardized assessment tools are useful in the clinical management of acute concussion, the underlying pathophysiology of SRC and the time course of physiological recovery after injury remain unclear. In this study, we used diffusion tensor imaging (DTI) to detect white-matter alterations in football players within 48 hours after SRC. As part of the NCAA-DoD CARE Consortium study of SRC, 30 American football players diagnosed with acute concussion, and 28 matched controls received clinical assessments and underwent advanced MRI scans. To avoid selection bias and partial voluming effects, whole-brain skeletonized white matter was examined via tract-based spatial statistics (TBSS) to investigate between group differences in DTI metrics and their associations with clinical outcome measures. Mean diffusivity was significantly higher in the brain white matter of the concussed athletes, particularly in frontal and sub-frontal long white-matter tracts. While no DTI metric was associated to any clinical measure in the contact-sport controls, in the concussed group, DTI exhibited correlations with clinical measures. Axial diffusivity demonstrated a significant positive correlation with the Brief Symptom Inventory (BSI) and a trend for a positive correlation with the symptom severity score of the Sports Concussion Assessment Tool (SCAT). In addition, concussed athletes with higher fractional anisotropy performed worse on the cognitive component of the Standardized Assessment of Concussion (SAC). Overall, the results of this study are consistent with the hypothesis that SRC is associated with changes in white-matter tracts shortly after injury, and these differences are correlated clinically with acute symptoms and functional impairments.

Selection of and Evidentiary Considerations for Wearable Devices and Their Measurements for Use in Regulatory Decision Making: Recommendations from the ePRO Consortium.

PubMed

Byrom, Bill; Watson, Chris; Doll, Helen; Coons, Stephen Joel; Eremenco, Sonya; Ballinger, Rachel; Mc Carthy, Marie; Crescioni, Mabel; O'Donohoe, Paul; Howry, Cindy

2018-06-01

Wearable devices offer huge potential to collect rich sources of data to provide insights into the effects of treatment interventions. Despite this, at the time of writing this report, limited regulatory guidance on the use of wearables in clinical trial programs has been published. To present recommendations from the Critical Path Institute's Electronic Patient-Reported Outcome Consortium regarding the selection and evaluation of wearable devices and their measurements for use in regulatory trials and to support labeling claims. The evaluation group was composed of Critical Path Institute's clinical outcome assessment (COA) scientists and COA specialists from pharmaceutical trial eCOA solution providers, including COA development and validation specialists. The resulting recommendations were drawn from a broad range of backgrounds, perspectives, and expertise that enriched the development of this report. Recommendations were developed through analysis of existing regulatory guidance relating to COA development and use in clinical trials, medical device certification/clearance regulations, literature-reported best practice, and practical experience of wearable technology application in clinical trials. We identify the essential properties of fit-for-purpose wearables and propose evidence needed to support their use. In addition, we overview the activities required to establish clinical endpoints derived from wearables data. Using this framework, we believe there is enough current understanding to promote the appropriate use of wearables in study protocols. We hope this will provide a basis for discussion among clinical trial stakeholders and catalyze the development of more robust regulatory guidance. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

25 CFR 1000.310 - What information must the Tribe's/Consortium's response contain?

Code of Federal Regulations, 2014 CFR

2014-04-01

... 25 Indians 2 2014-04-01 2014-04-01 false What information must the Tribe's/Consortium's response... INDIAN SELF-DETERMINATION AND EDUCATION ACT Reassumption § 1000.310 What information must the Tribe's/Consortium's response contain? (a) The Tribe's/Consortium's response must indicate the specific measures that...

25 CFR 1000.255 - May a Tribe/Consortium reallocate funds among construction programs?

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 2 2013-04-01 2013-04-01 false May a Tribe/Consortium reallocate funds among... INDIAN SELF-DETERMINATION AND EDUCATION ACT Construction § 1000.255 May a Tribe/Consortium reallocate funds among construction programs? Yes, a Tribe/Consortium may reallocate funds among construction...

25 CFR 1000.310 - What information must the Tribe's/Consortium's response contain?

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 2 2013-04-01 2013-04-01 false What information must the Tribe's/Consortium's response... INDIAN SELF-DETERMINATION AND EDUCATION ACT Reassumption § 1000.310 What information must the Tribe's/Consortium's response contain? (a) The Tribe's/Consortium's response must indicate the specific measures that...

25 CFR 1000.255 - May a Tribe/Consortium reallocate funds among construction programs?

Code of Federal Regulations, 2014 CFR

2014-04-01

... 25 Indians 2 2014-04-01 2014-04-01 false May a Tribe/Consortium reallocate funds among... INDIAN SELF-DETERMINATION AND EDUCATION ACT Construction § 1000.255 May a Tribe/Consortium reallocate funds among construction programs? Yes, a Tribe/Consortium may reallocate funds among construction...

24 CFR 943.124 - What elements must a consortium agreement contain?

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false What elements must a consortium agreement contain? 943.124 Section 943.124 Housing and Urban Development Regulations Relating to Housing and... elements must a consortium agreement contain? (a) The consortium agreement among the participating PHAs...

24 CFR 943.124 - What elements must a consortium agreement contain?

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false What elements must a consortium agreement contain? 943.124 Section 943.124 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND... elements must a consortium agreement contain? (a) The consortium agreement among the participating PHAs...

24 CFR 943.124 - What elements must a consortium agreement contain?

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 4 2012-04-01 2012-04-01 false What elements must a consortium agreement contain? 943.124 Section 943.124 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND... elements must a consortium agreement contain? (a) The consortium agreement among the participating PHAs...

24 CFR 943.124 - What elements must a consortium agreement contain?

Code of Federal Regulations, 2013 CFR

2013-04-01

... 24 Housing and Urban Development 4 2013-04-01 2013-04-01 false What elements must a consortium agreement contain? 943.124 Section 943.124 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND... elements must a consortium agreement contain? (a) The consortium agreement among the participating PHAs...

24 CFR 943.124 - What elements must a consortium agreement contain?

Code of Federal Regulations, 2014 CFR

2014-04-01

... 24 Housing and Urban Development 4 2014-04-01 2014-04-01 false What elements must a consortium agreement contain? 943.124 Section 943.124 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND... elements must a consortium agreement contain? (a) The consortium agreement among the participating PHAs...

Introducing a New Interface for the Online MagIC Database by Integrating Data Uploading, Searching, and Visualization

NASA Astrophysics Data System (ADS)

Jarboe, N.; Minnett, R.; Constable, C.; Koppers, A. A.; Tauxe, L.

2013-12-01

The Magnetics Information Consortium (MagIC) is dedicated to supporting the paleomagnetic, geomagnetic, and rock magnetic communities through the development and maintenance of an online database (http://earthref.org/MAGIC/), data upload and quality control, searches, data downloads, and visualization tools. While MagIC has completed importing some of the IAGA paleomagnetic databases (TRANS, PINT, PSVRL, GPMDB) and continues to import others (ARCHEO, MAGST and SECVR), further individual data uploading from the community contributes a wealth of easily-accessible rich datasets. Previously uploading of data to the MagIC database required the use of an Excel spreadsheet using either a Mac or PC. The new method of uploading data utilizes an HTML 5 web interface where the only computer requirement is a modern browser. This web interface will highlight all errors discovered in the dataset at once instead of the iterative error checking process found in the previous Excel spreadsheet data checker. As a web service, the community will always have easy access to the most up-to-date and bug free version of the data upload software. The filtering search mechanism of the MagIC database has been changed to a more intuitive system where the data from each contribution is displayed in tables similar to how the data is uploaded (http://earthref.org/MAGIC/search/). Searches themselves can be saved as a permanent URL, if desired. The saved search URL could then be used as a citation in a publication. When appropriate, plots (equal area, Zijderveld, ARAI, demagnetization, etc.) are associated with the data to give the user a quicker understanding of the underlying dataset. The MagIC database will continue to evolve to meet the needs of the paleomagnetic, geomagnetic, and rock magnetic communities.

Brain Tumor Database, a free relational database for collection and analysis of brain tumor patient information.

PubMed

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.

Indian Institute of Technology Bombay and Tata Memorial Centre Join the International Efforts in Clinical Proteogenomics Cancer Research | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute’s (NCI) Office of Cancer Clinical Proteomics Research, part of the National Institutes of Health, along with the Indian Institute of Technology Bombay (IITB) and Tata Memorial Centre (TMC) have signed a Memorandum of Understanding (MOU) on clinical proteogenomics cancer research. The MOU between NCI, IITB, and Tata Memorial Centre represents the thirtieth and thirty-first institutions and the twelfth country to join the International Cancer Proteogenome Consortium (ICPC). The purpose of the MOU is to facilitate scientific and programmatic collaborations between NCI, IITB, and TMC in basic and clinical proteogenomic studies leading to patient care and public dissemination and information sharing to the research community.

Creation of clinical research databases in the 21st century: a practical algorithm for HIPAA Compliance.

PubMed

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.

[Role and management of cancer clinical database in the application of gastric cancer precision medicine].

PubMed

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.